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BIOQUANT Topographer Handbook

BIOQUANT Topographer Handbook

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BIOQUANT Topographer

Help Procedures
This documents contains the help files for BIOQUANT Life Science or BIOQUANT OSTEO version 11.2.6 for Microsoft Windows 7. Use the Contents for quick direction to particular topics. Use the Index to find specific topics. Use the Search functionality for refined direction to specific topics. For directed help on individual items:
• • For Boxes: click the Help button or ? button to get help on that box. For Menu Items: Highlight a menu item with you mouse and click F1 on the keyboard for help on menu items that don’t have boxes.

This document is also available in PDF format on the BIOQUANT installation disk.

 Copyright 2010, 2011

BIOQUANT Image Analysis Corporation 5611 Ohio Avenue, Nashville, TN 37209 phone: 800-221-0549 or 615-350-7866 fax: 615-350-7282 email: bioquant.support@bioquant.com web: www.bioquant.com Revision 11.2, 2-28-2011

Table of Contents
Topographer Introduction- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1-1
The Topographer Three Work Areas ...................................................................... General Steps Required to Create a 2D Map ......................................................... General Steps Required to Create a 3D Model ...................................................... Additional Topographer Features ........................................................................... Viewing BIOQUANT Sample 2D Maps and 3D Models .......................................... 1-2 1-4 1-4 1-5 1-5

2D Mapping - Review & Optimize - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 2-1
Entering the Topographer ....................................................................................... 2-2 Part 1-Open the Desired Data Set .......................................................................... 2-3 Part 2-Select and Display the 2D Map.................................................................... 2-4 Part 3-Optimize the Map Display .......................................................................... 2-10 Part 4-Prepare to Edit the 2D Map........................................................................ 2-19 Part 5-Correct Errors In Topo Data....................................................................... 2-22

3D Modeling - Review & Optimize the 3D Data - - - - - - - - - - - - - - - - - - - - 3-1
Entering the Topographer ....................................................................................... 3-2 Part 1-Display The Atlas ......................................................................................... 3-2 Part 2-A Quick Look at the Surface Rendered Model ............................................. 3-5 Part 3-Save the Atlas to a New Array ..................................................................... 3-6 Part 4-General Section Review............................................................................... 3-7 Introduction To The Atlas Shop ............................................................................ 3-11 Color Editing Procedures ...................................................................................... 3-27 Section Alignment Procedures.............................................................................. 3-32 Z-Axis Re-Distribution Procedures........................................................................ 3-37 Special Formatting Features ................................................................................. 3-48 Other Atlas Shop Features ................................................................................... 3-53

3D Modeling: Surface Rending in the Atlas Modeler - - - - - - - - - - - - - - - - 4-1
Introduction to the Atlas Modeler ............................................................................ 4-2 Changing the Characteristics of the Model ............................................................. 4-7 Activating Continuous Rotation............................................................................. 4-11 Record or Play an AVI Movie................................................................................ 4-14 Saving and Loading a Surface Rendering Parameters File.................................. 4-17 Special Formatting Options................................................................................... 4-19 Printing, Saving, and Copying the Model .............................................................. 4-21 Exiting Atlas Modeler ............................................................................................ 4-25

The Atlas Viewer in Detail - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 5-1
Working With 3D Wire Frame Atlases .................................................................... 5-2 Printing, Copying, or Exporting an Atlas ............................................................... 5-34 Manipulating Data Arrays and Data Sets in the Atlas Viewer ............................... 5-38

The Atlas Shop in Detail - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 6-1
The File Menu ......................................................................................................... 6-2 The Select Menu..................................................................................................... 6-7 The View Menu ..................................................................................................... 6-16 The Edit Menu....................................................................................................... 6-27 Tools on the System Tool Bar............................................................................... 6-45
Table of Contents

Tools on the Vertical Tool Bar............................................................................... 6-47 Special Edits To Enhance Surface Rendering...................................................... 6-66 Taking Measurements from an Atlas .................................................................... 6-69

Planar & Contour Conversion - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 7-1
Understanding the Basics of Planar and Contour Conversion................................ 7-2 Planar Conversion .................................................................................................. 7-4 Displaying and Modifying the Planar Histogram ................................................... 7-17 Contour Conversion .............................................................................................. 7-25 Displaying and Modifying the Contour Converted Atlas........................................ 7-37

Index - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - index--i

Table of Contents

BIOQUANT Topographer Handbook

Topographer Introduction
This section explains important concepts and gives step by step instructions for viewing sample 2D maps and 3D surface-rendered models that can be installed from the BIOQUANT installation CD.
The Topographer Three Work Areas (page 1-2) General Steps Required to Create a 2D Map (page 1-4) General Steps Required to Create a 3D Model (page 1-4) Additional Topographer Features (page 1-5) Viewing BIOQUANT Sample 2D Maps and 3D Models (page 1-5)

Topographer Introduction

Page 1-2

THE TOPOGRAPHER THREE WORK AREAS
When the Save to Topo Array feature is active in the main BIOQUANT program, every mark and tracing generated during measurement is also recorded as a series of topographic data points. BIOQUANT’s Topographer Plug-in uses this topographic data to reconstruct first a wire frame atlas, then a three dimensional, surface rendered model of the measured structures. The Topographer program has three separate parts: • Atlas Viewer This is the Topographer’s “front room”. It is the where Topo arrays that contain the topographic data for the reconstruction are selected and displayed as a wire frame structure called an atlas. Once an atlas is displayed, “door ways” into the Atlas Shop and the Atlas Modeler become available. While in the Atlas Viewer, the user may experiment with color or rotational changes without fear of altering the original topo data. The atlas may also be printed or saved to a file while in the Atlas Viewer. (If you did not purchase the full Topographer plug-in, you have a subset of the Atlas Viewer called, “Topo Reader.”) The Atlas Viewer (Initial Display Environment)

Atlas Modeler This is the Topographer’s surface rendering environment, where a 3D atlas is rendered with a virtual skin to produce a solid or semi-solid model. Rotating models may be recorded as AVI movies.

BIOQUANT Topographer Handbook: Topographer Introduction

to convert an atlas to a planar histogram. There are tools to correct topographic errors that were introduced during measurement. area. and to take additional measurements directly from the reconstructed atlas. and distances between structures. Possible measurements include: volume. The Atlas Shop (Editing and Measurement Environment) BIOQUANT Topographer Handbook: Topographer Introduction . counts.Page 1-3 The Atlas Modeler (Surface Rendering Environment) • Atlas Shop This is the Topographer’s editing and measuring environment. to apply special formatting to an atlas that is to be surface rendered.

its tracings can be moved or modified in the Topographer’s Atlas Shop.). For a detailed procedure. For a detailed procedure. For each section in the series. collect Topo data while measuring a specimen.” in the Life Science or OSTEO help or PDF manual. adjust the display parameters (change line colors. 2. collect Topo data while measuring the serial sections. 2. • 2D MAPPING INSTRUCTIONS 2D Mapping .) Once displayed in the Atlas Viewer. STEPS 1. see the chapter entitled. then print or export the 2D map. In BIOQUANT Topographer’s Atlas Viewer.Review & Optimize (page 2-1) RELATED TOPICS • • • • The Topographer Three Work Areas (page 1-2) General Steps Required to Create a 3D Model (page 1-4) Additional Topographer Features (page 1-5) Viewing BIOQUANT Sample 2D Maps and 3D Models (page 1-5) GENERAL STEPS REQUIRED TO CREATE A 3D MODEL Following is a quick outline of the general steps required to create a 3-D Model. It is important to back up original data before edits are made in the Atlas Shop. if necessary. “3-D Modeling: Data Collection. During data collection the 2D map can be displayed in Life Science’s or OSTEO’s Overview window. (Color adjustments made in the Atlas Viewer do not change the default colors that are recorded in the Topo arrays. adjust the colors that are used in the atlas display. and a Z Offset value to identify the section’s position relative to other sections. select and display the initial wire frame reconstruction in an atlas window. In the BIOQUANT Life Science or BIOQUANT OSTEO measurement program.Page 1-4 RELATED TOPICS • • • • General Steps Required to Create a 2D Map (page 1-4) General Steps Required to Create a 3D Model (page 1-4) Additional Topographer Features (page 1-5) Viewing BIOQUANT Sample 2D Maps and 3D Models (page 1-5) GENERAL STEPS REQUIRED TO CREATE A 2D MAP Following is a quick outline of the general steps required to create a 2-D Map. you will set a reference Landmark for all tracings on that section.” in the Life Science or OSTEO help or PDF manual. In the BIOQUANT Life Science or BIOQUANT OSTEO measurement program. etc. In BIOQUANT Topographer’s Atlas Viewer select and display the map in an atlas window. back up the original data and. until the surface rendered model is both accurate and visually pleasing. STEPS 1. In BIOQUANT Data Manager. If desired. BIOQUANT Topographer Handbook: Topographer Introduction . 4. turn cell markers into symbols. the reconstruction is moved back and forth between the Atlas Modeler (where it is automatically surface rendered in the colors that were chosen in the Atlas Viewer) and the Atlas Shop (for editing). 3. If desired. “2-D Mapping: Data Collection. fill some areas with solid color. use the Topo Array Exporter to gather all of the Topo data for the reconstruction from multiple data sets into a single master 3D data set. If the map contains errors. see the chapter entitled.

keep in mind that the data and/or tracings of a particular reconstruction are called an atlas. using the topographic tracings that were recorded in BIOQUANT during measurement. The result is a Planar Histogram. section contour tracings retain their original configuration. RELATED TOPICS • • • • The Topographer Three Work Areas (page 1-2) General Steps Required to Create a 2D Map (page 1-4) General Steps Required to Create a 3D Model (page 1-4) Viewing BIOQUANT Sample 2D Maps and 3D Models (page 1-5) VIEWING BIOQUANT SAMPLE 2D MAPS AND 3D MODELS Looking at sample 2D maps and 3D Models will acquaint you with the Topographer and will show different types of finished reconstructions. With Planar Conversion. • • • The Atlas Viewer in Detail (page 5-1) The Atlas Shop in Detail (page 6-1) Planar & Contour Conversion (page 7-1)) Both Planar Conversion and Contour Conversion quantitatively map deferentially labeled cell populations across serial brain sections. One of the sample data sets is called General Atlas Set and contains finished 2D Maps and 3D models that can be displayed in the Topographer. the process pulls cell markers within the section to the nearest point on the section’s contour tracing. each of which is a separate specimen reconstruction. With Contour Conversion. The number of cells at each point are represented by proportionally sized symbols. SAMPLE 2D MAPS LIST The General Atlas Set contains the following two-dimensional atlases: • • • • • • • D4 Cerebellum (cerebellum section) D5 Colon (colon cross-section) D6 Glia (map that distinguishes single labeled and dual labeled cells) D7 LC Cells (map of cells labeled with lipocortin) D8 Cortex (brain cortex section) D9 Hippo (hippocampus section) D11 Symbols (shows cell markers replaced with symbols) BIOQUANT Topographer Handbook: Topographer Introduction . While working in the Topographer. There is a also a chapter dedicated to Planar and Contour Conversion. for each section. BIOQUANT Topographer has detailed instructions for using the Atlas Viewer and Atlas Shop outside of a procedural context. In both types of conversion. each section’s contour tracing is broken at a defined point and stretched into a vertical line. Sample Data Sets are installed from the BIOQUANT Life Science or BIOQUANT OSTEO installation CD. a special Topographer tool. The General Atlas Set has 18 Topo arrays.Page 1-5 3D MODELING INSTRUCTIONS 3D Modeling .Review & Optimize the 3D Data (page 3-1) 3D Modeling: Surface Rending in the Atlas Modeler (page 4-1) RELATED TOPICS • • • • The Topographer Three Work Areas (page 1-2) General Steps Required to Create a 2D Map (page 1-4) Additional Topographer Features (page 1-5) Viewing BIOQUANT Sample 2D Maps and 3D Models (page 1-5) ADDITIONAL TOPOGRAPHER FEATURES In addition procedures for 2D mapping and 3D modeling.

high resolution. The Topographer’s Atlas Viewer will open.OPEN THE GENERAL ATLAS SET 1. after it is displayed in the Atlas Viewer. ideal view of each sample wireframe atlas will be accomplished by loading the display Parameters (. On BIOQUANT Life Science’s or BIOQUANT OSTEO’s system menu bar click Topographer. The Open Data Set dialog box opens. On the Open Data Set dialog box. 2. it may be moved into the Atlas Modeler for surface rendering. surface-renders very slowly) D17 Spinal Cord Decrease Resolution (same as D16 but formatted with fewer data points to speed surface rendering) TO OPEN THE SAMPLES. The Change BQ Volume Search Directory dialog box opens. If the selected array contains a 3D atlas. A finished. choose Open Data Set. From the Atlas Viewer’s File menu. or on the system tool bar click the Open Data Set button. BIOQUANT Topographer Handbook: Topographer Introduction . Viewing the samples will begin with the selection of one of the Topo arrays in the General Atlas Set data set. CONTINUE TO • Procedures for Viewing Sample Reconstructions (page 1-6) RELATED TOPICS • • • • • Procedures for Viewing Sample Reconstructions (page 1-6) The Topographer Three Work Areas (page 1-2) General Steps Required to Create a 2D Map (page 1-4) General Steps Required to Create a 3D Model (page 1-4) Additional Topographer Features (page 1-5) PROCEDURES FOR VIEWING SAMPLE RECONSTRUCTIONS Both 2D and 3D atlases are displayed first in the Atlas Viewer window. formatted for surface-rendering that reveals internal structures) D3 Horizontals (brain sections showing sinuses and cells of interest) D10 Sections (sections that include two different cell populations) D12 Embryonic Rat Head (head sections showing major structure) D13 Milkweed (whole flower with petals and stamen) D14 Embryo Sagittal (sagittal sections of a rat embryo with internal structures) D15 Spinal Cord Small (spinal cord cross-sections) D16 Spinal Cord Large (more sections.set) file that was saved for that atlas.Page 1-6 • D18 Axon Counting (nerve cross-section for axon counting) SAMPLE 3D MODELS LIST The General Atlas Set contains the following three-dimensional atlases: • • • • • • • • • • D1 Rat Brain Normal (whole brain) D2 Rat Brain Caps (whole brain. PROCEDURE 1 . click the Browse button. 3.

Example Path: D:\BQLIFESCIENCE\Sample Data Sets\Atlas_Volume or D:\BQOSTEO\Sample Data Sets\Atlas_Volume. In the Data Sets list. Open Data Set Dialog Box 5. The index number of that atlas will be moved to the Selected column. click to highlight General Atlas Set. 6. Data sets within the volume will be displayed in the lower box. PROCEDURE 2 . Navigate to and open the Atlas Volume folder. There is only one data volume in this folder: Atlas Volume.Page 1-7 Change BQ Volume Search Dialog Box 4. On the Open Data Set dialog box. 7. click to highlight Atlas Volume.CHOOSE AND DISPLAY THE DESIRED ATLAS • To display a 2D map. on the Select Arrays dialog box. Click the Open button. Click the Select button to close the Change BQ Volume Search Directory dialog box. 8. The 18 atlases (Topo arrays) in this data set will be listed in the Select Arrays dialog box. scroll through the Available Arrays list of atlases and double-click one of the following arrays for viewing. The following arrays contain two-dimensional atlases: • • • • • • D4 Cerebellum (cerebellum section) D5 Colon (colon cross-section) D6 Glia (map that distinguishes single labeled and dual labeled cells) D7 LC Cells (map of cells labeled with lipocortin) D8 Cortex (brain cortex section) D9 Hippo (hippocampus section) BIOQUANT Topographer Handbook: Topographer Introduction .

scroll thought the Available Arrays list of atlases and double-click one of the following arrays for viewing: The index number of that atlas will be moved to the Selected column. BIOQUANT Topographer Handbook: Topographer Introduction . then click the New Atlas Window 2. Three dimensional atlases must be displayed in the Atlas Viewer before they can be moved into the Atlas Modeler for surface rendering. formatted for surface-rendering that reveals internal structures) D3 Horizontals (brain sections showing sinuses and cells of interest) D10 Sections (sections that include two different cell populations) D12 Embryonic Rat Head (head sections showing major structure) D13 Milkweed (whole flower with petals and stamen) D14 Embryo Sagittal (sagittal sections of a rat embryo with internal structures) D15 Spinal Cord Small (spinal cord cross-sections) D16 Spinal Cord Large (more sections. or choose Open from the Atlas menu. high resolution.set) files for each atlas in the General Atlas Set. 3.Page 1-8 • • • D11 Symbols (shows cell markers replaced with symbols) D18 Axon Counting (nerve cross-section for axon counting) To display a 3D reconstruction. on the Select Arrays dialog box. From the File menu. The atlas will be resized and centered in the window. On the system tool bar click the Resize To Fit button. 1. surface-renders very slowly) D17 Spinal Cord Decrease Resolution (same as D16 but formatted with fewer data points to speed surface rendering) button on the system tool bar. double click the Parameter Files Atlas Set folder. Load Parameters File Dialog Box b.set) file for this atlas by doing the following: a. The following arrays are three-dimensional atlases: • • • • • • • • • • D1 Rat Brain Normal (whole brain) D2 Rat Brain Caps (whole brain. Verify that the desired Topo array is in the Selected column of the Select Arrays dialog box. Load the parameters (. choose Load Parameters. In the large center box. This folder contains one or more parameter (.

In the Selected list of the Select Arrays dialog box. perform “Procedure 2 .bqr) files for each 3D atlas in the General Atlas Set. Repeat from step 2 to resize and display the new atlas. Open (Look in) the Parameter Files Atlas Set folder. click the Atlas Modeler button. Open Parameters File Dialog Box b. it means that more than one view of the atlas was saved. In the Available Arrays list. 2. d. On the Atlas Viewer’s tool bar. PROCEDURE 3 . choose Load Parameters. Click to highlight the . BIOQUANT Topographer Handbook: Topographer Introduction . On the system tool bar click the Redraw button. A finished. To display a different sample reconstruction. b.bqr) file for that model. do the following: a.SURFACE RENDER A 3D ATLAS After being displayed as a wire-frame in the Atlas Viewer. In the Atlas Viewer.set file that reflects the name of the currently displayed atlas. 3D atlases may be moved into the Atlas Modeler for surface rendering.Choose and Display the Desired Atlas” on page 1-7 to display the desired 3D atlas array and load its parameter file. This folder contains one or more Bioquant rendering (. The Atlas Modeler opens and displays a default version of the surface rendered model. ideal view of each surface rendered atlas may be accomplished by loading the Bioquant rendering (. c. 3. double-click the index number of the currently selected Topo array to remove it from the Selected list.Page 1-9 Open Parameters File Dialog Box c.set file that matches the name of the currently displayed atlas (the currently selected Topo array) and click the Open button. double-click to select the desired Topo array. If more than one Parameters (.set) file is available for an atlas. 4. 1. Load this model’s Bioquant rendering (. Choose any .bqr) file by doing the following: a. From the Atlas Modeler’s File menu.

• HAND ROTATING TIPS • • 5. click and slowly drag the cursor a short distance in the direction you wish the model to rotate. From the Atlas Modeler’s File menu. Click to highlight the . On the system tool bar. Choose any . To stop the rotation before the 360 degree cycle is complete. e. See Procedure 2. f. do the following: a. it means that more than one view of the model was saved. (Optional) To hand-rotate the model. choose Load Parameters and open the .bqr file that matches the name of the current model (the Topo array that was selected in the Atlas Viewer) and click the Open button. choose Exit Atlas Modeler. repeat from step 3 and choose an alternate . in the Available Arrays list. The Atlas Modeler closes and the Atlas Viewer re-opens. short line to the right. to see a different version of this same model. If more than one rendering parameters (. click the Auto Movie Rotate button to see the model automatically rotate 360 degrees. c. button to update the Atlas Window with the From the Atlas Viewer’s File menu. double-click to select the desired Topo array. b. Anywhere in the model window.bqr file for this model. Pause between each cursor-drag.Page 1-10 Open Surface Rendering Parameters File Dialog Box c. click and hold the right mouse button.set file that belongs to this atlas. then slowly move the cursor in a straight. d. 4. step 3 (1-8) Repeat from step 2 to view the new surface rendered model. Larger atlases will take a moment to respond. do the following: a. On the Atlas Viewer’s Select Arrays dialog box. If more than one Bioquant rendering file is available for this model. On the Atlas Viewer’s tool bar click the Redraw tracings from the new array. On the Atlas Viewer’s Select Arrays dialog box. double-click the current Topo array index number to remove it from the Selected list.bqr) file is available for a model. in the Selected list. On the system tool bar. Example: To rotate the model counter-clockwise (around its Z axis). b. Slow. 6. RELATED TOPICS • • • • • The Topographer Three Work Areas (page 1-2) General Steps Required to Create a 2D Map (page 1-4) General Steps Required to Create a 3D Model (page 1-4) Additional Topographer Features (page 1-5) Viewing BIOQUANT Sample 2D Maps and 3D Models (page 1-5) BIOQUANT Topographer Handbook: Topographer Introduction . short-distance drags of the cursor are best. click the Rotate button.bqr file that reflects the name of the currently displayed model. To open and view a completely different model. click the Auto Movie Rotate button again.

recorded in BOQUANT Life Science or BIOQUANT OSTEO. Entering the Topographer (page 2-2) Part 1-Open the Desired Data Set (page 2-3) Part 2-Select and Display the 2D Map (page 2-4) Part 3-Optimize the Map Display (page 2-10) Part 4-Prepare to Edit the 2D Map (page 2-19) Part 5-Correct Errors In Topo Data (page 2-22) 2D Mapping Review & Optimize .Review & Optimize Topographic data.BIOQUANT Topographer Handbook 2D Mapping . is displayed and reviewed in the Topographer. Errors introduced during measurement may be corrected and display parameters may be changed to enhance the quality of the specimen map.

Page 2-2 ENTERING THE TOPOGRAPHER Clicking the word “Topographer” on BIOQUANT Life Science’s or BIOQUANT OSTEO’s menu bar opens the Topographer’s Atlas Viewer. (The Atlas Modeler also becomes available. but is not used with 2D mapping. The atlas (map) may also be printed. TOPIC CONTENTS Part 1-Open the Desired Data Set (page 2-3) Part 2-Select and Display the 2D Map (page 2-4) Part 3-Optimize the Map Display (page 2-10) Part 4-Prepare to Edit the 2D Map (page 2-19) Part 5-Correct Errors In Topo Data (page 2-22) BIOQUANT Topographer Handbook: 2D Mapping .) While in the Atlas Viewer.Review & Optimize . The Atlas Viewer Desktop Before an Atlas is Selected and Displayed THE ATLAS VIEWER The Atlas Viewer is the Topographer’s “front room”.) In the Topographer. is called an atlas. then the Topo Reader. a reduced functionality free version of the Atlas Viewer opens. If the optional Topographer plug-in has not been purchased. The Select Arrays dialog box is visible and initially shows the arrays that are available in the data set that was open in Life Science or OSTEO when the Topographer was launched. (Opening an alternate data set will be discussed shortly. The topographic data that makes up a 2D map. saved to a file. a “door way” into the Atlas Shop becomes available. Once an atlas is displayed. as well as the display of the map. It is the where Topo arrays that contain the topographic data for the 2D map are selected and displayed. only Topo arrays are selected on the Select Arrays dialog box. or copied to the clipboard while in the Atlas Viewer. the user may experiment with color or positional changes without fear of altering the original topo data.

The Open a Data Set Dialog Box button. BIOQUANT Topographer Handbook: 2D Mapping . click to highlight the data volume that contains the data for the desired 2D map. 2.Review & Optimize .Page 2-3 RELATED TOPICS • • • • • • • • • Print the Map (page 2-6) Export the Map to a File (page 2-7) Copy and Paste the Map into a Different Program (page 2-9) Manipulating the Map (page 2-10) Change Background and Increase Thickness of Tracings (page 2-11) Change Color/Symbols Parameters (page 2-12) Saving and Loading Display Parameters (page 2-15) Save Data Set (page 2-18) Exit Atlas Viewer (page 2-19) PART 1-OPEN THE DESIRED DATA SET By default. If this is the data set that contains the desired 2D map. is open in the Topographer and its arrays are visible in the Select Arrays dialog box. If the desired data volume is not in the list do the following: a. otherwise. the data sets contained in that volume will be displayed in the Data Sets list. perform the following procedure to open the desired data set. the data set that was open in BIOQUANT Life Science or BIOQUANT OSTEO when the Topographer program was accessed. to When a data volume is selected. skip to Part 2. or from the File menu choose Open Data Set. On the system tool bar click the Open Data Set display the Open a Data Set dialog box. PROCEDURE 1. Click the Browse button to open the Choose BQ Volume Search Directory dialog box. In the Data Volumes list.

click the New Atlas Window Open. Only Topo arrays should be selected. 4. click to highlight the desired data set.Page 2-4 The Choose BQ Volume Search DIrectory Dialog Box b. PROCEDURE 1. 3. 5. In the Atlas Viewer. In the Folders list. double-clicking to open or close folders. choose 2. The arrays of the data set appear in the Select Arrays box.Review & Optimize . Click the OK button. In the Data Sets list. Continue with “Part 2-Select and Display the 2D Map” on page 2-4. Click the Open button. button. d. BIOQUANT Topographer Handbook: 2D Mapping . On the Atlas Viewer’s tool bar. in the Data Volumes list. The index number of the selected array(s) will appear in the Selected list. c. in the Available Arrays box. on the Select Arrays dialog box. Again on the Open Data Set dialog box. click to the desired data volume. open the folder that contains the desired data volume. the data for the 2D map is contained in one or more Topo arrays that are visible in the Available Arrays list of the Select Arrays dialog box. or from the Atlas menu. MORE 2-D MAP REVIEW & OPTIMIZING TOPICS Part 2-Select and Display the 2D Map (page 2-4) Part 3-Optimize the Map Display (page 2-10) Part 4-Prepare to Edit the 2D Map (page 2-19) Part 5-Correct Errors In Topo Data (page 2-22) RELATED TOPICS • • • • • • • • • Print the Map (page 2-6) Export the Map to a File (page 2-7) Copy and Paste the Map into a Different Program (page 2-9) Manipulating the Map (page 2-10) Change Background and Increase Thickness of Tracings (page 2-11) Change Color/Symbols Parameters (page 2-12) Saving and Loading Display Parameters (page 2-15) Save Data Set (page 2-18) Exit Atlas Viewer (page 2-19) PART 2-SELECT AND DISPLAY THE 2D MAP When the correct data set is open. double click any and all Topo arrays in the data set that contain data for the desired 2D map to move them to the Selected box.

this can result in structures of the same type (which were intended to be the same color) being different colors. then proceed to Part 5Correct Errors In Topo Data (page 2-22). b. The atlas (2D map) is visible in the Atlas Window and the Atlas Parameters dialog box opens. During automatic measurement an inaccurate tracing might be generated. For example. for example. if the user failed to notice. may have clicked points that were too far apart to accurately define segments of the structure’s edge. Do tracings accurately represent the shape of the objects that were measured? • • DATA CORRECTIONS ARE DONE IN THE ATLAS SHOP If data corrections are needed. Depending on circumstances. 5. Consider the following questions: a. Small positional problems may arise if two parts of the specimen were measured at different magnifications through microscope objectives that were not parfocaled. Are all of the tracings and/or cell markers positioned correctly. b. click the Resize To Fit button. if Spacebar to End was active.Page 2-5 3. or. might now appear to be outside the structure’s contour tracing that was created at 4X. Consider these questions: a. c. 2D Map Displayed in the Atlas Viewer 4. on cells that lay close to a structure’s edge. before clicking the Measure button. During manual measurement the user may have mis-traced a segment of a structure’s contour. On the Atlas Viewer’s tool bar. go to Part 4-Prepare to Edit the 2D Map (page 2-19). e.Review & Optimize . the user occasionally forgets to designate the intended Color in the Parameters region. that the automatic preview outline included something that was not intended to be measured. Are the default colors (those chosen during measurement) correct for all tracings and cell markers? • During measurement. cell markers that were generated at 40X. Do the default colors (those chosen during measurement) look good? Would the map be more visible against a black background? Would small objects such as cells look better represented by symbols? Would filling some areas with solid color enhance the map? Are there any duel-labeled structures? BIOQUANT Topographer Handbook: 2D Mapping . relative to one another? • c. d. Examine the atlas for aesthetic qualities. Examine the map for errors introduced during data collection.

Adjust any printing options.Review & Optimize . DISPLAY ENHANCEMENTS ARE DONE IN THE ATLAS VIEWER To enhance the appearance of the map. see Part 3-Optimize the Map Display (page 2-10). It titles the atlas with the names of the data volume and data set and the date.Page 2-6 The Fill and Overlap options can display overlapping areas in a distinctive third color. it is ready to be printed. The Print Box 2. • • • Print the Map (page 2-6) Export the Map to a File (page 2-7) Copy and Paste the Map into a Different Program (page 2-9) MORE 2-D MAP REVIEW & OPTIMIZING TOPICS Part 3-Optimize the Map Display (page 2-10) Part 4-Prepare to Edit the 2D Map (page 2-19) Part 5-Correct Errors In Topo Data (page 2-22) RELATED TOPICS • • • • • • • • • Print the Map (page 2-6) Export the Map to a File (page 2-7) Copy and Paste the Map into a Different Program (page 2-9) Manipulating the Map (page 2-10) Change Background and Increase Thickness of Tracings (page 2-11) Change Color/Symbols Parameters (page 2-12) Saving and Loading Display Parameters (page 2-15) Save Data Set (page 2-18) Exit Atlas Viewer (page 2-19) PRINT THE MAP Print Atlas is available when the Atlas Window is open. exported to a file.g. 3. When the map needs no further correction or enhancements. 6. PROCEDURE 1. or copied to the clipboard. To print the atlas at a different size. ADDITIONAL NOTE • Control-P opens the Print box. From the File menu. choose Print Atlas… to open the Print box. Topographer prints an atlas out at five inches by five inches. BIOQUANT Topographer Handbook: 2D Mapping . Click the OK button. Adobe Photoshop). export the atlas as a bitmap or metafile and print it from a graphics application (e.

Export options are available on the File menu when an atlas window is open.inkscape.Page 2-7 2-D MAP REVIEW & OPTIMIZING TOPICS Part 1-Open the Desired Data Set (page 2-3) Part 2-Select and Display the 2D Map (page 2-4) Part 3-Optimize the Map Display (page 2-10) Part 4-Prepare to Edit the 2D Map (page 2-19) Part 5-Correct Errors In Topo Data (page 2-22) RELATED TOPICS • • • • • • • • Export the Map to a File (page 2-7) Copy and Paste the Map into a Different Program (page 2-9) Manipulating the Map (page 2-10) Change Background and Increase Thickness of Tracings (page 2-11) Change Color/Symbols Parameters (page 2-12) Saving and Loading Display Parameters (page 2-15) Save Data Set (page 2-18) Exit Atlas Viewer (page 2-19) EXPORT THE MAP TO A FILE An atlas can be exported as a BMP or a SVG. SVG is a two-dimensional vector format. TOPIC CONTENTS Export to BMP Procedure (page 2-7) Export to SVG Procedure (page 2-8) 2-D MAP REVIEW & OPTIMIZING TOPICS Part 1-Open the Desired Data Set (page 2-3) Part 2-Select and Display the 2D Map (page 2-4) Part 3-Optimize the Map Display (page 2-10) Part 4-Prepare to Edit the 2D Map (page 2-19) Part 5-Correct Errors In Topo Data (page 2-22) RELATED TOPICS • • • • • • • • Print the Map (page 2-6) Copy and Paste the Map into a Different Program (page 2-9) Manipulating the Map (page 2-10) Change Background and Increase Thickness of Tracings (page 2-11) Change Color/Symbols Parameters (page 2-12) Saving and Loading Display Parameters (page 2-15) Save Data Set (page 2-18) Exit Atlas Viewer (page 2-19) EXPORT TO BMP PROCEDURE Export Current View to BMP will save the view in the Atlas window to the BMP format. They can be edited in graphics programs such as Inkscape or Adobe Illustrator. choose Export Current View to BMP. Inkscape is an open source graphics program that can be downloaded for free from www.Review & Optimize .org. A bitmap of the atlas can also be copied to the clipboard and then pasted into another application. SVG files can be opened and viewed directly in most web browsers. From the File menu. in essence a snapshot of the atlas. This format is useful because it can be resized to a larger size without loss of data in another program. PROCEDURE 1. BIOQUANT Topographer Handbook: 2D Mapping . To save to a vector based format. where the resolution of the map is maintained. The bitmap is a two dimensional format. see “Export to SVG Procedure” on page 2-8. This format is a two dimension “static” format. If a BMP is resized to a larger size in another program details of the map could be lost.

click to highlight the Topo array to be exported. When you return to the Atlas Viewer.Page 2-8 Save to BMP File Box 2. select only the single. in the Selected list. From the File menu. 2. On the Select Arrays box. This format is useful because it can be resized to a larger size without loss of data in another program. 3. Inkscape is an open source graphics program that can be downloaded for free from www. SVG is a two-dimensional vector format. BIOQUANT Topographer Handbook: 2D Mapping . choose Export Current Topo to SVG. As Export to SVG only works with one Topo array.Review & Optimize . SVG files can be opened and viewed directly in most web browsers. 2-D MAP REVIEW & OPTIMIZING TOPICS Part 1-Open the Desired Data Set (page 2-3) Part 2-Select and Display the 2D Map (page 2-4) Part 3-Optimize the Map Display (page 2-10) Part 4-Prepare to Edit the 2D Map (page 2-19) Part 5-Correct Errors In Topo Data (page 2-22) RELATED TOPICS • • • • • • • • • Print the Map (page 2-6) Export the Map to a File (page 2-7) Copy and Paste the Map into a Different Program (page 2-9) Manipulating the Map (page 2-10) Change Background and Increase Thickness of Tracings (page 2-11) Change Color/Symbols Parameters (page 2-12) Saving and Loading Display Parameters (page 2-15) Save Data Set (page 2-18) Exit Atlas Viewer (page 2-19) EXPORT TO SVG PROCEDURE Export Current Topo to SVG will save the current Topo array (highlighted Topo array in the Selected list) to the SVG format. To export to a “static” format that can not be as easily increased in size. They can be edited in graphics programs such as Inkscape or Adobe Illustrator.inkscape. Navigate to the folder in which the file should be saved. Click the Save button to create the file. type a name for the BMP file. simply select all Topo array and then go to the Atlas Shop and use Save As to save them to a new single Topo array. In the File name box. See “File > Save as” on page 6-3. combined Topo array for export. PROCEDURE 1. 4. see “Export to BMP Procedure” on page 2-7. if you have data from more than one Topo array that needs to be exported.org. The default folder for Topographer files is the C:\BQLifeScience\Topographer or C:\BQOSTEO\Topographer folder. but is accepted by more third party programs.

From the Edit menu of the other application. PROCEDURE 1. is to copy it to the clipboard. In the File name box. Navigate to the folder in which the file should be saved. type a name for the SVG file. choose Copy to Clipboard. 4. Check the documentation of the other application for details. ADDITIONAL NOTE • Choosing paste from the edit menu is the most common method of pasting in a bitmap. Switch to the other application. From the Atlas menu. choose Paste to insert the picture of the atlas. The Copy To Clipboard option is available on the Atlas menu when an Atlas window is open. 2-D MAP REVIEW & OPTIMIZING TOPICS Part 1-Open the Desired Data Set (page 2-3) Part 2-Select and Display the 2D Map (page 2-4) Part 3-Optimize the Map Display (page 2-10) Part 4-Prepare to Edit the 2D Map (page 2-19) Part 5-Correct Errors In Topo Data (page 2-22) RELATED TOPICS • • • • • • • • • Print the Map (page 2-6) Export the Map to a File (page 2-7) Copy and Paste the Map into a Different Program (page 2-9) Manipulating the Map (page 2-10) Change Background and Increase Thickness of Tracings (page 2-11) Change Color/Symbols Parameters (page 2-12) Saving and Loading Display Parameters (page 2-15) Save Data Set (page 2-18) Exit Atlas Viewer (page 2-19) COPY AND PASTE THE MAP INTO A DIFFERENT PROGRAM A quick way to transfer a bitmap of the 2D map to a different program. 3. The default folder for Topographer files is the C:\BQLifeScience\Topographer or C:\BQOSTEO\Topographer folder. 5.Review & Optimize . 2.Page 2-9 Save to SVG File Box 3. but applications vary. such as Microsoft PowerPoint or Adobe Photoshop. Click the Save button to create the file. BIOQUANT Topographer Handbook: 2D Mapping .

to instantly configure the atlas according to the saved parameters. REDRAW Redraw is used to refresh obscured tracings in the atlas window or to update the atlas window with a new set of tracings after a different Topo array has been selected. TOPIC CONTENTS Manipulating the Map (page 2-10) Change Background and Increase Thickness of Tracings (page 2-11) Change Color/Symbols Parameters (page 2-12) Saving and Loading Display Parameters (page 2-15) Save Data Set (page 2-18) Exit Atlas Viewer (page 2-19) MORE 2-D MAP REVIEW & OPTIMIZING TOPICS Part 1-Open the Desired Data Set (page 2-3) Part 2-Select and Display the 2D Map (page 2-4) Part 4-Prepare to Edit the 2D Map (page 2-19) Part 5-Correct Errors In Topo Data (page 2-22) RELATED TOPICS • • • • • • • • • Print the Map (page 2-6) Export the Map to a File (page 2-7) Copy and Paste the Map into a Different Program (page 2-9) Manipulating the Map (page 2-10) Change Background and Increase Thickness of Tracings (page 2-11) Change Color/Symbols Parameters (page 2-12) Saving and Loading Display Parameters (page 2-15) Save Data Set (page 2-18) Exit Atlas Viewer (page 2-19) MANIPULATING THE MAP The following tools are used to manipulate the map in the atlas window. BIOQUANT Topographer Handbook: 2D Mapping . the parameters for that view may be saved to a Parameters (.Review & Optimize .Page 2-10 2-D MAP REVIEW & OPTIMIZING TOPICS Part 1-Open the Desired Data Set (page 2-3) Part 2-Select and Display the 2D Map (page 2-4) Part 3-Optimize the Map Display (page 2-10) Part 4-Prepare to Edit the 2D Map (page 2-19) Part 5-Correct Errors In Topo Data (page 2-22) RELATED TOPICS • • • • • • • • Print the Map (page 2-6) Export the Map to a File (page 2-7) Manipulating the Map (page 2-10) Change Background and Increase Thickness of Tracings (page 2-11) Change Color/Symbols Parameters (page 2-12) Saving and Loading Display Parameters (page 2-15) Save Data Set (page 2-18) Exit Atlas Viewer (page 2-19) PART 3-OPTIMIZE THE MAP DISPLAY The Atlas Viewer has tools for altering the appearance of the 2D map. When a pleasing view of the atlas is established. Changing display parameters in the Atlas Viewer does not change the data in the Topo array.set) file that can be re-loaded any time in the future.

PAN Readies the cursor to move the atlas to a new location in the Atlas Window. CENTER Moves the topographic center of the atlas to the center of the Atlas Window. 2. Zoom button. click the window. To shrink. click the Redraw button. 3. Click the Resize to Fit button on the system tool bar. click the Pan button. 1. Click and drag the panning cursor to move the atlas. On the system tool bar. 1. RESIZE TO FIT Centers and resizes the atlas so it fills the Atlas Window. or choose Zoom from the Atlas menu. Magnification centers on the point clicked. choose Resize to Fit. • • From the Atlas menu. 2. To simultaneously zoom and pan to a particular location.Review & Optimize . click the to a magnifying glass. the cursor changes to a cross hair over the atlas. or from the Atlas menu choose Redraw. On the system tool bar. Click to release the Pan button to deactivate the panning cursor. Center button. To zoom. click and drag the cursor using the left mouse button.Page 2-11 • On the system tool bar. BIOQUANT Topographer Handbook: 2D Mapping . The cursor changes Click to release the Zoom button to deactivate the Zoom cursor. click and release the left mouse button over the atlas. ZOOM Activates the Zoom cursor so the atlas may be magnified or reduced in size. To magnify or reduce the atlas: • • • 3. click and release the right mouse button over the atlas. • On the system tool bar. The center of the atlas moves to the center of the atlas 2-D MAP REVIEW & OPTIMIZING TOPICS Part 1-Open the Desired Data Set (page 2-3) Part 2-Select and Display the 2D Map (page 2-4) Part 3-Optimize the Map Display (page 2-10) Part 4-Prepare to Edit the 2D Map (page 2-19) Part 5-Correct Errors In Topo Data (page 2-22) RELATED TOPICS • • • • • • • • Print the Map (page 2-6) Export the Map to a File (page 2-7) Copy and Paste the Map into a Different Program (page 2-9) Change Background and Increase Thickness of Tracings (page 2-11) Change Color/Symbols Parameters (page 2-12) Saving and Loading Display Parameters (page 2-15) Save Data Set (page 2-18) Exit Atlas Viewer (page 2-19) CHANGE BACKGROUND AND INCREASE THICKNESS OF TRACINGS BLACK BACKGROUND Changes the background color in the Atlas window from white to black.

BIOQUANT Topographer Handbook: 2D Mapping . To redraw the atlas with normal tracings. THICK TRACINGS Increases the thickness of atlas lines prior to printing. To re-display a white background. on the Atlas menu click to check Thick Tracings. which is ideal and recommended while making adjustments to the atlas display. PROCEDURE • • To redraw the atlas with thick tracings.Page 2-12 PROCEDURE • • To display a black background. Before and After Thick Tracings Thick tracings are recommended only when printing the atlas. 2-D MAP REVIEW & OPTIMIZING TOPICS Part 1-Open the Desired Data Set (page 2-3) Part 2-Select and Display the 2D Map (page 2-4) Part 3-Optimize the Map Display (page 2-10) Part 4-Prepare to Edit the 2D Map (page 2-19) Part 5-Correct Errors In Topo Data (page 2-22) RELATED TOPICS • • • • • • • • Print the Map (page 2-6) Export the Map to a File (page 2-7) Copy and Paste the Map into a Different Program (page 2-9) Manipulating the Map (page 2-10) Change Color/Symbols Parameters (page 2-12) Saving and Loading Display Parameters (page 2-15) Save Data Set (page 2-18) Exit Atlas Viewer (page 2-19) CHANGE COLOR/SYMBOLS PARAMETERS The Color/Symbols tab of the Atlas Parameters dialog box is used to change colors displayed in the map. The default thickness is 1 pixel. on the Atlas menu click to uncheck Thick Tracings. on the Atlas menu click to check Black Background.Review & Optimize . When printing an atlas it is sometimes better to thicken the tracings. on the Atlas menu click to uncheck Black Background.

) Entries in the Fill list are number 1 through 16 and each is a different color. Turn Fill on by clicking to check the Fill check box at the bottom of the Colors area. Find and click the entry that matches the current Fill color of the objects for which color is to be changed. Repeat for each color in the map you wish to change. In the Atlas window. 1. Choose a new color be clicking one of the 16 colored squares in the Colors area. 3. The entry in the Line/Sym list changes to the new color. To remove the Fill display. If symbols are currently being displayed. click to check the Fill check box at the bottom of the Colors area. 5. Find and click the entry that matches the current tracing color that is to be changed. The entry in the Fill list changes to the new color. BIOQUANT Topographer Handbook: 2D Mapping . click to uncheck the Overlap check box. notice the current fill color of the group of objects for which the fill color is to be changed. (The N square is for No Draw and the D square is for Default. 4. Choose a new color by clicking the cursor on one of the 16 color squares in the Colors area. To turn remove the overlap color. FILL LIST: CHANGE FILL COLOR 1. 3. symbol outlines of the targeted color will change. In the Atlas window. FILL CHECK BOX: FILL POLYGONAL TRACINGS WITH COLOR • • To display the default fill color. 2. 4. OVERLAP CHECK BOX: DISTINGUISH DUAL LABELED STRUCTURES • • To show areas of overlapping fill colors in a distinctive third color. Entries in the Line/Sym list are number 1 through 16 and each is a different color. click to uncheck the Fill check box.Review & Optimize .Page 2-13 Color/Symbol Tab of the Atlas Parameters Dialog Box LINE/SYM LIST: CHANGE LINE COLORS When Line/Symbol color changes are applied. 2. tracings of all items in the atlas window of the targeted color will change to the new color. Do not choose the N (No Draw) square or the D (Default) square. notice the current default color that you would like to change. Click the Apply button to update the atlas display to the new color(s). click to check both the Fill and Overlap check boxes at the bottom of the Colors area.

from the Atlas menu. Alternatively. Increase the value in the Maximum Object Size field and click the Apply button again. scroll through the available symbols and click to choose the desired symbol. click to check Symbols. Click the Apply button to display the changes. If all of the objects in the designated color group do not symbolize. Objects that appear in the atlas as single points or dots (such as those counted with an Object Count array). In the Maximum Object Size field. In this case the larger default symbol may be changed to the smaller “dot” symbol. if desirable. When there is a very large number of object count markers in the atlas (e. To adjust the width of the symbols. • 1. an Area array is sometimes used for cell counting in order to take advantage of BIOQUANT’s Auto Exclude feature. click to check the Symbols check box at the bottom of the Symbols area. In this case. 3. In the Symbols area. Symbols are most often used to replace “dots” in the atlas. it means that the group includes objects that are larger than the Maximum Object Size. there are two cases in which it is advantageous to assign the dot symbol to tracings. increase or decrease the value in the Symbol Size Height field by scrolling to or typing in a larger value. the area tracings can be replaced by the “dot” symbol. In the Atlas window. 5.Review & Optimize . MAXIMUM OBJECT SIZE: CHANGE THE SIZE OF THE SYMBOLS The default size of symbols is eight pixels by eight pixels. The symbol associated with that entry will change to the new symbol. 1. 6. or replace a larger symbol with a dot symbol: • During measurement. Continue to increase the Maximum Object Size until all the objects in the color group are replaced by the chosen symbol.Page 2-14 5. click the down arrowhead to display a small scroll list. To remove the symbolic display. Repeat steps 1 and 2 as needed until all of the desired tracings are symbolized. • AVAILABLE LIST: ASSIGN A DIFFERENT SYMBOL The default symbol assigned by the system to a particular color group may be changed to any of the alternate symbols on the Available symbol drop list. objects that have data points equal to or less than the Maximum Object Size value. scroll to or type in a higher number. • • To adjust the height of the symbols. identify the color of the group of objects for which the symbol should be changed. the default symbol assigned to the marker’s color may be too big and the symbolized display appears crowded. Using the two small scroll buttons.g. find and click the entry that matches the color of objects of interest (identified in step 2). Alternatively. Click the Apply button to update the atlas display with the new fill color(s). in the Available field. click to uncheck the Symbols check box. 4. SYMBOLS CHECK BOX: TURN ON/OFF SYMBOLS Small objects can be made more visible by marking them with symbols. 2. SYMBOL SIZE: SYMBOLIZE LARGER OBJECTS The Maximum Object Size value may be increased so slightly larger objects may be displayed as symbols. Click the Apply button to update the atlas display. click to uncheck Symbols. Display the current symbol(s) in the atlas by clicking to check the Symbols check box. the system sets the Maximum Object Size value to 2. actually have two data points with zero distance between them. from the Atlas menu. increase or decrease the value in the Symbol Size Width field. In the Symbol list. So the Maximum Object Size value must be at least 2. • To display the currently assigned symbol for small objects. Repeat for each fill color you wish to change. By default. 3. 2. But. This generates a tracing with multiple data points rather than a single dot. will be displayed with the currently assigned symbol. This can be increased or decreased as needed. cells). When the Symbols feature is activated. BIOQUANT Topographer Handbook: 2D Mapping . Changes in symbol size are applied to all symbols (not just the symbol of one selected color group). which allows only “single point” objects to be symbolized.

A value of 3 will display every third symbol. then click and drag the cursor across all the entries in the list. and Symbol assignments on the Colors/Symbols tab. To restore all the default Line/Sym. then click that entry in the list. its Parameter file may be loaded to instantly recall the preferred settings. 2. 1. 2-D MAP REVIEW & OPTIMIZING TOPICS Part 1-Open the Desired Data Set (page 2-3) Part 2-Select and Display the 2D Map (page 2-4) Part 3-Optimize the Map Display (page 2-10) Part 4-Prepare to Edit the 2D Map (page 2-19) Part 5-Correct Errors In Topo Data (page 2-22) RELATED TOPICS • • • • • • • • Print the Map (page 2-6) Export the Map to a File (page 2-7) Copy and Paste the Map into a Different Program (page 2-9) Manipulating the Map (page 2-10) Change Background and Increase Thickness of Tracings (page 2-11) Saving and Loading Display Parameters (page 2-15) Save Data Set (page 2-18) Exit Atlas Viewer (page 2-19) SAVING AND LOADING DISPLAY PARAMETERS This section covers saving and loading Display Parameter files. and so on. click the Restore button. Fill. If symbols are still too numerous. A value of 2 will display every second symbol. click the Default (D) square in the Colors area.Page 2-15 SHOW EVERY NTH SYMBOL: REDUCE THE NUMBER OF DENSELY PACKED SYMBOLS When Show Every (nth) Symbol is set to 1. RESTORE COLOR AND SYMBOL DEFAULTS • • • To restore the default assignment of one color entry in either the Line/Sym list or the Fill list. 3. TOPIC CONTENTS Save Parameters (page 2-16) Load Parameters (page 2-17) 2-D MAP REVIEW & OPTIMIZING TOPICS Part 1-Open the Desired Data Set (page 2-3) Part 2-Select and Display the 2D Map (page 2-4) Part 3-Optimize the Map Display (page 2-10) Part 4-Prepare to Edit the 2D Map (page 2-19) Part 5-Correct Errors In Topo Data (page 2-22) BIOQUANT Topographer Handbook: 2D Mapping . repeat steps 1 and 2. click the Default (D) square in the Colors area. Anytime in the future that the same data set is opened. Click the Apply button. The symbols representing a group of objects may be thinned out by increasing the “nth” value to a number greater than 1. In the Show Every (nth) Symbol field.Review & Optimize . To restore all the entries in the Line/Sym list or the Fill list to their default assignments. A Parameter file records which arrays were used to generate the reconstruction and saves the Perspective and Color/Symbols settings for a particular “view” of the atlas. a symbol is displayed for every single object that meets the Maximum Object Size criterion. increase the current value by 1.

Anytime in the future that the same data set is opened. On the system tool bar click the Save Parameters From the File menu choose Save Parameters.Review & Optimize . The Save Parameter File Dialog Box b. The Save Parameter File Dialog Box c. To do this: a. Double click the new folder to open it.Page 2-16 RELATED TOPICS • • • • • • • • Print the Map (page 2-6) Export the Map to a File (page 2-7) Copy and Paste the Map into a Different Program (page 2-9) Manipulating the Map (page 2-10) Change Background and Increase Thickness of Tracings (page 2-11) Change Color/Symbols Parameters (page 2-12) Save Data Set (page 2-18) Exit Atlas Viewer (page 2-19) SAVE PARAMETERS Save Parameters is available when the Atlas Window is open. button. PROCEDURE 1. Rename the New Folder to your Data Volume and Data Set Name. Open the Save Parameters dialog box using any of the following methods: • • • 2. Then when you later need to find and open the parameter files for a particular Data Set you can easily navigate to them. Click the Save button on either the Perspective or Color/Symbols tab of the Atlas Parameters dialog box. BIOQUANT Topographer Handbook: 2D Mapping . its Parameter file may be loaded to instantly recall the preferred settings. For ease of finding the parameters file again. it is recommended that you create a subdirectory in the Topographer folder that is named the same as your Data Volume and Data Set. Click the Create New Folder button. A Parameter file records which arrays were used to generate the reconstruction and saves the Perspective and Color/Symbols settings for a particular “view” of the atlas. The default Save in location is BQOSTEO\Topographer.

PROCEDURE 1. it will be listed here. button.Review & Optimize . or from the File menu choose Load Parameters. The default location for saving parameter files is BQOSTEO\Topographer.set” extensions. Navigate to the folder that contains the Parameter file for the current data set. 3. Click the Save button to save the file. Type a file name into the File name text box. If you created a subdirectory associated with your Data Volume and Data Set as recommended in the Save Parameters procedure. BIOQUANT Topographer Handbook: 2D Mapping . 2. The Save Parameter File Dialog Box 4. Loading a Parameters file instantly selects the arrays that were originally used to generate the atlas and resets the Perspective and Color/Symbol parameters that were active when the parameters file was saved. On the system tool bar click the Load Parameters to open the Open Parameter File dialog box. 2-D MAP REVIEW & OPTIMIZING TOPICS Part 1-Open the Desired Data Set (page 2-3) Part 2-Select and Display the 2D Map (page 2-4) Part 3-Optimize the Map Display (page 2-10) Part 4-Prepare to Edit the 2D Map (page 2-19) Part 5-Correct Errors In Topo Data (page 2-22) RELATED TOPICS • • • • • • • • • Print the Map (page 2-6) Export the Map to a File (page 2-7) Copy and Paste the Map into a Different Program (page 2-9) Manipulating the Map (page 2-10) Change Background and Increase Thickness of Tracings (page 2-11) Change Color/Symbols Parameters (page 2-12) Saving and Loading Display Parameters (page 2-15) Save Data Set (page 2-18) Exit Atlas Viewer (page 2-19) LOAD PARAMETERS Load Parameters is available both when the Atlas Window is closed and open.Page 2-17 You will save in this location. Parameter files have “. ADDITIONAL NOTES • • Control-S opens the Save Parameters box.

The Open Parameter File Dialog Box 4.” appears.Page 2-18 The Open Parameter File Dialog Box 3. The appearance of the atlas will change to reflect the loaded parameters. Click on the parameter file to be opened. the parameter file is for a different data set. Choose a different Parameter file or open the data set for which the file was saved. Click the Open button. BIOQUANT Topographer Handbook: 2D Mapping .Review & Optimize . Parameter files have “. Control-L opens the Load Parameters box.set” extensions. • • 2-D MAP REVIEW & OPTIMIZING TOPICS Part 1-Open the Desired Data Set (page 2-3) Part 2-Select and Display the 2D Map (page 2-4) Part 3-Optimize the Map Display (page 2-10) Part 4-Prepare to Edit the 2D Map (page 2-19) Part 5-Correct Errors In Topo Data (page 2-22) RELATED TOPICS • • • • • • • • • Print the Map (page 2-6) Export the Map to a File (page 2-7) Copy and Paste the Map into a Different Program (page 2-9) Manipulating the Map (page 2-10) Change Background and Increase Thickness of Tracings (page 2-11) Change Color/Symbols Parameters (page 2-12) Saving and Loading Display Parameters (page 2-15) Save Data Set (page 2-18) Exit Atlas Viewer (page 2-19) SAVE DATA SET The Save Data Set feature on the file menu will save changes to the current data set. ADDITIONAL NOTES • If the error message. “Parameter File Error: Sequence list not for this data set! File ignored.

Page 2-19 PROCEDURE • From the File menu. 1. 2-D MAP REVIEW & OPTIMIZING TOPICS Part 1-Open the Desired Data Set (page 2-3) Part 2-Select and Display the 2D Map (page 2-4) Part 3-Optimize the Map Display (page 2-10) Part 4-Prepare to Edit the 2D Map (page 2-19) Part 5-Correct Errors In Topo Data (page 2-22) RELATED TOPICS • • • • • • • • Print the Map (page 2-6) Export the Map to a File (page 2-7) Copy and Paste the Map into a Different Program (page 2-9) Manipulating the Map (page 2-10) Change Background and Increase Thickness of Tracings (page 2-11) Change Color/Symbols Parameters (page 2-12) Saving and Loading Display Parameters (page 2-15) Exit Atlas Viewer (page 2-19) EXIT ATLAS VIEWER The Exit menu is used to exit the Topographer and return to BIOQUANT Life Science or BIOQUANT OSTEO. Corrections are applied to the data in the new array. This insures that original data does not become corrupted during editing. choose Exit. BIOQUANT Topographer Handbook: 2D Mapping . NOTE: The Save Data Set option is only available when the Atlas Window is closed. In the Atlas Viewer. new array. 2-D MAP REVIEW & OPTIMIZING TOPICS Part 1-Open the Desired Data Set (page 2-3) Part 2-Select and Display the 2D Map (page 2-4) Part 3-Optimize the Map Display (page 2-10) Part 4-Prepare to Edit the 2D Map (page 2-19) Part 5-Correct Errors In Topo Data (page 2-22) RELATED TOPICS • • • • • • • • Print the Map (page 2-6) Export the Map to a File (page 2-7) Copy and Paste the Map into a Different Program (page 2-9) Manipulating the Map (page 2-10) Change Background and Increase Thickness of Tracings (page 2-11) Change Color/Symbols Parameters (page 2-12) Saving and Loading Display Parameters (page 2-15) Save Data Set (page 2-18) PART 4-PREPARE TO EDIT THE 2D MAP BACKUP ORIGINAL TOPO DATA Before any editing is done in the Atlas Shop.Review & Optimize . If the original data for the map is distributed in several different Topo arrays. the data for the 2D map is saved to a new Topo array. verify that the desired 2D map is displayed in the atlas window. The Topographer will close and BIOQUANT Life Science or BIOQUANT OSTEO will open. the backup process will consolidate the atlas into a single. choose Save Data Set. PROCEDURE • From the File menu.

Open the Atlas Shop by clicking the Atlas Shop button on the Atlas Viewer’s tool bar. Save Array As Dialog Box If there were any Topo arrays in the data set that were not selected as part of the current atlas. Consider upgrading to the full BIOQUANT Topographer plug-in for editing capabilities.) Different versions of the atlas data may be created using the Atlas Shop’s Save As option. From the Atlas Shop’s File menu. THE ATLAS SHOP Atlas Shop is the part of the Topographer that is used to backup original data and correct any color.Page 2-20 2. choose Select All Sections. empty Topo array to the data set. choose Save As. or by choosing Atlas Shop from the Tools menu. from the Select menu. NOTE: The Atlas Shop button is not available if you have the free Topo Reader.Review & Optimize . BIOQUANT Topographer Handbook: 2D Mapping . to insure that all parts of the atlas are selected. or tracing errors introduced during measurement. determine distance between structures.g. The Atlas Shop is also where several additional measurements may be taken from the 2D map (e. On the Save Array As dialog box. click the Resize To Fit Atlas Shop Desktop button. positional. In the Atlas Shop. 4. click the New Array button to add a new. 6. 5. If necessary. to open the Save Array As dialog box. count all objects of a certain type. etc. their names would be visible in the lower pane of the Save Array As dialog box. 3.

8. double-click the new Topo array that was added in the Atlas Shop. 9. on the Select Arrays dialog box. double-click the index number(s) of the currently selected array(s). In the Selected list.Page 2-21 Save Array As Dialog Box With New Topo Array Added and Renamed 7. 11. 10. Re-open the Atlas Shop by clicking the Atlas Shop Atlas Shop from the Tools menu. button on the Atlas Viewer’s tool bar. 12. then the Close button on the Save Array As dialog box. The data in the new Topo array is now ready for editing in the Atlas Shop (and the original data is safely preserved in its original array). to move its index number to the Selected list. In the Atlas Viewer. Click the Save button. then the Resize To Fit button.Review & Optimize . Edit the name of the new Topo array to reflect the fact that it will contain an edited or enhanced version of the atlas. MORE 2-D MAP REVIEW & OPTIMIZING TOPICS Part 1-Open the Desired Data Set (page 2-3) Part 2-Select and Display the 2D Map (page 2-4) Part 3-Optimize the Map Display (page 2-10) Part 5-Correct Errors In Topo Data (page 2-22) RELATED TOPICS • • • • • • • • • Print the Map (page 2-6) Export the Map to a File (page 2-7) Copy and Paste the Map into a Different Program (page 2-9) Manipulating the Map (page 2-10) Change Background and Increase Thickness of Tracings (page 2-11) Change Color/Symbols Parameters (page 2-12) Saving and Loading Display Parameters (page 2-15) Save Data Set (page 2-18) Exit Atlas Viewer (page 2-19) BIOQUANT Topographer Handbook: 2D Mapping . In the Available Arrays list. remove the currently selected array(s) from the Selected list by doing one of the following: • • From the Select menu on the Select Arrays dialog box. On the system tool bar click the Open Atlas button. or by choosing 13. choose Unselect All Arrays. Return to the Atlas Viewer by choosing Exit Atlas Shop from the File menu.

Tool tips appear for the system tool bar only when the system title bar is active (colored. When the cursor is held still over a tool bar button. a tool tip appears briefly to reveal the button’s name. Atlas Shop System Tool Bar In addition to buttons. Tool Tips for the Vertical Tool Bar appear only when the title bar of the Vertical Tool Bar is active. click the cursor on it. the system tool bar contains a Color Palette that is used with the Select By Color and Change Color tools on the Vertical Tool Bar. Most. instead of gray). To activate either title bar. MORE 2-D MAP REVIEW & OPTIMIZING TOPICS Part 1-Open the Desired Data Set (page 2-3) Part 2-Select and Display the 2D Map (page 2-4) Part 3-Optimize the Map Display (page 2-10) Part 4-Prepare to Edit the 2D Map (page 2-19) Part 5-Correct Errors In Topo Data (page 2-22) BIOQUANT Topographer Handbook: 2D Mapping . buttons on the system tool bar and on the Vertical Tool Bar are shortcuts to frequently used options on the system menus.Page 2-22 PART 5-CORRECT ERRORS IN TOPO DATA TOPIC CONTENTS Atlas Shop Tool Bars (page 2-22) The Three Selection Modes (page 2-23) Verify How Data are Grouped in the Atlas Topo Array (page 2-23) Selection Methods (page 2-24) About Saving Edits (page 2-26) Color Correction Procedures (page 2-26) The Line Editing Tools (page 2-30) Reposition or Resize Parts of the Map (page 2-35) MORE 2-D MAP REVIEW & OPTIMIZING TOPICS Part 1-Open the Desired Data Set (page 2-3) Part 2-Select and Display the 2D Map (page 2-4) Part 3-Optimize the Map Display (page 2-10) Part 4-Prepare to Edit the 2D Map (page 2-19) RELATED TOPICS • • • • • • • • • Print the Map (page 2-6) Export the Map to a File (page 2-7) Copy and Paste the Map into a Different Program (page 2-9) Manipulating the Map (page 2-10) Change Background and Increase Thickness of Tracings (page 2-11) Change Color/Symbols Parameters (page 2-12) Saving and Loading Display Parameters (page 2-15) Save Data Set (page 2-18) Exit Atlas Viewer (page 2-19) ATLAS SHOP TOOL BARS The Atlas Shop has two tool bars: the horizontal system tool bar and the Vertical Tool Bar. but not all.Review & Optimize .

meaning that the Section Mode depressed. the Atlas Shop opens in Section Mode. Usually there is only one topographic section in a 2D map (because usually there is only one Landmark set for a single-plane specimen). 2. there is usually only one topographic section in the atlas Topo array. Every tracing or marker in the map is a separate object. etc. Object Mode.Page 2-23 RELATED TOPICS • • • • • • • The Three Selection Modes (page 2-23) Verify How Data are Grouped in the Atlas Topo Array (page 2-23) Selection Methods (page 2-24) About Saving Edits (page 2-26) Color Correction Procedures (page 2-26) The Line Editing Tools (page 2-30) Reposition or Resize Parts of the Map (page 2-35) THE THREE SELECTION MODES In order to work with individual parts of the map. all operations apply only to the currently selected data point(s). all operations (e. choose Select All Sections. BIOQUANT Topographer Handbook: 2D Mapping .g. However. 3. it is important to be aware of the existence of multiple sections before data selection begins in the Atlas Shop. Rotate. PROCEDURE 1. By default. The number of topographic sections in the atlas Topo array can be determined by looking at the Section notation in the Atlas Shop’s title bar. all operations are applied only to the selected object(s). and Point Mode. because usually there was only one Landmark placed on the specimen during measurement. tracings or point markers appear white. Point Mode is rarely used when correcting errors in a 2D map. • • MORE 2-D MAP REVIEW & OPTIMIZING TOPICS Part 1-Open the Desired Data Set (page 2-3) Part 2-Select and Display the 2D Map (page 2-4) Part 3-Optimize the Map Display (page 2-10) Part 4-Prepare to Edit the 2D Map (page 2-19) Part 5-Correct Errors In Topo Data (page 2-22) RELATED TOPICS • • • • • • • Atlas Shop Tool Bars (page 2-22) Verify How Data are Grouped in the Atlas Topo Array (page 2-23) Selection Methods (page 2-24) About Saving Edits (page 2-26) Color Correction Procedures (page 2-26) The Line Editing Tools (page 2-30) Reposition or Resize Parts of the Map (page 2-35) VERIFY HOW DATA ARE GROUPED IN THE ATLAS TOPO ARRAY For a 2D map. A selected part of the atlas will be displayed in color in the Atlas Shop work space. From the Select menu. if this is not the case. • button on the system tool bar is In Section Mode . the particular tracing(s) or markers of interest must first be selected.) are applied to all tracings and markers in the selected topographic section(s).Review & Optimize . Click to activate the Section Mode button. There are three selection modes in the Atlas Shop: Section Mode. When the Object Mode button is depressed. In Point Mode . Translate. When not selected.

objects. • In the unusual case that the 2D map is contained in multiple topographic sections.Page 2-24 • • Section #0. Section #0-n. (where n = a number) means there is more than one topographic section. When working with 2D maps. objects (in Object Mode). Examples: Section #0-1. 1. or data points (in Point Mode).Review & Optimize . 1. means there is only one topographic section. means there are two topographic sections. remember that the section of interest must be selected in Section Mode before switching to Object Mode to work with individual tracings or markers. the section that contains objects of interest must always be selected in Section Mode before switching to Object Mode or Point Mode. click the Select By Color button On the system tool bar’s color palette. When working with 2D maps these tools are most often used in Object Mode to select individual tracings in a map that contains few or no cell markers. 2. Click to activate Object Mode . or one or more data points (in Point Mode). click the color that matches the color of the objects that need to be selected. On the Vertical Tool Bar. you will need to be familiar with the alternate methods. BIOQUANT Topographer Handbook: 2D Mapping . or single data points of interest. regardless of which Selection Mode is currently active. (see Verify How Data are Grouped in the Atlas Topo Array (page 2-23)). The system instantly selects all tracings and markers of that color. If even one data point of a tracing falls within the selection box or polygon. 2. buttons on the system tool bar to sequence through Click the Select Next or Select Previous individual tracings (or markers) in the map. Section #0-2 means there are three topographic sections. these tools are most often used in Object Mode to select individual or multiple objects (tracings or cell markers). but if that method proves to be awkward when working with a particular specimen. one or more objects (in Object Mode). Section numbering in the Atlas Shop always begins with 0. the whole tracing will be selected. SELECT NEXT / SELECT PREVIOUS The Select Next and Select Previous tools on the Vertical Tool Bar can be used to sequence through sections (in Section Mode). SELECT BY COLOR Select By Color operates across the entire atlas. MORE 2-D MAP REVIEW & OPTIMIZING TOPICS Part 1-Open the Desired Data Set (page 2-3) Part 2-Select and Display the 2D Map (page 2-4) Part 3-Optimize the Map Display (page 2-10) Part 4-Prepare to Edit the 2D Map (page 2-19) Part 5-Correct Errors In Topo Data (page 2-22) RELATED TOPICS • • • • • • • Atlas Shop Tool Bars (page 2-22) The Three Selection Modes (page 2-23) Selection Methods (page 2-24) About Saving Edits (page 2-26) Color Correction Procedures (page 2-26) The Line Editing Tools (page 2-30) Reposition or Resize Parts of the Map (page 2-35) SELECTION METHODS There are several different ways to select sections. With experience you may come to favor one selection method over another. SELECT USING RECTANGLE OR POLYGON The Select Using Rectangle and Select Using Polygon tools on the Vertical Tool Bar can be used to select one or more sections (in Section Mode). IMPORTANT • If multiple topographic sections exist.

then click each additional object that is to be selected. choose GoTo.Page 2-25 PROCEDURE: SELECT USING RECTANGLE a. Every cell marker is listed as a separate object. button. From the Select menu. click the first object. click the Select Using Rectangle Position the cursor close to the objects that need to be selected. click one object. SELECT FROM A LIST Sections (in Section Mode) and objects (in Object Mode) may be selected from a Go To list. Click to activate Object Mode . 1. then click a series of points to create a selection polygon around (or across tracings of) the objects of interest. so maps that have hundreds or thousands of cells will result in a very long list. To select multiple.Review & Optimize . 2. On the Vertical Tool Bar. to open the Go To Object list. c. Go To Object List With Four Objects Selected The Ctrl key was used to help select non-contiguous objects in the list. 1. then click and hold the left mouse button while dragging the cursor diagonally to from a selection box around (or across tracings of) the objects of interest. the Go To Object list is best used with maps that do not have lots of cell markers. then click the last object in the series. Tracings with one or more data points inside the polygon will be selected. press and hold the Ctrl key. b. click to highlight its entry in the list. Click to activate Object Mode . Click to activate Object Mode . BIOQUANT Topographer Handbook: 2D Mapping . Click to activate Object Mode . contiguous objects. Add Interior Object to Selection is used only in Object Mode. All objects between and including the first and the last will be selected. • SELECT BY ADDING INTERIOR OBJECTS Add Interior Objects to Selection is an option on the Select menu than can be used when a currently selected tracing encircles other tracings that need to be added to the selection. b. • • To select a single object. PROCEDURE: SELECT USING POLYGON a. non-contiguous objects. When working with 2D maps. button. To select multiple. click the Select Using Polygon Position the cursor close to the objects that need to be selected. On the Vertical Tool Bar. c. Tracings with one or more data points inside the box will be selected. press and hold the Shift key.

From the Select menu. 3. Use any convenient method to select the tracing (object) that encircles other objects. These edits are done only under special circumstances that will be explained later.Page 2-26 2. by simply choosing Save on the Atlas Shop File menu. or Internal Paste are used. Internal Copy. Save As may also be used to save selected parts of the map in a new Topo array. “Save As” is also an option on the Atlas Shop File menu. Three special editing routines actually rearrange the topographic data. and anytime Internal Cut. and is used any time a new version of the atlas needs to be saved. to produce a whole new map. choose Add Interior Object to Selection. MORE 2-D MAP REVIEW & OPTIMIZING TOPICS Part 1-Open the Desired Data Set (page 2-3) Part 2-Select and Display the 2D Map (page 2-4) Part 3-Optimize the Map Display (page 2-10) Part 4-Prepare to Edit the 2D Map (page 2-19) Part 5-Correct Errors In Topo Data (page 2-22) RELATED TOPICS • • • • • • • Atlas Shop Tool Bars (page 2-22) The Three Selection Modes (page 2-23) Verify How Data are Grouped in the Atlas Topo Array (page 2-23) Selection Methods (page 2-24) Color Correction Procedures (page 2-26) The Line Editing Tools (page 2-30) Reposition or Resize Parts of the Map (page 2-35) COLOR CORRECTION PROCEDURES This section covers color correction procedures used in the Atlas Shop. These routines are: Change Resolution. ADDITIONAL INFORMATION • The Atlas Shop has many features that are not used when working with a 2D map. BIOQUANT Topographer Handbook: 2D Mapping .Review & Optimize . and the only way to save the new arrangement is to write the data to a new Topo array (using Save As). MORE 2-D MAP REVIEW & OPTIMIZING TOPICS Part 1-Open the Desired Data Set (page 2-3) Part 2-Select and Display the 2D Map (page 2-4) Part 3-Optimize the Map Display (page 2-10) Part 4-Prepare to Edit the 2D Map (page 2-19) Part 5-Correct Errors In Topo Data (page 2-22) RELATED TOPICS • • • • • • • Atlas Shop Tool Bars (page 2-22) The Three Selection Modes (page 2-23) Verify How Data are Grouped in the Atlas Topo Array (page 2-23) About Saving Edits (page 2-26) Color Correction Procedures (page 2-26) The Line Editing Tools (page 2-30) Reposition or Resize Parts of the Map (page 2-35) ABOUT SAVING EDITS Most edits made to a map can be saved directly to the current atlas Topo array. These other features are explained in the 3D Modeling chapters.

MORE 2-D MAP REVIEW & OPTIMIZING TOPICS Part 1-Open the Desired Data Set (page 2-3) Part 2-Select and Display the 2D Map (page 2-4) Part 3-Optimize the Map Display (page 2-10) Part 4-Prepare to Edit the 2D Map (page 2-19) Part 5-Correct Errors In Topo Data (page 2-22) BIOQUANT Topographer Handbook: 2D Mapping . On the Vertical Tool Bar. 5. PROCEDURE 1. All objects (tracings and/or cell markers) in the atlas of the designated color will be selected. 4. click the Change Color tool. On the Vertical Tool Bar. choose Save.Review & Optimize . click to designate the desired new color. On the color palette. click to designate the current color of the objects of interest. it does not matter which topographic section is currently selected.Page 2-27 TOPIC CONTENTS Assign a New Color to a Group of Objects (page 2-27) Change A Single Tracing Color (page 2-28) Change the Color of One or More Cell Markers (page 2-29) MORE 2-D MAP REVIEW & OPTIMIZING TOPICS Part 1-Open the Desired Data Set (page 2-3) Part 2-Select and Display the 2D Map (page 2-4) Part 3-Optimize the Map Display (page 2-10) Part 4-Prepare to Edit the 2D Map (page 2-19) Part 5-Correct Errors In Topo Data (page 2-22) RELATED TOPICS • • • • • • • Atlas Shop Tool Bars (page 2-22) The Three Selection Modes (page 2-23) Verify How Data are Grouped in the Atlas Topo Array (page 2-23) Selection Methods (page 2-24) About Saving Edits (page 2-26) The Line Editing Tools (page 2-30) Reposition or Resize Parts of the Map (page 2-35) ASSIGN A NEW COLOR TO A GROUP OF OBJECTS A group of like-colored objects (tracings or cell markers) may be quickly selected using the Select By Color tool. On the color palette (on the system tool bar). 3. click the Select by Color tool. Since this procedure selects objects of the same color across all sections of the atlas. Click to depress the Section Mode button on the system tool bar. 6. From the File menu. The selected objects in the atlas will change to the new color. 2.

• If necessary. From the File menu. 3. click to choose the desired new color on the color palette. This is of no concern. until the object that needs to be changed to a new color is selected. object markers.Page 2-28 RELATED TOPICS • • • • • • • • • Change A Single Tracing Color (page 2-28) Change the Color of One or More Cell Markers (page 2-29) Atlas Shop Tool Bars (page 2-22) The Three Selection Modes (page 2-23) Verify How Data are Grouped in the Atlas Topo Array (page 2-23) Selection Methods (page 2-24) About Saving Edits (page 2-26) The Line Editing Tools (page 2-30) Reposition or Resize Parts of the Map (page 2-35) CHANGE A SINGLE TRACING COLOR PROCEDURE 1. If multiple topographic sections exist (see Verify How Data are Grouped in the Atlas Topo Array (page 223)).Review & Optimize . it is likely that the first object in the section is a tiny Object Count marker. choose Save. • TIP: If it appears that nothing in the map has been selected. 5. Repeat from step 3 for any other tracings in this section that need a color change. Only the first object in the section should remain colored. sequence through the individual sections in the map. Click the Object Mode button on the system tool bar. Choosing Save on the File menu permanently alters the data in the current atlas Topo array. For alternate selection methods. Using the Select Next and Select Previous buttons as needed. On the system tool bar. b. Using the most convenient selection method. MORE 2-D MAP REVIEW & OPTIMIZING TOPICS Part 1-Open the Desired Data Set (page 2-3) Part 2-Select and Display the 2D Map (page 2-4) Part 3-Optimize the Map Display (page 2-10) Part 4-Prepare to Edit the 2D Map (page 2-19) Part 5-Correct Errors In Topo Data (page 2-22) BIOQUANT Topographer Handbook: 2D Mapping . 6. This positions and sizes the atlas to fit the work space. The selected tracing will change to the chosen color. button. 2. select the desired tracing. click the Resize to Fit button on the Atlas Shop system tool bar. see Selection Methods (page 2-24). 4. All other objects will be displayed in white. click the Change Color a. do the following: a. On the Vertical Tool Bar. Verify that the Section Mode button is activated (depressed). Example: If there are very few. it may be convenient to use the Select Next and Select Previous buttons to sequence through individual objects. until a section that contains a tracing that needs to be changed to a new color is selected. or no.

use the Pan tool to reposition the zoomed tracings in the work space. do the following: a. 3. Using the left mouse button. it is often useful to magnify the area of interest before using the selection tools. ii. If necessary. click and drag the cursor diagonally to form a rectangular selection box around the objects of interest. click the Zoom tool. b. b. then do the following to select the cell markers of interest: • With the Select Using Rectangle tool. Click the Object Mode button on the system tool bar.Page 2-29 RELATED TOPICS • • • • • • • • • Assign a New Color to a Group of Objects (page 2-27) Change the Color of One or More Cell Markers (page 2-29) Atlas Shop Tool Bars (page 2-22) The Three Selection Modes (page 2-23) Verify How Data are Grouped in the Atlas Topo Array (page 2-23) Selection Methods (page 2-24) About Saving Edits (page 2-26) The Line Editing Tools (page 2-30) Reposition or Resize Parts of the Map (page 2-35) CHANGE THE COLOR OF ONE OR MORE CELL MARKERS One or more individual cell markers may be quickly selected with the Select Using Rectangle or Select Using Polygon tools. If multiple topographic sections exist (see Verify How Data are Grouped in the Atlas Topo Array (page 223)). click the Resize to Fit button on the Atlas Shop system tool bar. To zoom the area of interest. 2. On the Vertical Tool Bar. iii. c. Continue to click the area until the area is sufficiently magnified. ADDITIONAL INFORMATION • • 4. Place the hand-cursor over a point that you would like to move to the center of the work space. • If necessary. click the Select Using Rectangle button or the Select Using Polygon button. BIOQUANT Topographer Handbook: 2D Mapping . Using the Select Next and Select Previous buttons as needed. All other objects will be displayed in white.Review & Optimize . This is of no concern. Clicking the right mouse button will zoom out. • TIP: If it appears that nothing in the map has been selected. Only the first object in the section should remain colored. making the section tracings smaller. (Optional) When selecting small objects like cell markers. click the area of interest to zoom up one level. PROCEDURE 1. Click and drag the hand-cursor to reposition the tracings. click the Pan tool. This positions and sizes the atlas to fit the work space. do the following: a. until a section that contains a tracing that needs to be changed to a new color is selected. On the Vertical Tool Bar. as follows: i. it is likely that the first object in the section is a tiny Object Count marker. sequence through the individual sections in the map. Verify that the Section Mode button is activated (depressed). On the Vertical Tool Bar. Clicking the Resize To Fit button on the system tool bar will resize and center the atlas to fit the work space.

MORE 2-D MAP REVIEW & OPTIMIZING TOPICS Part 1-Open the Desired Data Set (page 2-3) Part 2-Select and Display the 2D Map (page 2-4) Part 3-Optimize the Map Display (page 2-10) Part 4-Prepare to Edit the 2D Map (page 2-19) Part 5-Correct Errors In Topo Data (page 2-22) RELATED TOPICS • • • • • • • • • Assign a New Color to a Group of Objects (page 2-27) Change A Single Tracing Color (page 2-28) Atlas Shop Tool Bars (page 2-22) The Three Selection Modes (page 2-23) Verify How Data are Grouped in the Atlas Topo Array (page 2-23) Selection Methods (page 2-24) About Saving Edits (page 2-26) The Line Editing Tools (page 2-30) Reposition or Resize Parts of the Map (page 2-35) THE LINE EDITING TOOLS The line editing tools on the vertical tool bar correct tracing errors made during data collection. All objects fully or partially contained within the box or polygon will be selected. The selected objects will change to the new color.” “Delete”. On the color palette (system tool bar). Choosing Save on the File menu permanently alters the data in the current atlas Topo array. From the File menu. On the Vertical Tool Bar.Page 2-30 • With the Select Using Polygon tool.Review & Optimize . click the Change Color tool. 6.” “Combine Two Objects. 5. TOPIC CONTENTS Straighten Edge (page 2-31) Combine Two Objects (page 2-32) Separate Two Objects separate (page 2-33) Redefining an Object’s Edge (page 2-34) Deleting Objects (page 2-34) BIOQUANT Topographer Handbook: 2D Mapping . The Line Editing Tools on the Vertical Toolbar From top to bottom the tools are “Straighten Edge. 7.” “Redefine Edge. click to designate the desired new color. click a series of points to form a selection polygon around the objects of interest.” “Separate Two Objects. choose Save.

2. 3. PROCEDURE 1. The second point must always lie counterclockwise from the first point. Click the other end of the segment. MORE 2-D MAP REVIEW & OPTIMIZING TOPICS Part 1-Open the Desired Data Set (page 2-3) Part 2-Select and Display the 2D Map (page 2-4) Part 3-Optimize the Map Display (page 2-10) Part 4-Prepare to Edit the 2D Map (page 2-19) Part 5-Correct Errors In Topo Data (page 2-22) BIOQUANT Topographer Handbook: 2D Mapping . Select the tracing that needs to be Line edited. Keep in mind that the other end of the segment must lie counterclockwise from the first point clicked.Page 2-31 MORE 2-D MAP REVIEW & OPTIMIZING TOPICS Part 1-Open the Desired Data Set (page 2-3) Part 2-Select and Display the 2D Map (page 2-4) Part 3-Optimize the Map Display (page 2-10) Part 4-Prepare to Edit the 2D Map (page 2-19) Part 5-Correct Errors In Topo Data (page 2-22) RELATED TOPICS • • • • • • • • • Assign a New Color to a Group of Objects (page 2-27) Change A Single Tracing Color (page 2-28) Change the Color of One or More Cell Markers (page 2-29) Atlas Shop Tool Bars (page 2-22) The Three Selection Modes (page 2-23) Verify How Data are Grouped in the Atlas Topo Array (page 2-23) Selection Methods (page 2-24) About Saving Edits (page 2-26) Reposition or Resize Parts of the Map (page 2-35) STRAIGHTEN EDGE The Straighten Edge tool is used to replace a segment of tracing. click the Straighten Edge button. 4. with a straight line. Click one end of the segment to be straightened.Review & Optimize . Click the undo button to undo the last line edit. between two clicked points. ADDITIONAL NOTES • • Click the right mouse button to cancel after the first click. The Straighten Edge tool is used only when the distance between the clicked points is small and a straight line between the points is an adequate redefinition of the line. On the Vertical tool bar.

Review & Optimize . 5. Click the Combine Objects button. ADDITIONAL NOTES • • Click the right mouse button to cancel before the series of 4 clicks is finished. The Combine Two Objects tool on the vertical tool bar connects two objects with straight lines which are defined by a series of 4 mouse clicks. Click where one end of the connecting line should be on object A. Click where the other end of the connecting line should be on object B. 6. 4. Click where the other end of the connecting line should be on object A. MORE 2-D MAP REVIEW & OPTIMIZING TOPICS Part 1-Open the Desired Data Set (page 2-3) Part 2-Select and Display the 2D Map (page 2-4) Part 3-Optimize the Map Display (page 2-10) Part 4-Prepare to Edit the 2D Map (page 2-19) Part 5-Correct Errors In Topo Data (page 2-22) BIOQUANT Topographer Handbook: 2D Mapping . Click where one end of the second connecting line should be on object B. 3. Combine Objects Example Clicking in the order shown will connect these two objects 1. 2. This procedure corrects this.Page 2-32 RELATED TOPICS • • • • • • • • • • • • • Combine Two Objects (page 2-32) Separate Two Objects separate (page 2-33) Redefining an Object’s Edge (page 2-34) Deleting Objects (page 2-34) Assign a New Color to a Group of Objects (page 2-27) Change A Single Tracing Color (page 2-28) Change the Color of One or More Cell Markers (page 2-29) Atlas Shop Tool Bars (page 2-22) The Three Selection Modes (page 2-23) Verify How Data are Grouped in the Atlas Topo Array (page 2-23) Selection Methods (page 2-24) About Saving Edits (page 2-26) Reposition or Resize Parts of the Map (page 2-35) COMBINE TWO OBJECTS Sometimes a single object will be thresholded and traced as two separate halves. Click the Undo button to undo the last edit. Select the objects that are to be combined.

Click the undo button to undo the separation. then click the opposite side. Click one side of the single tracing. Clicking two points defines the location for a gap that will separate the single tracing into two separate objects. PROCEDURE 1.Review & Optimize . Click the Separate Two Objects button on the vertical toolbar.Page 2-33 RELATED TOPICS • • • • • • • • • • • • • Straighten Edge (page 2-31) Separate Two Objects separate (page 2-33) Redefining an Object’s Edge (page 2-34) Deleting Objects (page 2-34) Assign a New Color to a Group of Objects (page 2-27) Change A Single Tracing Color (page 2-28) Change the Color of One or More Cell Markers (page 2-29) Atlas Shop Tool Bars (page 2-22) The Three Selection Modes (page 2-23) Verify How Data are Grouped in the Atlas Topo Array (page 2-23) Selection Methods (page 2-24) About Saving Edits (page 2-26) Reposition or Resize Parts of the Map (page 2-35) SEPARATE TWO OBJECTS SEPARATE Sometimes. creating two separate tracings. two objects that lie close together are traced as one. A dividing gap will appear. 3. Select the tracing that needs to be separated into two objects. This procedure corrects this. 2. MORE 2-D MAP REVIEW & OPTIMIZING TOPICS Part 1-Open the Desired Data Set (page 2-3) Part 2-Select and Display the 2D Map (page 2-4) Part 3-Optimize the Map Display (page 2-10) Part 4-Prepare to Edit the 2D Map (page 2-19) Part 5-Correct Errors In Topo Data (page 2-22) RELATED TOPICS • • • • • • • • • • • • • Straighten Edge (page 2-31) Combine Two Objects (page 2-32) Redefining an Object’s Edge (page 2-34) Deleting Objects (page 2-34) Assign a New Color to a Group of Objects (page 2-27) Change A Single Tracing Color (page 2-28) Change the Color of One or More Cell Markers (page 2-29) Atlas Shop Tool Bars (page 2-22) The Three Selection Modes (page 2-23) Verify How Data are Grouped in the Atlas Topo Array (page 2-23) Selection Methods (page 2-24) About Saving Edits (page 2-26) Reposition or Resize Parts of the Map (page 2-35) BIOQUANT Topographer Handbook: 2D Mapping . ADDITIONAL NOTES • • Click the right mouse button after the first click to cancel the separation.

BIOQUANT Topographer Handbook: 2D Mapping . The end point must always lie counterclockwise from the beginning point. Define the end points of the segment that is to be redefined. Keep in mind that the end of the segment must lie counterclockwise from the segment’s beginning point. b. or by responding YES to the Save Data message when exiting the Atlas Shop. Click to mark the end of the segment. Line segments are re-defined by first identifying the beginning and end points of the segment. click a series of data points to define the new contour. The object immediately disappears from the atlas window. 3. SAVING THE EDIT After Redefine Edge is used. Click the right mouse button to end the construction of the new edge. the data in the original atlas Topo array are permanently changed. ADDITIONAL NOTES: • Click the Undo button on the vertical tool bar to undo the redefinition of the contour. then clicking a series of points in a counterclockwise direction from the beginning point.Review & Optimize . This tool is recommended (instead of the Straighten Edge tool) any time a significant portion of an object’s tracing needs to be altered. Starting from the segment’s beginning point and moving in a counterclockwise direction. 2. to save the edited version of the atlas to a new Topo array.Page 2-34 REDEFINING AN OBJECT’S EDGE A segment of a section or object’s contour tracing can be redrawn with the Redefine Edge tool. by doing the following: a. if the atlas is saved using Save on the File menu. PROCEDURE: 1. MORE 2-D MAP REVIEW & OPTIMIZING TOPICS Part 1-Open the Desired Data Set (page 2-3) Part 2-Select and Display the 2D Map (page 2-4) Part 3-Optimize the Map Display (page 2-10) Part 4-Prepare to Edit the 2D Map (page 2-19) Part 5-Correct Errors In Topo Data (page 2-22) RELATED TOPICS • • • • • • • • • • • • • Straighten Edge (page 2-31) Combine Two Objects (page 2-32) Separate Two Objects separate (page 2-33) Deleting Objects (page 2-34) Assign a New Color to a Group of Objects (page 2-27) Change A Single Tracing Color (page 2-28) Change the Color of One or More Cell Markers (page 2-29) Atlas Shop Tool Bars (page 2-22) The Three Selection Modes (page 2-23) Verify How Data are Grouped in the Atlas Topo Array (page 2-23) Selection Methods (page 2-24) About Saving Edits (page 2-26) Reposition or Resize Parts of the Map (page 2-35) DELETING OBJECTS The Delete tool on the vertical toolbar is used to permanently remove the data of a chosen object from the original Topo array. If desirable. 4. Click to mark the beginning point of the segment that is to be redefined. Click the Redefine Edge tool on the vertical tool bar. Save As on the File menu may be used instead.

Review & Optimize . MORE 2-D MAP REVIEW & OPTIMIZING TOPICS Part 1-Open the Desired Data Set (page 2-3) Part 2-Select and Display the 2D Map (page 2-4) Part 3-Optimize the Map Display (page 2-10) Part 4-Prepare to Edit the 2D Map (page 2-19) Part 5-Correct Errors In Topo Data (page 2-22) RELATED TOPICS • • • • • • • • • • • • • Straighten Edge (page 2-31) Combine Two Objects (page 2-32) Separate Two Objects separate (page 2-33) Redefining an Object’s Edge (page 2-34) Assign a New Color to a Group of Objects (page 2-27) Change A Single Tracing Color (page 2-28) Change the Color of One or More Cell Markers (page 2-29) Atlas Shop Tool Bars (page 2-22) The Three Selection Modes (page 2-23) Verify How Data are Grouped in the Atlas Topo Array (page 2-23) Selection Methods (page 2-24) About Saving Edits (page 2-26) Reposition or Resize Parts of the Map (page 2-35) REPOSITION OR RESIZE PARTS OF THE MAP This section covers tools used to reposition or resize parts of the map. ADDITIONAL NOTES: • • The most recent unsaved deletion may be canceled by clicking the Undo button on the vertical tool bar. 2. Note: The removed data is temporarily stored in the Topographer’s backup buffer and the delete does not become permanent until the edits are saved using Save on the File menu or by responding YES to the Save Data message on exiting the Atlas Shop. Click the Delete Object tool on the vertical tool bar. TOPIC CONTENTS Rotate (page 2-36) Translate (page 2-37) Resize (page 2-38) MORE 2-D MAP REVIEW & OPTIMIZING TOPICS Part 1-Open the Desired Data Set (page 2-3) Part 2-Select and Display the 2D Map (page 2-4) Part 3-Optimize the Map Display (page 2-10) Part 4-Prepare to Edit the 2D Map (page 2-19) Part 5-Correct Errors In Topo Data (page 2-22) BIOQUANT Topographer Handbook: 2D Mapping . All unsaved edits may be canceled by choosing Restore Original from the File menu. Click on the tracing of the object to be deleted.Page 2-35 PROCEDURE: 1.

4. place the cursor any where in the atlas window. in Section mode rotated.Review & Optimize . then click and drag the cursor straight down. Selection Methods (page 2-24) Click to activate Object Mode Selection Methods (page 2-24) . then click and drag the cursor straight up. To rotate the object counter-clockwise. SAVING THE EDIT After Rotate is used. 3. if the atlas is saved using Save on the File menu. If multiple sections exist. or by responding YES to the Save Data message when exiting the Atlas Shop. Choosing Restore Original from the File menu will undo all unsaved changes to the atlas. MORE 2-D MAP REVIEW & OPTIMIZING TOPICS Part 1-Open the Desired Data Set (page 2-3) Part 2-Select and Display the 2D Map (page 2-4) Part 3-Optimize the Map Display (page 2-10) Part 4-Prepare to Edit the 2D Map (page 2-19) Part 5-Correct Errors In Topo Data (page 2-22) BIOQUANT Topographer Handbook: 2D Mapping . The object will rotate around this marker. To rotate the object clockwise. If desirable. 5. place the cursor anywhere in the atlas window. to save the edited version of the atlas to a new Topo array.Page 2-36 RELATED TOPICS • • • • • • • • • • • • • • Straighten Edge (page 2-31) Combine Two Objects (page 2-32) Separate Two Objects separate (page 2-33) Redefining an Object’s Edge (page 2-34) Deleting Objects (page 2-34) Assign a New Color to a Group of Objects (page 2-27) Change A Single Tracing Color (page 2-28) Change the Color of One or More Cell Markers (page 2-29) Atlas Shop Tool Bars (page 2-22) The Three Selection Modes (page 2-23) Verify How Data are Grouped in the Atlas Topo Array (page 2-23) Selection Methods (page 2-24) About Saving Edits (page 2-26) Reposition or Resize Parts of the Map (page 2-35) ROTATE PROCEDURE 1. ADDITIONAL INFORMATION • • The Undo button on the vertical tool bar will undo the last rotation. the data in the original atlas Topo array(s) are permanently changed. select the section that contains the object(s) that need to be 2. Click the Rotate button on the vertical tool bar. If desirable. A red marker will appear on the selected object. Save As on the File menu may be used instead. click and drag the red marker to a different location on the object. . the select the object(s) that need to be rotated.

4. If necessary. button on the vertical tool bar. If multiple sections exist. If desirable. . the data in the original atlas Topo array(s) are permanently changed.Page 2-37 RELATED TOPICS • • • • • • • • • • • • • • • • Translate (page 2-37) Resize (page 2-38) Straighten Edge (page 2-31) Combine Two Objects (page 2-32) Separate Two Objects separate (page 2-33) Redefining an Object’s Edge (page 2-34) Deleting Objects (page 2-34) Assign a New Color to a Group of Objects (page 2-27) Change A Single Tracing Color (page 2-28) Change the Color of One or More Cell Markers (page 2-29) Atlas Shop Tool Bars (page 2-22) The Three Selection Modes (page 2-23) Verify How Data are Grouped in the Atlas Topo Array (page 2-23) Selection Methods (page 2-24) About Saving Edits (page 2-26) Reposition or Resize Parts of the Map (page 2-35) TRANSLATE Choosing Translate from the Edit menu or clicking the Translate button on the vertical tool bar readies the cursor to reposition the selected part of the atlas in the XY plane. 3. or choose Translate from the Edit menu.Review & Optimize . to save the edited version of the atlas to a new Topo array. the select the object(s) that need to be rotated. then use the arrow keys on the keyboard to move the selected item up. select the section that contains the object(s) that need to be 2. down. Save As on the File menu may be used instead. click the Undo button on the vertical tool bar to undo the last translation. Move the selected item using one of the following methods: a. Press and hold the Control key. 5. MORE 2-D MAP REVIEW & OPTIMIZING TOPICS Part 1-Open the Desired Data Set (page 2-3) Part 2-Select and Display the 2D Map (page 2-4) Part 3-Optimize the Map Display (page 2-10) Part 4-Prepare to Edit the 2D Map (page 2-19) Part 5-Correct Errors In Topo Data (page 2-22) BIOQUANT Topographer Handbook: 2D Mapping . Selection Methods (page 2-24) Click to activate Object Mode Selection Methods (page 2-24) Click the Translate . or by responding YES to the Save Data message when exiting the Atlas Shop. click and drag the selected item(s) to the new position. or left. if the atlas is saved using Save on the File menu. Using the left mouse button. right. PROCEDURE: 1. b. in Section mode rotated. SAVING THE EDIT After Translate is used. or choose Restore Original from the File menu to undo all unsaved changes to the atlas.

if the atlas is saved using Save on the File menu.Page 2-38 RELATED TOPICS • • • • • • • • • • • • • • • • Rotate (page 2-36) Resize (page 2-38) Straighten Edge (page 2-31) Combine Two Objects (page 2-32) Separate Two Objects separate (page 2-33) Redefining an Object’s Edge (page 2-34) Deleting Objects (page 2-34) Assign a New Color to a Group of Objects (page 2-27) Change A Single Tracing Color (page 2-28) Change the Color of One or More Cell Markers (page 2-29) Atlas Shop Tool Bars (page 2-22) The Three Selection Modes (page 2-23) Verify How Data are Grouped in the Atlas Topo Array (page 2-23) Selection Methods (page 2-24) About Saving Edits (page 2-26) Reposition or Resize Parts of the Map (page 2-35) RESIZE PROCEDURE 1. sequencing to the Next item will cause the resize box to automatically adjust to fit the size of the new selection.Review & Optimize . • BIOQUANT Topographer Handbook: 2D Mapping . Save As on the File menu may be used instead. If desirable. To expand or shrink the object while maintaining its current height and width ratio. click and drag the resize control point on the top of the resize box. or by responding YES to the Save Data message when exiting the Atlas Shop. in Section mode rotated. select the section that contains the object(s) that need to be 2. To increase or decrease the height of the object while maintaining its current width. Selection Methods (page 2-24) Click to activate Object Mode Selection Methods (page 2-24) Click the Resize . button on the vertical tool bar. • • • . If multiple sections exist. When resizing is finished for the currently selected item. the data in the original atlas Topo array(s) are permanently changed. ADDITIONAL INFORMATION • • Clicking the Undo button on the vertical tool bar will undo the last resizing. SAVING THE EDIT After Resize is used. 3. click an alternate tool on the vertical tool bar. to save the edited version of the atlas to a new Topo array. To remove the resize box from the atlas. click and drag the resize control point in the lower left corner of the resize box. Choosing Restore Original from the File menu will undo all unsaved edits. the select the object(s) that need to be resized. To narrow or widen the object while maintaining its current height. A resizing box will appear around the selected object(s). The selection may be resized without maintaining the height to width ratio using Numeric Transform. click and drag the resize control point on the right side of the resize box.

Page 2-39 MORE 2-D MAP REVIEW & OPTIMIZING TOPICS Part 1-Open the Desired Data Set (page 2-3) Part 2-Select and Display the 2D Map (page 2-4) Part 3-Optimize the Map Display (page 2-10) Part 4-Prepare to Edit the 2D Map (page 2-19) Part 5-Correct Errors In Topo Data (page 2-22) RELATED TOPICS • • • • • • • • • • • • • • • • Rotate (page 2-36) Translate (page 2-37) Straighten Edge (page 2-31) Combine Two Objects (page 2-32) Separate Two Objects separate (page 2-33) Redefining an Object’s Edge (page 2-34) Deleting Objects (page 2-34) Assign a New Color to a Group of Objects (page 2-27) Change A Single Tracing Color (page 2-28) Change the Color of One or More Cell Markers (page 2-29) Atlas Shop Tool Bars (page 2-22) The Three Selection Modes (page 2-23) Verify How Data are Grouped in the Atlas Topo Array (page 2-23) Selection Methods (page 2-24) About Saving Edits (page 2-26) Reposition or Resize Parts of the Map (page 2-35) BIOQUANT Topographer Handbook: 2D Mapping .Review & Optimize .

Page 2-40 BIOQUANT Topographer Handbook: 2D Mapping .Review & Optimize .

Procedures below that begin with the word “Part” should be performed in the given order. Entering the Topographer (page 3-2) Part 1-Display The Atlas (page 3-2) Part 2-A Quick Look at the Surface Rendered Model (page 3-5) Part 3-Save the Atlas to a New Array (page 3-6) Part 4-General Section Review (page 3-7) Introduction To The Atlas Shop (page 3-11) Color Editing Procedures (page 3-27) Section Alignment Procedures (page 3-32) Z-Axis Re-Distribution Procedures (page 3-37) Special Formatting Features (page 3-48) Other Atlas Shop Features (page 3-53) .Review & Review & Optimize the 3D Data Optimize the This section gives instructions for finding and 3D Data BIOQUANT Topographer Handbook correcting errors introduced during measurement and for applying special formatting to enhance the quality of a surface rendered model.3D Modeling 3D Modeling .

or recorded in a movie while it rotates. choose Close to close the Atlas Window. resized. The model can be saved in various file formats. While in the Atlas Viewer. the user may experiment with color or rotational changes without fear of altering the original topo data. If the Atlas Window is open.Page 3-2 ENTERING THE TOPOGRAPHER When the word “Topographer” is clicked on the Life Science or OSTEO menu bar. choose Open Data Set to display the Open a Data Set dialog box. Look at the Data Volume and Data Set listed on the Topographer’s title bar. then from the Atlas menu. the reconstruction may be moved. rotated. the data set that was open in BIOQUANT Life Science or BIOQUANT OSTEO when the Topographer program was accessed is open in the Topographer and its arrays are visible in the Select Arrays dialog box. Atlas Shop . BIOQUANT Topographer Handbook: 3D Modeling . Different versions of the atlas may be saved using the Atlas Shop’s Save As option. The atlas may also be printed or saved to a file while in the Atlas Viewer. From the File menu.) may be taken directly from the 3D atlas. volume. It is the where Topo arrays that contain the topographic data for the reconstruction are selected and displayed as a wire frame structure called an atlas. If this is not the data set you would like opened. • Atlas Viewer . The Atlas Shop is also were measurements (e. Following is a brief review of the Topographer’s three parts. surfaces may be made more transparent or hidden completely. a. “door ways” into the Atlas Shop and the Atlas Modeler become available. To reveal internal structures. etc. b. and lighted in various ways.This is the Topographer’s “front room”. Once an atlas is displayed. the Topographer’s Atlas Viewer opens.This is the part of the Topographer that is used to check for and correct any errors introduced during measurement. Different versions of the surface rendered model may be saved in the Atlas Modeler. printed. do the following to open the desired data set: By default. distance between structures.g. Atlas Modeler . make adjustments that increase the speed of rendering. • • TOPIC CONTENTS Part 1-Display The Atlas (page 3-2) Part 2-A Quick Look at the Surface Rendered Model (page 3-5) Part 3-Save the Atlas to a New Array (page 3-6) Part 4-General Section Review (page 3-7) RELATED TOPICS • • • • • Color Editing Procedures (page 3-27) Section Alignment Procedures (page 3-32) Z-Axis Re-Distribution Procedures (page 3-37) Special Formatting Features (page 3-48) Other Atlas Shop Features (page 3-53) PART 1-DISPLAY THE ATLAS 1.The final surface rendered model is generated in the Atlas Modeler. In the Atlas Modeler. or add formatting that will produce special effects in the surface rendered model.Review & Optimize the 3D Data .

on the Select Arrays dialog box. In the Atlas Viewer. The arrays of the data set appear in the Select Arrays box. to move its index number into the Selected list. may be removed from the Selected list by double clicking the array’s index number in the Selected list. click the Resize To Fit button. Click the Open button. On the Atlas Viewer’s tool bar. e. Click the Browse button to open the Choose BQ Volume Search Directory box. 2. iii. 3. 4.Page 3-3 The Open a Data Set Dialog Box c. any measurement arrays or Topo arrays. The Choose BQ Volume Search DIrectory Box ii.Review & Optimize the 3D Data . On the Atlas Viewer’s tool bar. or from the Atlas menu choose New. Alternately: All of the arrays in the set may be selected at once by choosing Select All Arrays from the Select menu on the Select Arrays dialog box. double click each of the Topo arrays that contain data for the desired reconstruction. BIOQUANT Topographer Handbook: 3D Modeling . f. that do not contain relevant data. Click on the desired data set in the Data Sets list. The wire frame atlas will be visible in the Atlas Window and the Atlas Parameters dialog box will open. Click on a data volume in the Data Volumes list to display its data sets in the Data Sets list. d. Click the Select button. If the desired data volume is not shown: i. Select the directory that contains the desired data volume. click the New Atlas Window button. Then.

even if the rendering appears adequate at first glance. Atlas Viewer features. Working With 3D Wire Frame Atlases (page 5-2) The Atlas Viewer Desktop With an Open Atlas Window When the Topographer first opens. containing data for the desired reconstruction.Page 3-4 ADDITIONAL INFORMATION In the Atlas Viewer. An Atlas Window is opened after Topo arrays. Afterward. For instance. MORE 3-D MODELING REVIEWING & OPTIMIZATION TOPICS Part 1-Display The Atlas (page 3-2) Part 2-A Quick Look at the Surface Rendered Model (page 3-5) Part 3-Save the Atlas to a New Array (page 3-6) Part 4-General Section Review (page 3-7) RELATED TOPICS • • • • • Color Editing Procedures (page 3-27) Section Alignment Procedures (page 3-32) Z-Axis Re-Distribution Procedures (page 3-37) Special Formatting Features (page 3-48) Other Atlas Shop Features (page 3-53) BIOQUANT Topographer Handbook: 3D Modeling .Review & Optimize the 3D Data . are selected. it usually indicates that all section maps currently have the same Z Value. Print. only the Select Arrays dialog box is visible in the Atlas Viewer’s work space. This is easily corrected in the Atlas Shop. Fill. Taking a quick look at the atlas in its surface rendered form is both fun and informative. and many others. the wire frame atlas may also be manipulated in various ways and/or printed. it is sometimes useful to create a version of the wire frame atlas in the Atlas Viewer that shows internal structure tracings filled with color. 5. Do not be concerned if the model does not look good at this point. Small changes made in the Atlas Shop can make a dramatic difference in how the model is rendered. in addition to creating a fully surface rendered model. Continue with “Part 2-A Quick Look at the Surface Rendered Model” on page 3-5. it is important to move the atlas into the Atlas Shop for closer examination. If a surface rendered model does not show up at all.

A large atlas will take a few seconds to load. Afterward. it combines all of the data into a single array. Make a note to use the Redefine Edge tool on the affected sections. make a note that additional sections may need to be measured. Do slow. Repeat slow. b. Continue with “Part 3-Save the Atlas to a New Array” on page 3-6. short drags in the same direction to increase the rotation in one direction. MORE 3-D MODELING REVIEWING & OPTIMIZATION TOPICS Part 1-Display The Atlas (page 3-2) Part 2-A Quick Look at the Surface Rendered Model (page 3-5) Part 3-Save the Atlas to a New Array (page 3-6) Part 4-General Section Review (page 3-7) BIOQUANT Topographer Handbook: 3D Modeling . or holes? A variety of imperfections in the surface rendering will disappear after section maps are properly aligned in the Atlas Shop. if the data for the atlas exists in multiple Topo arrays. it usually indicates that all section maps currently have the same Z Value. Before work in the Atlas Shop begins. The Atlas Modeler will open and automatically display a rendered model. • • • 4. That procedure is: Reduce Atlas Resolution (page 3-48). even if the rendering appears adequate at first glance. cracks. it insures that an original copy of the data is readily accessible if needed. Do not be concerned if the model does not look good at this point. Make a note that Z-Values must be corrected in the Atlas Shop and skip ahead to: Introduction To The Atlas Shop (page 3-11). straight. or right to left). Close the Atlas Modeler by choosing Close from the File menu. click the Atlas Modeler button . it is important to move the atlas into the Atlas Shop for closer examination. PROCEDURE 1. The Atlas Viewer will reopen. click and hold the left mouse button. Note any other problems that you immediately recognize. Doing this serves two purposes: First. shelves. Second. horizontal line (either left to right. short drags in the opposite direction to reverse the rotation. Answer the following questions: • Does the model’s shape reflect the shape of the physical specimen before it was sectioned? If not. it is prudent to save the original atlas data to a new Topo array.Page 3-5 PART 2-A QUICK LOOK AT THE SURFACE RENDERED MODEL Taking a quick look at the atlas in its surface rendered form is both fun and informative. The model will rotate in the direction the cursor moves. Small changes made in the Atlas Shop can make a dramatic difference in how the model is rendered. Verify that the Rotate button on the tool bar is depressed. With the cursor any where in the model display space. nicks. If the model took a long time to load. Large atlases will take a moment to respond to the cursor’s movement. 5. • If a surface rendered model does not appear at all. Rotate the model back and forth a few times by doing the following: a. If a surface rendered model does not show up at all. This is easily corrected in the Atlas Shop. then very slowly drag the cursor in a short. 3. Are there unnaturally” flat” places in the rendered surface? This sometimes occurs if sections were manually traced by clicking points (with Keyboard Termination active) and there were insufficient points clicked to describe the curve of section outlines. it probably means that all of the sections maps currently have the same Z Offset value. make a note to decrease the resolution of the tracings that define the outermost surface. • 2. The cause and solution of problems becomes more apparent in the Atlas Shop. or a few of the existing section tracings may need to be duplicated to “fill in” for missing sections.Review & Optimize the 3D Data . Does the model’s surface have folds. which is easier to manipulate. On the Atlas Viewer’s tool bar.

Its name will appear in the Array Name edit field. Second.Page 3-6 RELATED TOPICS • • • • • Color Editing Procedures (page 3-27) Section Alignment Procedures (page 3-32) Z-Axis Re-Distribution Procedures (page 3-37) Special Formatting Features (page 3-48) Other Atlas Shop Features (page 3-53) PART 3-SAVE THE ATLAS TO A NEW ARRAY Before work in the Atlas Shop begins. click the Atlas Shop button to update the Atlas Window with the new atlas. click the Arrays menu. then choose Unselect All Arrays. it combines all of the data into a single array. and so on. 10. If there are Topo arrays in the data set that were NOT selected as part of the current atlas. 2. 3. On the system tool bar. All of the data for the atlas will be copied into the one new array. you may select it instead of adding another Topo array.Review & Optimize the 3D Data . choose Exit Atlas Shop to return to the Atlas Viewer. to move its index number into the Selected list. if it becomes necessary to save another new version of the atlas. click the New Array button to add a new Topo array to the data set. button to reopen the Atlas Shop. Use a name that distinguishes it from the original. If one of the listed arrays is empty (has no data). The original atlas arrays must now be unselected and the new atlas array selected for use. 9. Example: If the original atlas data are distributed in multiple Topo arrays. it insures that an original copy of the data is readily accessible if needed. Click the Save button. rename the empty or newly added Topo array. scroll to and double click the new Atlas Topo array. In the Array Name edit field. From the File menu. In the Available Arrays list of the Select Arrays dialog box. the next version might be named “Atlas 2”. choose Save As to open the Save Array As dialog box. Save Array As Dialog Box (before and after atlas data is saved to a new Topo array) The atlas data (whether it is currently in a single Topo array or distributed in many Topo arrays) is saved to a new Topo array to preserve the original data in its unedited form. it is prudent to save the original atlas data to a new Topo array. If still in the Atlas Viewer. BIOQUANT Topographer Handbook: 3D Modeling . Later. from the File menu. on the Select Arrays dialog box. click the Redraw On the system tool bar. since the new Topo array will contain all the data for the atlas. On the Save Array As dialog box. button on the system tool bar (or choose Tools menu> Atlas In the Atlas Shop. 7. Click to highlight the empty array in the Topo array list. 8. 6. you might name this copy of the atlas “Atlas 1”. 4. which is easier to manipulate. All of the arrays in the Selected list will be removed. click the Atlas Shop Shop) to open the Atlas Shop. their names will be listed on the Save Array As dialog box. if the data for the atlas exists in multiple Topo arrays. 5. In the Atlas Viewer. PROCEDURE 1. Doing this serves two purposes: First.

button is depressed on the system tool bar. IF SECTIONS WERE MEASURED OUT OF ORDER. and/or will provided an opportunity to make desirable color changes or add special formatting to improve the appearance of the rendered model. and/or will provided an opportunity to make desirable color changes or add special formatting to improve the appearance of the rendered model. (Optional) If you want to hide all tracings that are not part of the selected section map. During the review and editing process. click to place a check mark next to Selection Only. If physical sections were measured out of order. section by section. Part 2-A Quick Look at the Surface Rendered Model (page 3-5) The system numbers topographic sections according to their positions in the Topo array. . sometimes not. 3. on the View menu. Continue with “Part 4-General Section Review” on page 3-7. 2. looking for and correcting any of the problems that are listed below.Page 3-7 11. This positions and sizes the atlas to fit the work space. will reveal the sources of any problems that were apparent in the surfaced rendered model. before beginning the General Section Review. Using the Select Next and Select Previous buttons on the system tool bar. keep in mind the following points: • Anytime an edited version of the atlas is saved to a new array. MORE 3-D MODELING REVIEWING & OPTIMIZATION TOPICS Part 1-Display The Atlas (page 3-2) Part 2-A Quick Look at the Surface Rendered Model (page 3-5) Part 3-Save the Atlas to a New Array (page 3-6) Part 4-General Section Review (page 3-7) RELATED TOPICS • • • • • Color Editing Procedures (page 3-27) Section Alignment Procedures (page 3-32) Z-Axis Re-Distribution Procedures (page 3-37) Special Formatting Features (page 3-48) Other Atlas Shop Features (page 3-53) PART 4-GENERAL SECTION REVIEW Scrolling through the atlas. the out-of-order section numbers may be confusing. during the section by section review. • Possible Color Problems (page 3-8) BIOQUANT Topographer Handbook: 3D Modeling . Verify that the Section Mode Select Section 0. Glance at the system title bar to verify that Section 0 is selected. to see the effects of editing. During the process of finding and correcting problems. you will sequence through all of the sections in the atlas several times. it is useful to exit the Atlas Shop occasionally. The Z Sort option rearranges topographic sections according to their assigned Z Values. will reveal the sources of any problems that were apparent in the surfaced rendered model. you must momentarily exit the Atlas Shop and in the Atlas Viewer select the new array. before any further edits are made. Use this option when there is a clear reason to do so. Hiding all but the tracings of the currently selected section is sometimes helpful. Click the Resize to Fit button on the Atlas Shop system tool bar. section by section. and take another quick look at the atlas in the Atlas Modeler. perform the procedure: Z-Sort Topographic Sections (page 3-40) • • PROCEDURE 1.Review & Optimize the 3D Data • 4. Scrolling through the atlas. See steps 6-10 of the procedure: Part 3-Save the Atlas to a New Array (page 3-6). See “The Selection Methods” on 3-15.

use the suggested corrective procedure. The default surface rendering of an atlas may be modified to enhance the final three dimensional model. usually the shortest. unique color to a tracing use the procedure: Change A Single Tracing Color (page 3-27). to assign a new. must be assigned a different color in the Atlas Shop to insure proper rendering. If this is not the case.Page 3-8 • • • 5. • • • • • RETURN TO Part 4-General Section Review (page 3-7) BIOQUANT Topographer Handbook: 3D Modeling . Tracings that comprise one branch.Review & Optimize the 3D Data . If your atlas does not have these characteristics. Within any individual section map: Every tracing will be a unique color.) For any un-branched structure that spans multiple sections. also see the next bullet point. change the color of each incorrectly colored outline using the procedure: Change A Single Tracing Color (page 3-27). MORE 3-D MODELING REVIEWING & OPTIMIZATION TOPICS Part 1-Display The Atlas (page 3-2) Part 2-A Quick Look at the Surface Rendered Model (page 3-5) Part 3-Save the Atlas to a New Array (page 3-6) Part 4-General Section Review (page 3-7) RELATED TOPICS • • • • • Color Editing Procedures (page 3-27) Section Alignment Procedures (page 3-32) Z-Axis Re-Distribution Procedures (page 3-37) Special Formatting Features (page 3-48) Other Atlas Shop Features (page 3-53) POSSIBLE COLOR PROBLEMS An atlas that has been correctly colored for surface rendering will have certain characteristics. tracings will be the same color in every section map in which the structure appears. Possible Alignment Problems (page 3-9) Possible Z-Axis Spacing Problems (page 3-9) Possibility of a Branched Structure (page 3-11) Continue with “3D Modeling: Surface Rending in the Atlas Modeler” on page 4-1. (If a change is necessary. change the color of each incorrectly colored tracing using the procedure: Change A Single Tracing Color (page 3-27). anywhere in the atlas. tracings will initially be the same color on all sections. If this is not the case. The exception to this rule is small tracings or markers that represent clusters of the same type cell. If this is not the case. to a new color using the procedure: Assign a New Color to a Group of Objects (page 3-28). • The surface-defining outlines of sections in all section maps will be the same color. If a 3D branched structure exists in the atlas. you may simultaneously change all tracings or markers of that color. use the procedure: Change the Color Of One Branch of a Y or VShaped Structure (page 3-30) Cell markers or cell area tracings for any one type of cell will be the same color in all section maps. use the procedure: Change the Color of One or More Cell Markers (page 3-28) If a color that was used during measurement is not satisfactory. The rotating model can be recorded in an AVI movie. For any branched (Y or V-shaped) structure that spans multiple sections. If this is not the case.

Page 3-9 RELATED TOPICS • • • • • Color Editing Procedures (page 3-27) Section Alignment Procedures (page 3-32) Z-Axis Re-Distribution Procedures (page 3-37) Special Formatting Features (page 3-48) Other Atlas Shop Features (page 3-53) POSSIBLE ALIGNMENT PROBLEMS The system initially stacks topographic sections (the individual section maps) by aligning their landmarks. Misalignment of section maps can be caused by forgetting to place a Landmark on one or more sections during measurement. the black panel to the right of the atlas work space. reveals the spacing of section maps along the Z axis. If there is any evidence of misalignment. be sure to return to the Atlas Viewer. deselect the currently selected atlas array. it is obvious that some sections need to be moved or rotated to line up properly with adjacent sections. or may be due simply to differences in size or orientation of the original physical sections. perform the section alignment procedures that seem relevant and save the edits. non-adjacent section outlines appeared to have been connected during surface rendering.Review & Optimize the 3D Data . As often as necessary or desirable. placing the Landmark indiscriminately on sections that do not contain the landmark structure that was used on other sections. BIOQUANT Topographer Handbook: 3D Modeling . Section Alignment Procedures (page 3-32) In the Atlas Modeler. move the atlas into the Atlas Modeler to see the effects of editing. before continuing with the section by section review in the Atlas Shop. The Line Editing Tools (page 3-24) • • RETURN TO Part 4-General Section Review (page 3-7) RELATED TOPICS • • • • • Color Editing Procedures (page 3-27) Section Alignment Procedures (page 3-32) Z-Axis Re-Distribution Procedures (page 3-37) Special Formatting Features (page 3-48) Other Atlas Shop Features (page 3-53) POSSIBLE Z-AXIS SPACING PROBLEMS In Z Perspective. there were unexpected nicks. (The surface should connect a section outline with the ones that are immediately adjacent to it. it is obvious that some object tracings are incorrect and need to be deleted or redefined using the Line Edit tools. but the initial alignment almost always needs to be refined. ADDITIONAL INFORMATION • If the edited version of the atlas is saved to a new Topo array (using Save As).) Section Alignment Procedures (page 3-32) In the Atlas Shop. This is a good start. shelves. Section Alignment Procedures (page 3-32) In the Atlas Shop. • EVIDENCE OF MISALIGNMENT • • In the Atlas Modeler. and select the new array. or open spaces in the rendered surface.

There are conjoint section maps due to the lack of a landmark on one or more sections. On the system tool bar. to evaluate the situation further and make corrections if necessary. An existing section map may be duplicated and reassigned an appropriate Z Value. This indicates that all sections currently have the same Z Offset Value. The number of section lines in the black Perspective panel is less than the number of total sections indicted in the Atlas Shop’s title bar. Use the corrective procedure: Reposition Misplaced Points (page 3-47) • • • • • • REMINDER Anytime an edited version of the atlas is saved to a new Topo array (using Save As or using any of the special Save Array As dialog boxes that open during editing). and select the new array. This also indicates conjoint section maps due to the lack of a landmark on one or more sections. instead of only one. In the Atlas Shop’s title bar. RETURN TO Part 4-General Section Review (page 3-7) BIOQUANT Topographer Handbook: 3D Modeling . Occasionally. Use the corrective procedure: Distribute Section Maps Evenly Along the Z-Axis (page 3-37) The section lines in the Perspective panel are positioned as expected. verify that both the Section Mode and the Z Perspective buttons are depressed. choose Select All Sections. The Z Offset value currently assigned to one or more sections is incorrect. In Z Perspective mode. From the Select menu. when you click Next Section. Use the procedure: Dealing With Conjoint Sections (page 3-42). Use the corrective procedure: Change the Z Value of a Section Map (page 3-38) The physical sections you measured were equal distances apart. be sure to return to the Atlas Viewer. but section lines in the black Perspective panel are not. 2.Review & Optimize the 3D Data . If data point in one of the sections is corrupted or misplaced. One or more section maps currently have the same Z Offset value. before continuing with the section by section review in the Atlas Shop. 3. afterwards return to this page and check for other Z-axis spacing problems. to evaluate the situation further and make corrections if necessary. deselect the currently selected atlas array.Page 3-10 PROCEDURE 1. Use the procedure: Dealing With Conjoint Sections (page 3-42). note the total number of section maps in the atlas. Use the corrective procedure: Distribute Section Maps Evenly Along the Z-Axis (page 3-37) The total number of section maps reported in the Atlas Shop’s title bar is less than the number of physical sections you measured. two or more section maps are selected. the vertical line in the black Perspective panel represents the Z axis. Example: If there are 20 section maps in the atlas. 4. to fill-in for missing sections. If it is necessary to turn to a corrective procedure. but there are unwanted gaps in their spacing. due the fact that one or more physical sections were missing and could not be measured. Horizontal lines represent individual section maps as they are currently defined in the Topo array. but there is only one horizontal line in the black Perspective panel. there is a stray vertical line (other than the Z axis line) between two of the horizontal section lines. the title bar will show: Section #0-19 Decide if there is evidence of Z-axis spacing problems by scrolling through the atlas and comparing what you see to the points below. EVIDENCE OF Z-AXIS SPACING PROBLEMS • The atlas has multiple section maps. Use the procedure: Duplicate A Section (page 3-45) In the Perspective panel.

Review & Optimize the 3D Data . go to the procedure: Change the Color Of One Branch of a Y or V-Shaped Structure (page 3-30) RETURN TO Part 4-General Section Review (page 3-7) RELATED TOPICS • • • • • Color Editing Procedures (page 3-27) Section Alignment Procedures (page 3-32) Z-Axis Re-Distribution Procedures (page 3-37) Special Formatting Features (page 3-48) Other Atlas Shop Features (page 3-53) INTRODUCTION TO THE ATLAS SHOP IMPORTANT Selection Modes and Selection Methods.Page 3-11 RELATED TOPICS • • • • • Color Editing Procedures (page 3-27) Section Alignment Procedures (page 3-32) Z-Axis Re-Distribution Procedures (page 3-37) Special Formatting Features (page 3-48) Other Atlas Shop Features (page 3-53) POSSIBILITY OF A BRANCHED STRUCTURE The system creates surfaces by looking for corresponding points of the same color on adjacent section maps. When the Z Perspective is chosen. PROCEDURE 1. the defining surface outline breaks into two sets of outlines and the system must deal with the sudden appearance of “too many points” that do not correspond. Making the “shorter” branch of the Y or V shaped structure a different color. THINK 3D. the Perspective panel shows the section maps as horizontal lines distributed along the vertical Z axis. As you scroll through the 2D section maps in the atlas. For branched (Y or V shaped) structures. included in this Introduction. The atlas is displayed for review. or measurement on the Atlas Shop’s work space. are important to understand. eliminates the confusion. because you will be using them repeatedly during the section review. than the longer branch. If there are any branched structures in the atlas that span multiple section maps. editing. BIOQUANT Topographer Handbook: 3D Modeling . Look for tracings on adjacent section maps that define a three dimensional branched structure. A two-axis sketch of the atlas is also shown in the black Perspective panel along the right hand side of the work space. The “shorter” branch will have fewer total tracings (will appear on fewer section maps). 2.

Review & Optimize the 3D Data .Page 3-12 The Atlas Shop Interface The system tool bar (horizontal) and the Vertical Tool Bar hold action buttons. The system tool bar also holds a color palette. TOPIC CONTENTS Title Bar and Tool Bars (page 3-13) Save Versus Save As (page 3-13) The Three Selection Modes (page 3-14) The Selection Methods (page 3-15) The Line Editing Tools (page 3-24) RELATED TOPICS • • • • • • • • • • • • • • • Possible Color Problems (page 3-8) Possible Alignment Problems (page 3-9) Possible Z-Axis Spacing Problems (page 3-9) Distribute Section Maps Evenly Along the Z-Axis (page 3-37) Change the Z Value of a Section Map (page 3-38) Z-Sort Topographic Sections (page 3-40) Dealing With Conjoint Sections (page 3-42) Duplicate A Section (page 3-45) Reposition Misplaced Points (page 3-47) Color Editing Procedures (page 3-27) Section Alignment Procedures (page 3-32) Z-Axis Re-Distribution Procedures (page 3-37) Other Atlas Shop Features (page 3-53) Numeric Transform (page 3-54) Special Atlas Shop FEatures (page 3-58) 3-D MODELING REVIEWING & OPTIMIZATION TOPICS • • • • Part 1-Display The Atlas (page 3-2) Part 2-A Quick Look at the Surface Rendered Model (page 3-5) Part 3-Save the Atlas to a New Array (page 3-6) Part 4-General Section Review (page 3-7) BIOQUANT Topographer Handbook: 3D Modeling .

Three special editing routines actually rearrange the topographic data. To activate either title bar. Section numbers always begin at 0.6) Atlas Shop Title. “Save As” is also an option on the Atlas Shop File menu. Tool Tips for the Vertical Tool Bar appear only when the title bar of the Vertical Tool Bar is active. with different colors or special formatting. Menu. click the cursor on it. by simply choosing Save on the Atlas Shop File menu.Review & Optimize the 3D Data . In the title bar below. or Internal Paste are used. RELATED TOPICS • • • • • • • • • • • • • • • • • • • Save Versus Save As (page 3-13) The Three Selection Modes (page 3-14) The Selection Methods (page 3-15) The Line Editing Tools (page 3-24) Possible Color Problems (page 3-8) Possible Alignment Problems (page 3-9) Possible Z-Axis Spacing Problems (page 3-9) Distribute Section Maps Evenly Along the Z-Axis (page 3-37) Change the Z Value of a Section Map (page 3-38) Z-Sort Topographic Sections (page 3-40) Dealing With Conjoint Sections (page 3-42) Duplicate A Section (page 3-45) Reposition Misplaced Points (page 3-47) Color Editing Procedures (page 3-27) Section Alignment Procedures (page 3-32) Z-Axis Re-Distribution Procedures (page 3-37) Other Atlas Shop Features (page 3-53) Numeric Transform (page 3-54) Special Atlas Shop FEatures (page 3-58) 3-D MODELING REVIEWING & OPTIMIZATION TOPICS • • • • Part 1-Display The Atlas (page 3-2) Part 2-A Quick Look at the Surface Rendered Model (page 3-5) Part 3-Save the Atlas to a New Array (page 3-6) Part 4-General Section Review (page 3-7) SAVE VERSUS SAVE AS Most edits can be saved directly to the current atlas Topo array. Save As may also be used in order to make multiple versions of the atlas. BIOQUANT Topographer Handbook: 3D Modeling . and is used any time a new version of the atlas needs to be saved. buttons on the system tool bar and on the Vertical Tool Bar are shortcuts to frequently used options on the system menus. and the only way to save the new arrangement is to write the data to a new Topo array (using Save As). Internal Copy. These routines are: Z-Sort. Most. and System Tool Bars Tool Tips (button labels that appear briefly to reveal a button’s name) appear for the system tool bar only when the system title bar is active (colored. instead of gray).Page 3-13 TITLE BAR AND TOOL BARS The Atlas Shop title bar not only displays the name of the program. but also the section number of the currently selected section (or the range of multiple sections that are currently selected). These edits are done only under special circumstances that will be explained later. it is apparent that seven sections are selected (Section # 0 . but not all. This display will be used for reference many times during the editing process. and anytime Internal Cut.

meaning that the Section Mode button on the system tool bar is depressed. objects. If you are an experienced user. all operations are applied only to the selected object(s). or single points of interest. or point marker. Selected sections. In Section Mode all operations (e.) are applied to the selected section(s).g. all operations apply only to the currently selected data point(s). By default. section.Page 3-14 RELATED TOPICS • • • • • • • • • • • • • • • • • • • Title Bar and Tool Bars (page 3-13) The Three Selection Modes (page 3-14) The Selection Methods (page 3-15) The Line Editing Tools (page 3-24) Possible Color Problems (page 3-8) Possible Alignment Problems (page 3-9) Possible Z-Axis Spacing Problems (page 3-9) Distribute Section Maps Evenly Along the Z-Axis (page 3-37) Change the Z Value of a Section Map (page 3-38) Z-Sort Topographic Sections (page 3-40) Dealing With Conjoint Sections (page 3-42) Duplicate A Section (page 3-45) Reposition Misplaced Points (page 3-47) Color Editing Procedures (page 3-27) Section Alignment Procedures (page 3-32) Z-Axis Re-Distribution Procedures (page 3-37) Other Atlas Shop Features (page 3-53) Numeric Transform (page 3-54) Special Atlas Shop FEatures (page 3-58) 3-D MODELING REVIEWING & OPTIMIZATION TOPICS • • • • Part 1-Display The Atlas (page 3-2) Part 2-A Quick Look at the Surface Rendered Model (page 3-5) Part 3-Save the Atlas to a New Array (page 3-6) Part 4-General Section Review (page 3-7) THE THREE SELECTION MODES In order to work with parts of the atlas. Translate. the particular section. When not selected. objects. object. or point tracings appear gray. in the following procedures. or points of interest must first be selected. feel free to substitute your preferred selection method any time you are asked to select a section. etc. or points are displayed in color both in the Atlas Shop work space and in the black Axis Perspective panel. the Atlas Shop opens in Section Mode. With experience you may come to favor one selection method over another. When the Object Mode button is depressed. object. object. Rotate.Review & Optimize the 3D Data . BIOQUANT Topographer Handbook: 3D Modeling . In Point Mode . As you go through the procedures below you will become aware that there are several different ways to select sections.

but if that method proves to be awkward when working with a particular specimen. objects. TOPIC CONTENTS Select By Color (page 3-16) Select Next / Select Previous (page 3-17) Select Using Rectangle or Polygon (page 3-18) Select From a List (page 3-21) Select by Adding Interior Objects (page 3-23) BIOQUANT Topographer Handbook: 3D Modeling .Page 3-15 RELATED TOPICS • • • • • • • • • • • • • • • • • • • Title Bar and Tool Bars (page 3-13) Save Versus Save As (page 3-13) The Selection Methods (page 3-15) The Line Editing Tools (page 3-24) Possible Color Problems (page 3-8) Possible Alignment Problems (page 3-9) Possible Z-Axis Spacing Problems (page 3-9) Distribute Section Maps Evenly Along the Z-Axis (page 3-37) Change the Z Value of a Section Map (page 3-38) Z-Sort Topographic Sections (page 3-40) Dealing With Conjoint Sections (page 3-42) Duplicate A Section (page 3-45) Reposition Misplaced Points (page 3-47) Color Editing Procedures (page 3-27) Section Alignment Procedures (page 3-32) Z-Axis Re-Distribution Procedures (page 3-37) Other Atlas Shop Features (page 3-53) Numeric Transform (page 3-54) Special Atlas Shop FEatures (page 3-58) 3-D MODELING REVIEWING & OPTIMIZATION TOPICS • • • • Part 1-Display The Atlas (page 3-2) Part 2-A Quick Look at the Surface Rendered Model (page 3-5) Part 3-Save the Atlas to a New Array (page 3-6) Part 4-General Section Review (page 3-7) THE SELECTION METHODS There are several different ways to select sections. With experience you may come to favor one selection method over another. or single data points of interest. you will need to be familiar with the alternate methods.Review & Optimize the 3D Data .

click the color that matches the color of the objects that need to be selected. BIOQUANT Topographer Handbook: 3D Modeling . throughout the entire atlas. System Tool Bar With Color Palette When the Select By Color tool on the Vertical Tool Bar is active. 2. click the Select By Color button On the system tool bar’s color palette. regardless of which Selection Mode is currently active. On the Vertical Tool Bar.Review & Optimize the 3D Data .Page 3-16 RELATED TOPICS • • • • • • • • • • • • • • • • • • • • Title Bar and Tool Bars (page 3-13) Save Versus Save As (page 3-13) The Three Selection Modes (page 3-14) The Selection Methods (page 3-15) The Line Editing Tools (page 3-24) Possible Color Problems (page 3-8) Possible Alignment Problems (page 3-9) Possible Z-Axis Spacing Problems (page 3-9) Distribute Section Maps Evenly Along the Z-Axis (page 3-37) Change the Z Value of a Section Map (page 3-38) Z-Sort Topographic Sections (page 3-40) Dealing With Conjoint Sections (page 3-42) Duplicate A Section (page 3-45) Reposition Misplaced Points (page 3-47) Color Editing Procedures (page 3-27) Section Alignment Procedures (page 3-32) Z-Axis Re-Distribution Procedures (page 3-37) Other Atlas Shop Features (page 3-53) Numeric Transform (page 3-54) Special Atlas Shop FEatures (page 3-58) 3-D MODELING REVIEWING & OPTIMIZATION TOPICS • • • • Part 1-Display The Atlas (page 3-2) Part 2-A Quick Look at the Surface Rendered Model (page 3-5) Part 3-Save the Atlas to a New Array (page 3-6) Part 4-General Section Review (page 3-7) SELECT BY COLOR Select By Color operates across the entire atlas. PROCEDURE 1. It simply selects all tracings and/or markers of the same color. clicking a colored square on the system tool bar’s Color Palette selects all objects in the atlas of that color.

BIOQUANT Topographer Handbook: 3D Modeling .Review & Optimize the 3D Data . or data points (in Point Mode). you may sequence through individual objects (tracings and cell markers) within that section by doing the following: a. .Page 3-17 RELATED TOPICS • • • • • • • • • • • • • • • • • • • • • • • • Select Next / Select Previous (page 3-17) Select Using Rectangle or Polygon (page 3-18) Select From a List (page 3-21) Select by Adding Interior Objects (page 3-23) Title Bar and Tool Bars (page 3-13) Save Versus Save As (page 3-13) The Three Selection Modes (page 3-14) The Selection Methods (page 3-15) The Line Editing Tools (page 3-24) Possible Color Problems (page 3-8) Possible Alignment Problems (page 3-9) Possible Z-Axis Spacing Problems (page 3-9) Distribute Section Maps Evenly Along the Z-Axis (page 3-37) Change the Z Value of a Section Map (page 3-38) Z-Sort Topographic Sections (page 3-40) Dealing With Conjoint Sections (page 3-42) Duplicate A Section (page 3-45) Reposition Misplaced Points (page 3-47) Color Editing Procedures (page 3-27) Section Alignment Procedures (page 3-32) Z-Axis Re-Distribution Procedures (page 3-37) Other Atlas Shop Features (page 3-53) Numeric Transform (page 3-54) Special Atlas Shop FEatures (page 3-58) 3-D MODELING REVIEWING & OPTIMIZATION TOPICS • • • • Part 1-Display The Atlas (page 3-2) Part 2-A Quick Look at the Surface Rendered Model (page 3-5) Part 3-Save the Atlas to a New Array (page 3-6) Part 4-General Section Review (page 3-7) SELECT NEXT / SELECT PREVIOUS The Select Next and Select Previous tools on the Vertical Tool Bar can be used to sequence through sections (in Section Mode). although there is rarely a reason to do so. 2. • Click to activate Section Mode Click the Select Next individual sections. PROCEDURE 1. buttons on the system tool bar to sequence through or Select Previous Within any currently selected section. Click to activate Object Mode . • Within any currently selected object you may sequence through individual data points. Click the Select Next or Select Previous buttons on the system tool bar to sequence through individual data points within the current object. Click the Select Next or Select Previous buttons on the system tool bar to sequence through individual tracings (or markers) within the current section. objects (in Object Mode). b. Click to activate Point Mode . a. b.

If Select Using Polygon is active. tool or the Select Using Polygon tool. or one or more data points (in Point Mode). click either the Select Using Rectangle then do the following: • If Select Using Rectangle is active. click and hold the left mouse button while dragging the cursor diagonally to form a small selection box that crosses the outline of the section(s) that you want to select. On the Vertical Tool Bar. Click to activate Section Mode . RELATED TOPICS • • • • • • • • • • • • • • • • • • • • • • • • Select By Color (page 3-16) Select Using Rectangle or Polygon (page 3-18) Select From a List (page 3-21) Select by Adding Interior Objects (page 3-23) Title Bar and Tool Bars (page 3-13) Save Versus Save As (page 3-13) The Three Selection Modes (page 3-14) The Selection Methods (page 3-15) The Line Editing Tools (page 3-24) Possible Color Problems (page 3-8) Possible Alignment Problems (page 3-9) Possible Z-Axis Spacing Problems (page 3-9) Distribute Section Maps Evenly Along the Z-Axis (page 3-37) Change the Z Value of a Section Map (page 3-38) Z-Sort Topographic Sections (page 3-40) Dealing With Conjoint Sections (page 3-42) Duplicate A Section (page 3-45) Reposition Misplaced Points (page 3-47) Color Editing Procedures (page 3-27) Section Alignment Procedures (page 3-32) Z-Axis Re-Distribution Procedures (page 3-37) Other Atlas Shop Features (page 3-53) Numeric Transform (page 3-54) Special Atlas Shop FEatures (page 3-58) 3-D MODELING REVIEWING & OPTIMIZATION TOPICS • • • • Part 1-Display The Atlas (page 3-2) Part 2-A Quick Look at the Surface Rendered Model (page 3-5) Part 3-Save the Atlas to a New Array (page 3-6) Part 4-General Section Review (page 3-7) SELECT USING RECTANGLE OR POLYGON The Select Using Rectangle and Select Using Polygon tools on the Vertical Tool Bar can be used to select one or more sections (in Section Mode). A cell marker.Review & Optimize the 3D Data .Page 3-18 ADDITIONAL INFORMATION • • A object’s tracing may have hundreds or thousands of data points. one or more objects (in Object Mode). If even one data point of a section or object falls within the selection box or polygon. which appears to the eye to be a single point. actually contains two data points with zero distance between them. click a series of points to create a selection polygon of any shape that crosses the outline of the section(s) you want to select. PROCEDURE: SELECT SECTIONS 1. the whole section or object will be selected. 2. • BIOQUANT Topographer Handbook: 3D Modeling .

• 3. In Section mode . click the Zoom tool. b.Review & Optimize the 3D Data . position the cursor anywhere in the work space. With the cursor positioned over the objects of interest. The result is shown on the right: All tracings and markers within those three sections are selected. Release the cursor button. verify that the Zoom tool is active. Repeat if needed to return the atlas to fully un-zoomed state. BIOQUANT Topographer Handbook: 3D Modeling . verify that the Zoom tool is active. In Object mode. PROCEDURE: SELECT OBJECTS An “object” is any individual tracing or cell marker. and click the left mouse button once. select the section of interest. the Select Using Rectangle and Select Using Polygon tools operate only on the current section. click a series of points to create a selection polygon of any shape that encloses or touches all the objects you want to select. click either the Select Using Rectangle then do the following: • • tool or the Select Using Polygon tool. If the objects of interest are small and need to be magnified to make selection easier. ADDITIONAL INFORMATION • If even one data point of a section falls within the rectangle or polygon. on the Select menu.Page 3-19 Selecting Sections Using the Select With Rectangle or Polygon Tool On the left is a selection rectangle across the outlines of three sections. If Select Using Polygon is active. 2. click and drag the atlas to the desired location. Repeat as needed. on the Vertical Tool bar. 4. To pan with out zooming. click and hold the left mouse button while dragging the cursor diagonally to form a small selection box that encloses or touches all the objects you want to select. Click to activate Object Mode If you want the system to select objects on all sections that correspond to the objects you intend to select on this section. using the left mouse button. In the middle is a selection polygon across the same outlines. all tracings and markers within that section are selected. then using the left mouse button. To return to an un-zoomed state. position the cursor anywhere in the work space. using the most convenient method. The Select Across Sections feature works only in Object mode and tells the system to select objects on all sections in an area that corresponds to the selection box or polygon that is being created on the current section. . On the vertical tool bar. you may simultaneously zoom and pan them to the middle of the work space by doing the following: a. click to activate the Pan tool. If Select Using Rectangle is active. A selection polygon can be any shape. then Object mode is activated. ADDITIONAL INFORMATION • • • To Zoom without panning. unless a special feature called Select Across Sections is turned on. On the Vertical Tool Bar. Repeat as needed to increase the zoom level. click to check Select Across Sections. To work with objects. a section must first be selected in Section mode. click and drag the objects of interest toward the center of the work space. and click the right mouse button once. 1.

With the cursor positioned over the selected objects. then the object within that section that contains the data points of interest.Review & Optimize the 3D Data . Repeat as needed. click either the Select Using Rectangle then do the following: • • If Select Using Rectangle is active. click the Zoom tool. Release the cursor button. using the left mouse button. Using the most convenient method. button. 4. click a series of points to create a selection polygon of any shape that encloses all of the data points you want to select. 3. On the system tool bar. you may simultaneously zoom and pan them to the middle of the work space by doing the following: a. b. while still in Object mode. click and drag the object(s) toward the center of the work space. tool or the Select Using Polygon tool. If Select Using Polygon is active. If the data points of interest need to be magnified to make selection easier. On the vertical tool bar. 2. click the Points Mode On the Vertical Tool Bar. BIOQUANT Topographer Handbook: 3D Modeling . cells of interest are selected with the Select Using Rectangle tool (upper right) or the Select Using Polygon tool (lower right).Page 3-20 Selecting Objects Using the Select With Rectangle or Polygon Tool During Zoom The illustrated section has small cell markers in the middle that need to be selected. click and hold the left mouse button while dragging the cursor diagonally to form a small selection box that encloses all the data points you want to select. After the atlas is zoomed. select first the section map. PROCEDURE: SELECT DATA POINTS 1.

PROCEDURE: SELECT SECTIONS 1. unless the current section has dozens or hundreds of cell markers. The GoTo Object list is a quick way to select objects. In this case the object list would be very long and possibly tedious to use.Page 3-21 RELATED TOPICS • • • • • • • • • • • • • • • • • • • • • • • • Select By Color (page 3-16) Select Next / Select Previous (page 3-17) Select From a List (page 3-21) Select by Adding Interior Objects (page 3-23) Title Bar and Tool Bars (page 3-13) Save Versus Save As (page 3-13) The Three Selection Modes (page 3-14) The Selection Methods (page 3-15) The Line Editing Tools (page 3-24) Possible Color Problems (page 3-8) Possible Alignment Problems (page 3-9) Possible Z-Axis Spacing Problems (page 3-9) Distribute Section Maps Evenly Along the Z-Axis (page 3-37) Change the Z Value of a Section Map (page 3-38) Z-Sort Topographic Sections (page 3-40) Dealing With Conjoint Sections (page 3-42) Duplicate A Section (page 3-45) Reposition Misplaced Points (page 3-47) Color Editing Procedures (page 3-27) Section Alignment Procedures (page 3-32) Z-Axis Re-Distribution Procedures (page 3-37) Other Atlas Shop Features (page 3-53) Numeric Transform (page 3-54) Special Atlas Shop FEatures (page 3-58) 3-D MODELING REVIEWING & OPTIMIZATION TOPICS • • • • Part 1-Display The Atlas (page 3-2) Part 2-A Quick Look at the Surface Rendered Model (page 3-5) Part 3-Save the Atlas to a New Array (page 3-6) Part 4-General Section Review (page 3-7) SELECT FROM A LIST Sections (in Section Mode) and objects (in Object Mode) may be selected from a GoTo list. to open the GoTo Section list box. From the Select menu. BIOQUANT Topographer Handbook: 3D Modeling . The GoTo Section list is almost always the fastest way to select the desired section(s). choose GoTo.Review & Optimize the 3D Data . 2. Click to activate the Section mode button.

then click each additional section that is to be selected. . press and hold the Ctrl key. press and hold the Shift key. non-contiguous sections. click the first section. To select multiple. Example GoTo Object Lists The Ctrl key was used to help select non-contiguous objects. contiguous objects. click to highlight its entry in the list. to open the Go To Object list.Page 3-22 GoTo Section List With the First Section Selected • • To select a single section. using the most convenient method. click to highlight its entry in the list. To select multiple. In Section mode interest. All objects between and including the first and the last will be selected. click the first object. • • To select a single object. click one section. choose GoTo. 3. To select multiple. Click to activate Object Mode From the Select menu. BIOQUANT Topographer Handbook: 3D Modeling . press and hold the Shift key. then click the last object in the series. contiguous sections. • PROCEDURE: SELECT OBJECTS 1. select the section that contains the objects of .Review & Optimize the 3D Data . All sections between and including the first and the last will be selected. 2. then click the last section in the series that is to be selected.

using the most convenient method. From the Select menu. Click to activate Object Mode Using the most convenient method. . select the tracing (object) that surrounds another set of objects that need to be selected.Review & Optimize the 3D Data . click one object. 2. 3. PROCEDURE 1. non-contiguous objects. choose Add Interior Objects to Selection. then click each additional object that is to be selected. 4. select the section that contains the objects of . In Section mode interest. Add Interior Object to Selection is used only in Object Mode. press and hold the Ctrl key.Page 3-23 • To select multiple. BIOQUANT Topographer Handbook: 3D Modeling . RELATED TOPICS • • • • • • • • • • • • • • • • • • • • • • • • Select By Color (page 3-16) Select Next / Select Previous (page 3-17) Select Using Rectangle or Polygon (page 3-18) Select by Adding Interior Objects (page 3-23) Title Bar and Tool Bars (page 3-13) Save Versus Save As (page 3-13) The Three Selection Modes (page 3-14) The Selection Methods (page 3-15) The Line Editing Tools (page 3-24) Possible Color Problems (page 3-8) Possible Alignment Problems (page 3-9) Possible Z-Axis Spacing Problems (page 3-9) Distribute Section Maps Evenly Along the Z-Axis (page 3-37) Change the Z Value of a Section Map (page 3-38) Z-Sort Topographic Sections (page 3-40) Dealing With Conjoint Sections (page 3-42) Duplicate A Section (page 3-45) Reposition Misplaced Points (page 3-47) Color Editing Procedures (page 3-27) Section Alignment Procedures (page 3-32) Z-Axis Re-Distribution Procedures (page 3-37) Other Atlas Shop Features (page 3-53) Numeric Transform (page 3-54) Special Atlas Shop FEatures (page 3-58) 3-D MODELING REVIEWING & OPTIMIZATION TOPICS • • • • Part 1-Display The Atlas (page 3-2) Part 2-A Quick Look at the Surface Rendered Model (page 3-5) Part 3-Save the Atlas to a New Array (page 3-6) Part 4-General Section Review (page 3-7) SELECT BY ADDING INTERIOR OBJECTS Add Interior Objects to Selection is an option on the Select menu than can be used when a currently selected tracing (object) encircles other tracings that need to be added to the selection.

” “Redefine Edge.” “Combine Two Objects. click the Straighten Edge button. On the vertical tool bar.” “Separate Two Objects.” “Delete”.Review & Optimize the 3D Data . The Line Editing Tools on the Vertical Toolbar From top to bottom the tools are “Straighten Edge. the second of two clicked points must lie counterclockwise from the first. STRAIGHTEN EDGE In this procedure. BIOQUANT Topographer Handbook: 3D Modeling . 1.Page 3-24 RELATED TOPICS • • • • • • • • • • • • • • • • • • • • • • • • Select By Color (page 3-16) Select Next / Select Previous (page 3-17) Select Using Rectangle or Polygon (page 3-18) Select From a List (page 3-21) Title Bar and Tool Bars (page 3-13) Save Versus Save As (page 3-13) The Three Selection Modes (page 3-14) The Selection Methods (page 3-15) The Line Editing Tools (page 3-24) Possible Color Problems (page 3-8) Possible Alignment Problems (page 3-9) Possible Z-Axis Spacing Problems (page 3-9) Distribute Section Maps Evenly Along the Z-Axis (page 3-37) Change the Z Value of a Section Map (page 3-38) Z-Sort Topographic Sections (page 3-40) Dealing With Conjoint Sections (page 3-42) Duplicate A Section (page 3-45) Reposition Misplaced Points (page 3-47) Color Editing Procedures (page 3-27) Section Alignment Procedures (page 3-32) Z-Axis Re-Distribution Procedures (page 3-37) Other Atlas Shop Features (page 3-53) Numeric Transform (page 3-54) Special Atlas Shop FEatures (page 3-58) 3-D MODELING REVIEWING & OPTIMIZATION TOPICS • • • • Part 1-Display The Atlas (page 3-2) Part 2-A Quick Look at the Surface Rendered Model (page 3-5) Part 3-Save the Atlas to a New Array (page 3-6) Part 4-General Section Review (page 3-7) THE LINE EDITING TOOLS The line editing tools on the vertical tool bar correct tracing errors made when the topographic data were collected in the measurement software. A new straight line segment will be constructed (counterclockwise) from the first point to the second point. Select the tracing that needs to be Line edited. 2.

4. Click the Undo button to undo the separation. Click the Separate Two Objects button on the vertical toolbar.Review & Optimize the 3D Data . two objects are traced as one. REDEFINING AN OBJECT’S EDGE A segment of an object’s contour tracing can be redrawn with the Redefine Edge tool. Click the other end of the segment. Select the objects that are to be combined. ADDITIONAL NOTES • • Click the right mouse button to cancel after the first click. BIOQUANT Topographer Handbook: 3D Modeling . Click the button to undo the last edit. Click one end of the segment to be straightened. This procedure corrects this. Click where one end of the connecting line should be on object A. Select the objects that need to be separated. Click where the other end of the connecting line should be on object B. ADDITIONAL NOTES • • Click the right mouse button after the first click to cancel the separation. 3. Combine Objects Example Clicking in the order shown will connect these two objects 1. creating two separate tracings. Click the Combine Objects button. ADDITIONAL NOTES • • Click the right mouse button to cancel before the series of 4 clicks is finished. 1. then click the opposite side. Click where the other end of the connecting line should be on object A. A dividing gap will appear. The Combine Two Objects tool on the vertical toolbar connects two objects with straight lines which are defined by mouse clicks. 1. 6. Click the Undo button to undo the last edit. COMBINE TWO OBJECTS Sometimes a single object will be thresholded and traced as two separate halves. 2. Clicking two points defines the location for a gap that will separate the object into two. Click one side of the single tracing. Click where one end of the second connecting line should be on object B. SEPARATE TWO OBJECTS Sometimes. Click the Redefine Edge tool on the vertical tool bar. 3.Page 3-25 3. This tool is recommended (instead of the Straighten Edge tool) when editing atlases that are to be surface rendered or any other time that a significant portion of an object’s tracing needs to be altered. 5. 4. This procedure corrects this. 2.

If the atlas is to be surface rendered. Starting from the first point. The object immediately disappears from the atlas window. ADDITIONAL NOTES: • • The most recent unsaved deletion may be canceled by clicking the Undo tool bar. Note: The removed data is temporarily stored in the Topographer’s backup buffer and the delete does not become permanent until the data is saved using Save on the File menu or by responding YES to the Save Data message on exiting the Atlas Shop. 5. Click to mark one end of the segment that is to be redefined.Page 3-26 2. RELATED TOPICS • • • • • • • • • • • • • • • Numeric Transform (page 3-54) Special Atlas Shop FEatures (page 3-58) Possible Color Problems (page 3-8) Possible Alignment Problems (page 3-9) Possible Z-Axis Spacing Problems (page 3-9) Distribute Section Maps Evenly Along the Z-Axis (page 3-37) Change the Z Value of a Section Map (page 3-38) Z-Sort Topographic Sections (page 3-40) Dealing With Conjoint Sections (page 3-42) Duplicate A Section (page 3-45) Reposition Misplaced Points (page 3-47) Color Editing Procedures (page 3-27) Section Alignment Procedures (page 3-32) Z-Axis Re-Distribution Procedures (page 3-37) Other Atlas Shop Features (page 3-53) 3-D MODELING REVIEWING & OPTIMIZATION TOPICS • • • • Part 1-Display The Atlas (page 3-2) Part 2-A Quick Look at the Surface Rendered Model (page 3-5) Part 3-Save the Atlas to a New Array (page 3-6) Part 4-General Section Review (page 3-7) BIOQUANT Topographer Handbook: 3D Modeling . Click on the tracing of the object to be deleted. the data in the original atlas Topo array(s) are permanently changed. 4. ADDITIONAL NOTES: • • The most recent unsaved deletion may be canceled by clicking the Undo tool bar. or by responding YES to the Save Data message when exiting the Atlas Shop. click the series of data points fairly close together.Review & Optimize the 3D Data . If desirable. DELETING OBJECTS The Delete tool on the vertical toolbar is used to permanently remove the data of a chosen object from the original Topo array. Save As on the File menu may be used instead. SAVING THE EDIT After Redefine Edge is used. button on the vertical All unsaved edits may be canceled by choosing Restore Original from the File menu. 1. button on the vertical All unsaved edits may be canceled by choosing Restore Original from the File menu. Click to mark the other end of the segment. 2. to save the edited version of the atlas to a new Topo array. if the atlas is saved using Save on the File menu. Click the right mouse button to end the construction of the new edge. 3. Click the Delete Object tool on the vertical tool bar. click a series of data points to define the new contour.

Page 3-27

COLOR EDITING PROCEDURES
This sections covers how to modify the color of sections, objects, and points in the Atlas Shop.

COLOR EDITING TOPIC CONTENTS
Change A Single Tracing Color (page 3-27) Assign a New Color to a Group of Objects (page 3-28) Change the Color of One or More Cell Markers (page 3-28) Change the Color Of One Branch of a Y or V-Shaped Structure (page 3-30) Close Gap in a Branched Structure (page 3-31)

3-D MODELING REVIEWING & OPTIMIZATION TOPICS
Part 1-Display The Atlas (page 3-2) Part 2-A Quick Look at the Surface Rendered Model (page 3-5) Part 3-Save the Atlas to a New Array (page 3-6) Part 4-General Section Review (page 3-7)

RELATED TOPICS
• • • • • Section Alignment Procedures (page 3-32) Z-Axis Re-Distribution Procedures (page 3-37) Special Formatting Features (page 3-48) The Line Editing Tools (page 3-24) Other Atlas Shop Features (page 3-53)

CHANGE A SINGLE TRACING COLOR
PROCEDURE
1. 2. 3. 4. If necessary, in Section Mode , select the section of interest. The Selection Methods (page 3-15) Click Object Mode button, to activate Object mode.

Select the object (tracing or marker) for which the color needs to be changed. The Selection Methods (page 3-15) On the Vertical Tool Bar, click the Change Color a. button.

On the system tool bar, click to choose the desired new color on the color palette. The selected tracing will change to the chosen color.

5. 6. 7.

Repeat from step 3 for any tracing in this section that needs a color change. From the File menu, choose Save. Choosing Save on the File menu permanently alters the data in the current atlas Topo array. If appropriate, return to: Part 4-General Section Review (page 3-7).

RELATED TOPICS
• • • • • • • • • • Assign a New Color to a Group of Objects (page 3-28) Change the Color of One or More Cell Markers (page 3-28) Change the Color Of One Branch of a Y or V-Shaped Structure (page 3-30) Close Gap in a Branched Structure (page 3-31) Color Editing Procedures (page 3-27) Section Alignment Procedures (page 3-32) Z-Axis Re-Distribution Procedures (page 3-37) The Line Editing Tools (page 3-24) Special Formatting Features (page 3-48) Other Atlas Shop Features (page 3-53) BIOQUANT Topographer Handbook: 3D Modeling - Review & Optimize the 3D Data

Page 3-28 3-D MODELING REVIEWING & OPTIMIZATION TOPICS
• • • • Part 1-Display The Atlas (page 3-2) Part 2-A Quick Look at the Surface Rendered Model (page 3-5) Part 3-Save the Atlas to a New Array (page 3-6) Part 4-General Section Review (page 3-7)

ASSIGN A NEW COLOR TO A GROUP OF OBJECTS
A group of like-colored objects (tracings or cell markers) may be quickly selected using the Select By Color tool.

PROCEDURE
1. Click to depress the Section Mode button on the system tool bar. Since this procedure selects objects of the same color across all sections of the atlas, it does not matter which section map is currently selected. On the Vertical Tool Bar, click the Select by Color tool.

2. 3. 4. 5. 6. 7.

On the color palette (on the system tool bar), click to designate the current color of the objects of interest. All objects (tracings and/or cell markers) in the atlas of the designated color will be selected. On the Vertical Tool Bar, click the Change Color tool.

On the color palette, click to designate the desired new color. The selected objects in the atlas will change to the new color. From the File menu, choose Save. If appropriate, return to: Part 4-General Section Review (page 3-7).

RELATED TOPICS
• • • • • • • • • • Change A Single Tracing Color (page 3-27) Change the Color of One or More Cell Markers (page 3-28) Change the Color Of One Branch of a Y or V-Shaped Structure (page 3-30) Close Gap in a Branched Structure (page 3-31) Color Editing Procedures (page 3-27) Section Alignment Procedures (page 3-32) Z-Axis Re-Distribution Procedures (page 3-37) Special Formatting Features (page 3-48) The Line Editing Tools (page 3-24) Other Atlas Shop Features (page 3-53)

3-D MODELING REVIEWING & OPTIMIZATION TOPICS
• • • • Part 1-Display The Atlas (page 3-2) Part 2-A Quick Look at the Surface Rendered Model (page 3-5) Part 3-Save the Atlas to a New Array (page 3-6) Part 4-General Section Review (page 3-7)

CHANGE THE COLOR OF ONE OR MORE CELL MARKERS
One or more individual cell markers (single point objects) may be quickly selected with the Select Using Rectangle or Select Using Polygon tools.

PROCEDURE
1. 2. Verify that the Section Mode button is depressed on the system tool bar.

Select a section that contains mis-colored cell markers (single point objects) using one of the following methods:

BIOQUANT Topographer Handbook: 3D Modeling - Review & Optimize the 3D Data

Page 3-29
• • Use the Select Next or Select Previous buttons to sequence through sections. Use the GoTo Section dialog box (Select menu> GoTo). Click to highlight the desired section in the GoTo Section list. The dialog box may be closed by clicking the Close button. If it remains open, it will change to the GoTo Objects list when Object Mode is activated (in step 3), but the object list will not be needed for this procedure. button.

3. 4.

On the system tool bar, click to depress the Object Mode

(Optional) When selecting single point objects, it is often useful to magnify the area of interest before using the selection tools. To zoom the area of interest, do the following: a. b. c. On the Vertical Tool Bar, click the Zoom tool. Using the left mouse button, click the area of interest to zoom up one level. Continue to click the area until the area is sufficiently magnified. If necessary, use the Pan tool to reposition the zoomed tracings in the work space, as follows: i. ii. On the Vertical Tool Bar, click the Pan tool. Place the hand-cursor over a point that you would like to move to the center of the work space.

iii. Click and drag the hand-cursor to reposition the tracings. NOTE: Clicking the right mouse button will zoom out, making the section tracings smaller. Clicking the Resize To Fit 5. button on the system tool bar will resize and center the atlas to fit the work space. button or the Select Using Polygon button,

On the Vertical Tool Bar, click the Select Using Rectangle then do the following to select the cell markers of interest: • •

With the Select Using Rectangle tool, click and drag the cursor diagonally to form a rectangular selection box around the objects of interest.

With the Select Using Polygon tool, click a series of points to form a selection polygon around the objects of interest. All objects fully or partially contained within the box or polygon will be selected. 6. 7. 8. 9. On the Vertical Tool Bar, click the Change Color tool.

On the color palette (system tool bar), click to designate the desired new color. The selected single point objects will change to the new color. From the File menu, choose Save. Choosing Save on the File menu permanently alters the data in the current atlas Topo array. If appropriate, return to: Part 4-General Section Review (page 3-7).

ADDITIONAL INFORMATION
• • If the Zoom tool was used, clicking the Resize to Fit button on the system tool bar will redraw and center the atlas to fit the work space. When the Select Across Sections option is checked on the Select menu, the Select Using Rectangle and Select Using Polygon tools may also be used to select objects in corresponding regions on all sections at once. See “Select Using Rectangle or Polygon” on 3-18.

RELATED TOPICS
• • • • • • • • • • Change A Single Tracing Color (page 3-27) Assign a New Color to a Group of Objects (page 3-28) Change the Color Of One Branch of a Y or V-Shaped Structure (page 3-30) Close Gap in a Branched Structure (page 3-31) Color Editing Procedures (page 3-27) Section Alignment Procedures (page 3-32) The Line Editing Tools (page 3-24) Z-Axis Re-Distribution Procedures (page 3-37) Special Formatting Features (page 3-48) Other Atlas Shop Features (page 3-53)

BIOQUANT Topographer Handbook: 3D Modeling - Review & Optimize the 3D Data

Page 3-30 3-D MODELING REVIEWING & OPTIMIZATION TOPICS
• • • • Part 1-Display The Atlas (page 3-2) Part 2-A Quick Look at the Surface Rendered Model (page 3-5) Part 3-Save the Atlas to a New Array (page 3-6) Part 4-General Section Review (page 3-7)

CHANGE THE COLOR OF ONE BRANCH OF A Y OR V-SHAPED STRUCTURE
When a structure branches, the Atlas Modeler has difficulty distinguishing which data points belong to which branch if all of the data points for the structure are the same color. For this reason, tracings that define the smaller branch are assigned a different color. A Y or V-shaped structure will always have 3 parts: two branches and an un-divided base to which each branch is connected. The connecting base may be very thin and may be defined by a single tracing in only one section map. When working with a branched structure it is usually best to focus entirely on that structure, locating its tracings on each section and making color changes as needed. This means switching back and forth between Object Mode and Section Mode several times, and ignoring other types of color-related issues until all of the tracings for the structure’s smallest branch have been changed to a new color.

PROCEDURE
1. Decide which color to use for the tracings of the structure’s smaller branch. When possible, choose a color that has a similar hue or brightness as the original color (e.g. red and pink, blue and dark blue, purple and brown). It may not be possible to use a similar color, since the new color must also be one that has NOT already been used for another type of structure in the atlas. In Section Mode , select the first section map that has a tracing that belongs to the structure’s shortest branch. The Selection Methods (page 3-15) Click to depress the Object Mode button, to activate Object mode.

2.

3. 4. 5. 6.

Select the tracing that belongs to the shortest branch of the structure. The Selection Methods (page 3-15) On the Vertical Tool Bar, click the Change Color tool.

On the color palette (system tool bar), click to designate the desired new color. The selected tracing will change to the new color. On the system tool bar, click the Section Mode section), then click the Object Mode button, click the Select Next button (to select the next

7.

button (to re-activate Object mode).

8. 9.

Repeat from step 4 until all of the tracings that define the smaller branch have been changed to the desired color. From the File menu, choose Save. Choosing Save on the File menu permanently alters the data in the current atlas Topo array.

ADDITIONAL INFORMATION
Now, when the atlas is moved into the Atlas Modeler, the uniquely colored branch will render correctly as an object that is separate from the other branch. However, treating it as separate object, may introduce a visible gap between the uniquely colored branch and the rest of the structure. If this proves to be the case, the gap may be closed by changing the Z-Value of the tracing in the color-altered branch that is closest to the base, to match the Z-Value of the closest base tracing. This procedure is given below.

BIOQUANT Topographer Handbook: 3D Modeling - Review & Optimize the 3D Data

Page 3-31 RELATED TOPICS
• • • • • • • • • • Change A Single Tracing Color (page 3-27) Assign a New Color to a Group of Objects (page 3-28) Change the Color of One or More Cell Markers (page 3-28) Close Gap in a Branched Structure (page 3-31) Color Editing Procedures (page 3-27) Section Alignment Procedures (page 3-32) The Line Editing Tools (page 3-24) Z-Axis Re-Distribution Procedures (page 3-37) Special Formatting Features (page 3-48) Other Atlas Shop Features (page 3-53)

3-D MODELING REVIEWING & OPTIMIZATION TOPICS
• • • • Part 1-Display The Atlas (page 3-2) Part 2-A Quick Look at the Surface Rendered Model (page 3-5) Part 3-Save the Atlas to a New Array (page 3-6) Part 4-General Section Review (page 3-7)

CLOSE GAP IN A BRANCHED STRUCTURE
PROCEDURE
1. 2. Verify that the Section Mode button is depressed on the system tool bar.

Using any convenient method, select the section map that contains the desired base-tracing (the one that is closest to the section map that contains the first tracing of the shortest branch), and determine its Z-Value doing the following: a. b. c. On the Vertical Tool Bar, click the Change Z open the Change Z dialog box. button (or from the Edit menu, choose Change Z) to

Note the section’s Z-Value in the “Change All Sections To” field. You will change nothing at this point. Simply view the Z Value of the currently selected section map. Click the Close button.

3. 4.

Use the Select Next or Select Previous button to select the adjacent section map that contains the first tracing for the uniquely colored branch. Click the Object Mode button on the system tool bar and select the tracing of the uniquely colored branch. The Selection Methods (page 3-15) On the Vertical Tool Bar, click the Change Z the Change Z dialog box. button (or from the Edit menu, choose Change Z) to open

5.

The Change Z Dialog Box in Change Selected Sections Mode

6. 7.

On the Change Z dialog box, change the value in the “Change All Z-Values To” field to match the Z-Value observed in step 2. Click the Apply button, then click the Close button. BIOQUANT Topographer Handbook: 3D Modeling - Review & Optimize the 3D Data

Page 3-32
8. 9. From the File menu, choose Save. If appropriate, return to: Part 4-General Section Review (page 3-7).

RELATED TOPICS
• • • • • • • • • • Change A Single Tracing Color (page 3-27) Assign a New Color to a Group of Objects (page 3-28) Change the Color of One or More Cell Markers (page 3-28) Change the Color Of One Branch of a Y or V-Shaped Structure (page 3-30) Color Editing Procedures (page 3-27) Section Alignment Procedures (page 3-32) Z-Axis Re-Distribution Procedures (page 3-37) Special Formatting Features (page 3-48) The Line Editing Tools (page 3-24) Other Atlas Shop Features (page 3-53)

3-D MODELING REVIEWING & OPTIMIZATION TOPICS
• • • • Part 1-Display The Atlas (page 3-2) Part 2-A Quick Look at the Surface Rendered Model (page 3-5) Part 3-Save the Atlas to a New Array (page 3-6) Part 4-General Section Review (page 3-7)

SECTION ALIGNMENT PROCEDURES
For a variety of reasons, the sections maps in the atlas may not line up optimally to produce a smooth and beautiful 3D model. The Atlas Shop provides tools for section realignment. The first tool is the automatic Align Sections feature that simultaneously rotates section map Start Points into alignment. However, this option is only useful if, during measurement, the user controlled the starting point of each section’s outline and placed that point at corresponding locations on each section. Individual section maps, or objects within individual section maps, may be manually translated, rotated, or resized to better line up with tracings in adjacent sections. Tracings from other section maps may be overlaid for visual reference while moving, rotating, or resizing a selected section map.

TOPIC CONTENTS
Simultaneously Align All Sections That have Corresponding Start Points (page 3-32) Manually Align Section Maps (page 3-33) Translate (Move) a Section Map (page 3-34) Rotate A Section Map (page 3-35) Resize A Section Map (page 3-36)

RELATED TOPICS
• • • • • • Color Editing Procedures (page 3-27) Section Alignment Procedures (page 3-32) Z-Axis Re-Distribution Procedures (page 3-37) Special Formatting Features (page 3-48) The Line Editing Tools (page 3-24) Other Atlas Shop Features (page 3-53)

3-D MODELING REVIEWING & OPTIMIZATION TOPICS
• • • • Part 1-Display The Atlas (page 3-2) Part 2-A Quick Look at the Surface Rendered Model (page 3-5) Part 3-Save the Atlas to a New Array (page 3-6) Part 4-General Section Review (page 3-7)

SIMULTANEOUSLY ALIGN ALL SECTIONS THAT HAVE CORRESPONDING START
BIOQUANT Topographer Handbook: 3D Modeling - Review & Optimize the 3D Data

or resized.Page 3-33 POINTS The automatic Align Sections feature should only be used if during data collection. In Section Mode . RELATED TOPICS • • • • • • • • • • Manually Align Section Maps (page 3-33) Translate (Move) a Section Map (page 3-34) Rotate A Section Map (page 3-35) Resize A Section Map (page 3-36) Color Editing Procedures (page 3-27) Section Alignment Procedures (page 3-32) Z-Axis Re-Distribution Procedures (page 3-37) Special Formatting Features (page 3-48) The Line Editing Tools (page 3-24) Other Atlas Shop Features (page 3-53) 3-D MODELING REVIEWING & OPTIMIZATION TOPICS • • • • Part 1-Display The Atlas (page 3-2) Part 2-A Quick Look at the Surface Rendered Model (page 3-5) Part 3-Save the Atlas to a New Array (page 3-6) Part 4-General Section Review (page 3-7) MANUALLY ALIGN SECTION MAPS Before translating. The Selection Methods (page 3-15) Overlay at least one unselected section map for visual reference by doing the following: a. All section maps in the atlas will automatically rotate so that the measurement Start Points on the outermost section outlines line up. 2. return to the section by section review (3-9). measurement Start Points of section outlines were deliberately placed in corresponding positions on all sections. This will keep the dialog box from obscuring the atlas during the edit procedure. The overlaid tracings will be gray. 2. If appropriate. With the cursor on its title bar. PROCEDURE 1. it is best to overlay one or more adjacent maps to use for visual reference. The automatic Align Sections feature acts on all section maps in the atlas. PROCEDURE: OVERLAY REFERENCE SECTIONS 1. or resizing an individual section map. Rotate. rotated. rotating.Review & Optimize the 3D Data . choose Align Sections. The Overlay Section dialog box must remain open as long as the reference tracings are needed. select a section map that needs to be translated (moved in the XY plane). From the View menu. regardless of which selection mode is currently active. From the Edit menu. BIOQUANT Topographer Handbook: 3D Modeling . and Resize procedures that follow. click and drag the Overlay Section dialog box to the back Perspective Panel. The procedure for overlaying reference sections is given immediately below and referred to in the Translate. choose Overlay Sections to open the Overlay Section dialog box.

Although various combinations of reference maps may be used. From the View menu. ADDITIONAL INFORMATION • • The tracings in overlaid section maps will remain gray. To learn more about Overly Section options see: View> Overlay Sections (page 6-20) RELATED TOPICS • • • • • • • • • • Simultaneously Align All Sections That have Corresponding Start Points (page 3-32) Translate (Move) a Section Map (page 3-34) Rotate A Section Map (page 3-35) Resize A Section Map (page 3-36) Color Editing Procedures (page 3-27) Section Alignment Procedures (page 3-32) Z-Axis Re-Distribution Procedures (page 3-37) The Line Editing Tools (page 3-24) Special Formatting Features (page 3-48) Other Atlas Shop Features (page 3-53) 3-D MODELING REVIEWING & OPTIMIZATION TOPICS • • • • Part 1-Display The Atlas (page 3-2) Part 2-A Quick Look at the Surface Rendered Model (page 3-5) Part 3-Save the Atlas to a New Array (page 3-6) Part 4-General Section Review (page 3-7) TRANSLATE (MOVE) A SECTION MAP 1. In Section mode . On the Overlay Section dialog box.Page 3-34 Overlay Section Dialog Box b. indicating that they are not currently selected. type 1 in the previous section edit field and verify that there is a check mark next to it. This will keep the dialog box from obscuring the atlas during the edit procedure. choose Overlay Sections to open the Overlay Section dialog box. select a section map that needs to be moved in the same XY plane to a new location. To use the simplest approach. The Selection Methods (page 3-15) Overlay at least one adjacent section map for visual reference by doing the following: a. click and drag the Overlay Section dialog box to the back Perspective Panel. BIOQUANT Topographer Handbook: 3D Modeling . ii. 2. the simplest is to superimpose only the previous section.Review & Optimize the 3D Data . With the cursor on its title bar. Click the Apply button. do the following: i.

the moved tracing will settle into its new position. 3. Although various combinations of reference maps may be used. click and drag the section map so that its tracings are better aligned with the reference (gray) section. RELATED TOPICS • • • • • • • • • • Simultaneously Align All Sections That have Corresponding Start Points (page 3-32) Manually Align Section Maps (page 3-33) Rotate A Section Map (page 3-35) Resize A Section Map (page 3-36) Color Editing Procedures (page 3-27) Section Alignment Procedures (page 3-32) Z-Axis Re-Distribution Procedures (page 3-37) Special Formatting Features (page 3-48) The Line Editing Tools (page 3-24) Other Atlas Shop Features (page 3-53) 3-D MODELING REVIEWING & OPTIMIZATION TOPICS • • • • Part 1-Display The Atlas (page 3-2) Part 2-A Quick Look at the Surface Rendered Model (page 3-5) Part 3-Save the Atlas to a New Array (page 3-6) Part 4-General Section Review (page 3-7) ROTATE A SECTION MAP 1. Click the Apply button. ALTERNATE PROCEDURE • Sections may also be moved a known micron distance using Numeric Transform. On the Overlay Section dialog box. the simplest is to superimpose only the previous section. repeat step 4 to refine the placement. select a section map that needs to be rotated. 4. In Section mode . ii. ADDITIONAL INFORMATION • • • To remove the overlaid tracings. To use the simplest approach. type 1 in the previous section edit field and verify that there is a check mark next to it.Review & Optimize the 3D Data .Page 3-35 Overlay Section Dialog Box b. To learn more about Overly Section options see: View> Overlay Sections (page 6-20) Choosing Save on the File menu permanently saves the edit in the current atlas Topo array. do the following: i. The Selection Methods (page 3-15) BIOQUANT Topographer Handbook: 3D Modeling . See “Numeric Transform” on 354. Place the cursor over the selected section. click the Translate The cursor takes the shape of crossed arrows. When the cursor button is released. close the Overlay Section dialog box. If needed. then using the left mouse button. 5. tool. On the Vertical Tool Bar.

The Selection Methods (page 3-15) Overlay at least one adjacent section map for visual reference. 5. 5. When the cursor button is released. Choosing Save on the File menu permanently saves the edit in the current atlas Topo array. 4. select a section map that needs to be resized. BIOQUANT Topographer Handbook: 3D Modeling . In Section mode . the rotated section will settle into its new orientation. 4. ALTERNATE PROCEDURE • Sections may also be rotated by a degree using Numeric Transform. the resized tracing will settle into its new position. click the Rotate The special rotate cursor will appear. ALTERNATE PROCEDURE • Sections may also be resized by a known percentage using Numeric Transform.Page 3-36 2. then click and hold the left mouse button while moving the cursor in either a clockwise or counter-clockwise circle. When the cursor button is released. View> Overlay Sections (page 6-20) On the Vertical Tool Bar. close the Overlay Section dialog box. 2. RELATED TOPICS • • • • • • • • • • Simultaneously Align All Sections That have Corresponding Start Points (page 3-32) Manually Align Section Maps (page 3-33) Translate (Move) a Section Map (page 3-34) Resize A Section Map (page 3-36) Color Editing Procedures (page 3-27) Section Alignment Procedures (page 3-32) Z-Axis Re-Distribution Procedures (page 3-37) The Line Editing Tools (page 3-24) Special Formatting Features (page 3-48) Other Atlas Shop Features (page 3-53) 3-D MODELING REVIEWING & OPTIMIZATION TOPICS • • • • Part 1-Display The Atlas (page 3-2) Part 2-A Quick Look at the Surface Rendered Model (page 3-5) Part 3-Save the Atlas to a New Array (page 3-6) Part 4-General Section Review (page 3-7) RESIZE A SECTION MAP 1. Click and drag one of the pull-points outward to increase the size or inward to decrease the size. Place the cursor anywhere on the Atlas Shop work space. Choosing Save on the File menu permanently saves the edit in the current atlas Topo array. A box with a pull-point at each corner will appear around the section. 3.Review & Optimize the 3D Data . See “Numeric Transform” on 3-54. click the Resize tool. 3.) ADDITIONAL INFORMATION • • To remove the overlaid tracings. See “Numeric Transform” on 354. If needed. tool. Overlay at least one adjacent section map for visual reference. repeat step 4 to refine the size. View> Overlay Sections (page 6-20) On the Vertical Tool Bar. repeat step 4 to refine the rotation.) ADDITIONAL INFORMATION • • To remove the overlaid tracings. close the Overlay Section dialog box. If needed.

If either of these is the case. do the following: BIOQUANT Topographer Handbook: 3D Modeling . TOPIC CONTENTS Distribute Section Maps Evenly Along the Z-Axis (page 3-37) Change the Z Value of a Section Map (page 3-38) Z-Sort Topographic Sections (page 3-40) Dealing With Conjoint Sections (page 3-42) Duplicate A Section (page 3-45) Reposition Misplaced Points (page 3-47) RELATED TOPICS • • • • • • Color Editing Procedures (page 3-27) Section Alignment Procedures (page 3-32) Z-Axis Re-Distribution Procedures (page 3-37) Special Formatting Features (page 3-48) The Line Editing Tools (page 3-24) Other Atlas Shop Features (page 3-53) 3-D MODELING REVIEWING & OPTIMIZATION TOPICS • • • • Part 1-Display The Atlas (page 3-2) Part 2-A Quick Look at the Surface Rendered Model (page 3-5) Part 3-Save the Atlas to a New Array (page 3-6) Part 4-General Section Review (page 3-7) DISTRIBUTE SECTION MAPS EVENLY ALONG THE Z-AXIS If there is only one horizontal section line displayed in the Perspective panel. it means all topographic sections have the same Z-Value. There are one or more short vertical lines connecting the horizontal section lines in the black Perspective panel. If sections were originally taken at regular intervals from the physical tissue.Page 3-37 RELATED TOPICS • • • • • • • • • • Simultaneously Align All Sections That have Corresponding Start Points (page 3-32) Manually Align Section Maps (page 3-33) Translate (Move) a Section Map (page 3-34) Rotate A Section Map (page 3-35) Color Editing Procedures (page 3-27) Section Alignment Procedures (page 3-32) The Line Editing Tools (page 3-24) Z-Axis Re-Distribution Procedures (page 3-37) Special Formatting Features (page 3-48) Other Atlas Shop Features (page 3-53) 3-D MODELING REVIEWING & OPTIMIZATION TOPICS • • • • Part 1-Display The Atlas (page 3-2) Part 2-A Quick Look at the Surface Rendered Model (page 3-5) Part 3-Save the Atlas to a New Array (page 3-6) Part 4-General Section Review (page 3-7) Z-AXIS RE-DISTRIBUTION PROCEDURES Problems with section distribution along the Z axis show up in the black Perspective panel.Review & Optimize the 3D Data . There may be unnatural gaps along the Z axis. because one of more physical tissue sections in the series was lost or damaged and could not be measured. Some of the section maps may be conjoint (meaning that there is more than one section map in a topographic section). but the section lines are unevenly spaced along the Z-axis.) The following procedures address these problems. it means that incorrect Z-Values were assigned to one or more sections. There are several different sources of Z-axis problems: Individual section maps may have the wrong Z Offset value. (This sometime happens when a data point becomes misplaced during editing.

5. click the Change Z the Change Z dialog box. Click the Close button. The Change Z Dialog Box in Change All Sections Mode 3. 2. From the system File menu. On the Vertical Tool Bar. choose Change Z) to open the Change Z dialog box. Click the Apply button. 2.Page 3-38 1. RELATED TOPICS • • • • • • • • • • Change the Z Value of a Section Map (page 3-38) Z-Sort Topographic Sections (page 3-40) Dealing With Conjoint Sections (page 3-42) Duplicate A Section (page 3-45) Reposition Misplaced Points (page 3-47) Color Editing Procedures (page 3-27) Section Alignment Procedures (page 3-32) Z-Axis Re-Distribution Procedures (page 3-37) Special Formatting Features (page 3-48) Other Atlas Shop Features (page 3-53) 3-D MODELING REVIEWING & OPTIMIZATION TOPICS • • • • Part 1-Display The Atlas (page 3-2) Part 2-A Quick Look at the Surface Rendered Model (page 3-5) Part 3-Save the Atlas to a New Array (page 3-6) Part 4-General Section Review (page 3-7) CHANGE THE Z VALUE OF A SECTION MAP Use this procedure to change the Z Offset Value of any one section. In the “Z Offset Between Sections” edit field.Review & Optimize the 3D Data . 4. The Z-Offset of First Section is usually kept at zero. Click the Change Z button (or from the Edit menu. If the desired section map cannot be selected independently because it is conjoined to the tracings of another section: See “Dealing With Conjoint Sections” on 3-42. Verify that Section Mode is active. then select the section for which the Z-Value is incorrect. type in the micron distance that should separate one section from the next. 1. click to activate the Change All Sections radio button. button (or from the Edit menu. choose Save. BIOQUANT Topographer Handbook: 3D Modeling . choose Change Z) to open On the Change Z dialog box. By default the “Change Selected Section(s)” radio button is active and the current Z-Value of the selected section is displayed in the “Change All Z Values to” edit field.

Page 3-39 The Change Z Dialog Box in Change Selected Sections Mode 3. Click the Apply button. (See illustration below. CORRECTION: Perform the Separate Conjoint Sections procedure on (3-42).) Atlas With Tracings From 2 Physical Sections • 4. Use Z Sort to rearrange topographic sections in the Topo array in a logical. choose Save. sequential order. “Change All Z Values” refers only to the selected sections. Click the Select Next button (or click the next section in the GoTo Section list) to select the next topographic section in the series. With the “Change Selected Sections” radio button is active. This indicates that the selected topographic section contains sets of tracings from two (or more) physical tissue sections and all of the tracings share a common Z-Value. Type the correct Z-Offset Value for this section into the “Change All Z Values to” edit field. ATLAS: Tracings belonging to two (or more) physical sections are selected. PERSPECTIVE PANEL: Only one line is selected. The value in the “Raise/Lower All Z Values By” field should remain 0. Z-Sort Topographic Sections (page 3-40) BIOQUANT Topographer Handbook: 3D Modeling . Corrective procedures that include Internal Cut and Internal Paste alter the number of topographic sections in the atlas. Repeat from step 3 until all topographic sections in the atlas have been reviewed and Z-Values corrected if necessary. 5. then the Close button. Keep this fact in mind when reviewing sections after these types of edits are made.Review & Optimize the 3D Data . From the system File menu. IMPORTANT ADDITIONAL INFORMATION • 8. 7. then perform the indicated corrective procedure. The GoTo Section dialog box shows that a conjoint set of section tracings exist in a single topographic section. 6.

sequential order and this can cause considerable confusion during the section by section review. Sort Sections by Z Value dialog box button in that field to open the • • If the Topo array that is currently designated in the Destination Array field is not suitable (if it already contains data or if you do not like its name). NOTE 2: If the last Topo array in the data set is empty and you do not object to its current name. The confusion can be eliminated by using Z Sort. and asks if you want to add a new array.Page 3-40 RELATED TOPICS • • • • • • • • • • Distribute Section Maps Evenly Along the Z-Axis (page 3-37) Z-Sort Topographic Sections (page 3-40) Dealing With Conjoint Sections (page 3-42) Duplicate A Section (page 3-45) Reposition Misplaced Points (page 3-47) Color Editing Procedures (page 3-27) Section Alignment Procedures (page 3-32) Z-Axis Re-Distribution Procedures (page 3-37) Special Formatting Features (page 3-48) Other Atlas Shop Features (page 3-53) 3-D MODELING REVIEWING & OPTIMIZATION TOPICS • • • • Part 1-Display The Atlas (page 3-2) Part 2-A Quick Look at the Surface Rendered Model (page 3-5) Part 3-Save the Atlas to a New Array (page 3-6) Part 4-General Section Review (page 3-7) Z-SORT TOPOGRAPHIC SECTIONS The system numbers topographic sections according to their order in the Topo array. Z Sort should be used before the section by section review begins. If sections were measured out of order.Review & Optimize the 3D Data . It should also be used any time Z Values are changed. the message box will disappear and the Sort Sections by Z Value dialog box will open with the last Topo array in the data set selected in the Destination Array field. it may be selected from the Destination Array field’s drop list (by clicking the down-arrow drop list). On the message box. This default name cannot be changed. the message box will disappear and the Sort Sections by Z Value dialog box will open with the automatically added “Z Sorted Topo” selected in the Destination Array field. or if section maps have been copied and pasted during the editing process. do the following: BIOQUANT Topographer Handbook: 3D Modeling . A message box will open to inform you that the Z sorted atlas must be saved to a new array. which rearranges all topographic sections in the Topo array according to their assigned Z Values. • • • NOTE 1: The Destination Array must be empty (must have no values). When YES is clicked. From the Edit menu. empty Topo array exists in the data set. NOTE 3: If a different. topographic sections will not be arranged in a logical. When NO is clicked. choose Z Sort. click NO if you prefer to add a new Topo array with a different name or you would like to use an empty Topo array that already exists in the data set. Do one of the following: • On the message box. If physical sections were measured out or order. it may be retained as the Destination Array. click YES if you want the system to automatically add a Topo array named “Z Sorted Topo”. PROCEDURE 1.

Click the Redraw Click the Atlas Shop button (to update the Atlas Window with the new version in the atlas). In the Array Name field. button to re-open the Atlas Shop.Page 3-41 i. In the Atlas Shop. • On the Save Data message. On the Sort Sections by Z Values dialog box. double-click the array index to remove it from the Selected list. When the NO button is clicked. return to the Section By Section Review (3-7). do the following: a. In the Atlas Viewer. click the New Array button to open the New Array dialog box. click YES if all of the unsaved changes to the atlas were meant to be saved.Review & Optimize the 3D Data . any unsaved changes that were made either before or after Z-Sort was performed. When the YES button is clicked. choose Exit Atlas Shop. type in the desired name for the new Topo array. click to choose either the Ascending or Descending radio button. c. If appropriate. you must take the following steps. From the File menu. Alternately. b. the Atlas Shop closes and the Atlas Viewer opens. choose Unselect All Arrays (to deselect the original atlas array). will be saved to both the currently open atlas array (which is not sorted by Z-Values) and to the newly added Z-Sorted atlas array. Click the Apply button to record the edited version of the atlas into the array that is specified in the Destination Array field. d. In the Z Sort Options area of the Sort Sections by Z Value dialog box. click the Resize to Fit button. iii. • 3. Do one of the following. Ascending places Section 0 at the bottom of the atlas. scroll to and double-click to select the array that holds the Z Sorted version of the atlas. Descending places Section 0 at the top of the atlas. Click the OK button to close the New Array box. Z-sorted state). In the Available Arrays list. it means that edits other than Z-Sort (which has already been saved) were made to the atlas and those changes have not yet been saved. If a Save Data message appears. On the Save Data message. 4. click NO if the unsaved changes to the atlas were not meant to be saved. The Atlas Shop closes and the Atlas Viewer opens. In order to continue the atlas review (using the atlas in its new. Click Close. iv. ii. in the Selected column. 2. RELATED TOPICS • • • • • • • • • • Distribute Section Maps Evenly Along the Z-Axis (page 3-37) Change the Z Value of a Section Map (page 3-38) Dealing With Conjoint Sections (page 3-42) Duplicate A Section (page 3-45) Reposition Misplaced Points (page 3-47) Color Editing Procedures (page 3-27) Section Alignment Procedures (page 3-32) Z-Axis Re-Distribution Procedures (page 3-37) Special Formatting Features (page 3-48) Other Atlas Shop Features (page 3-53) 3-D MODELING REVIEWING & OPTIMIZATION TOPICS • • • • Part 1-Display The Atlas (page 3-2) Part 2-A Quick Look at the Surface Rendered Model (page 3-5) Part 3-Save the Atlas to a New Array (page 3-6) Part 4-General Section Review (page 3-7) BIOQUANT Topographer Handbook: 3D Modeling . From the Select Arrays dialog box’s Select menu.

There are two ways to deal with conjoint sections that need editing: • Select and cut the tracings that belong to one physical section. select the conjoint section maps. In Section Mode . when the user forgot to put a landmark on one (or more) of the sections during measurement. reposition the GoTo Section dialog box over the Perspective panel to keep from obscuring the tracings in the atlas.Page 3-42 DEALING WITH CONJOINT SECTIONS The maps of two (or more) physical tissue sections will show up as one topographic section in the atlas. This will remove all but the conjoint section tracings from the work space. Create New Topographic Sections (page 3-42) Perform any needed edits for the conjoint sections by selecting their individual tracings in Object Mode. If necessary.Review & Optimize the 3D Data . and paste them to create new topographic sections that can be independently selected in Section Mode. 2. choose GoTo. If the GoTo Section dialog box is not already open. 1. from the Select menu. Use the following procedures as needed: Possible Color Problems (page 3-8) Possible Alignment Problems (page 3-9) Possible Z-Axis Spacing Problems (page 3-9) • REMINDER • If each conjoint section has the correct Z Offset value (appears in its proper place on the Z axis) and none need to be independently moved or rotated. the conjoint sections do not need to be separated. BIOQUANT Topographer Handbook: 3D Modeling . choose Selection Only. RELATED TOPICS • • • • • • • • • • Distribute Section Maps Evenly Along the Z-Axis (page 3-37) Change the Z Value of a Section Map (page 3-38) Z-Sort Topographic Sections (page 3-40) Duplicate A Section (page 3-45) Reposition Misplaced Points (page 3-47) Color Editing Procedures (page 3-27) Section Alignment Procedures (page 3-32) Z-Axis Re-Distribution Procedures (page 3-37) Special Formatting Features (page 3-48) Other Atlas Shop Features (page 3-53) 3-D MODELING REVIEWING & OPTIMIZATION TOPICS • • • • Part 1-Display The Atlas (page 3-2) Part 2-A Quick Look at the Surface Rendered Model (page 3-5) Part 3-Save the Atlas to a New Array (page 3-6) Part 4-General Section Review (page 3-7) CREATE NEW TOPOGRAPHIC SECTIONS PROCEDURE 1. From the View menu. This is a problem only if the conjoined section maps have the same Z Offset Value and/or if one of the maps needs to be rotated or moved independently to improve its alignment with other maps.

The GoTo Section dialog box changes to GoTo Object. will be automatically selected. click to momentarily select each successive object in the list until the first tracing from the second physical section is located (and selected). 5. Click the Object Mode button on the system tool bar. With the first tracing from the second physical section highlighted. then in the GoTo Object list. beginning with the object just below the initially selected one. GoTo Object Dialog Box With One Object Selected Here. press and hold the Control (Ctrl) key on the keyboard. BIOQUANT Topographer Handbook: 3D Modeling . 4.Page 3-43 GoTo Section Dialog Box Tracings from two different physical tissue sections residing in the one topographic section that is selected in the GoTo Section dialog box 3. belonging to the first set of physical tissue section tracings. was the contour outline of the physical tissue section that received the Landmark. the first tracing (object) that was recorded in the topographic section. continue to click successive objects until all of the tracings (objects) that belong to the second physical section are selected. The very first object. In the GoTo Object list.Review & Optimize the 3D Data .

click Redraw section by section review. the new topographic sections created by Internal Paste will still exist at the original Z-Offset position. One new topographic section was created for each tracing that was cut from the conjoint section. c. click to choose the Ascending or Descending radio button. In the Z Sort Options area. b. The Atlas Shop closes and the Atlas Viewer reopens. a. 11. (Usually ascending) Click the Apply button to record the edited version of the atlas to the new array. Click OK to acknowledge the notice. b. At this point. Choose Internal Cut from the Edit menu. Click Close on the Z-Sort dialog box. BIOQUANT Topographer Handbook: 3D Modeling . 8. choose Z Sort. you must do the following: a. A message box appears to let you know that each cut element (tracing) will ultimately be pasted as a new topographic section in the last array in the data set. In Section Mode . (Clicking Cancel will cancel the Internal Cut command. 9. select one of the new topographic sections that was created when Internal Paste was used. click NO (since the changed version of the atlas has already been saved). From the Edit menu.Page 3-44 GoTo Object Dialog Box With Three Objects Selected 6. in the Destination Array field. Click the YES button to open the Sort Sections By Z Value dialog box. click the Resize to Fit button. On the Sort Sections By Z Value dialog box. On the Save Data message. A Warning box will open to inform you that the Z sorted atlas must be saved to a new array. In the Atlas Shop. At this point the pasted tracings are actually being held in a system buffer. A Warning box will open to remind you that the altered atlas must be saved to a new array. 12.Review & Optimize the 3D Data . 10. choose Exit Atlas Shop. b. and to continue the button to reopen the Atlas Shop. In order to display or continue editing the changed version of the atlas. Click OK to acknowledge the warning and cut the selected tracings(s) from the displayed atlas. From the File menu. and asks if you want to add a new array. A new Topo array will be added to the data set in step 9. click the Atlas Shop on the system tool bar. Click the New Array button to add a new Topo array to the end of the data set array list.) Choose Internal Paste from the Edit menu. on the Select Arrays dialog box. d. In the Atlas Viewer. deselect the original atlas array(s) and select the Topo array that holds the revised version of the atlas. 7. do the following: a. A Save Data message will appear. To display the revised version of the atlas.

button (or from the Edit menu. In the “Change All Z Values to” field. Click the Apply button. 20. choose Save. Use Z Sort to rearrange topographic sections in the Topo array in a logical. Z-Sort Topographic Sections (page 3-40) From the File menu. 18. BIOQUANT Topographer Handbook: 3D Modeling . On the Vertical Tool Bar. choose Change Z) to open The current Z-Value of the selected section will be displayed in the “Change All Z-Values To” field. 14. Missing sections may be filled with duplicates made from near by sections.Page 3-45 13. sequential order. PROCEDURE 1. The Change Z Dialog Box in Change Selected Sections Mode 16. type in the Z-Value (Z-Offset Value) that should have been assigned to the physical section from which the displayed tracing was taken.Review & Optimize the 3D Data . On the Change Z dialog box. 19. 17. The value in the “Raise/Lower All Z Values By” field should remain 0. In Section mode select a section that approximates the size and shape of the missing section. Repeat from step 12 for any additional new topographic sections that were created when Internal Paste was used. click the Change Z the Change Z dialog box. verify that the Change Selected Sections radio button is active. RELATED TOPICS • • • • • • • • • • • • • • Possible Color Problems (page 3-8) Possible Alignment Problems (page 3-9) Possible Z-Axis Spacing Problems (page 3-9) Distribute Section Maps Evenly Along the Z-Axis (page 3-37) Change the Z Value of a Section Map (page 3-38) Z-Sort Topographic Sections (page 3-40) Dealing With Conjoint Sections (page 3-42) Duplicate A Section (page 3-45) Reposition Misplaced Points (page 3-47) Color Editing Procedures (page 3-27) Section Alignment Procedures (page 3-32) Z-Axis Re-Distribution Procedures (page 3-37) Special Formatting Features (page 3-48) Other Atlas Shop Features (page 3-53) 3-D MODELING REVIEWING & OPTIMIZATION TOPICS • • • • Part 1-Display The Atlas (page 3-2) Part 2-A Quick Look at the Surface Rendered Model (page 3-5) Part 3-Save the Atlas to a New Array (page 3-6) Part 4-General Section Review (page 3-7) DUPLICATE A SECTION Occasionally one or more tissue sections in a series is lost or damaged during tissue processing and the absence of those sections is obvious in the reconstructed atlas. 15.

f. Use Z Sort to rearrange topographic sections in the Topo array in a logical. or click the down arrow in the Destination Array field and choose an existing Topo array from the drop list. From the File menu. Keyboard shortcut: Control-V is the same as choosing Internal Paste from the Edit menu. sequential order. do the following: a. click to choose the Ascending or Descending radio button. choose Internal Paste again for each additional tracing that is needed. (Or. b. On the Save Data message. (Alternately. Click the New Array button to add a new Topo array. A Warning box will open to inform you that the Z sorted atlas must be saved to a new array. (Clicking Cancel will cancel the Internal Copy command. Keyboard shortcut: Control-C is the same as choosing Internal Cut from the Edit menu. 5. On the Sort Sections By Z Value dialog box.) From the Edit menu.) From the Edit menu. on the Select Arrays dialog box. Click the Apply button to record the edited version of the atlas to the array in the Destination Array field. (In this case the last array will be the new array that will be added in step 6.) Click OK to acknowledge the notice. and asks if you want to add a new array. click the Atlas Shop button. Click OK to acknowledge the Warning and copy the selected section. In the Atlas Viewer. In order to display or continue editing the changed version of the atlas. 3.Review & Optimize the 3D Data . g. select a different section to duplicate and repeat steps 2 and 3. The Atlas Shop closes and the Atlas Viewer reopens. choose Internal Paste. A Save Data message will appear. 4. Click the YES button to open the Sort Sections By Z Value dialog box. 7. If more than one duplicate of the selected tracing is needed. A Warning box will open to remind you that the altered atlas must be saved to a new array. d. you must do the following: e. 6. click NO (since the changed version of the atlas has already been saved). From the Edit menu.) In the Z Sort Options area. or to continue editing. then add a New Array. deselect the original atlas array and select the Topo array that holds the revised version of the atlas.) Click Close. click Cancel. (The chosen Topo array cannot be one of the current atlas arrays. To display the revised version of the atlas. choose Z Sort. choose Internal Copy. If the chosen array is not new. click Redraw on the system tool bar.Page 3-46 2. ADDITIONAL NOTE • • 8. c. A Notice box appears to let you know that Elements will be pasted as a new section in the last array. Z-Sort Topographic Sections (page 3-40) RELATED TOPICS • • • • • • • • • • • • • Possible Color Problems (page 3-8) Possible Alignment Problems (page 3-9) Possible Z-Axis Spacing Problems (page 3-9) Distribute Section Maps Evenly Along the Z-Axis (page 3-37) Change the Z Value of a Section Map (page 3-38) Z-Sort Topographic Sections (page 3-40) Dealing With Conjoint Sections (page 3-42) Reposition Misplaced Points (page 3-47) Color Editing Procedures (page 3-27) Section Alignment Procedures (page 3-32) Z-Axis Re-Distribution Procedures (page 3-37) Special Formatting Features (page 3-48) Other Atlas Shop Features (page 3-53) BIOQUANT Topographer Handbook: 3D Modeling . click the OK button on the Warning box that says existing data will be overwritten. choose Exit Atlas Shop.

click the Change Z the Change Z dialog box. button (or from the Edit menu. occasionally result in a misplaced data point. choose Save. choose Change Z) to open The Change Z Dialog Box in Change Selected Sections Mode 4. This will automatically re-set the misplaced data point to the same Z-Value as the rest of the section. When this happens. The point may be correctly repositioned by this procedure. On the Change Z dialog box. then click the Close button. using the Select Next button or the GoTo Section dialog box (Select menu> GoTo).Page 3-47 3-D MODELING REVIEWING & OPTIMIZATION TOPICS • • • • Part 1-Display The Atlas (page 3-2) Part 2-A Quick Look at the Surface Rendered Model (page 3-5) Part 3-Save the Atlas to a New Array (page 3-6) Part 4-General Section Review (page 3-7) REPOSITION MISPLACED POINTS Atlas Shop editing routines that change the locations of sections on the Z-axis. RELATED TOPICS • • • • • • • • • • • • • Possible Color Problems (page 3-8) Possible Alignment Problems (page 3-9) Possible Z-Axis Spacing Problems (page 3-9) Distribute Section Maps Evenly Along the Z-Axis (page 3-37) Change the Z Value of a Section Map (page 3-38) Z-Sort Topographic Sections (page 3-40) Dealing With Conjoint Sections (page 3-42) Duplicate A Section (page 3-45) Color Editing Procedures (page 3-27) Section Alignment Procedures (page 3-32) Z-Axis Re-Distribution Procedures (page 3-37) Special Formatting Features (page 3-48) Other Atlas Shop Features (page 3-53) 3-D MODELING REVIEWING & OPTIMIZATION TOPICS • • • • Part 1-Display The Atlas (page 3-2) Part 2-A Quick Look at the Surface Rendered Model (page 3-5) Part 3-Save the Atlas to a New Array (page 3-6) Part 4-General Section Review (page 3-7) BIOQUANT Topographer Handbook: 3D Modeling . simply click the Apply button. until the stray vertical line (and its parent section) is selected. 3. Sequence through the sections. 2. the misplaced point becomes evident as a stray vertical line between two horizontal section lines in the Perspective panel. Verify that the Section Mode button is depressed on the system tool bar.Review & Optimize the 3D Data . 5. On the Vertical Tool Bar. the current Z Value of that section is displayed in the “Change All Z Values to” edit field. PROCEDURE 1. if there is only one section selected. From the File menu. because when the Change Z dialog box first opens.

these may be selected quickly using Select by Color.The “cap” or “open” markers on a tracing may be removed to return the tracing to its original “Middle of Object” default status. the resolution of the entire atlas or at least the resolution of the surface tracings should be reduced. through which interior objects may be viewed.Review & Optimize the 3D Data . When resolution is changed. (3-48) Cap Object .A number of tracings in the atlas may be marked as “open” to create a transparent window in a surface rendered model. (3-51) Middle of Object . COMMON ADJUSTMENTS THAT ENHANCE SURFACE RENDERING • • • Change Resolution . are needed. If corrective edits. After editing is finished. Hint: If all section outlines (or other objects of interest) are of the same unique color. especially in larger atlases. (3-52) • RELATED TOPICS • • • • • • • • • • • • • Possible Color Problems (page 3-8) Possible Alignment Problems (page 3-9) Possible Z-Axis Spacing Problems (page 3-9) Distribute Section Maps Evenly Along the Z-Axis (page 3-37) Change the Z Value of a Section Map (page 3-38) Z-Sort Topographic Sections (page 3-40) Dealing With Conjoint Sections (page 3-42) Duplicate A Section (page 3-45) Reposition Misplaced Points (page 3-47) Color Editing Procedures (page 3-27) Section Alignment Procedures (page 3-32) Z-Axis Re-Distribution Procedures (page 3-37) Other Atlas Shop Features (page 3-53) 3-D MODELING REVIEWING & OPTIMIZATION TOPICS • • • • Part 1-Display The Atlas (page 3-2) Part 2-A Quick Look at the Surface Rendered Model (page 3-5) Part 3-Save the Atlas to a New Array (page 3-6) Part 4-General Section Review (page 3-7) REDUCE ATLAS RESOLUTION When the atlas is displayed in the Atlas Modeler.The first and last contour tracings in an atlas can be marked as “caps” that will cover the open ends of a surface rendered model. the edited version of the atlas must be saved to a new Topo array. the edited atlas is opened again in the Atlas Modeler.The resolution (number of data points) in large atlases may be decreased to increase the speed at which a model is rendered or to produce a smoother surface. The original resolution was set by the smoothing limit in BIOQUANT Life Science or BIOQUANT OSTEO (the lower the Smoothing Limit the higher the resolution). The following procedures are all done in the Atlas Shop. CAUTION: Do not attempt to change the resolution of an entire atlas at one time. without reducing the opacity of the entire model. if it takes a long time to render the surface or redraw the model after it has been moved in the Model Window. it is best that these be done prior to adding special surface rendering formats. BIOQUANT Topographer Handbook: 3D Modeling . all section outlines) for which the resolution needs to be changed. To do so will most likely corrupt the data. PROCEDURE: 1. Select a limited number of objects(s) (e.g. See “Assign a New Color to a Group of Objects” on 3-28.Page 3-48 SPECIAL FORMATTING FEATURES Particular editing and formatting tools in the Topographer’s Atlas Shop help improve the quality of a surface rendered model. (3-51) End of Object/Leave Open . such as aligning sections and correcting errors in Z positioning.

4. Otherwise. click the down arrow in the Destination Array field and click to choose the desired empty Topo array from the drop list. it may be necessary to repeat steps 4 and 5 several times before the desired effect would be apparent in a surface rendered model. click Yes. b. (Excess data points are discarded to maintain the original size of the tracings). The initial default value in the Resolution Distance field is the minimum distance the system found between any two data points in the selected portion of the atlas. b. The New Array dialog box opens. If a single smoothing limit was maintained during measurement. unless you think the data set already contains an empty Topo array that can be used. increase the micron value between data points (to decrease the resolution). (the new micron distance) is only applied between pairs of data points in the selected outlines. d. remove the original Topo arrays from the Selected list. and all will be increased simultaneously to the new value. c. Choose Resolution from the Edit menu to open the Set Image Resolution dialog box. 5. In the Resolution Distance field. In the Array Name field. Click the Apply button to generate the lower resolution atlas in the selected Topo array. a. repeat steps 4 and 5. IMPORTANT: If a single Smoothing Limit was not maintained during data collection for the selected outlines. Click the Close button to close the Set Image Resolution dialog box. On the Set Image Resolution dialog box. Verify that the intended Destination Array is selected. Click the OK button to close the New Array dialog box. The lower resolution atlas is now ready to be displayed in the Atlas Viewer. When asked if you want to add a new Topo array. or Atlas Shop. is usually enough to produce the desired effect. Atlas Modeler. 7. the distance between all data points will match the minimum value. read the following carefully.Review & Optimize the 3D Data . for which the original distance matched the minimum (initial) value in the Resolution Distance field. if a new Topo array was added in step 2. If there is not an empty Topo array. by doubling or tripling the initial default value in the Resolution Distance field. simply doubling or tripling the default Resolution Distance and clicking the Apply button once. and select the Topo array that contains the lower resolution version of the atlas. if the smoothing limit was changed during data collection. if it seems necessary. In this case. the number of data set pairs that are separated by the minimum distance may be small. exit the Atlas Shop. Set Image Resolution 3. In this case. do the following: a. then.Page 3-49 2. edit the name of the Topo array to indicate that this is a lower resolution version of the atlas. 6. then click OK. However. The change in resolution. A warning will appear to remind you that any data in the selected array will be overwritten. To display or edit the new resolution atlas. on the Select Arrays dialog box. it will already be selected in the Destination Array field. Click the Add Topo button. c. In the Atlas Viewer. BIOQUANT Topographer Handbook: 3D Modeling .

End of Object/Leave Open . Surface Render Formatting Tools buttons on the system tool bar add TOPIC CONTENTS Cap Open Ends of A Model (page 3-51) Define a Transparent Window in a Model (page 3-51) Restore Middle of Object Status (page 3-52) RELATED TOPICS • • • • • • • • • • • • • • Reduce Atlas Resolution (page 3-48) Possible Color Problems (page 3-8) Possible Alignment Problems (page 3-9) Possible Z-Axis Spacing Problems (page 3-9) Distribute Section Maps Evenly Along the Z-Axis (page 3-37) Change the Z Value of a Section Map (page 3-38) Z-Sort Topographic Sections (page 3-40) Dealing With Conjoint Sections (page 3-42) Duplicate A Section (page 3-45) Reposition Misplaced Points (page 3-47) Color Editing Procedures (page 3-27) Section Alignment Procedures (page 3-32) Z-Axis Re-Distribution Procedures (page 3-37) Other Atlas Shop Features (page 3-53) 3-D MODELING REVIEWING & OPTIMIZATION TOPICS • • • • Part 1-Display The Atlas (page 3-2) Part 2-A Quick Look at the Surface Rendered Model (page 3-5) Part 3-Save the Atlas to a New Array (page 3-6) Part 4-General Section Review (page 3-7) BIOQUANT Topographer Handbook: 3D Modeling .Review & Optimize the 3D Data . and Middle of Object special formatting to an atlas that is to be surface rendered.Page 3-50 RELATED TOPICS • • • • • • • • • • • • • • • Reduce Atlas Resolution (page 3-48) Format Contour Lines (page 3-50) Possible Color Problems (page 3-8) Possible Alignment Problems (page 3-9) Possible Z-Axis Spacing Problems (page 3-9) Distribute Section Maps Evenly Along the Z-Axis (page 3-37) Change the Z Value of a Section Map (page 3-38) Z-Sort Topographic Sections (page 3-40) Dealing With Conjoint Sections (page 3-42) Duplicate A Section (page 3-45) Reposition Misplaced Points (page 3-47) Color Editing Procedures (page 3-27) Section Alignment Procedures (page 3-32) Z-Axis Re-Distribution Procedures (page 3-37) Other Atlas Shop Features (page 3-53) 3-D MODELING REVIEWING & OPTIMIZATION TOPICS • • • • Part 1-Display The Atlas (page 3-2) Part 2-A Quick Look at the Surface Rendered Model (page 3-5) Part 3-Save the Atlas to a New Array (page 3-6) Part 4-General Section Review (page 3-7) FORMAT CONTOUR LINES The Cap Object .

without reducing the opacity of the entire BIOQUANT Topographer Handbook: 3D Modeling . Because surface rendering connects points of the same color on adjacent surface defining outlines (usually section outlines). and there is no outline before the first tracing or after the last. Select the topographic section that contains the first or last surface defining outline for the model. leaving open holes at the top and bottom of the rendered model. Click the Cap Object button on the system toolbar to mark the selected tracing as a "cap". 2. (3-52) RELATED TOPICS • • • • • • • • • • • • • • • • • • Define a Transparent Window in a Model (page 3-51) Restore Middle of Object Status (page 3-52) Reduce Atlas Resolution (page 3-48) Format Contour Lines (page 3-50) Reduce Atlas Resolution (page 3-48) Possible Color Problems (page 3-8) Possible Alignment Problems (page 3-9) Possible Z-Axis Spacing Problems (page 3-9) Distribute Section Maps Evenly Along the Z-Axis (page 3-37) Change the Z Value of a Section Map (page 3-38) Z-Sort Topographic Sections (page 3-40) Dealing With Conjoint Sections (page 3-42) Duplicate A Section (page 3-45) Reposition Misplaced Points (page 3-47) Color Editing Procedures (page 3-27) Section Alignment Procedures (page 3-32) Z-Axis Re-Distribution Procedures (page 3-37) Other Atlas Shop Features (page 3-53) 3-D MODELING REVIEWING & OPTIMIZATION TOPICS • • • • Part 1-Display The Atlas (page 3-2) Part 2-A Quick Look at the Surface Rendered Model (page 3-5) Part 3-Save the Atlas to a New Array (page 3-6) Part 4-General Section Review (page 3-7) DEFINE A TRANSPARENT WINDOW IN A MODEL The End of Object/Leave Open tool in the Atlas Shop makes it possible to create a limited transparent window in a surface rendered model. use the Select Next button on the system toolbar to cycle through the objects in the selected section.Review & Optimize the 3D Data . the rendered surface stops abruptly. If necessary. These holes may be closed using the Cap Object tool in the Atlas Shop. Click the Object Mode button to activate Object Mode. Repeat steps 1 through 5 to mark (as a cap) the tracing at the opposite end of the model. Click the Section Mode button on the system tool bar to activate Section Mode. 6. NOTE: For the bottom cap this is usually. 3. 4. RELATED PROCEDURE Middle of Object . Section 0. 5. through which interior objects may be viewed. until the correct contour outline is selected. but not always. PROCEDURE 1. An outline that is tagged as a cap will automatically fill with the surface color when the atlas is opened in the Atlas Modeler.The “cap” or “open” markers on a tracing may be removed to return the tracing to its original “Middle of Object” default status.Page 3-51 CAP OPEN ENDS OF A MODEL The Cap Object tool is used to tag the first and last outlines in the model as surface rendering caps.

Page 3-52 model. Click the Section Mode button on the system tool bar to activate Section Mode. Click the Object Mode button to activate Object Mode. Before special formatting is added. all tracings in an atlas are termed Middle of Object. Click the End of Object/Leave Open "Leave Open". When the atlas is opened in the Atlas Modeler. Select the topographic section that contains the first (or next) outline that is to be marked with Leave Open. 4. The very first and last outlines in a marked series. The End of Object/Leave Open tool is used to mark a series of surface defining outlines that are to be “left open”. If necessary. RELATED TOPICS • • • • • • • • • • • • • • • • • • Cap Open Ends of A Model (page 3-51) Restore Middle of Object Status (page 3-52) Reduce Atlas Resolution (page 3-48) Format Contour Lines (page 3-50) Reduce Atlas Resolution (page 3-48) Possible Color Problems (page 3-8) Possible Alignment Problems (page 3-9) Possible Z-Axis Spacing Problems (page 3-9) Distribute Section Maps Evenly Along the Z-Axis (page 3-37) Change the Z Value of a Section Map (page 3-38) Z-Sort Topographic Sections (page 3-40) Dealing With Conjoint Sections (page 3-42) Duplicate A Section (page 3-45) Reposition Misplaced Points (page 3-47) Color Editing Procedures (page 3-27) Section Alignment Procedures (page 3-32) Z-Axis Re-Distribution Procedures (page 3-37) Other Atlas Shop Features (page 3-53) 3-D MODELING REVIEWING & OPTIMIZATION TOPICS • • • • Part 1-Display The Atlas (page 3-2) Part 2-A Quick Look at the Surface Rendered Model (page 3-5) Part 3-Save the Atlas to a New Array (page 3-6) Part 4-General Section Review (page 3-7) RESTORE MIDDLE OF OBJECT STATUS The "cap" or "open" markers on a tracing may be removed to return a tracing to its original "Middle of Object" default status. 3. The Middle of Object tool on the system tool bar removes the special formatting that was applied to a tracing using the Cap Object or End of Object/Leave Open tools BIOQUANT Topographer Handbook: 3D Modeling . PROCEDURE 1. serve as End of Object markers that allow the system to recognize the intervening outlines as a separate object. 5. all but the first and last outlines marked “Leave Open” will automatically be constructed as a transparent window. tool button on the system tool bar to mark the selected tracing as Repeat steps 1 through 5 to mark (as Leave Open) all the tracings that are to be part of the transparent window. 6. even though the color of the “open” lines is identical to the rest of the surface. until only the correct contour outline is selected. use the Select Next button on the system tool bar to cycle through the objects in the selected section. 2.Review & Optimize the 3D Data .

3. use the Select Next button on the system tool bar to cycle through the objects in the selected section. until only the specially formatted outline is selected. TOPIC CONTENTS Numeric Transform (page 3-54) The Line Editing Tools (page 3-24) Special Atlas Shop FEatures (page 3-58) BIOQUANT Topographer Handbook: 3D Modeling .Page 3-53 PROCEDURE 1. If necessary.Review & Optimize the 3D Data . Select the topographic section that contains the outline for which the Cap or End of Object/Leave Open formatting is to be removed. Click the Object Mode button to activate Object Mode. Click the Middle of Object button on the system toolbar to remove the special formatting and restore the tracing’s default Middle of Object status. 2. RELATED TOPICS • • • • • • • • • • • • • • • • • • Cap Open Ends of A Model (page 3-51) Define a Transparent Window in a Model (page 3-51) Reduce Atlas Resolution (page 3-48) Format Contour Lines (page 3-50) Reduce Atlas Resolution (page 3-48) Possible Color Problems (page 3-8) Possible Alignment Problems (page 3-9) Possible Z-Axis Spacing Problems (page 3-9) Distribute Section Maps Evenly Along the Z-Axis (page 3-37) Change the Z Value of a Section Map (page 3-38) Z-Sort Topographic Sections (page 3-40) Dealing With Conjoint Sections (page 3-42) Duplicate A Section (page 3-45) Reposition Misplaced Points (page 3-47) Color Editing Procedures (page 3-27) Section Alignment Procedures (page 3-32) Z-Axis Re-Distribution Procedures (page 3-37) Other Atlas Shop Features (page 3-53) 3-D MODELING REVIEWING & OPTIMIZATION TOPICS • • • • Part 1-Display The Atlas (page 3-2) Part 2-A Quick Look at the Surface Rendered Model (page 3-5) Part 3-Save the Atlas to a New Array (page 3-6) Part 4-General Section Review (page 3-7) OTHER ATLAS SHOP FEATURES Following are Atlas Shop procedures that were not covered above. 4. 5. Click the Section Mode button on the system tool bar to activate Section Mode.

2. or resizes the selected parts of the atlas by a known amount. PROCEDURE: SETUP 1. rotates. The Numeric Transform dialog box is opened by choosing Numeric Transform from the Edit menu.Review & Optimize the 3D Data . From the Atlas Shop Edit menu. Numeric Transform Dialog Box TOPIC CONTENTS Translate by Numeric Transform (page 3-55) Resize by Numeric Transform (page 3-56) Rotate by Numeric Transform (page 3-57) BIOQUANT Topographer Handbook: 3D Modeling .Page 3-54 RELATED TOPICS • • • • • • • • • • • • • Possible Color Problems (page 3-8) Possible Alignment Problems (page 3-9) Possible Z-Axis Spacing Problems (page 3-9) Distribute Section Maps Evenly Along the Z-Axis (page 3-37) Change the Z Value of a Section Map (page 3-38) Z-Sort Topographic Sections (page 3-40) Dealing With Conjoint Sections (page 3-42) Duplicate A Section (page 3-45) Reposition Misplaced Points (page 3-47) Color Editing Procedures (page 3-27) Section Alignment Procedures (page 3-32) Z-Axis Re-Distribution Procedures (page 3-37) Other Atlas Shop Features (page 3-53) 3-D MODELING REVIEWING & OPTIMIZATION TOPICS • • • • Part 1-Display The Atlas (page 3-2) Part 2-A Quick Look at the Surface Rendered Model (page 3-5) Part 3-Save the Atlas to a New Array (page 3-6) Part 4-General Section Review (page 3-7) NUMERIC TRANSFORM Numeric Transform translates. Select the section(s) or objects(s) or point(s) of interest. choose Numeric Transform to open the Numeric Transform dialog box.

Down: In the Y field.) • If Relative is checked. enter a negative micron distance (the selection will be moved this distance upwards. it should be noted that the XY plane of the coordinate system used by the Windows operating system is unconventional.: • • If Relative is checked. type the positive or negative Y coordinate to which the first point in the first object should be moved. enter a positive micron distance (the selection will be moved this distance to the right). b. On the Numeric Transform dialog box. In the Y field. type the positive or negative X coordinate to which the first point in the first object should be moved. the atlas landmark always occupies the XYZ(0. enter a positive micron distance (the selection will be moved this distance downwards).0. 2. +) BIOQUANT Topographer Handbook: 3D Modeling . The X and Y signs (x. click to check the Translate check box. Left: In the X field.Page 3-55 RELATED TOPICS • • • • • • • • • • • • • • • The Line Editing Tools (page 3-24) Special Atlas Shop FEatures (page 3-58) Possible Color Problems (page 3-8) Possible Alignment Problems (page 3-9) Possible Z-Axis Spacing Problems (page 3-9) Distribute Section Maps Evenly Along the Z-Axis (page 3-37) Change the Z Value of a Section Map (page 3-38) Z-Sort Topographic Sections (page 3-40) Dealing With Conjoint Sections (page 3-42) Duplicate A Section (page 3-45) Reposition Misplaced Points (page 3-47) Color Editing Procedures (page 3-27) Section Alignment Procedures (page 3-32) Z-Axis Re-Distribution Procedures (page 3-37) Other Atlas Shop Features (page 3-53) 3-D MODELING REVIEWING & OPTIMIZATION TOPICS • • • • Part 1-Display The Atlas (page 3-2) Part 2-A Quick Look at the Surface Rendered Model (page 3-5) Part 3-Save the Atlas to a New Array (page 3-6) Part 4-General Section Review (page 3-7) TRANSLATE BY NUMERIC TRANSFORM PROCEDURE 1. enter a negative micron distance (the selection will be moved this distance to the left).y) in the various quadrants are given below: • Lower Right Quadrant (+ .Review & Optimize the 3D Data . (All other points in the selection will be moved to maintain their positional relationship to the first point. If Relative is not checked. Helpful Hint: As expected. to move the selected item(s) … • • • • Right: In the X field. the values that are typed into the X and Y fields designate the micron distance that the selection is to be moved relative to its current position in the atlas. However. the values that are typed into the X and Y fields designate actual X and Y coordinates to which the first point in the selection is to be moved. In the X field. • If Relative is not checked.0 Offset) position of the current coordinate system. Decide whether or not the Relative check box should be checked. Up: In the Y field. to move the first point of the first object in the selection to a specific XY location … a.

or by responding YES to the Save Data message when exiting the Atlas Shop. On the Numeric Transform dialog box. Click the Apply button. If desirable. in the Width or/and Height field(s) type a percentage value that is greater than 100. • • 3. 2... to save the edited version of the atlas to a new Topo array. in the Width or/and Height field(s) enter a percentage value that is less than 100. +) Upper Right Quadrant (+ . If the Maintain Aspect Ratio check box is checked. BIOQUANT Topographer Handbook: 3D Modeling . if the atlas is saved using Save on the File menu. -) Lower Left Quadrant (. Height and Width resizing are independent of each other. click to uncheck the Maintain Aspect Ratio check box. To decrease the size of the selected item(s). Upper Left Quadrant (. when a value is entered in either the Height or Width field. the new size just applied is now the current size and is considered the 100% value for the selected item(s). -) Click the Apply button. The selected item(s) are shown at the new size in the Atlas Window. RELATED TOPICS • • • • • • • • • • • • • • • • • • Numeric Transform (page 3-54) Resize by Numeric Transform (page 3-56) Rotate by Numeric Transform (page 3-57) The Line Editing Tools (page 3-24) Special Atlas Shop FEatures (page 3-58) Possible Color Problems (page 3-8) Possible Alignment Problems (page 3-9) Possible Z-Axis Spacing Problems (page 3-9) Distribute Section Maps Evenly Along the Z-Axis (page 3-37) Change the Z Value of a Section Map (page 3-38) Z-Sort Topographic Sections (page 3-40) Dealing With Conjoint Sections (page 3-42) Duplicate A Section (page 3-45) Reposition Misplaced Points (page 3-47) Color Editing Procedures (page 3-27) Section Alignment Procedures (page 3-32) Z-Axis Re-Distribution Procedures (page 3-37) Other Atlas Shop Features (page 3-53) 3-D MODELING REVIEWING & OPTIMIZATION TOPICS • • • • Part 1-Display The Atlas (page 3-2) Part 2-A Quick Look at the Surface Rendered Model (page 3-5) Part 3-Save the Atlas to a New Array (page 3-6) Part 4-General Section Review (page 3-7) RESIZE BY NUMERIC TRANSFORM PROCEDURE 1. If it is unchecked.Review & Optimize the 3D Data . The current size of the selection is designated 100%. If desirable. the other field automatically updates to the same value. click to check the Resize check box. the data in the current atlas Topo array(s) are permanently changed. To increase the size of the selected item(s).Page 3-56 • • • 3. SAVING THE NUMERIC TRANSFORM EDIT • After Numeric Transform is used. NOTE: If subsequent resizing is done. Save As on the File menu may be used instead.

Review & Optimize the 3D Data . Click the Apply button. Save As on the File menu may be used instead.Page 3-57 SAVING THE NUMERIC TRANSFORM EDIT • After Numeric Transform is used. in the Angle field type the number of degrees the selected item(s) should be rotated. click to check the Rotate check box. if the atlas is saved using Save on the File menu. If desirable. If desirable. the data in the current atlas Topo array(s) are permanently changed. BIOQUANT Topographer Handbook: 3D Modeling . • • 2. if the atlas is saved using Save on the File menu. RELATED TOPICS • • • • • • • • • • • • • • • • • • Numeric Transform (page 3-54) Translate by Numeric Transform (page 3-55) Rotate by Numeric Transform (page 3-57) The Line Editing Tools (page 3-24) Special Atlas Shop FEatures (page 3-58) Possible Color Problems (page 3-8) Possible Alignment Problems (page 3-9) Possible Z-Axis Spacing Problems (page 3-9) Distribute Section Maps Evenly Along the Z-Axis (page 3-37) Change the Z Value of a Section Map (page 3-38) Z-Sort Topographic Sections (page 3-40) Dealing With Conjoint Sections (page 3-42) Duplicate A Section (page 3-45) Reposition Misplaced Points (page 3-47) Color Editing Procedures (page 3-27) Section Alignment Procedures (page 3-32) Z-Axis Re-Distribution Procedures (page 3-37) Other Atlas Shop Features (page 3-53) 3-D MODELING REVIEWING & OPTIMIZATION TOPICS • • • • Part 1-Display The Atlas (page 3-2) Part 2-A Quick Look at the Surface Rendered Model (page 3-5) Part 3-Save the Atlas to a New Array (page 3-6) Part 4-General Section Review (page 3-7) ROTATE BY NUMERIC TRANSFORM PROCEDURE 1. SAVING THE NUMERIC TRANSFORM EDIT • After Numeric Transform is used. On the Numeric Transform dialog box. to save the edited version of the atlas to a new Topo array. or by responding YES to the Save Data message when exiting the Atlas Shop. in the Angle field type the negative number of degrees the selected item(s) should be rotated. To rotate clockwise. to save the edited version of the atlas to a new Topo array. or by responding YES to the Save Data message when exiting the Atlas Shop. the data in the current atlas Topo array(s) are permanently changed. To rotate counter-clockwise. Save As on the File menu may be used instead.

Page 3-58 RELATED TOPICS • • • • • • • • • • • • • • • • • • Numeric Transform (page 3-54) Resize by Numeric Transform (page 3-56) Translate by Numeric Transform (page 3-55) The Line Editing Tools (page 3-24) Special Atlas Shop FEatures (page 3-58) Possible Color Problems (page 3-8) Possible Alignment Problems (page 3-9) Possible Z-Axis Spacing Problems (page 3-9) Distribute Section Maps Evenly Along the Z-Axis (page 3-37) Change the Z Value of a Section Map (page 3-38) Z-Sort Topographic Sections (page 3-40) Dealing With Conjoint Sections (page 3-42) Duplicate A Section (page 3-45) Reposition Misplaced Points (page 3-47) Color Editing Procedures (page 3-27) Section Alignment Procedures (page 3-32) Z-Axis Re-Distribution Procedures (page 3-37) Other Atlas Shop Features (page 3-53) 3-D MODELING REVIEWING & OPTIMIZATION TOPICS • • • • Part 1-Display The Atlas (page 3-2) Part 2-A Quick Look at the Surface Rendered Model (page 3-5) Part 3-Save the Atlas to a New Array (page 3-6) Part 4-General Section Review (page 3-7) SPECIAL ATLAS SHOP FEATURES There are three special Atlas Shop features that are not covered in this section: Taking Measurements From the Atlas. These are briefly described below. and Contour Conversion. Planar Conversion.Review & Optimize the 3D Data . and discussed detail in Section 8: The Atlas Viewer in Detail (page 5-1) RELATED TOPICS • • • • • • • • • • • • • • • • • • • Title Bar and Tool Bars (page 3-13) Save Versus Save As (page 3-13) The Three Selection Modes (page 3-14) The Selection Methods (page 3-15) Possible Color Problems (page 3-8) Possible Alignment Problems (page 3-9) Possible Z-Axis Spacing Problems (page 3-9) Distribute Section Maps Evenly Along the Z-Axis (page 3-37) Change the Z Value of a Section Map (page 3-38) Z-Sort Topographic Sections (page 3-40) Dealing With Conjoint Sections (page 3-42) Duplicate A Section (page 3-45) Reposition Misplaced Points (page 3-47) Color Editing Procedures (page 3-27) Section Alignment Procedures (page 3-32) Z-Axis Re-Distribution Procedures (page 3-37) Other Atlas Shop Features (page 3-53) Numeric Transform (page 3-54) Special Atlas Shop FEatures (page 3-58) BIOQUANT Topographer Handbook: 3D Modeling .

Review & Optimize the 3D Data .Page 3-59 3-D MODELING REVIEWING & OPTIMIZATION TOPICS • • • • Part 1-Display The Atlas (page 3-2) Part 2-A Quick Look at the Surface Rendered Model (page 3-5) Part 3-Save the Atlas to a New Array (page 3-6) Part 4-General Section Review (page 3-7) BIOQUANT Topographer Handbook: 3D Modeling .

Review & Optimize the 3D Data .Page 3-60 BIOQUANT Topographer Handbook: 3D Modeling .

Introduction to the Atlas Modeler (page 4-2) Changing the Characteristics of the Model (page 4-7) Activating Continuous Rotation (page 4-11) Record or Play an AVI Movie (page 4-14) Saving and Loading a Surface Rendering Parameters File (page 4-17) Special Formatting Options (page 4-19) Printing. Saving.3D Modeling: 3D Modeling: Surface RendSurface ing in the Atlas Modeler Rending in the The default surface rendering of an atlas may be Atlas Modeler BIOQUANT Topographer Handbook modified to enhance the final three dimensional model. The rotating model can be recorded in an AVI movie. and Copying the Model (page 4-21) Exiting Atlas Modeler (page 4-25) .

The model can be set to auto rotate and recorded as an AVI movie. click the Show Surface as Lines choose Wireframe from the View menu. panned. to points. and Copying the Model (page 4-21) Exiting Atlas Modeler (page 4-25) AVAILABLE SURFACE TYPES VIEW> SOLID • To display the surfaces of the rendered model as solid. button on the tool bar or BIOQUANT Topographer Handbook: 3D Modeling: Surface Rending in the Atlas Modeler . click the Show Surface as Filled bar or choose Solid from the View menu. Saving. The model can be zoomed in or out. or rotated. In the Atlas model. they can be saved as a Parameters file that can be reloaded upon returning to the Atlas Modeler for this model for quick retrieval. to wire frame. Surfaces Shown As Filled button on the tool VIEW> WIRE FRAME • To display the surface as a series of lines. TOPIC CONTENTS Available Surface Types (page 4-2) Smoothing (page 4-3) Render Option 2 (page 4-4) Manipulating the Model (page 4-4) Using Ideal Test Forms (page 4-6) RELATED TOPICS • • • • • • • • Introduction to the Atlas Modeler (page 4-2) Changing the Characteristics of the Model (page 4-7) Activating Continuous Rotation (page 4-11) Record or Play an AVI Movie (page 4-14) Saving and Loading a Surface Rendering Parameters File (page 4-17) Special Formatting Options (page 4-19) Printing. the surface rending environment of the Topographer plug-in. the view can be changed from modeled. Once settings have been refined.Page 4-2 INTRODUCTION TO THE ATLAS MODELER The Atlas Modeler’s Toolbar This sections is an introduction to the Atlas Modeler. The lighting and opacity can be changed.

click the Show Surface as Points choose Points from the View menu.Page 4-3 Surfaces Shown As Lines VIEW> POINTS • To display the surface as a series of dots. The Smoothing option modifies the BIOQUANT Topographer Handbook: 3D Modeling: Surface Rending in the Atlas Modeler . Saving. Surfaces Show As Points button on the tool bar or RELATED TOPICS • • • • • • • • • • • • Smoothing (page 4-3) Render Option 2 (page 4-4) Manipulating the Model (page 4-4) Using Ideal Test Forms (page 4-6) Introduction to the Atlas Modeler (page 4-2) Changing the Characteristics of the Model (page 4-7) Activating Continuous Rotation (page 4-11) Record or Play an AVI Movie (page 4-14) Saving and Loading a Surface Rendering Parameters File (page 4-17) Special Formatting Options (page 4-19) Printing. and Copying the Model (page 4-21) Exiting Atlas Modeler (page 4-25) SMOOTHING The Atlas Modeler's rendering algorithm produces a matt finish on the model.

click and drag the cursor straight downwards on the screen. click to check this option on the Options menu. 2. Saving. To decrease the size of the atlas. click to check Smoothing on the Options menu. To show a glossier surface. click the Scale Image button. BIOQUANT Topographer Handbook: 3D Modeling: Surface Rending in the Atlas Modeler . 2. click to un-check Smoothing on the Options menu.Page 4-4 surface to appear glossy. Render Option 2 uses a different algorithm that can sometimes render more accurately a specimen that includes one or more folded or accordion type structures. 3. and Copying the Model (page 4-21) Exiting Atlas Modeler (page 4-25) MANIPULATING THE MODEL VIEW> SCALE IMAGE The size of the surface rendered model may be scaled up or down. click to uncheck Rendering Option 2 on the Options menu. and Copying the Model (page 4-21) Exiting Atlas Modeler (page 4-25) RENDER OPTION 2 The Atlas Modeler’s primary rendering algorithm usually produces the most pleasing display. click and drag the cursor straight upwards on the screen. RELATED TOPICS • • • • • • • • • • • • Available Surface Types (page 4-2) Render Option 2 (page 4-4) Manipulating the Model (page 4-4) Using Ideal Test Forms (page 4-6) Introduction to the Atlas Modeler (page 4-2) Changing the Characteristics of the Model (page 4-7) Activating Continuous Rotation (page 4-11) Record or Play an AVI Movie (page 4-14) Saving and Loading a Surface Rendering Parameters File (page 4-17) Special Formatting Options (page 4-19) Printing. 1. Saving. with the cursor anywhere in the image window. PROCEDURE • • To apply Render Option 2. RELATED TOPICS • • • • • • • • • • • • Available Surface Types (page 4-2) Smoothing (page 4-3) Manipulating the Model (page 4-4) Using Ideal Test Forms (page 4-6) Introduction to the Atlas Modeler (page 4-2) Changing the Characteristics of the Model (page 4-7) Activating Continuous Rotation (page 4-11) Record or Play an AVI Movie (page 4-14) Saving and Loading a Surface Rendering Parameters File (page 4-17) Special Formatting Options (page 4-19) Printing. with the cursor anywhere in the image window. To re-apply the primary rendering algorithm. PROCEDURE 1. On the tool bar. To increase the size of the atlas. To remove the smoothing format.

Page 4-5 VIEW> PAN IMAGE
The surface rendered model may be moved around on the Atlas Modeler’s desktop. 1. 2. On the tool bar, click the Pan button.

With the cursor over the atlas, click and drag the cursor (and the atlas) to the desired location.

VIEW> ROTATE IMAGE
The perspective of the surface rendered model may be changed by rotating it in small increments using the arrow keys on the keyboard or by clicking and dragging the cursor in the model window. If Rotate and Auto Rotate are both active when the click and drag method is used, the model will continue to rotate in the indicated direction until the Auto Rotate button is released.

OPTION 1: ROTATE THE MODEL USING THE ARROW KEYS
1. 2. 3. Click the Rotate button on the tool bar, or choose Rotate from the View menu.

Use the right and left arrow keys to incrementally rotate the model clockwise and counter-clockwise respectively around the Z axis. Use the up and down arrow keys to incrementally rotate the model clockwise and counter-clockwise respectively around the X axis.

HELPFUL HINTS
• • Arrow key rotation is the easiest and most controlled method of changing the perspective of a model. It is the recommended method especially for large models. After a model has been rotated 180 degrees, clockwise and counter-clockwise directions will appear reversed on the screen.

OPTION 2: ROTATE THE MODEL USING THE CURSOR
1. 2. 3. Click the Rotate on the tool bar, or choose Rotate from the View menu.

With the cursor anywhere in the image window, click and slowly drag the cursor a short distance in the direction you want the atlas to rotate. Repeat step 2 until the desired perspective is reached.

HELPFUL HINTS
• • • • Slow, short moves of the cursor in a straight line in either the right or left direction, are recommended for starters. The speed at which the cursor moves on the screen dictates the speed at which the atlas model is rotated to its new perspective. The angle at which the cursor is dragged on the screen influences the axis around which the model rotates. To rotate the model at a precise angle use the controls on the Movie Parameters dialog box.

VIEW> BLACK BACKGROUND
A brightly colored surface rendered model on a black background makes a dramatic presentation. When printing a bitmap of the model, however, a black background is usually not ideal. • • To turn on Black Background, click to check this option on the View menu. To replace a black background with a white one, click to uncheck Black Background on the View menu.

HELPFUL HINT
• When using a white background, light tracings can be made darker by returning to the Atlas Viewer and making a different Color assignment on the Color/Symbol tab of the Atlas Parameters dialog box.

BIOQUANT Topographer Handbook: 3D Modeling: Surface Rending in the Atlas Modeler

Page 4-6 RELATED TOPICS
• • • • • • • • • • • • Available Surface Types (page 4-2) Render Option 2 (page 4-4) Smoothing (page 4-3) Using Ideal Test Forms (page 4-6) Introduction to the Atlas Modeler (page 4-2) Changing the Characteristics of the Model (page 4-7) Activating Continuous Rotation (page 4-11) Record or Play an AVI Movie (page 4-14) Saving and Loading a Surface Rendering Parameters File (page 4-17) Special Formatting Options (page 4-19) Printing, Saving, and Copying the Model (page 4-21) Exiting Atlas Modeler (page 4-25)

USING IDEAL TEST FORMS
Lighting adjustments on complex three dimensional forms are made easier by pre-adjusting the lights on simplified geometric test forms. When Test Sphere, Test Isohedron, or Test Plane is chosen from the Atlas Modeler’s View menu, the idealized form temporarily replaces the surface rendered model in the Model window.

VIEW> TEST SPHERE
The test sphere is used to facilitate light adjustments for surface rendered models that are roughly spherical in shape. When Test Sphere is chosen from the View menu, the surface rendered model is temporarily replaced by an ideal sphere. 1. 2. 3. From the View menu, choose Test Sphere. Adjust the lighting to best show off the test form. Choose Topo Data from the View menu to restore the surface rendered model to the Model Window. The lighting that was applied to the test form is automatically applied to the rendered model.

VIEW> TEST ISOHEDRON
The test isohedron is used to facilitate light adjustments for surface rendered models that have complex or multisided shapes. When Test Isohedron is chosen from the View menu, the surface rendered model is temporarily replaced by an ideal Isohedron. 1. 2. 3. From the View menu, choose Test Isohedron. Adjust the lighting to best show off the test form. Choose Topo Data from the View menu to restore the surface rendered model to the Model Window. The lighting that was applied to the test form is automatically applied to the rendered model.

VIEW> TEST PLANE
The test plane is used to facilitate light adjustments for surface rendered models that are relatively flat. When Test Plane is chosen from the View menu, the surface rendered model is temporarily replaced by an ideal flat plane. 1. 2. 3. From the View menu, choose Test Plane. Adjust the lighting to best show off the test form. Choose Topo Data from the View menu to restore the surface rendered model to the Model Window. The lighting that was applied to the test form is automatically applied to the rendered model.

VIEW>TOPO DATA
• After adjusting the lighting on an test form, choose Topo Data from the View menu to restore the surface rendered model to the Model Window.

BIOQUANT Topographer Handbook: 3D Modeling: Surface Rending in the Atlas Modeler

Page 4-7 RELATED TOPICS
• • • • • • • • • • • • Available Surface Types (page 4-2) Render Option 2 (page 4-4) Manipulating the Model (page 4-4) Smoothing (page 4-3) Introduction to the Atlas Modeler (page 4-2) Changing the Characteristics of the Model (page 4-7) Activating Continuous Rotation (page 4-11) Record or Play an AVI Movie (page 4-14) Saving and Loading a Surface Rendering Parameters File (page 4-17) Special Formatting Options (page 4-19) Printing, Saving, and Copying the Model (page 4-21) Exiting Atlas Modeler (page 4-25)

CHANGING THE CHARACTERISTICS OF THE MODEL
Characteristics of the model may be changed in the Atlas Modeler. On the Color Parameters dialog box, the opacity of surface colors may by adjusted and objects of a particular color may be hidden. The Lighting Parameters dialog box allows the adjustment of the brightness of Global Ambient Light, parameters for a Spotlight Positioned on the Camera, and Surrounding Light.

TOPIC CONTENTS
Set Color Parameters (page 4-7) Set Lighting Parameters (page 4-9)

RELATED TOPICS
• • • • • • • • • • • • • Available Surface Types (page 4-2) Smoothing (page 4-3) Render Option 2 (page 4-4) Manipulating the Model (page 4-4) Smoothing (page 4-3) Introduction to the Atlas Modeler (page 4-2) Changing the Characteristics of the Model (page 4-7) Activating Continuous Rotation (page 4-11) Record or Play an AVI Movie (page 4-14) Saving and Loading a Surface Rendering Parameters File (page 4-17) Special Formatting Options (page 4-19) Printing, Saving, and Copying the Model (page 4-21) Exiting Atlas Modeler (page 4-25)

SET COLOR PARAMETERS
On the Color Parameters dialog box, the opacity of surface colors may by adjusted and objects of a particular color may be hidden.

IMPORTANT
If the ultimate goal is to record a rotating atlas in an AVI movie, set the Movie Bounding Box and resize the model to fit the Bounding Box before setting the desired lighting parameters. See “Options> Set Movie Parameters” on page 4-11. The Color Parameters dialog box is opened by clicking the Set Color Parameters button on the system toolbar or choosing Set Color Parameters from the Options menu. It is closed by clicking the dialog box Close button.

BIOQUANT Topographer Handbook: 3D Modeling: Surface Rending in the Atlas Modeler

Page 4-8
The Color Parameters Dialog Box

COLOR INDEX VERSES COLOR SHOWN
Clicking one of the 16 colored squares on the Color Parameters dialog box, selects objects in the model based on their color index numbers in the Topo array. An object’s Color Index (in the Topo array) and Color Shown (in the model) are the same, unless the object’s default Fill color was changed in the Atlas Viewer, before entering the Atlas Modeler. The colors shown in the surface rendered model always match the Fill colors last applied in the Atlas Viewer. If the default Fill color for an object was changed on the Color/Symbols tab of the Atlas Parameters dialog box (in the Atlas Viewer), the Color Shown in the model (for that object) will not match the object’s Color Index. This makes selecting objects for color adjustments in the Atlas Modeler tricky. In short, if the default Fill color for any object was changed in the Atlas Viewer, in the Atlas Modeler, you must remember the object’s original, default color in order to select it on the Color Parameters dialog box. It will help to keep the following points in mind: • • • Clicking a colored square on the Color Parameters dialog box will cause the system to search through the model’s Topo array and identify any objects with a Color Index that matches the selected square. When the “Show Objects of this Color Index” box is unchecked, all objects in the model that have the indicated Color Index (in the Topo array) will be hidden from view when the Apply button is clicked. When the Opacity slider is adjusted, the opacity of surfaces constructed between all objects in the model that have the indicated Color Index (in the Topo array) will be adjusted appropriately.

ADJUST THE TRANSPARENCY OF THE SURFACE
The opacity of an outer surface may be reduced so internal objects may be seen. 1. 2. 3. 4. On the color palette click the default color of the surface you wish to make less opaque. Click and drag the Opacity slider to a value less than 100%. Click the Apply button. Repeat steps 2 and 3 until the desired transparency is reached.

RELATED PROCEDURE
An alternate way to reveal internal structures, without reducing the opacity of the entire surface, is to apply a special “Leave Open” formatting to a selected number of surface tracings, thus creating a transparent window. Special formatting is applied in the Atlas Shop. See “Format Contour Lines” on page 3-50.

HIDE ALL OBJECTS OF A PARTICULAR COLOR
1. 2. On the color palette, click the default color of an object you wish to hide (remove from the display). Click to un-check the Show Objects of This Color check box. All objects of that color will be removed (hidden) from the surface rendered display.

ADDITIONAL INFORMATION
Lighting, Color, and Movie parameters may be saved to a Surface Rendering Parameters file, then loaded for subsequent showings. See “Saving and Loading a Surface Rendering Parameters File” on page 4-17.

BIOQUANT Topographer Handbook: 3D Modeling: Surface Rending in the Atlas Modeler

Page 4-9 RELATED TOPICS
• • • • • • • • • • • • • • • Set Color Parameters (page 4-7) Set Lighting Parameters (page 4-9) Available Surface Types (page 4-2) Smoothing (page 4-3) Render Option 2 (page 4-4) Manipulating the Model (page 4-4) Smoothing (page 4-3) Introduction to the Atlas Modeler (page 4-2) Changing the Characteristics of the Model (page 4-7) Activating Continuous Rotation (page 4-11) Record or Play an AVI Movie (page 4-14) Saving and Loading a Surface Rendering Parameters File (page 4-17) Special Formatting Options (page 4-19) Printing, Saving, and Copying the Model (page 4-21) Exiting Atlas Modeler (page 4-25)

SET LIGHTING PARAMETERS
The Lighting Parameters dialog box allows the adjustment of the brightness of Global Ambient Light, parameters for a Spotlight Positioned on the Camera, and Surrounding Light.

ADDITIONAL INFORMATION
• If the ultimate goal is to record a rotating atlas in an AVI movie, set the Movie Bounding Box and resize the model to fit the Bounding Box before setting the desired lighting parameters. Options> Set Movie Parameters (page 4-11) It is usually beneficial to adjust lighting on the ideal Test shape that most closely resembles the shape of the atlas model, then display the atlas model using those settings. Using Ideal Test Forms (page 4-6)

Global Ambient Light and Spotlight Positioned On Camera are often used together. When Surrounding Light is used, it is usually better to turn off Global Ambient Light and Spotlight Positioned on Camera. The Lighting Parameters dialog box is opened by clicking the Set Lighting Parameters button on the system tool bar or choosing Set Lighting Parameters from the Options menu. It is closed by clicking the dialog box Close button.

BIOQUANT Topographer Handbook: 3D Modeling: Surface Rending in the Atlas Modeler

Page 4-10
The Lighting Parameters Dialog Box

ADJUST GLOBAL AMBIENT LIGHT
1. • • Click to check the Global Ambient Light check box. To decrease the brightness of the ambient light, click and drag the slider toward the left end (-1) of the Brightness scale. To increase the brightness of the ambient light, click and drag the slider toward the right end (1) of the Brightness scale.

ADJUST SPOTLIGHT POSITIONED ON CAMERA
1. • • • • Click to check the Spotlight Positioned on Camera check box. To decrease the brightness of the spotlight, click and drag the slider toward the left end (-1) of the Brightness scale. To increase the brightness of the spotlight, click and drag the slider toward the right end (1) of the Brightness scale. To diffuse the beam of the spotlight, click and drag the slider toward the left end (128) of the Intensity Distribution scale. To concentrate the beam of the spotlight, click and drag the slider toward the right end (0) of the Intensity Distribution scale.

ADJUST SURROUNDING LIGHT
The surrounding light is cast from six different spotlights: Front, Right, Left, Top, Bottom, and Back. Each spotlight has its own control tab on the Set Lighting Parameters dialog box. It may be necessary to use the left or right scroll buttons to see either the left most (Back) tab, or the rightmost (Front) tab. By default all surrounding spotlights are turned Off. 1. 2. 3. Click to check the Adjust Surrounding Light check box, then for each spotlight do the following: Click to choose the tab for a spotlight that is to be used. Click the spotlight’s On radio button. • • • • To decrease the brightness of the spotlight, click and drag the slider toward the left end (-1) of the Brightness scale. To increase the brightness of the spotlight, click and drag the slider toward the right end (1) of the Brightness scale. To diffuse the beam of the spotlight, click and drag the slider toward the left end (128) of the Intensity Distribution scale. To concentrate the beam of the spotlight, click and drag the slider toward the right end (0) of the Intensity Distribution scale.

BIOQUANT Topographer Handbook: 3D Modeling: Surface Rending in the Atlas Modeler

Color. Saving and Loading a Surface Rendering Parameters File (page 4-17) RELATED TOPICS • • • • • • • • • • • • • • Set Color Parameters (page 4-7) Available Surface Types (page 4-2) Smoothing (page 4-3) Render Option 2 (page 4-4) Manipulating the Model (page 4-4) Smoothing (page 4-3) Introduction to the Atlas Modeler (page 4-2) Changing the Characteristics of the Model (page 4-7) Activating Continuous Rotation (page 4-11) Record or Play an AVI Movie (page 4-14) Saving and Loading a Surface Rendering Parameters File (page 4-17) Special Formatting Options (page 4-19) Printing. speed. The rotating model may also be recorded and played as an AVI movie. and Copying the Model (page 4-21) Exiting Atlas Modeler (page 4-25) ACTIVATING CONTINUOUS ROTATION Controls on the Movie Parameters dialog box are used to precisely control the angle. It is closed by clicking the dialog box Close button. Saving. Saving. BIOQUANT Topographer Handbook: 3D Modeling: Surface Rending in the Atlas Modeler . TOPIC CONTENTS Options> Set Movie Parameters (page 4-11) Options> Auto Movie Rotate (page 4-13) Options> Auto Rotate (page 4-13) RELATED TOPICS • • • • • • • • • • • • • • Set Color Parameters (page 4-7) Available Surface Types (page 4-2) Smoothing (page 4-3) Render Option 2 (page 4-4) Manipulating the Model (page 4-4) Smoothing (page 4-3) Introduction to the Atlas Modeler (page 4-2) Changing the Characteristics of the Model (page 4-7) Activating Continuous Rotation (page 4-11) Record or Play an AVI Movie (page 4-14) Saving and Loading a Surface Rendering Parameters File (page 4-17) Special Formatting Options (page 4-19) Printing. and Movie parameters may be saved to a Surface Rendering Parameters file. and number of times a surface rendered model is rotated. and Copying the Model (page 4-21) Exiting Atlas Modeler (page 4-25) OPTIONS> SET MOVIE PARAMETERS The Movie Parameters dialog box is opened by clicking the Set Movie Parameters button on the system tool bar or choosing Set Movie Parameters from the Options menu. then loaded for subsequent showings.Page 4-11 ADDITIONAL INFORMATION • Lighting.

To view one 360 degree rotation of the atlas. The model will continue to rotate even if the Movie Parameters dialog box is closed.g. b. 3. Color. if the atlas has been deliberately rotated to a preferred starting perspective. click to release the Auto Movie Rotate button . To change the speed of the rotation. press the Apply button. Determine the number of frames required for one complete 360 degree rotation as follows: Divide 360 by the number of degrees the atlas will be rotated in each frame (e. • • ADDITIONAL INFORMATION • Lighting. or choose Set Movie Parameters from the Options menu. (See Helpful Hints below. Decide around which axis the atlas is to be rotated (X. Saving and Loading a Surface Rendering Parameters File (page 4-17) BIOQUANT Topographer Handbook: 3D Modeling: Surface Rending in the Atlas Modeler . The original model perspective defaults to zero (no rotation) on each axis. then subtract 1. Then decrease the value and press Apply until the desired speed is reached. click the Set Movie Parameters button.) In the Degree Rotation per Frame field for the desired axis. On the tool bar. However. To end a continuous rotation of the atlas. or Z). c. • In the Number of Frames field. 4. click the Use Current Position button. (e. The Delay field defaults to 100 (1/100 th of a second).g. 2. This is the recommended Delay if the rotating atlas is to be recorded as an AVI movie. type the value determined in step 3 (e.Page 4-12 The Movie Parameters Dialog Box SET ROTATION PARAMETERS 1. 10). type the number of degrees the atlas will rotate per frame.g. and Movie parameters may be saved to a Surface Rendering Parameters file. 10 degrees). then loaded for subsequent showings.1 = 35. to open the Record Movie dialog box. Y. Example calculation: (360/10) . try 500 in the Delay field and press Apply again. d. 35). To view a continuous rotation of the atlas. click to depress the Auto Movie Rotate button on the tool bar. Set the Rotation Parameters as follows: a.

and Copying the Model (page 4-21) Exiting Atlas Modeler (page 4-25) OPTIONS> AUTO ROTATE When Auto Rotate is active. click to depress the Auto Movie Rotate choose Auto Movie Rotate on the Options menu. PROCEDURE 1. or click to uncheck Auto Movie Rotate on the Options menu. a surface rendered model continues to rotate according to parameters set on the Movie Parameters dialog box until Auto Movie Rotate is deactivated. Saving.Page 4-13 RELATED TOPICS • • • • • • • • • • • • • • • • Options> Auto Movie Rotate (page 4-13) Options> Auto Rotate (page 4-13) Set Color Parameters (page 4-7) Available Surface Types (page 4-2) Smoothing (page 4-3) Render Option 2 (page 4-4) Manipulating the Model (page 4-4) Smoothing (page 4-3) Introduction to the Atlas Modeler (page 4-2) Changing the Characteristics of the Model (page 4-7) Activating Continuous Rotation (page 4-11) Record or Play an AVI Movie (page 4-14) Saving and Loading a Surface Rendering Parameters File (page 4-17) Special Formatting Options (page 4-19) Printing. the current speed and direction of the rotating surface rendered model continues until Auto Rotate is deactivated. To activate Auto Movie Rotate. Saving. 2. click to release the Auto Movie Rotate button. and Copying the Model (page 4-21) Exiting Atlas Modeler (page 4-25) OPTIONS> AUTO MOVIE ROTATE When Auto Movie Rotate is active. button on the system toolbar. BIOQUANT Topographer Handbook: 3D Modeling: Surface Rending in the Atlas Modeler . RELATED TOPICS • • • • • • • • • • • • • • • • Options> Set Movie Parameters (page 4-11) Options> Auto Rotate (page 4-13) Set Color Parameters (page 4-7) Available Surface Types (page 4-2) Smoothing (page 4-3) Render Option 2 (page 4-4) Manipulating the Model (page 4-4) Smoothing (page 4-3) Introduction to the Atlas Modeler (page 4-2) Changing the Characteristics of the Model (page 4-7) Activating Continuous Rotation (page 4-11) Record or Play an AVI Movie (page 4-14) Saving and Loading a Surface Rendering Parameters File (page 4-17) Special Formatting Options (page 4-19) Printing. or To deactivate Auto Movie Rotate.

Page 4-14 PROCEDURE 1. lighting. RELATED TOPICS • • • • • • • • • • • • • • • • Options> Set Movie Parameters (page 4-11) Options> Auto Movie Rotate (page 4-13) Set Color Parameters (page 4-7) Available Surface Types (page 4-2) Smoothing (page 4-3) Render Option 2 (page 4-4) Manipulating the Model (page 4-4) Smoothing (page 4-3) Introduction to the Atlas Modeler (page 4-2) Changing the Characteristics of the Model (page 4-7) Activating Continuous Rotation (page 4-11) Record or Play an AVI Movie (page 4-14) Saving and Loading a Surface Rendering Parameters File (page 4-17) Special Formatting Options (page 4-19) Printing. 2. Saving. or click to uncheck Auto Rotate on the Options menu. Saving. and rotational settings are made. and Copying the Model (page 4-21) Exiting Atlas Modeler (page 4-25) BIOQUANT Topographer Handbook: 3D Modeling: Surface Rending in the Atlas Modeler . or click to check Auto To deactivate Auto Rotate. TOPIC CONTENTS Record And Review an AVI Movie (page 4-15) About the Bounding Box (page 4-16) RELATED TOPICS • • • • • • • • • • • • • • • • • Options> Set Movie Parameters (page 4-11) Options> Auto Movie Rotate (page 4-13) Options> Auto Rotate (page 4-13) Set Color Parameters (page 4-7) Available Surface Types (page 4-2) Smoothing (page 4-3) Render Option 2 (page 4-4) Manipulating the Model (page 4-4) Smoothing (page 4-3) Introduction to the Atlas Modeler (page 4-2) Changing the Characteristics of the Model (page 4-7) Activating Continuous Rotation (page 4-11) Record or Play an AVI Movie (page 4-14) Saving and Loading a Surface Rendering Parameters File (page 4-17) Special Formatting Options (page 4-19) Printing. button on the tool bar. and Copying the Model (page 4-21) Exiting Atlas Modeler (page 4-25) RECORD OR PLAY AN AVI MOVIE Controls on the Movie Parameters dialog box allow a rotating model to be recorded as an AVI movie file. The movie resolution is determined by the size of a Bounding Box that defines how much of the background space is included in the movie. click to depress the Auto Rotate Rotate on the Options menu. To activate Auto Rotate. click to release the Auto Rotate button. The Bounding Box should be chosen and the model scaled to fit within the Bounding Box before color.

set the desired Rotation parameters. to open it. 11. Click the OK button on the Video Compression dialog box. choose the desired Resolution (meaning the area of the Atlas Modeler’s display space that is to be included in the movie): For more information. The Set Bounding Box dialog box opens. open the Color Parameters button on the tool bar or choosing Set Color Parameters dialog box by clicking the Set Color Parameters from the Options menu. 6. The model will rotate through one complete rotational cycle as the movie is being recorded. see About the Bounding Box (page 4-16).Page 4-15 RECORD AND REVIEW AN AVI MOVIE This procedure outlines recording and reviewing an AVI movie. click to release the Auto Movie Rotate rotations. if necessary. then close the Lighting Parameters dialog box. Video Resolution . On the Set Bounding box dialog box. 17. click the Record button to open the Save Surface Modeler Movie dialog box. The Video Compression dialog box will open. The Options dialog box opens. click the Set Movie Parameters Movie Parameters from the Options menu. tool to resize the model to 4. 12.Includes the space defined by the user. If the opacity of the surface needs to be changed or particular colors hidden. PROCEDURE 1.Includes a 320 x 240 area of the display space. click the Set Lighting Parameters button. navigate to the desired Save In folder. click the Play button. click the Set Bounding Box button. in the Recording Parameters region. . BIOQUANT Topographer Handbook: 3D Modeling: Surface Rending in the Atlas Modeler 8. Web Resolution . click the down arrow at the end of the Compressor field to open a drop list of compression routines. If the lighting on the model needs to be adjusted. A three letter extension (. type a name that is easily associated with the current model. 15. click the Edit menu and choose Options from the drop list. button to stop the button.Includes 1020 x 700 display space. on the tool bar. If the model is currently rotating.Includes a 640 x 480 area of the display space. 3. On the Save Surface Modeler Movie dialog box. use the Scale Image fit within the Bounding Box. or choose Set On the Movie Parameters dialog box. The Windows Media Player opens. or choose Set Lighting Parameters from the Options menu to open the Lighting Parameters dialog box. On the Media Player dialog box.avi) will be automatically appended to the name when the Save button is pressed. Set Lighting Parameters (page 4-9) On the Movie Parameters dialog box. Make the desired adjustments. Click to choose Microsoft Video 1 (recommended compression type). Close the Set Bounding Box dialog box and. • • • • High Resolution . 9. Set Color Parameters (page 4-7) 7. When the desired destination folder is open in the Save In field. then click the OK button. 2. 10. If the Movie Parameters dialog box is not open. in the Name field. 14. 5. To review the movie. 13. Make the desired changes. On the Video Compression dialog box. On the Options dialog box click to check Auto Repeat. The Options dialog box will close. Click the Save button. 16. then close the Color Parameters dialog box. Set Rotation Parameters (page 4-12) On the Movie Parameters dialog box. Custom Resolution .

• • RELATED TOPICS • • • • • • • • • • • • • • • • • • About the Bounding Box (page 4-16) Options> Set Movie Parameters (page 4-11) Options> Auto Movie Rotate (page 4-13) Options> Auto Rotate (page 4-13) Set Color Parameters (page 4-7) Available Surface Types (page 4-2) Smoothing (page 4-3) Render Option 2 (page 4-4) Manipulating the Model (page 4-4) Smoothing (page 4-3) Introduction to the Atlas Modeler (page 4-2) Changing the Characteristics of the Model (page 4-7) Activating Continuous Rotation (page 4-11) Record or Play an AVI Movie (page 4-14) Saving and Loading a Surface Rendering Parameters File (page 4-17) Special Formatting Options (page 4-19) Printing. (To produce 10 frames per second the default Delay of 100 should is used.Includes 1020 x 700 display space. The frames per second may be loosely determined by dividing 1. Open the Set Bounding Box dialog box by clicking the Bounding Box button on the Movie Parameters dialog box. BIOQUANT Topographer Handbook: 3D Modeling: Surface Rending in the Atlas Modeler . On the Set Bounding Box dialog box. 2. check Show Bounding Box. To stop the movie click the left mouse button. from the View menu. ADDITIONAL INFORMATION • Using Microsoft Video 1 compression and Full Resolution. the bounding box may be displayed or hidden by clicking the Movie Bounding Box button on the tool bar. This produces a movie file of about 16 MB. Saving. PROCEDURE 1. each movie frame will save as a 1024x768 image. and Copying the Model (page 4-21) Exiting Atlas Modeler (page 4-25) ABOUT THE BOUNDING BOX Controls on the Movie Parameters dialog box allow a rotating model to be recorded and played as an AVI movie file. SHOW BOUNDING BOX NOTE To show the bounding box at all times. Adjusting the size of the Bounding Box controls the size or resolution of the movie file. A Bounding Box defines how much of the Atlas Modeler's background space is included in the movie. choose the desired Resolution (meaning the area of the Atlas Modeler's display space that is to be included in the movie): • • • • High Resolution . The movie will appear choppy if it runs at anything more than 10 frames per second. click to release the Auto Movie Rotate button and stop the rotation. If Auto Movie Rotate is active. or by choosing Set Movie Size from the Options menu. On the Media Player’s button bar.) After the Movie Bounding Box dialog box is closed. click the Play button to start the movie.000 by the Delay value. Video Resolution .Page 4-16 18. An alternate resolution may be selected on the Movie Bounding Box dialog box if a smaller movie file is desirable. 19. Web Resolution . 3.Includes a 640 x 480 area of the display space.Includes a 320 x 240 area of the display space. on the tool bar.Includes a space defined by the user. Custom Resolution .

use the within the Bounding Box. Saving.Page 4-17 4. and Copying the Model (page 4-21) Exiting Atlas Modeler (page 4-25) BIOQUANT Topographer Handbook: 3D Modeling: Surface Rending in the Atlas Modeler . TOPIC CONTENTS File> Save Parameters (page 4-18) File> Load Parameters (page 4-18) RELATED TOPICS • • • • • • • • • • • • • • • • • • • Record And Review an AVI Movie (page 4-15) About the Bounding Box (page 4-16) Options> Set Movie Parameters (page 4-11) Options> Auto Movie Rotate (page 4-13) Options> Auto Rotate (page 4-13) Set Color Parameters (page 4-7) Available Surface Types (page 4-2) Smoothing (page 4-3) Render Option 2 (page 4-4) Manipulating the Model (page 4-4) Smoothing (page 4-3) Introduction to the Atlas Modeler (page 4-2) Changing the Characteristics of the Model (page 4-7) Activating Continuous Rotation (page 4-11) Record or Play an AVI Movie (page 4-14) Saving and Loading a Surface Rendering Parameters File (page 4-17) Special Formatting Options (page 4-19) Printing. Lighting. Anytime in the future that the model is reopened in the Atlas Modeler. Scale Image tool to resize the model to fit RELATED TOPICS • • • • • • • • • • • • • • • • • • Record And Review an AVI Movie (page 4-15) Options> Set Movie Parameters (page 4-11) Options> Auto Movie Rotate (page 4-13) Options> Auto Rotate (page 4-13) Set Color Parameters (page 4-7) Available Surface Types (page 4-2) Smoothing (page 4-3) Render Option 2 (page 4-4) Manipulating the Model (page 4-4) Smoothing (page 4-3) Introduction to the Atlas Modeler (page 4-2) Changing the Characteristics of the Model (page 4-7) Activating Continuous Rotation (page 4-11) Record or Play an AVI Movie (page 4-14) Saving and Loading a Surface Rendering Parameters File (page 4-17) Special Formatting Options (page 4-19) Printing. and Copying the Model (page 4-21) Exiting Atlas Modeler (page 4-25) SAVING AND LOADING A SURFACE RENDERING PARAMETERS FILE The preferred Color. the Parameter file may be loaded to instantly restore the preferred settings. and Movie parameters for a rendered model may be saved to a Surface Rendering Parameters file. Close the Set Bounding Box dialog box. If necessary. Saving.

BIOQUANT Topographer Handbook: 3D Modeling: Surface Rending in the Atlas Modeler . Click the Load Parameters button on the system tool bar or from the File menu. When the desired folder is open in the Save In field. A three letter extension (. This will place its name in the File Name field. and Copying the Model (page 4-21) Exiting Atlas Modeler (page 4-25) FILE> LOAD PARAMETERS If a Surface Rendering Parameters file was saved for the current model. the Parameters file may be reloaded to automatically restore previously set Color. The default location for saving parameter files is BQOSTEO\Topographer. Click the Save Parameters button on the system tool bar or from the File menu.bqr) will be automatically appended to the new name.Page 4-18 FILE> SAVE PARAMETERS The preferred Color. type a name that is easily associated with the current model. 2. choose Load Parameters to open the Open Surface Rendering Parameters dialog box. For ease of finding the parameters file again. Click to highlight the desired Parameters field. 3. If you created a subdirectory associated with your Data Volume and Data Set as recommended in the Save Parameters procedure. choose Save Parameters to open the Save Surface Rendering Parameters dialog box. 2. 4. Lighting. The default Save in location is BQOSTEO\Topographer or BQLifescience\Topographer. Lighting. Click the Open button. it will be listed here. PROCEDURE 1. and Movie parameters. 4. Navigate to the folder that contains the Parameter file for the current data set. Saving. in the File Name field. and Movie parameters for a rendered model may be saved to a Surface Rendering Parameters file. it is recommended that you create a subdirectory in the Topographer folder that is named the same as your Data Volume and Data Set. 3. RELATED TOPICS • • • • • • • • • • • • • • • • • • • • File> Save Parameters (page 4-18) Record And Review an AVI Movie (page 4-15) About the Bounding Box (page 4-16) Options> Set Movie Parameters (page 4-11) Options> Auto Movie Rotate (page 4-13) Options> Auto Rotate (page 4-13) Set Color Parameters (page 4-7) Available Surface Types (page 4-2) Smoothing (page 4-3) Render Option 2 (page 4-4) Manipulating the Model (page 4-4) Smoothing (page 4-3) Introduction to the Atlas Modeler (page 4-2) Changing the Characteristics of the Model (page 4-7) Activating Continuous Rotation (page 4-11) Record or Play an AVI Movie (page 4-14) Saving and Loading a Surface Rendering Parameters File (page 4-17) Special Formatting Options (page 4-19) Printing. Then when you later need to find and open the parameter files for a particular Data Set you can easily navigate to them. PROCEDURE 1. Click the Save button.

Saving. Saving. and Copying the Model (page 4-21) Exiting Atlas Modeler (page 4-25) BIOQUANT Topographer Handbook: 3D Modeling: Surface Rending in the Atlas Modeler . TOPIC CONTENTS Adjustment in the Atlas Viewer that Enhances Surface Rendering (page 4-20) Adjustments in the Atlas Shop that enhance surface rendering. and Copying the Model (page 4-21) Exiting Atlas Modeler (page 4-25) SPECIAL FORMATTING OPTIONS Particular formatting tools in the Topographer’s Atlas Viewer and Atlas Shop help improve the quality of a surface rendered model. (page 4-20) RELATED TOPICS • • • • • • • • • • • • • • • • • • • • • File> Save Parameters (page 4-18) File> Load Parameters (page 4-18) Record And Review an AVI Movie (page 4-15) About the Bounding Box (page 4-16) Options> Set Movie Parameters (page 4-11) Options> Auto Movie Rotate (page 4-13) Options> Auto Rotate (page 4-13) Set Color Parameters (page 4-7) Available Surface Types (page 4-2) Smoothing (page 4-3) Render Option 2 (page 4-4) Manipulating the Model (page 4-4) Smoothing (page 4-3) Introduction to the Atlas Modeler (page 4-2) Changing the Characteristics of the Model (page 4-7) Activating Continuous Rotation (page 4-11) Record or Play an AVI Movie (page 4-14) Saving and Loading a Surface Rendering Parameters File (page 4-17) Special Formatting Options (page 4-19) Printing.Page 4-19 RELATED TOPICS • • • • • • • • • • • • • • • • • • • • File> Load Parameters (page 4-18) Record And Review an AVI Movie (page 4-15) About the Bounding Box (page 4-16) Options> Set Movie Parameters (page 4-11) Options> Auto Movie Rotate (page 4-13) Options> Auto Rotate (page 4-13) Set Color Parameters (page 4-7) Available Surface Types (page 4-2) Smoothing (page 4-3) Render Option 2 (page 4-4) Manipulating the Model (page 4-4) Smoothing (page 4-3) Introduction to the Atlas Modeler (page 4-2) Changing the Characteristics of the Model (page 4-7) Activating Continuous Rotation (page 4-11) Record or Play an AVI Movie (page 4-14) Saving and Loading a Surface Rendering Parameters File (page 4-17) Special Formatting Options (page 4-19) Printing.

3. signals the Atlas Modeler to render the designated tracings as discrete objects. Using the two small scroll buttons. click the down arrow to display a small scroll list. Change the Color Of One Branch of a Y or V-Shaped Structure (page 3-30) • BIOQUANT Topographer Handbook: 3D Modeling: Surface Rending in the Atlas Modeler . scroll to and click to choose the Dot symbol. • Change Resolution . Reduce Atlas Resolution (page 3-48) Change Colors in a Branched Structure . for example when an Area array was used to trace cells within a structure. Exit the Atlas Modeler. 6. In the Symbols section. In the Atlas Viewer. click on the color (and current symbol) of the group for which the Dot symbol is to be applied. Click the Apply button. and Copying the Model (page 4-21) Exiting Atlas Modeler (page 4-25) ADJUSTMENTS IN THE ATLAS SHOP THAT ENHANCE SURFACE RENDERING. Assigning the Dot symbol to such tracings and turning on Symbols in the Atlas Viewer.The resolution (number of data points) in large atlases may be decreased to speed surface rendering.Y or V shaped three dimensional structures will surface render more accurately if one of the “legs” of the Y or V is assigned a different color. Click the Atlas Modeler discrete objects. 5. button to reopen the Atlas Modeler. Display the current default symbol(s) in the atlas by clicking to check the Symbol check box. the Atlas Modeler has no way to recognize them as separate individual objects. 2. (page 4-20) File> Save Parameters (page 4-18) File> Load Parameters (page 4-18) Record And Review an AVI Movie (page 4-15) About the Bounding Box (page 4-16) Options> Set Movie Parameters (page 4-11) Options> Auto Movie Rotate (page 4-13) Options> Auto Rotate (page 4-13) Set Color Parameters (page 4-7) Available Surface Types (page 4-2) Smoothing (page 4-3) Render Option 2 (page 4-4) Manipulating the Model (page 4-4) Smoothing (page 4-3) Introduction to the Atlas Modeler (page 4-2) Changing the Characteristics of the Model (page 4-7) Activating Continuous Rotation (page 4-11) Record or Play an AVI Movie (page 4-14) Saving and Loading a Surface Rendering Parameters File (page 4-17) Special Formatting Options (page 4-19) Printing. on the Atlas Parameters dialog box click the Colors/Symbols tab. In the color coded Symbols list. 4. 7. Saving. The small area tracings will now render as RELATED TOPICS • • • • • • • • • • • • • • • • • • • • • • Adjustments in the Atlas Shop that enhance surface rendering. PROCEDURE: ASSIGN THE DOT SYMBOL TO REPLACE SMALL AREA TRACINGS 1. in the Available field.Page 4-20 ADJUSTMENT IN THE ATLAS VIEWER THAT ENHANCES SURFACE RENDERING When an atlas contains multiple small area tracings of the same color.

The first and last contour tracings in an atlas can be marked as “caps” that will cover the open ends of a surface rendered model. and copy the model to the clipboard. and Copying the Model (page 4-21) Exiting Atlas Modeler (page 4-25) PRINTING. through which interior objects may be viewed. AND COPYING THE MODEL This section describes how to save the model as a bitmap or DXF file.The “cap” or “open” markers on a tracing may be removed to return the tracing to its original “Middle of Object” default status. Define a Transparent Window in a Model (page 3-51) Middle of Object . without reducing the opacity of the entire model. print the model. Cap Open Ends of A Model (page 3-51) End of Object/Leave Open .Page 4-21 • Cap Object . Restore Middle of Object Status (page 3-52) • • RELATED TOPICS • • • • • • • • • • • • • • • • • • • • • • Adjustment in the Atlas Viewer that Enhances Surface Rendering (page 4-20) File> Save Parameters (page 4-18) File> Load Parameters (page 4-18) Record And Review an AVI Movie (page 4-15) About the Bounding Box (page 4-16) Options> Set Movie Parameters (page 4-11) Options> Auto Movie Rotate (page 4-13) Options> Auto Rotate (page 4-13) Set Color Parameters (page 4-7) Available Surface Types (page 4-2) Smoothing (page 4-3) Render Option 2 (page 4-4) Manipulating the Model (page 4-4) Smoothing (page 4-3) Introduction to the Atlas Modeler (page 4-2) Changing the Characteristics of the Model (page 4-7) Activating Continuous Rotation (page 4-11) Record or Play an AVI Movie (page 4-14) Saving and Loading a Surface Rendering Parameters File (page 4-17) Special Formatting Options (page 4-19) Printing. TOPIC CONTENTS File>Save Image As (page 4-22) File> Print Image (page 4-23) File> Copy Image to Clipboard (page 4-24) BIOQUANT Topographer Handbook: 3D Modeling: Surface Rending in the Atlas Modeler . Saving. SAVING.A number of tracings in the atlas may be marked as “open” to create a transparent window in a surface rendered model.

3. In the Name field. Click the Save button. When the desired destination folder is open in the Save In field. PROCEDURE 1. A three letter extension (.Page 4-22 RELATED TOPICS • • • • • • • • • • • • • • • • • • • • • • Adjustment in the Atlas Viewer that Enhances Surface Rendering (page 4-20) File> Save Parameters (page 4-18) File> Load Parameters (page 4-18) Record And Review an AVI Movie (page 4-15) About the Bounding Box (page 4-16) Options> Set Movie Parameters (page 4-11) Options> Auto Movie Rotate (page 4-13) Options> Auto Rotate (page 4-13) Set Color Parameters (page 4-7) Available Surface Types (page 4-2) Smoothing (page 4-3) Render Option 2 (page 4-4) Manipulating the Model (page 4-4) Smoothing (page 4-3) Introduction to the Atlas Modeler (page 4-2) Changing the Characteristics of the Model (page 4-7) Activating Continuous Rotation (page 4-11) Record or Play an AVI Movie (page 4-14) Saving and Loading a Surface Rendering Parameters File (page 4-17) Special Formatting Options (page 4-19) Printing. Click the Save Image As button on the tool bar or choose Save Image As from the File menu.bmp or . Saving.dxf) will be automatically appended to the name when the Save button is pressed. 4. Click to choose Windows Bitmap or Autocad DXF. and Copying the Model (page 4-21) Exiting Atlas Modeler (page 4-25) FILE>SAVE IMAGE AS A surface rendered model may be saved as a Windows bitmap or an Autocad DXF file. 2. navigate to the drive and folder to which the bitmap image file should be saved. click the down arrow to reveal a drop list of available file types. 5. type a name that is easily associated with the current model. at the end of the Files of Type field. On the Save As dialog box. BIOQUANT Topographer Handbook: 3D Modeling: Surface Rending in the Atlas Modeler .

etc. click to uncheck Black Background. Click the Print Image dialog box opens. 2. The Print On the Print dialog box. BIOQUANT Topographer Handbook: 3D Modeling: Surface Rending in the Atlas Modeler . if necessary adjust printing options as follows: • • • Click the down-arrow in the Printer field to choose an alternate printer. change paper size. Click the Properties button to select Portrait or Landscape.Page 4-23 RELATED TOPICS • • • • • • • • • • • • • • • • • • • • • • • • File> Print Image (page 4-23) File> Copy Image to Clipboard (page 4-24) Adjustment in the Atlas Viewer that Enhances Surface Rendering (page 4-20) File> Save Parameters (page 4-18) File> Load Parameters (page 4-18) Record And Review an AVI Movie (page 4-15) About the Bounding Box (page 4-16) Options> Set Movie Parameters (page 4-11) Options> Auto Movie Rotate (page 4-13) Options> Auto Rotate (page 4-13) Set Color Parameters (page 4-7) Available Surface Types (page 4-2) Smoothing (page 4-3) Render Option 2 (page 4-4) Manipulating the Model (page 4-4) Smoothing (page 4-3) Introduction to the Atlas Modeler (page 4-2) Changing the Characteristics of the Model (page 4-7) Activating Continuous Rotation (page 4-11) Record or Play an AVI Movie (page 4-14) Saving and Loading a Surface Rendering Parameters File (page 4-17) Special Formatting Options (page 4-19) Printing. 1. Change the number of copies to be printed. 3. button on the system tool bar or from the File menu. From the View menu. Click the Print button. 4. For most printers. and Copying the Model (page 4-21) Exiting Atlas Modeler (page 4-25) FILE> PRINT IMAGE The surface rendered model may be printed. Saving. it is better to change the model’s background color to white. choose Print Image.

choose Copy Image to Clipboard. From the File menu. Saving. and Copying the Model (page 4-21) Exiting Atlas Modeler (page 4-25) FILE> COPY IMAGE TO CLIPBOARD A bitmap image of the surface rendered model may be copied to the clipboard.Page 4-24 RELATED TOPICS • • • • • • • • • • • • • • • • • • • • • • • • File>Save Image As (page 4-22) File> Copy Image to Clipboard (page 4-24) Adjustment in the Atlas Viewer that Enhances Surface Rendering (page 4-20) File> Save Parameters (page 4-18) File> Load Parameters (page 4-18) Record And Review an AVI Movie (page 4-15) About the Bounding Box (page 4-16) Options> Set Movie Parameters (page 4-11) Options> Auto Movie Rotate (page 4-13) Options> Auto Rotate (page 4-13) Set Color Parameters (page 4-7) Available Surface Types (page 4-2) Smoothing (page 4-3) Render Option 2 (page 4-4) Manipulating the Model (page 4-4) Smoothing (page 4-3) Introduction to the Atlas Modeler (page 4-2) Changing the Characteristics of the Model (page 4-7) Activating Continuous Rotation (page 4-11) Record or Play an AVI Movie (page 4-14) Saving and Loading a Surface Rendering Parameters File (page 4-17) Special Formatting Options (page 4-19) Printing. PROCEDURE 1. BIOQUANT Topographer Handbook: 3D Modeling: Surface Rending in the Atlas Modeler .

choose Exit Atlas Modeler. and Copying the Model (page 4-21) Exiting Atlas Modeler (page 4-25) BIOQUANT Topographer Handbook: 3D Modeling: Surface Rending in the Atlas Modeler . RELATED TOPICS • • • • • • • • • • • • • • • • • • • • • • • • File> Print Image (page 4-23) File> Copy Image to Clipboard (page 4-24) Adjustment in the Atlas Viewer that Enhances Surface Rendering (page 4-20) File> Save Parameters (page 4-18) File> Load Parameters (page 4-18) Record And Review an AVI Movie (page 4-15) About the Bounding Box (page 4-16) Options> Set Movie Parameters (page 4-11) Options> Auto Movie Rotate (page 4-13) Options> Auto Rotate (page 4-13) Set Color Parameters (page 4-7) Available Surface Types (page 4-2) Smoothing (page 4-3) Render Option 2 (page 4-4) Manipulating the Model (page 4-4) Smoothing (page 4-3) Introduction to the Atlas Modeler (page 4-2) Changing the Characteristics of the Model (page 4-7) Activating Continuous Rotation (page 4-11) Record or Play an AVI Movie (page 4-14) Saving and Loading a Surface Rendering Parameters File (page 4-17) Special Formatting Options (page 4-19) Printing. Saving. from the File menu.Page 4-25 RELATED TOPICS • • • • • • • • • • • • • • • • • • • • • • • • File> Print Image (page 4-23) File>Save Image As (page 4-22) Adjustment in the Atlas Viewer that Enhances Surface Rendering (page 4-20) File> Save Parameters (page 4-18) File> Load Parameters (page 4-18) Record And Review an AVI Movie (page 4-15) About the Bounding Box (page 4-16) Options> Set Movie Parameters (page 4-11) Options> Auto Movie Rotate (page 4-13) Options> Auto Rotate (page 4-13) Set Color Parameters (page 4-7) Available Surface Types (page 4-2) Smoothing (page 4-3) Render Option 2 (page 4-4) Manipulating the Model (page 4-4) Smoothing (page 4-3) Introduction to the Atlas Modeler (page 4-2) Changing the Characteristics of the Model (page 4-7) Activating Continuous Rotation (page 4-11) Record or Play an AVI Movie (page 4-14) Saving and Loading a Surface Rendering Parameters File (page 4-17) Special Formatting Options (page 4-19) Printing. and Copying the Model (page 4-21) Exiting Atlas Modeler (page 4-25) EXITING ATLAS MODELER • To exit the Atlas Modeler and return to the Atlas Viewer. Saving.

Page 4-26 BIOQUANT Topographer Handbook: 3D Modeling: Surface Rending in the Atlas Modeler .

BIOQUANT Topographer Handbook The Atlas Viewer in Detail This section covers working with 3D wire frame models in the Atlas Viewer and Atlas Viewer functions that were not covered in detail in previous sections. Working With 3D Wire Frame Atlases (page 5-2) Printing. or Exporting an Atlas (page 5-34) Manipulating Data Arrays and Data Sets in the Atlas Viewer (page 5-38) The Atlas Viewer in Detail . Copying.

To hide the Control Bar.Page 5-2 WORKING WITH 3D WIRE FRAME ATLASES The wire frame reconstruction in the Atlas Viewer can sometimes show off important aspects of a specimen. and/or resize the wire frame atlas in the Atlas Window. in ways that the surface rendered model does not. Copying. depending on whether or not an Atlas Window is open.Colors/Symbols Tab (page 5-10) Setting Atlas Parameters . or Exporting an Atlas (page 5-34) Manipulating Data Arrays and Data Sets in the Atlas Viewer (page 5-38) ATLAS VIEWER MENU AND TOOL BARS The Atlas Viewer’s menu bar and tool bar have two different configurations.Rotation Tab (page 5-25) Using Alternate Display Options (page 5-29) Saving and Loading an Atlas Parameter File (page 5-30) RELATED TOPICS • • Printing. click to check Show Control Bar.Rotation Tab (page 5-25) Using Alternate Display Options (page 5-29) Saving and Loading an Atlas Parameter File (page 5-30) Working With 3D Wire Frame Atlases (page 5-2) Printing. on the Atlas menu. or Exporting an Atlas (page 5-34) Manipulating Data Arrays and Data Sets in the Atlas Viewer (page 5-38) MANIPULATING THE ATLAS IN THE ATLAS WINDOW The following tools are used to open. RELATED TOPICS • • • • • • • • • • Manipulating the Atlas in the Atlas Window (page 5-2) Using the Atlas Parameters Dialog Box (page 5-7) Setting Atlas Parameters .Colors/Symbols Tab (page 5-10) Setting Atlas Parameters . THE CONTROL BAR .BEFORE AN ATLAS WINDOW IS OPEN THE MENU AND CONTROL BAR .AFTER AN ATLAS WINDOW IS OPEN PROCEDURE • • To hide the Control Bar.Perspective Tab (page 5-7) Setting Atlas Parameters . TOPIC CONTENTS Atlas Viewer Menu and Tool Bars (page 5-2) Manipulating the Atlas in the Atlas Window (page 5-2) Using the Atlas Parameters Dialog Box (page 5-7) Setting Atlas Parameters .Perspective Tab (page 5-7) Setting Atlas Parameters . BIOQUANT Topographer Handbook: The Atlas Viewer in Detail . re-position. on the Atlas menu. Copying. The tool bar is also called the control bar. click to uncheck Show Control Bar.

Click the Close button in the upper right corner of the Atlas Window. To close the Atlas Window. choose Close. an Atlas window needs to be opened. BIOQUANT Topographer Handbook: The Atlas Viewer in Detail . or Exporting an Atlas (page 5-34) Manipulating Data Arrays and Data Sets in the Atlas Viewer (page 5-38) ATLAS> OPEN OR CLOSE When Topographer’s Atlas Viewer first opens. only the Select Arrays dialog box is visible on the desk top. select the one or more Topo arrays that contain the topographic data that is to be viewed.Rotation Tab (page 5-25) Using Alternate Display Options (page 5-29) Saving and Loading an Atlas Parameter File (page 5-30) Working With 3D Wire Frame Atlases (page 5-2) Printing. The Atlas Window A simple reconstruction PROCEDURE 1.Perspective Tab (page 5-7) Setting Atlas Parameters .Page 5-3 TOPIC CONTENTS Atlas> Open or Close (page 5-3) Atlas> Resize to Fit (page 5-4) Atlas> Zoom (page 5-4) Atlas> Pan (page 5-5) Atlas> Center (page 5-6) Atlas> Redraw (page 5-6) RELATED TOPICS • • • • • • • • • • Manipulating the Atlas in the Atlas Window (page 5-2) Using the Atlas Parameters Dialog Box (page 5-7) Setting Atlas Parameters . do one of the following: • • From the Atlas menu. Open the Atlas Window by doing one of the following: • • • Click the New Atlas Window button on the tool bar. 2. From the Atlas menu choose Open. On the Select Arrays dialog box. To see the topographic map or 3D reconstruction (known as the “Atlas” in the Topographer).Colors/Symbols Tab (page 5-10) Setting Atlas Parameters . Copying. Close becomes available on the Atlas menu any time an Atlas window is open.

PROCEDURES • • From the Atlas menu. the cursor changes to a magnifying glass.Page 5-4 RELATED TOPICS • • • • • • • • • • • • • • • Atlas> Resize to Fit (page 5-4) Atlas> Zoom (page 5-4) Atlas> Pan (page 5-5) Atlas> Center (page 5-6) Atlas> Redraw (page 5-6) Manipulating the Atlas in the Atlas Window (page 5-2) Using the Atlas Parameters Dialog Box (page 5-7) Setting Atlas Parameters . Reduction occurs when the right mouse button is pressed and released. Clicking and dragging the Zoom cursor with the left mouse button. RELATED TOPICS • • • • • • • • • • • • • • • Atlas> Open or Close (page 5-3) Atlas> Zoom (page 5-4) Atlas> Pan (page 5-5) Atlas> Center (page 5-6) Atlas> Redraw (page 5-6) Manipulating the Atlas in the Atlas Window (page 5-2) Using the Atlas Parameters Dialog Box (page 5-7) Setting Atlas Parameters .Rotation Tab (page 5-25) Using Alternate Display Options (page 5-29) Saving and Loading an Atlas Parameter File (page 5-30) Working With 3D Wire Frame Atlases (page 5-2) Printing. or Exporting an Atlas (page 5-34) Manipulating Data Arrays and Data Sets in the Atlas Viewer (page 5-38) ATLAS> ZOOM Activates the Zoom cursor so the atlas may be magnified or reduced in size. PROCEDURE 1. Click the Resize to Fit button on the system tool bar. choose Resize to Fit.Colors/Symbols Tab (page 5-10) Setting Atlas Parameters . BIOQUANT Topographer Handbook: The Atlas Viewer in Detail . On the Control Bar.Colors/Symbols Tab (page 5-10) Setting Atlas Parameters . Copying. click the To magnify or reduce the atlas: Zoom button. simultaneously Zooms and Pans.Perspective Tab (page 5-7) Setting Atlas Parameters .Perspective Tab (page 5-7) Setting Atlas Parameters . or Exporting an Atlas (page 5-34) Manipulating Data Arrays and Data Sets in the Atlas Viewer (page 5-38) ATLAS> RESIZE TO FIT Simultaneously centers and resizes the atlas so it fills the Atlas Window. Magnification centered on the point clicked. occurs when the left mouse button is pressed and released.Rotation Tab (page 5-25) Using Alternate Display Options (page 5-29) Saving and Loading an Atlas Parameter File (page 5-30) Working With 3D Wire Frame Atlases (page 5-2) Printing. 2. Copying.

Page 5-5 • • • 3. ADDITIONAL INFORMATION • • A precise zoom can be set numerically on the Perspective tab of the Atlas Parameters box. click and release the left mouse button over the atlas. 3. On the system tool bar. PROCEDURE 1. button on the system tool RELATED TOPICS • • • • • • • • • • • • • • • Atlas> Open or Close (page 5-3) Atlas> Resize to Fit (page 5-4) Atlas> Pan (page 5-5) Atlas> Center (page 5-6) Atlas> Redraw (page 5-6) Manipulating the Atlas in the Atlas Window (page 5-2) Using the Atlas Parameters Dialog Box (page 5-7) Setting Atlas Parameters . Click to release the Zoom button to deactivate the Zoom cursor. Click to release the Pan button to deactivate the panning cursor.Perspective Tab (page 5-7) Setting Atlas Parameters .Colors/Symbols Tab (page 5-10) Setting Atlas Parameters . click the Pan button.Rotation Tab (page 5-25) Using Alternate Display Options (page 5-29) Saving and Loading an Atlas Parameter File (page 5-30) Working With 3D Wire Frame Atlases (page 5-2) Printing. Copying. click and release the right mouse button over the atlas. To zoom. or Exporting an Atlas (page 5-34) Manipulating Data Arrays and Data Sets in the Atlas Viewer (page 5-38) BIOQUANT Topographer Handbook: The Atlas Viewer in Detail . RELATED TOPICS • • • • • • • • • • • • • • • Atlas> Open or Close (page 5-3) Atlas> Resize to Fit (page 5-4) Atlas> Zoom (page 5-4) Atlas> Center (page 5-6) Atlas> Redraw (page 5-6) Manipulating the Atlas in the Atlas Window (page 5-2) Using the Atlas Parameters Dialog Box (page 5-7) Setting Atlas Parameters . Copying. Click and drag the panning cursor to move the atlas.Perspective Tab (page 5-7) Setting Atlas Parameters .Colors/Symbols Tab (page 5-10) Setting Atlas Parameters . To shrink. To zoom and pan to a particular location.Rotation Tab (page 5-25) Using Alternate Display Options (page 5-29) Saving and Loading an Atlas Parameter File (page 5-30) Working With 3D Wire Frame Atlases (page 5-2) Printing. or Exporting an Atlas (page 5-34) Manipulating Data Arrays and Data Sets in the Atlas Viewer (page 5-38) ATLAS> PAN Readies the cursor to move the atlas to a new location in the Atlas Window. 2. Zoom Factor (page 5-8) To automatically resize the atlas to fill the Atlas Window. the cursor changes to a cross hair over the atlas. click and drag with the left mouse button. click the Resize to Fit bar.

Colors/Symbols Tab (page 5-10) Setting Atlas Parameters . Copying.Perspective Tab (page 5-7) Setting Atlas Parameters .Rotation Tab (page 5-25) Using Alternate Display Options (page 5-29) Saving and Loading an Atlas Parameter File (page 5-30) Working With 3D Wire Frame Atlases (page 5-2) Printing. or Exporting an Atlas (page 5-34) Manipulating Data Arrays and Data Sets in the Atlas Viewer (page 5-38) BIOQUANT Topographer Handbook: The Atlas Viewer in Detail . Copying. A alternate array or set of arrays has been selected on the Select Arrays dialog box and the Atlas Window needs to be updated with the new atlas. or Exporting an Atlas (page 5-34) Manipulating Data Arrays and Data Sets in the Atlas Viewer (page 5-38) ATLAS> REDRAW Redraw is used any time the Atlas Window is open and either of the following is the case: • • The current atlas needs to be refreshed. click the window. PROCEDURE • On the Control Bar. click the Redraw button.Perspective Tab (page 5-7) Setting Atlas Parameters .Colors/Symbols Tab (page 5-10) Setting Atlas Parameters .Page 5-6 ATLAS> CENTER Moves the center of the atlas to the center of the Atlas Window.Rotation Tab (page 5-25) Using Alternate Display Options (page 5-29) Saving and Loading an Atlas Parameter File (page 5-30) Working With 3D Wire Frame Atlases (page 5-2) Printing. PROCEDURE • On the Control Bar. RELATED TOPICS • • • • • • • • • • • • • • • Atlas> Open or Close (page 5-3) Atlas> Resize to Fit (page 5-4) Atlas> Zoom (page 5-4) Atlas> Pan (page 5-5) Atlas> Center (page 5-6) Manipulating the Atlas in the Atlas Window (page 5-2) Using the Atlas Parameters Dialog Box (page 5-7) Setting Atlas Parameters . Center button. The center of the atlas moves to the center of the atlas RELATED TOPICS • • • • • • • • • • • • • • • Atlas> Open or Close (page 5-3) Atlas> Resize to Fit (page 5-4) Atlas> Zoom (page 5-4) Atlas> Center (page 5-6) Atlas> Redraw (page 5-6) Manipulating the Atlas in the Atlas Window (page 5-2) Using the Atlas Parameters Dialog Box (page 5-7) Setting Atlas Parameters .

and color overlap for tracings of dual labeled structures may be visualized by a distinctive third color. and the amount of spread (Z Shift) between sections. Rotation. With controls on the Color/Symbol tab. Choose Set Parameters on the Atlas menu. The Atlas Parameters dialog box may be opened in the following ways: • • • Open a New Atlas Window Click the (Atlas Parameters simultaneously opens). closed polygonal tracings can be filled. Copying. The rotation can be displayed frame by frame or looped to produce a continuous rotation.Colors/Symbols Tab (page 5-10) Setting Atlas Parameters . Y. the atlas may be displayed in different colors.Perspective Tab (page 5-7) Setting Atlas Parameters . or Z Perspective (page 5-9) BIOQUANT Topographer Handbook: The Atlas Viewer in Detail . the point around which its perspective is adjusted. A rotating atlas may be recorded as an AVI movie. Edit Parameters button on the system tool bar. The Rotation tab controls the rotation of the atlas through time and the recording of AVI movies. or Exporting an Atlas (page 5-34) Manipulating Data Arrays and Data Sets in the Atlas Viewer (page 5-38) SETTING ATLAS PARAMETERS .Colors/Symbols Tab (page 5-10) Setting Atlas Parameters . single point objects or small tracings may be displayed as symbols.Rotation Tab (page 5-25) Using Alternate Display Options (page 5-29) Saving and Loading an Atlas Parameter File (page 5-30) Working With 3D Wire Frame Atlases (page 5-2) Printing.Rotation Tab (page 5-25) RELATED TOPICS • • • • • • • • • • • Atlas Viewer Menu and Tool Bars (page 5-2) Manipulating the Atlas in the Atlas Window (page 5-2) Using the Atlas Parameters Dialog Box (page 5-7) Setting Atlas Parameters . and Color/Symbol.Perspective Tab (page 5-7) Setting Atlas Parameters .PERSPECTIVE TAB TOPIC CONTENTS Zoom Factor (page 5-8) Z-Shift (page 5-9) Adjust X. The total number of frames and the degree rotation per frame are specified. angle from which the atlas is viewed. The Perspective tab controls the size. The Atlas Parameters dialog box has three tabs: Perspective. TOPIC CONTENTS Setting Atlas Parameters .Page 5-7 USING THE ATLAS PARAMETERS DIALOG BOX The Atlas Parameters dialog box holds all the primary controls for adjusting the display of the wire frame atlas.

Copying.Page 5-8 The Atlas Parameters: Perspective Tab RELATED TOPICS • • • • • • • • • Manipulating the Atlas in the Atlas Window (page 5-2) Using the Atlas Parameters Dialog Box (page 5-7) Setting Atlas Parameters . increase the value in the Zoom Factor field.Rotation Tab (page 5-25) Using Alternate Display Options (page 5-29) Saving and Loading an Atlas Parameter File (page 5-30) Working With 3D Wire Frame Atlases (page 5-2) Printing. decrease the value in the Zoom Factor field. tool PROCEDURE: CHANGE ZOOM FACTOR • • To increase the zoom of the atlas.Colors/Symbols Tab (page 5-10) Setting Atlas Parameters . the Zoom setting defaults to the current zoomed state of the atlas. on the Perspective tab of Atlas Parameters. To decrease the zoom. BIOQUANT Topographer Handbook: The Atlas Viewer in Detail . or Exporting an Atlas (page 5-34) Manipulating Data Arrays and Data Sets in the Atlas Viewer (page 5-38) ZOOM FACTOR When the Atlas Parameters dialog box is first opened. The zoomed state of the atlas in the Atlas window may be increased or decreased using either the Zoom (5-4) or by changing the Zoom Factor.

Colors/Symbols Tab (page 5-10) Setting Atlas Parameters . type a positive micron distance in the Z Shift field.Perspective Tab (page 5-7) Setting Atlas Parameters . by the micron distance in the Z Shift field. or Exporting an Atlas (page 5-34) Manipulating Data Arrays and Data Sets in the Atlas Viewer (page 5-38) ADJUST X. Each successive section is shifted to the right relative to the previous section. To shift sections to the left. Z Shift allows each successive section to be displaced a bit to the right or left for better viewing. or Z Perspective (page 5-9) Manipulating the Atlas in the Atlas Window (page 5-2) Using the Atlas Parameters Dialog Box (page 5-7) Setting Atlas Parameters . Y. OR Z PERSPECTIVE The X. type a negative micron distance in the Z Shift field.Rotation Tab (page 5-25) Using Alternate Display Options (page 5-29) Saving and Loading an Atlas Parameter File (page 5-30) Working With 3D Wire Frame Atlases (page 5-2) Printing. The first section in the series remains in its initial position.Colors/Symbols Tab (page 5-10) Setting Atlas Parameters .Rotation Tab (page 5-25) Using Alternate Display Options (page 5-29) Saving and Loading an Atlas Parameter File (page 5-30) Working With 3D Wire Frame Atlases (page 5-2) Printing. • RELATED TOPICS • • • • • • • • • • • • Zoom Factor (page 5-8) Adjust X.Perspective Tab (page 5-7) Setting Atlas Parameters . and Z Perspective fields specify the degree the atlas is to be rotated on each axis to reach the desired perspective. or Exporting an Atlas (page 5-34) Manipulating Data Arrays and Data Sets in the Atlas Viewer (page 5-38) Z-SHIFT Initially the atlas is displayed with sections stacked one on top of the other. Y. Copying.Page 5-9 RELATED TOPICS • • • • • • • • • • • • Z-Shift (page 5-9) Adjust X. Copying. Y. or Z Perspective (page 5-9) Manipulating the Atlas in the Atlas Window (page 5-2) Using the Atlas Parameters Dialog Box (page 5-7) Setting Atlas Parameters . BIOQUANT Topographer Handbook: The Atlas Viewer in Detail . Positive values rotate the atlas clockwise as seen from the positive end of the axis. The Effect of Z Shift PROCEDURE • To shift sections to the right. Y.

PROCEDURE 1. Choose one of the Rotate Around radio buttons to determine the point around which the atlas will rotate. BIOQUANT Topographer Handbook: The Atlas Viewer in Detail . 0. or Z perspective text boxes. The Center button rotates around the center of the atlas. its settings may be saved in a Parameters file that can be reloaded at a later time to instantly restore the preferred display. The positive X axis points right. In most cases. Copying. 0. Click the Apply button to display the new orientation. The Rotate Around radio buttons control the point around which the atlas rotates. The positive Z axis points out of the monitor.Page 5-10 Windows uses a left-handed system for its axes: • • • The positive Y axis points down. See “Saving and Loading an Atlas Parameter File” on 5-30.g. Center is the most commonly used point.Colors/Symbols Tab (page 5-10) Setting Atlas Parameters .Perspective Tab (page 5-7) Setting Atlas Parameters . or Exporting an Atlas (page 5-34) Manipulating Data Arrays and Data Sets in the Atlas Viewer (page 5-38) SETTING ATLAS PARAMETERS .e. (If there is a reason to permanently change the default colors in the Topo array. those created with area measurements) can be filled in any of 16 colors or can be set not to fill while other objects do. 2. Closed polygon objects (e. The Start Point button rotates around the first point in the atlas. this may be done in the Topographer’s Atlas Shop. RELATED TOPICS • • • • • • • • • • • • Zoom Factor (page 5-8) Z-Shift (page 5-9) Manipulating the Atlas in the Atlas Window (page 5-2) Using the Atlas Parameters Dialog Box (page 5-7) Setting Atlas Parameters . Y. 3. i. In the X.). The color used to draw an object can be changed to any of 16 colors or can be set not to draw at all.) All objects of the same color comprise a group. The Landmark button rotates around the landmark of the atlas.Rotation Tab (page 5-25) Using Alternate Display Options (page 5-29) Saving and Loading an Atlas Parameter File (page 5-30) Working With 3D Wire Frame Atlases (page 5-2) Printing. Small objects can be marked with any of 16 symbol shapes of customizable sizes. ADDITIONAL NOTE • When an ideal or pleasing display is accomplished. enter the desired degree of rotation. Changing the color properties of the atlas on the Color/Symbols tab does not change the default colors recorded in the Topo array. rotation around the center of the atlas (Object) is used. Changes made on the Colors/Symbols tab are applied to all objects in the atlas that are the specified color. the origin (0.COLORS/SYMBOLS TAB A topographic object’s default color is the color that was used to trace or count the object in BIOQUANT.

or assigning a different symbol to represent particular objects.Rotation Tab (page 5-25) Using Alternate Display Options (page 5-29) Saving and Loading an Atlas Parameter File (page 5-30) Working With 3D Wire Frame Atlases (page 5-2) Printing.Colors/Symbols Tab (page 5-10) Setting Atlas Parameters . Since everything in the displayed atlas must be one of these 16 colors. these lists are used to identify for the system which parts of the atlas you want to change. or Exporting an Atlas (page 5-34) Manipulating Data Arrays and Data Sets in the Atlas Viewer (page 5-38) HOW TO USE THE SELECTION LISTS Each of the three long selection lists (Line/Sym. each entry is a different color. and Symbols) has 16 entries and. In other words.Perspective Tab (page 5-7) Setting Atlas Parameters . Fill. before any changes are made by the user.Page 5-11 TOPIC CONTENTS How To Use the Selection Lists (page 5-11) About The Apply. Save. or the fill color for particular objects. and Restore Buttons (page 5-12) Change Tracing (Line or Symbol) Color (page 5-13) Fill Polygonal Tracings With Color (page 5-14) Distinguish Dual Labeled Structures (page 5-15) Change Fill Color (page 5-16) Restore Color and Symbol Defaults (page 5-17) Exclude Certain Objects or Symbols (page 5-18) Fill Some Objects But Not Others (page 5-19) Display Small Objects As Symbols (page 5-20) Symbolize Larger Objects (page 5-21) Assign a Different Symbol (page 5-22) Change the Size of the Symbols (page 5-23) Reduce The Number of Densely Packed Symbols (page 5-24) The Colors/Symbols Dialog Box RELATED TOPICS • • • • • • • • • • Manipulating the Atlas in the Atlas Window (page 5-2) Using the Atlas Parameters Dialog Box (page 5-7) Setting Atlas Parameters . Copying. Whether changing the color of tracings. the basic steps are the same: BIOQUANT Topographer Handbook: The Atlas Viewer in Detail . selecting items to be changed is a color matching process.

its default color or default symbol changes to the new one. Copying. The user chooses a new color on the color palette. and Restore Buttons (page 5-12) Change Tracing (Line or Symbol) Color (page 5-13) Fill Polygonal Tracings With Color (page 5-14) Distinguish Dual Labeled Structures (page 5-15) Change Fill Color (page 5-16) Restore Color and Symbol Defaults (page 5-17) Exclude Certain Objects or Symbols (page 5-18) Fill Some Objects But Not Others (page 5-19) Display Small Objects As Symbols (page 5-20) Symbolize Larger Objects (page 5-21) Assign a Different Symbol (page 5-22) Change the Size of the Symbols (page 5-23) Reduce The Number of Densely Packed Symbols (page 5-24) Manipulating the Atlas in the Atlas Window (page 5-2) Using the Atlas Parameters Dialog Box (page 5-7) Setting Atlas Parameters . Anytime in the future when the atlas is displayed.Page 5-12 a. c. or a new symbol from the Available symbols drop list.Colors/Symbols Tab (page 5-10) Setting Atlas Parameters .Rotation Tab (page 5-25) Using Alternate Display Options (page 5-29) Saving and Loading an Atlas Parameter File (page 5-30) Working With 3D Wire Frame Atlases (page 5-2) Printing. The user clicks the entry in the relevant list that matches the current color of the item in the Atlas window. When the entry in the list is clicked.Perspective Tab (page 5-7) Setting Atlas Parameters . The Restore button erases all changes from the Color/Symbols tab and restores all original default color and symbol settings. RELATED TOPICS • • • • • • • • • • • • • • • • • • • • • • • About The Apply. Save. The Save buttons on all three Atlas Parameters tabs. When an ideal atlas display is created. or Exporting an Atlas (page 5-34) Manipulating Data Arrays and Data Sets in the Atlas Viewer (page 5-38) ABOUT THE APPLY. The user clicks the Apply button. AND RESTORE BUTTONS • • The Apply button causes the atlas to be redrawn to include any changes that were made on the Color/ Symbols tab. and all items in the Atlas window that matched the original. The user notes the current color of the item in the Atlas window. its parameter file can be loaded to instantly recreate the ideal view.set) file. b. changes to the new color or to the new symbol. d. the settings that generate that particular view of the atlas may be saved to a Parameter (. default color of the clicked entry. SAVE. open the Save Parameters dialog box. • BIOQUANT Topographer Handbook: The Atlas Viewer in Detail .

Rotation Tab (page 5-25) Using Alternate Display Options (page 5-29) Saving and Loading an Atlas Parameter File (page 5-30) Working With 3D Wire Frame Atlases (page 5-2) Printing.Page 5-13 RELATED TOPICS • • • • • • • • • • • • • • • • • • • • • • • How To Use the Selection Lists (page 5-11) Change Tracing (Line or Symbol) Color (page 5-13) Fill Polygonal Tracings With Color (page 5-14) Distinguish Dual Labeled Structures (page 5-15) Change Fill Color (page 5-16) Restore Color and Symbol Defaults (page 5-17) Exclude Certain Objects or Symbols (page 5-18) Fill Some Objects But Not Others (page 5-19) Display Small Objects As Symbols (page 5-20) Symbolize Larger Objects (page 5-21) Assign a Different Symbol (page 5-22) Change the Size of the Symbols (page 5-23) Reduce The Number of Densely Packed Symbols (page 5-24) Manipulating the Atlas in the Atlas Window (page 5-2) Using the Atlas Parameters Dialog Box (page 5-7) Setting Atlas Parameters . 3. Repeat steps 1 through 3 for each color group you wish to change. or Exporting an Atlas (page 5-34) Manipulating Data Arrays and Data Sets in the Atlas Viewer (page 5-38) CHANGE TRACING (LINE OR SYMBOL) COLOR The Line/Sym list and the Fill list in the Colors area of the Colors/Symbols tab are used to change the display color for a particular group of objects. (The N square is for No Draw and the D square is for Default.Colors/Symbols Tab (page 5-10) Setting Atlas Parameters . Since item selection is based entirely on color. Choose a new color by clicking one of the 16 color squares in the Colors area. When clicked. any change that is made to Color/Symbol parameters is applied to all items in the Atlas window that match the selected color. the entry in the list changes to the new color. PROCEDURE 1. notice the current default color of the group of objects for which the color is to be changed. Do not use these for this procedure. Copying. 5. In the Atlas window. Click the Apply button to update the atlas display to the new color(s). 4.Perspective Tab (page 5-7) Setting Atlas Parameters . 2. BIOQUANT Topographer Handbook: The Atlas Viewer in Detail .) Find and click the entry in the Line/Sym list that matches the current color of the objects for which color is to be changed.

Perspective Tab (page 5-7) Setting Atlas Parameters . Copying. or choose Fill from the Atlas menu.Rotation Tab (page 5-25) Using Alternate Display Options (page 5-29) Saving and Loading an Atlas Parameter File (page 5-30) Working With 3D Wire Frame Atlases (page 5-2) Printing. or Exporting an Atlas (page 5-34) Manipulating Data Arrays and Data Sets in the Atlas Viewer (page 5-38) FILL POLYGONAL TRACINGS WITH COLOR PROCEDURE • • To display the default fill color. The Atlas Shop’s Open Polygon feature allows the closed-tracings made with area arrays to be opened. so they will NOT fill with color when the Fill option is active in the Atlas Viewer.Colors/Symbols Tab (page 5-10) Setting Atlas Parameters . click to uncheck the Fill check box. and Restore Buttons (page 5-12) Fill Polygonal Tracings With Color (page 5-14) Distinguish Dual Labeled Structures (page 5-15) Change Fill Color (page 5-16) Restore Color and Symbol Defaults (page 5-17) Exclude Certain Objects or Symbols (page 5-18) Fill Some Objects But Not Others (page 5-19) Display Small Objects As Symbols (page 5-20) Symbolize Larger Objects (page 5-21) Assign a Different Symbol (page 5-22) Change the Size of the Symbols (page 5-23) Reduce The Number of Densely Packed Symbols (page 5-24) Manipulating the Atlas in the Atlas Window (page 5-2) Using the Atlas Parameters Dialog Box (page 5-7) Setting Atlas Parameters . so they will fill with color when the Fill option is active in the Atlas Viewer. Save. BIOQUANT Topographer Handbook: The Atlas Viewer in Detail . or uncheck Fill on the Atlas menu. To remove the Fill display.Page 5-14 RELATED TOPICS • • • • • • • • • • • • • • • • • • • • • • • How To Use the Selection Lists (page 5-11) About The Apply. click to check the Fill check box at the bottom of the Colors area. ADDITIONAL INFORMATION • • The Atlas Shop’s Close Polygon feature allows open-tracings made with Length arrays to be closed.

Perspective Tab (page 5-7) Setting Atlas Parameters . Save. and Restore Buttons (page 5-12) Change Tracing (Line or Symbol) Color (page 5-13) Distinguish Dual Labeled Structures (page 5-15) Change Fill Color (page 5-16) Restore Color and Symbol Defaults (page 5-17) Exclude Certain Objects or Symbols (page 5-18) Fill Some Objects But Not Others (page 5-19) Display Small Objects As Symbols (page 5-20) Symbolize Larger Objects (page 5-21) Assign a Different Symbol (page 5-22) Change the Size of the Symbols (page 5-23) Reduce The Number of Densely Packed Symbols (page 5-24) Manipulating the Atlas in the Atlas Window (page 5-2) Using the Atlas Parameters Dialog Box (page 5-7) Setting Atlas Parameters . To remove the overlap color. Copying. click to uncheck the Overlap check box. or Exporting an Atlas (page 5-34) Manipulating Data Arrays and Data Sets in the Atlas Viewer (page 5-38) DISTINGUISH DUAL LABELED STRUCTURES PROCEDURE • To show areas of overlapping fill colors in a distinctive third color. Alternately. check both these options on the Atlas menu. or uncheck Overlap on the Atlas menu. click to check both the Fill and Overlap check boxes at the bottom of the Colors area.Page 5-15 RELATED TOPICS • • • • • • • • • • • • • • • • • • • • • • • How To Use the Selection Lists (page 5-11) About The Apply.Rotation Tab (page 5-25) Using Alternate Display Options (page 5-29) Saving and Loading an Atlas Parameter File (page 5-30) Working With 3D Wire Frame Atlases (page 5-2) Printing.Colors/Symbols Tab (page 5-10) Setting Atlas Parameters . • BIOQUANT Topographer Handbook: The Atlas Viewer in Detail .

Page 5-16 RELATED TOPICS • • • • • • • • • • • • • • • • • • • • • • • How To Use the Selection Lists (page 5-11) About The Apply. In the Atlas window.Colors/Symbols Tab (page 5-10) Setting Atlas Parameters . The entry in the Fill list changes to the new color. Choose a new color be clicking one of the 16 colored squares in the Colors area. Find and click the entry that matches the current Fill color of the objects for which color is to be changed. or Exporting an Atlas (page 5-34) Manipulating Data Arrays and Data Sets in the Atlas Viewer (page 5-38) CHANGE FILL COLOR PROCEDURE 1. notice the current fill color of the group of objects for which the fill color is to be changed.Perspective Tab (page 5-7) Setting Atlas Parameters .Rotation Tab (page 5-25) Using Alternate Display Options (page 5-29) Saving and Loading an Atlas Parameter File (page 5-30) Working With 3D Wire Frame Atlases (page 5-2) Printing. 6. 2. Copying. Click the Apply button to update the atlas display with the new fill color(s). NOTE • The fill color assigned on the Atlas Parameters dialog box is the color used to surface render the atlas if the Atlas Modeler is opened. BIOQUANT Topographer Handbook: The Atlas Viewer in Detail . 5. Repeat steps 2 through 4 for each fill color you wish to change. and Restore Buttons (page 5-12) Change Tracing (Line or Symbol) Color (page 5-13) Fill Polygonal Tracings With Color (page 5-14) Change Fill Color (page 5-16) Restore Color and Symbol Defaults (page 5-17) Exclude Certain Objects or Symbols (page 5-18) Fill Some Objects But Not Others (page 5-19) Display Small Objects As Symbols (page 5-20) Symbolize Larger Objects (page 5-21) Assign a Different Symbol (page 5-22) Change the Size of the Symbols (page 5-23) Reduce The Number of Densely Packed Symbols (page 5-24) Manipulating the Atlas in the Atlas Window (page 5-2) Using the Atlas Parameters Dialog Box (page 5-7) Setting Atlas Parameters . Turn Fill on by clicking to check the Fill check box at the bottom of the Colors area. (The N square is for No Draw and the D square is for Default. Save. 4. 3.) Entries in the Fill list are number 1 through 16 and each is a different color.

Save.Colors/Symbols Tab (page 5-10) Setting Atlas Parameters . Copying. To restore all the entries in the Line/Sym list or the Fill list to their default assignments. then click and drag the cursor across all the entries in the list.Perspective Tab (page 5-7) Setting Atlas Parameters . To restore all the default Line/Sym. BIOQUANT Topographer Handbook: The Atlas Viewer in Detail . click the Restore button. and Symbol assignments on the Colors/Symbols tab. click the Default (D) square in the Colors area.Rotation Tab (page 5-25) Using Alternate Display Options (page 5-29) Saving and Loading an Atlas Parameter File (page 5-30) Working With 3D Wire Frame Atlases (page 5-2) Printing. Fill.Page 5-17 RELATED TOPICS • • • • • • • • • • • • • • • • • • • • • • • How To Use the Selection Lists (page 5-11) About The Apply. or Exporting an Atlas (page 5-34) Manipulating Data Arrays and Data Sets in the Atlas Viewer (page 5-38) RESTORE COLOR AND SYMBOL DEFAULTS PROCEDURE • • • To restore the default assignment of one color entry in either the Line/Sym list or the Fill list. then click that entry in the list. and Restore Buttons (page 5-12) Change Tracing (Line or Symbol) Color (page 5-13) Fill Polygonal Tracings With Color (page 5-14) Distinguish Dual Labeled Structures (page 5-15) Restore Color and Symbol Defaults (page 5-17) Exclude Certain Objects or Symbols (page 5-18) Fill Some Objects But Not Others (page 5-19) Display Small Objects As Symbols (page 5-20) Symbolize Larger Objects (page 5-21) Assign a Different Symbol (page 5-22) Change the Size of the Symbols (page 5-23) Reduce The Number of Densely Packed Symbols (page 5-24) Manipulating the Atlas in the Atlas Window (page 5-2) Using the Atlas Parameters Dialog Box (page 5-7) Setting Atlas Parameters . click the Default (D) square in the Colors area.

Page 5-18 RELATED TOPICS • • • • • • • • • • • • • • • • • • • • • • • How To Use the Selection Lists (page 5-11) About The Apply. notice the current color of the group of objects that need to be hidden. PROCEDURE 1. Repeat steps 1 through 3 for each color group you wish to hide. click the No Draw (N) square. Find and click the entry in the Line/Sym list that matches the current color of the objects that are to be hidden. 4. and Restore Buttons (page 5-12) Change Tracing (Line or Symbol) Color (page 5-13) Fill Polygonal Tracings With Color (page 5-14) Distinguish Dual Labeled Structures (page 5-15) Change Fill Color (page 5-16) Exclude Certain Objects or Symbols (page 5-18) Fill Some Objects But Not Others (page 5-19) Display Small Objects As Symbols (page 5-20) Symbolize Larger Objects (page 5-21) Assign a Different Symbol (page 5-22) Change the Size of the Symbols (page 5-23) Reduce The Number of Densely Packed Symbols (page 5-24) Manipulating the Atlas in the Atlas Window (page 5-2) Using the Atlas Parameters Dialog Box (page 5-7) Setting Atlas Parameters .Colors/Symbols Tab (page 5-10) Setting Atlas Parameters . On the color palette.Perspective Tab (page 5-7) Setting Atlas Parameters . Click the Apply button to update the atlas display. Save. BIOQUANT Topographer Handbook: The Atlas Viewer in Detail . symbols.Rotation Tab (page 5-25) Using Alternate Display Options (page 5-29) Saving and Loading an Atlas Parameter File (page 5-30) Working With 3D Wire Frame Atlases (page 5-2) Printing. or Exporting an Atlas (page 5-34) Manipulating Data Arrays and Data Sets in the Atlas Viewer (page 5-38) EXCLUDE CERTAIN OBJECTS OR SYMBOLS The No Draw (N) square on the color palette in the Colors area of the Colors/Symbol tab is used to hide the tracings. 2. or fill color for a specified group of objects. 5. 3. Copying. In the Atlas window.

Colors/Symbols Tab (page 5-10) Setting Atlas Parameters . click the No Draw (N) square. or Exporting an Atlas (page 5-34) Manipulating Data Arrays and Data Sets in the Atlas Viewer (page 5-38) FILL SOME OBJECTS BUT NOT OTHERS No Draw is assigned to entries in the Fill list when there are multiple types of objects (each associated with a unique color) and you want some types to display as filled and not others.Perspective Tab (page 5-7) Setting Atlas Parameters . On the color palette. In the Atlas window. 2. and Restore Buttons (page 5-12) Change Tracing (Line or Symbol) Color (page 5-13) Fill Polygonal Tracings With Color (page 5-14) Distinguish Dual Labeled Structures (page 5-15) Change Fill Color (page 5-16) Restore Color and Symbol Defaults (page 5-17) Fill Some Objects But Not Others (page 5-19) Display Small Objects As Symbols (page 5-20) Symbolize Larger Objects (page 5-21) Assign a Different Symbol (page 5-22) Change the Size of the Symbols (page 5-23) Reduce The Number of Densely Packed Symbols (page 5-24) Manipulating the Atlas in the Atlas Window (page 5-2) Using the Atlas Parameters Dialog Box (page 5-7) Setting Atlas Parameters . 5. notice the current fill color of the group of objects for which the fill color is to be hidden. BIOQUANT Topographer Handbook: The Atlas Viewer in Detail .Page 5-19 RELATED TOPICS • • • • • • • • • • • • • • • • • • • • • • • How To Use the Selection Lists (page 5-11) About The Apply. PROCEDURE 1. Save.Rotation Tab (page 5-25) Using Alternate Display Options (page 5-29) Saving and Loading an Atlas Parameter File (page 5-30) Working With 3D Wire Frame Atlases (page 5-2) Printing. 4. Turn Fill on by clicking to check the Fill check box at the bottom of the Colors area. Copying. Click the Apply button to update the atlas display. 3. In the Fill list find and click the entry that matches the current fill color of the objects for which the fill color is to be hidden.

or Exporting an Atlas (page 5-34) Manipulating Data Arrays and Data Sets in the Atlas Viewer (page 5-38) DISPLAY SMALL OBJECTS AS SYMBOLS Small objects can be made more visible by marking them with symbols. which allows only “single point” objects to be symbolized. Copying. By default.Rotation Tab (page 5-25) Using Alternate Display Options (page 5-29) Saving and Loading an Atlas Parameter File (page 5-30) Working With 3D Wire Frame Atlases (page 5-2) Printing. from the Atlas menu. To remove the symbolic display. When the Symbols feature is activated. click to check the Symbols check box at the bottom of the Symbols area.Page 5-20 RELATED TOPICS • • • • • • • • • • • • • • • • • • • • • • • How To Use the Selection Lists (page 5-11) About The Apply. will be displayed with the currently assigned symbol. Save. Alternatively.Perspective Tab (page 5-7) Setting Atlas Parameters . PROCEDURE • To display the currently assigned symbol for small objects. objects that have data points equal to or less than the Maximum Object Size value. click to check Symbols. actually have two data points with zero distance between them. the system sets the Maximum Object Size value to 2. from the Atlas menu. • BIOQUANT Topographer Handbook: The Atlas Viewer in Detail . So the Maximum Object Size value must be at least 2. and Restore Buttons (page 5-12) Change Tracing (Line or Symbol) Color (page 5-13) Fill Polygonal Tracings With Color (page 5-14) Distinguish Dual Labeled Structures (page 5-15) Change Fill Color (page 5-16) Restore Color and Symbol Defaults (page 5-17) Exclude Certain Objects or Symbols (page 5-18) Display Small Objects As Symbols (page 5-20) Symbolize Larger Objects (page 5-21) Assign a Different Symbol (page 5-22) Change the Size of the Symbols (page 5-23) Reduce The Number of Densely Packed Symbols (page 5-24) Manipulating the Atlas in the Atlas Window (page 5-2) Using the Atlas Parameters Dialog Box (page 5-7) Setting Atlas Parameters . click to uncheck the Symbols check box. Objects that appear in the atlas as single points or dots (such as those counted with an Object Count array). click to uncheck Symbols. Alternatively.Colors/Symbols Tab (page 5-10) Setting Atlas Parameters .

Rotation Tab (page 5-25) Using Alternate Display Options (page 5-29) Saving and Loading an Atlas Parameter File (page 5-30) Working With 3D Wire Frame Atlases (page 5-2) Printing. In the Maximum Object Size field. 1.Colors/Symbols Tab (page 5-10) Setting Atlas Parameters . Save. Click the Apply button to display the changes. scroll to or type in a higher number. or Exporting an Atlas (page 5-34) Manipulating Data Arrays and Data Sets in the Atlas Viewer (page 5-38) SYMBOLIZE LARGER OBJECTS The Maximum Object Size value may be increased so slightly larger objects may be displayed as symbols. 2. Repeat steps 1 and 2 as needed until all of the desired tracings are symbolized.Perspective Tab (page 5-7) Setting Atlas Parameters .Page 5-21 RELATED TOPICS • • • • • • • • • • • • • • • • • • • • • • • How To Use the Selection Lists (page 5-11) About The Apply. Copying. BIOQUANT Topographer Handbook: The Atlas Viewer in Detail . and Restore Buttons (page 5-12) Change Tracing (Line or Symbol) Color (page 5-13) Fill Polygonal Tracings With Color (page 5-14) Distinguish Dual Labeled Structures (page 5-15) Change Fill Color (page 5-16) Restore Color and Symbol Defaults (page 5-17) Exclude Certain Objects or Symbols (page 5-18) Fill Some Objects But Not Others (page 5-19) Symbolize Larger Objects (page 5-21) Assign a Different Symbol (page 5-22) Change the Size of the Symbols (page 5-23) Reduce The Number of Densely Packed Symbols (page 5-24) Manipulating the Atlas in the Atlas Window (page 5-2) Using the Atlas Parameters Dialog Box (page 5-7) Setting Atlas Parameters . 3.

Page 5-22 RELATED TOPICS • • • • • • • • • • • • • • • • • • • • • • • How To Use the Selection Lists (page 5-11) About The Apply. find and click the entry that matches the color of objects of interest (identified in step 2). and Restore Buttons (page 5-12) Change Tracing (Line or Symbol) Color (page 5-13) Fill Polygonal Tracings With Color (page 5-14) Distinguish Dual Labeled Structures (page 5-15) Change Fill Color (page 5-16) Restore Color and Symbol Defaults (page 5-17) Exclude Certain Objects or Symbols (page 5-18) Fill Some Objects But Not Others (page 5-19) Display Small Objects As Symbols (page 5-20) Assign a Different Symbol (page 5-22) Change the Size of the Symbols (page 5-23) Reduce The Number of Densely Packed Symbols (page 5-24) Manipulating the Atlas in the Atlas Window (page 5-2) Using the Atlas Parameters Dialog Box (page 5-7) Setting Atlas Parameters . the default symbol assigned to the marker’s color may be too big and the symbolized display appears crowded. In the Symbols area. or replace a larger symbol with a dot symbol: a. 5. Using the two small scroll buttons. there are two cases in which it is advantageous to assign the dot symbol to tracings. This generates a tracing with multiple data points rather than a single dot. cells). Increase the value in the Maximum Object Size field and click the Apply button again. When there is a very large number of object count markers in the atlas (e. In this case. in the Available field.g. In this case the larger default symbol may be changed to the smaller “dot” symbol. the area tracings can be replaced by the “dot” symbol. b. In the Symbol list. Continue to increase the Maximum Object Size until all the objects in the color group are replaced by the chosen symbol. it means that the group includes objects that are larger than the Maximum Object Size. Display the current symbol(s) in the atlas by clicking to check the Symbols check box. In the Atlas window. click the down arrowhead to display a small scroll list.Perspective Tab (page 5-7) Setting Atlas Parameters . BIOQUANT Topographer Handbook: The Atlas Viewer in Detail . PROCEDURE 1.Rotation Tab (page 5-25) Using Alternate Display Options (page 5-29) Saving and Loading an Atlas Parameter File (page 5-30) Working With 3D Wire Frame Atlases (page 5-2) Printing. During measurement. identify the color of the group of objects for which the symbol should be changed. If all of the objects in the designated color group do not symbolize. 4. scroll through the available symbols and click to choose the desired symbol. 2. The symbol associated with that entry will change to the new symbol. Symbols are most often used to replace “dots” in the atlas. Save. Copying. Click the Apply button to update the atlas display.Colors/Symbols Tab (page 5-10) Setting Atlas Parameters . if desirable. an Area array is sometimes used for cell counting in order to take advantage of BIOQUANT’s Auto Exclude feature. 3. But. or Exporting an Atlas (page 5-34) Manipulating Data Arrays and Data Sets in the Atlas Viewer (page 5-38) ASSIGN A DIFFERENT SYMBOL The default symbol assigned by the system to a particular color group may be changed to any of the alternate symbols on the Available symbol drop list.

Page 5-23 RELATED TOPICS • • • • • • • • • • • • • • • • • • • • • • • How To Use the Selection Lists (page 5-11) About The Apply. increase or decrease the value in the Symbol Size Height field by scrolling to or typing in a larger value. increase or decrease the value in the Symbol Size Width field.Rotation Tab (page 5-25) Using Alternate Display Options (page 5-29) Saving and Loading an Atlas Parameter File (page 5-30) Working With 3D Wire Frame Atlases (page 5-2) Printing. or Exporting an Atlas (page 5-34) Manipulating Data Arrays and Data Sets in the Atlas Viewer (page 5-38) CHANGE THE SIZE OF THE SYMBOLS The default size of symbols is eight pixels by eight pixels. Changes in symbol size are applied to all symbols (not just the symbol of one selected color group). Copying. This can be increased or decreased as needed. BIOQUANT Topographer Handbook: The Atlas Viewer in Detail . Save.Perspective Tab (page 5-7) Setting Atlas Parameters .Colors/Symbols Tab (page 5-10) Setting Atlas Parameters . PROCEDURE • • To adjust the height of the symbols. To adjust the width of the symbols. and Restore Buttons (page 5-12) Change Tracing (Line or Symbol) Color (page 5-13) Fill Polygonal Tracings With Color (page 5-14) Distinguish Dual Labeled Structures (page 5-15) Change Fill Color (page 5-16) Restore Color and Symbol Defaults (page 5-17) Exclude Certain Objects or Symbols (page 5-18) Fill Some Objects But Not Others (page 5-19) Display Small Objects As Symbols (page 5-20) Symbolize Larger Objects (page 5-21) Change the Size of the Symbols (page 5-23) Reduce The Number of Densely Packed Symbols (page 5-24) Manipulating the Atlas in the Atlas Window (page 5-2) Using the Atlas Parameters Dialog Box (page 5-7) Setting Atlas Parameters .

BIOQUANT Topographer Handbook: The Atlas Viewer in Detail . Click the Apply button. a symbol is displayed for every single object that meets the Maximum Object Size criterion.Rotation Tab (page 5-25) Using Alternate Display Options (page 5-29) Saving and Loading an Atlas Parameter File (page 5-30) Working With 3D Wire Frame Atlases (page 5-2) Printing.Colors/Symbols Tab (page 5-10) Setting Atlas Parameters . Save.Page 5-24 RELATED TOPICS • • • • • • • • • • • • • • • • • • • • • • • How To Use the Selection Lists (page 5-11) About The Apply.Perspective Tab (page 5-7) Setting Atlas Parameters . The symbols representing a group of objects may be thinned out by increasing the “nth” value to a number greater than 1. increase the current value by 1. If symbols are still too numerous. 3. Copying. 2. or Exporting an Atlas (page 5-34) Manipulating Data Arrays and Data Sets in the Atlas Viewer (page 5-38) REDUCE THE NUMBER OF DENSELY PACKED SYMBOLS When Show Every (nth) Symbol is set to 1. repeat steps 1 and 2. In the Show Every (nth) Symbol field. A value of 3 will display every third symbol. and Restore Buttons (page 5-12) Change Tracing (Line or Symbol) Color (page 5-13) Fill Polygonal Tracings With Color (page 5-14) Distinguish Dual Labeled Structures (page 5-15) Change Fill Color (page 5-16) Restore Color and Symbol Defaults (page 5-17) Exclude Certain Objects or Symbols (page 5-18) Fill Some Objects But Not Others (page 5-19) Display Small Objects As Symbols (page 5-20) Symbolize Larger Objects (page 5-21) Assign a Different Symbol (page 5-22) Reduce The Number of Densely Packed Symbols (page 5-24) Manipulating the Atlas in the Atlas Window (page 5-2) Using the Atlas Parameters Dialog Box (page 5-7) Setting Atlas Parameters . and so on. PROCEDURE 1. A value of 2 will display every second symbol.

Colors/Symbols Tab (page 5-10) Setting Atlas Parameters . Save. and Restore Buttons (page 5-12) Change Tracing (Line or Symbol) Color (page 5-13) Fill Polygonal Tracings With Color (page 5-14) Distinguish Dual Labeled Structures (page 5-15) Change Fill Color (page 5-16) Restore Color and Symbol Defaults (page 5-17) Exclude Certain Objects or Symbols (page 5-18) Fill Some Objects But Not Others (page 5-19) Display Small Objects As Symbols (page 5-20) Symbolize Larger Objects (page 5-21) Assign a Different Symbol (page 5-22) Change the Size of the Symbols (page 5-23) Manipulating the Atlas in the Atlas Window (page 5-2) Using the Atlas Parameters Dialog Box (page 5-7) Setting Atlas Parameters .ROTATION TAB TOPIC CONTENTS Dynamically Rotate the Wire Frame Atlas (page 5-26) Record a Movie of a Rotating Wire Frame Atlas (page 5-27) Play a Movie of a Rotating Atlas (page 5-28) BIOQUANT Topographer Handbook: The Atlas Viewer in Detail .Rotation Tab (page 5-25) Using Alternate Display Options (page 5-29) Saving and Loading an Atlas Parameter File (page 5-30) Working With 3D Wire Frame Atlases (page 5-2) Printing. or Exporting an Atlas (page 5-34) Manipulating Data Arrays and Data Sets in the Atlas Viewer (page 5-38) SETTING ATLAS PARAMETERS .Page 5-25 RELATED TOPICS • • • • • • • • • • • • • • • • • • • • • • • How To Use the Selection Lists (page 5-11) About The Apply.Perspective Tab (page 5-7) Setting Atlas Parameters . Copying.

g. The Delay value specifies the millisecond pause before the next frame is loaded.1 = 35 Type this value in the Number of Frames field. 10). In the Atlas Viewer. 3. The Step button advances through the rotation frame by frame. If Loop is checked. then subtract 1 from that number. Dynamically rotating an atlas is done much like animation: a series of still images. Divide 360 by the number of degrees the atlas is to rotate for each frame (e. Provide the number of frames required for one complete 360 degree rotation by doing the following: a. are played in rapid succession to create the illusion of motion.g. Example:(360/10) .Page 5-26 The Atlas Parameters: Rotation Tab RELATED TOPICS • • • • • • • • • Manipulating the Atlas in the Atlas Window (page 5-2) Using the Atlas Parameters Dialog Box (page 5-7) Setting Atlas Parameters . b. The Cancel button stops the rotation. the rotation repeats itself. BIOQUANT Topographer Handbook: The Atlas Viewer in Detail .) Rotations on the Atlas Parameters dialog box are limited to a maximum of 360 frames. Decide around which axis the atlas is to rotate (X. Copying. The atlas may be rotated by the following methods. the smoother the motion. or Z). This motion will appear “choppy” until it is recorded and played back in an AVI movie. • To view one complete rotation. In the Degree Rotation per Frame field for the desired axis. 10).Colors/Symbols Tab (page 5-10) Using Alternate Display Options (page 5-29) Saving and Loading an Atlas Parameter File (page 5-30) Working With 3D Wire Frame Atlases (page 5-2) Printing. each slightly changed from the one before. or Exporting an Atlas (page 5-34) Manipulating Data Arrays and Data Sets in the Atlas Viewer (page 5-38) DYNAMICALLY ROTATE THE WIRE FRAME ATLAS A rotating wire frame atlas may be recorded as an AVI movie. the Rotation tab of the Atlas Parameters dialog box is where AVI movie parameters are set. PROCEDURE 1. 2. (The smaller the change between images. Y. type the number of degrees that the atlas should be rotated (e.Perspective Tab (page 5-7) Setting Atlas Parameters . 4. click the Rotate button.

Clicking the New Folder button will add a new folder to the drive or folder that is currently displayed in the Save In field. • 3. PROCEDURE 1. navigate to the desired destination drive using the following guide lines: • • • • The movie file will be saved to the drive or folder that is in the Save In field. then in the Recording Parameters area click the Record button to open the Save Movie File navigation box.Perspective Tab (page 5-7) Setting Atlas Parameters .Rotation Tab (page 5-25) Using Alternate Display Options (page 5-29) Saving and Loading an Atlas Parameter File (page 5-30) Working With 3D Wire Frame Atlases (page 5-2) Printing. click the Cancel button. BIOQUANT Topographer Handbook: The Atlas Viewer in Detail .Page 5-27 • • • To change the speed of rotation. Clicking the down arrow folder may be chosen. To record a movie. and type a name for the movie file. click the Step button. the full BIOQUANT Topographer Plug-In is required. Double clicking a folder in the center list will place it in the Save In field. When the desired destination folder is in the Save In field. Clicking the Up Folder in the Save In field will open a drop list. The Save Movie File Box 2. from which an alternate drive or button will close the folder in the Save In field and open its parent folder. Copying. click to check the Loop check box. click the cursor in the File Name text box. To advance the rotation one frame at a time. increase or decrease the millisecond value in the Delay field and click the Rotate button. To view a continuous rotation. then press the Rotate button. or Exporting an Atlas (page 5-34) Manipulating Data Arrays and Data Sets in the Atlas Viewer (page 5-38) RECORD A MOVIE OF A ROTATING WIRE FRAME ATLAS Note: The freeware BIOQUANT Topo Reader cannot be used to record AVI movies. On the Save Movie File box. Set the desired rotation parameters. RELATED TOPICS • • • • • • • • • • • • Record a Movie of a Rotating Wire Frame Atlas (page 5-27) Play a Movie of a Rotating Atlas (page 5-28) Manipulating the Atlas in the Atlas Window (page 5-2) Using the Atlas Parameters Dialog Box (page 5-7) Setting Atlas Parameters . To stop a continuous rotation.Colors/Symbols Tab (page 5-10) Setting Atlas Parameters . Click the cursor in the New Folder edit field and type an appropriate name for the new folder.

Click the Play Movie button on the system tool bar. The Video Compression Box 6. Click the OK button to create the AVI file. the Video Compression dialog box opens. The first frame of the movie will display in the atlas window. RELATED TOPICS • • • • • • • • • • • • Dynamically Rotate the Wire Frame Atlas (page 5-26) Play a Movie of a Rotating Atlas (page 5-28) Manipulating the Atlas in the Atlas Window (page 5-2) Using the Atlas Parameters Dialog Box (page 5-7) Setting Atlas Parameters . Open the Load Movie File dialog box in any of the following ways: • • • On the Rotate tab of the Atlas Parameters dialog box. click the Load button. Choosing Play Movie from the File menu. 3. From the Compressor drop list.avi). The Load Movie Box 2. Click the Save button to create frames of the movie. 5. or Exporting an Atlas (page 5-34) Manipulating Data Arrays and Data Sets in the Atlas Viewer (page 5-38) PLAY A MOVIE OF A ROTATING ATLAS PROCEDURE 1. choose Microsoft Video 1.Rotation Tab (page 5-25) Using Alternate Display Options (page 5-29) Saving and Loading an Atlas Parameter File (page 5-30) Working With 3D Wire Frame Atlases (page 5-2) Printing.Perspective Tab (page 5-7) Setting Atlas Parameters . BIOQUANT Topographer Handbook: The Atlas Viewer in Detail . Copying. Click the Open button. Navigate to the folder that contains the movie file (.Page 5-28 4. Depending on the number of frames. this may take a while. When all the frames have been captured. Click to highlight the movie file to be opened. 4.Colors/Symbols Tab (page 5-10) Setting Atlas Parameters .

Colors/Symbols Tab (page 5-10) Setting Atlas Parameters . Copying. PROCEDURE • • To display a black background. or Exporting an Atlas (page 5-34) Manipulating Data Arrays and Data Sets in the Atlas Viewer (page 5-38) USING ALTERNATE DISPLAY OPTIONS TOPIC CONTENTS Atlas> Black Background (page 5-29) Atlas> Thick Tracings (page 5-30) RELATED TOPICS • • • • • • • • • Using the Atlas Parameters Dialog Box (page 5-7) Setting Atlas Parameters . RELATED TOPICS • • • • • • • • • • • • Dynamically Rotate the Wire Frame Atlas (page 5-26) Record a Movie of a Rotating Wire Frame Atlas (page 5-27) Manipulating the Atlas in the Atlas Window (page 5-2) Using the Atlas Parameters Dialog Box (page 5-7) Setting Atlas Parameters .Colors/Symbols Tab (page 5-10) Setting Atlas Parameters . on the Atlas menu click to check Black Background. ADDITIONAL NOTES • • • AVI video files can also be played using the Media Player (found in the multi-media accessories) or by simply double clicking on the AVI file in My Computer or the Explorer. Copying. or Exporting an Atlas (page 5-34) Manipulating Data Arrays and Data Sets in the Atlas Viewer (page 5-38) ATLAS> BLACK BACKGROUND The colors in the atlas sometimes show better against a black background. Click the Play button to play the movie. on the Atlas menu click to uncheck Black Background.Perspective Tab (page 5-7) Setting Atlas Parameters . Control-M will also open the Load Movie File box.Rotation Tab (page 5-25) Using Alternate Display Options (page 5-29) Saving and Loading an Atlas Parameter File (page 5-30) Working With 3D Wire Frame Atlases (page 5-2) Printing.Perspective Tab (page 5-7) Setting Atlas Parameters . AVI video files can be viewed on any computer with the Windows Media Player. The computer does not need to have BIOQUANT’s Topographer installed. BIOQUANT Topographer Handbook: The Atlas Viewer in Detail . ADDITIONAL INFORMATION • A black background is generally not recommended when printing an atlas.Rotation Tab (page 5-25) Using Alternate Display Options (page 5-29) Saving and Loading an Atlas Parameter File (page 5-30) Working With 3D Wire Frame Atlases (page 5-2) Printing.Page 5-29 5. To re-display a white background.

Copying. PROCEDURE • • To redraw the atlas with thick tracings. it is often helpful to increase the thickness of atlas tracings.Colors/Symbols Tab (page 5-10) Setting Atlas Parameters . RELATED TOPICS • • • • • • • • • • Atlas> Black Background (page 5-29) Using the Atlas Parameters Dialog Box (page 5-7) Setting Atlas Parameters . Copying.Rotation Tab (page 5-25) Using Alternate Display Options (page 5-29) Saving and Loading an Atlas Parameter File (page 5-30) Working With 3D Wire Frame Atlases (page 5-2) Printing. or Exporting an Atlas (page 5-34) Manipulating Data Arrays and Data Sets in the Atlas Viewer (page 5-38) ATLAS> THICK TRACINGS Prior to printing. To redraw the atlas with normal tracings. which is ideal and recommended while making adjustments to the atlas display. The default thickness is 1 pixel. on the Atlas menu click to uncheck Thick Tracings. on the Atlas menu click to check Thick Tracings.Rotation Tab (page 5-25) Using Alternate Display Options (page 5-29) Saving and Loading an Atlas Parameter File (page 5-30) Working With 3D Wire Frame Atlases (page 5-2) Printing.Perspective Tab (page 5-7) Setting Atlas Parameters .Page 5-30 RELATED TOPICS • • • • • • • • • • Atlas> Thick Tracings (page 5-30) Using the Atlas Parameters Dialog Box (page 5-7) Setting Atlas Parameters . or Exporting an Atlas (page 5-34) Manipulating Data Arrays and Data Sets in the Atlas Viewer (page 5-38) SAVING AND LOADING AN ATLAS PARAMETER FILE TOPIC CONTENTS File> Save Parameters (page 5-31) File> Load Parameters (page 5-32) BIOQUANT Topographer Handbook: The Atlas Viewer in Detail . Before and After Thick Tracings Thick tracings are recommended only when printing the atlas.Colors/Symbols Tab (page 5-10) Setting Atlas Parameters .Perspective Tab (page 5-7) Setting Atlas Parameters .

Click the Create New Folder button.Colors/Symbols Tab (page 5-10) Setting Atlas Parameters . Open the Save Parameters dialog box using any of the following methods: • • • 2. The Save Parameter File Dialog Box b. Then when you later need to find and open the parameter files for a particular Data Set you can easily navigate to them. Anytime in the future that the same data set is opened. To do this: a. On the system tool bar click the Save Parameters From the File menu choose Save Parameters. or Exporting an Atlas (page 5-34) Manipulating Data Arrays and Data Sets in the Atlas Viewer (page 5-38) FILE> SAVE PARAMETERS Save Parameters is available when the Atlas Window is open. A Parameter file records which arrays were used to generate the reconstruction and saves the Perspective and Color/Symbols settings for a particular “view” of the atlas. button.Rotation Tab (page 5-25) Using Alternate Display Options (page 5-29) Saving and Loading an Atlas Parameter File (page 5-30) Working With 3D Wire Frame Atlases (page 5-2) Printing.Page 5-31 RELATED TOPICS • • • • • • • • • Using the Atlas Parameters Dialog Box (page 5-7) Setting Atlas Parameters . For ease of finding the parameters file again. The default Save in location is BQOSTEO\Topographer. it is recommended that you create a subdirectory in the Topographer folder that is named the same as your Data Volume and Data Set. PROCEDURE 1.Perspective Tab (page 5-7) Setting Atlas Parameters . BIOQUANT Topographer Handbook: The Atlas Viewer in Detail . Click the Save button on either the Perspective or Color/Symbols tab of the Atlas Parameters dialog box. Copying. its Parameter file may be loaded to instantly recall the preferred settings. Rename the New Folder to your Data Volume and Data Set Name.

ADDITIONAL NOTES • • Control-S opens the Save Parameters box. RELATED TOPICS • • • • • • • • • • File> Load Parameters (page 5-32) Using the Atlas Parameters Dialog Box (page 5-7) Setting Atlas Parameters . Loading a Parameters file instantly selects the arrays that were originally used to generate the atlas and resets the Perspective and Color/Symbol parameters that were active when the parameters file was saved. The Save Parameter File Dialog Box 4. or Exporting an Atlas (page 5-34) Manipulating Data Arrays and Data Sets in the Atlas Viewer (page 5-38) FILE> LOAD PARAMETERS Load Parameters is available both when the Atlas Window is closed and open. Copying.Rotation Tab (page 5-25) Using Alternate Display Options (page 5-29) Saving and Loading an Atlas Parameter File (page 5-30) Working With 3D Wire Frame Atlases (page 5-2) Printing.set” extensions. You will save in this location. Type a file name into the File name text box. Parameter files have “. On the system tool bar click the Load Parameters to open the Open Parameter File dialog box. Click the Save button to save the file. Double click the new folder to open it.Page 5-32 The Save Parameter File Dialog Box c. or from the File menu choose Load Parameters. 3.Colors/Symbols Tab (page 5-10) Setting Atlas Parameters .Perspective Tab (page 5-7) Setting Atlas Parameters . PROCEDURE 1. button. BIOQUANT Topographer Handbook: The Atlas Viewer in Detail .

Copying. ADDITIONAL NOTES • If the error message. or Exporting an Atlas (page 5-34) Manipulating Data Arrays and Data Sets in the Atlas Viewer (page 5-38) BIOQUANT Topographer Handbook: The Atlas Viewer in Detail .Page 5-33 2.Colors/Symbols Tab (page 5-10) Setting Atlas Parameters . The Open Parameter File Dialog Box 3. Parameter files have “. • • RELATED TOPICS • • • • • • • • • • File> Save Parameters (page 5-31) Using the Atlas Parameters Dialog Box (page 5-7) Setting Atlas Parameters . it will be listed here. “Parameter File Error: Sequence list not for this data set! File ignored. If you created a subdirectory associated with your Data Volume and Data Set as recommended in the Save Parameters procedure. the parameter file is for a different data set.set” extensions.Rotation Tab (page 5-25) Using Alternate Display Options (page 5-29) Saving and Loading an Atlas Parameter File (page 5-30) Working With 3D Wire Frame Atlases (page 5-2) Printing. Choose a different Parameter file or open the data set for which the file was saved. Control-L opens the Load Parameters box. The Open Parameter File Dialog Box 4. Click the Open button. The default location for saving parameter files is BQOSTEO\Topographer.” appears. Click on the parameter file to be opened. The appearance of the atlas will change to reflect the loaded parameters.Perspective Tab (page 5-7) Setting Atlas Parameters . Navigate to the folder that contains the Parameter file for the current data set.

Adjust any printing options. The Print Box 2.g. COPYING. To print the atlas at a different size. Topographer prints an atlas out at five inches by five inches. Adobe Photoshop or JASC Paint Shop Pro). From the Atlas Viewer’s File menu. export the atlas as a bitmap or metafile and print it from a graphics application (e. BIOQUANT Topographer Handbook: The Atlas Viewer in Detail .Page 5-34 PRINTING. choose Print Atlas. OR EXPORTING AN ATLAS TOPIC CONTENTS Printing a Wire Frame Atlas (page 5-34) Copying a Wire Frame Atlas (page 5-35) Exporting a 2D Atlas (page 5-35) RELATED TOPICS • • • • • • • • • • Atlas Viewer Menu and Tool Bars (page 5-2) Manipulating the Atlas in the Atlas Window (page 5-2) Using the Atlas Parameters Dialog Box (page 5-7) Setting Atlas Parameters .Perspective Tab (page 5-7) Setting Atlas Parameters . ADDITIONAL NOTE • Control-P opens the Print dialog box.Rotation Tab (page 5-25) Using Alternate Display Options (page 5-29) Saving and Loading an Atlas Parameter File (page 5-30) Working With 3D Wire Frame Atlases (page 5-2) Manipulating Data Arrays and Data Sets in the Atlas Viewer (page 5-38) PRINTING A WIRE FRAME ATLAS Print Atlas is available on the Atlas Viewer’s File menu when the Atlas Window is open. PROCEDURE 1. to open the Print dialog box. Click the OK button. It titles the atlas with the names of the data volume and data set and the date.Colors/Symbols Tab (page 5-10) Setting Atlas Parameters . 3.

This image can then be pasted into other applications such as Microsoft PowerPoint or Adobe Photoshop.Colors/Symbols Tab (page 5-10) Setting Atlas Parameters . in essence a snapshot of the atlas.Rotation Tab (page 5-25) Using Alternate Display Options (page 5-29) Saving and Loading an Atlas Parameter File (page 5-30) Working With 3D Wire Frame Atlases (page 5-2) Printing. ADDITIONAL NOTE • Choosing paste from the edit menu is the most common method of pasting in a bitmap.Colors/Symbols Tab (page 5-10) Setting Atlas Parameters . Copying. Switch to the other application.Page 5-35 RELATED TOPICS • • • • • • • • • • • • • Copying a Wire Frame Atlas (page 5-35) Exporting a 2D Atlas (page 5-35) Atlas Viewer Menu and Tool Bars (page 5-2) Manipulating the Atlas in the Atlas Window (page 5-2) Using the Atlas Parameters Dialog Box (page 5-7) Setting Atlas Parameters . but applications vary. Copying. SVG is a two-dimensional vector format that can be opened with many programs.Perspective Tab (page 5-7) Setting Atlas Parameters . RELATED TOPICS • • • • • • • • • • • • • Printing a Wire Frame Atlas (page 5-34) Exporting a 2D Atlas (page 5-35) Atlas Viewer Menu and Tool Bars (page 5-2) Manipulating the Atlas in the Atlas Window (page 5-2) Using the Atlas Parameters Dialog Box (page 5-7) Setting Atlas Parameters . PROCEDURE 1. including Inkscape. or Exporting an Atlas (page 5-34) Manipulating Data Arrays and Data Sets in the Atlas Viewer (page 5-38) EXPORTING A 2D ATLAS Export Atlas is available on the Atlas Viewer’s File menu when the Atlas Window is open. Check the documentation of the other application for details. An 2D atlas can be exported in two formats: bitmap and SVG. From the Atlas Viewer’s Atlas menu.Perspective Tab (page 5-7) Setting Atlas Parameters . The bitmap is a two dimensional format. 2. choose Copy to Clipboard. choose Paste to insert the picture of the atlas.Rotation Tab (page 5-25) Using Alternate Display Options (page 5-29) Saving and Loading an Atlas Parameter File (page 5-30) Working With 3D Wire Frame Atlases (page 5-2) Printing. Chrome. Firefox. 3. From the Edit menu of the other application. or Exporting an Atlas (page 5-34) Manipulating Data Arrays and Data Sets in the Atlas Viewer (page 5-38) COPYING A WIRE FRAME ATLAS Copy To Clipboard on the Atlas Viewer’s Atlas menu copies a bitmap of the Atlas Window to the Windows clipboard. TOPIC CONTENTS Using Export Current View to BMP (page 5-36) Using Export Current Topo to SVG (page 5-37) BIOQUANT Topographer Handbook: The Atlas Viewer in Detail . This menu item is available if the Atlas window is open.

4. A bitmap loses integrity if the size is enlarged in another program. see Using Export Current Topo to SVG (page 5-37). BIOQUANT Topographer Handbook: The Atlas Viewer in Detail . or Exporting an Atlas (page 5-34) Manipulating Data Arrays and Data Sets in the Atlas Viewer (page 5-38) USING EXPORT CURRENT VIEW TO BMP The bitmap is a two dimensional format. Copying.Rotation Tab (page 5-25) Using Alternate Display Options (page 5-29) Saving and Loading an Atlas Parameter File (page 5-30) Working With 3D Wire Frame Atlases (page 5-2) Printing. 3. Navigate to the folder where the file should be saved. Type a filename into the File Name text box.Page 5-36 RELATED TOPICS • • • • • • • • • • • • • Printing a Wire Frame Atlas (page 5-34) Copying a Wire Frame Atlas (page 5-35) Atlas Viewer Menu and Tool Bars (page 5-2) Manipulating the Atlas in the Atlas Window (page 5-2) Using the Atlas Parameters Dialog Box (page 5-7) Setting Atlas Parameters . including Adobe Photoshop. PROCEDURE 1. Microsoft Word.Colors/Symbols Tab (page 5-10) Setting Atlas Parameters .Perspective Tab (page 5-7) Setting Atlas Parameters . in essence a snapshot of the atlas. choose Export Current View to BMP. To save in a 2D vector format that can be resized in another program. Click the OK button to create the file. From the Atlas Viewer’s File menu. Export to BMP Box 2. and Microsoft PowerPoint. It can be opened by many programs.

Type a filename into the File Name text box. click the Resize to Fit button to center and size the Topo data. and then permanently change the colors. Then export it. and Chrome. including Inkscape. From the Atlas Viewer’s File menu.Colors/Symbols Tab (page 5-10) Setting Atlas Parameters . • BIOQUANT currently exports the raw Topo data colors. PROCEDURE 1. If you need a free SVG view. select the Topo array to export. BIOQUANT currently exports only the current Topo array. 5. download Inkscape from http://www. If you want to change colors. If there are several Topo arrays you would like exported. or Exporting an Atlas (page 5-34) Manipulating Data Arrays and Data Sets in the Atlas Viewer (page 5-38) USING EXPORT CURRENT TOPO TO SVG Scalable Vector Graphic (SVG) is a two-dimensional vector format that can be opened with many programs. use the Atlas Shop to first save to a new Topo array. choose Export Current Topo to SVG. Navigate to the folder where the file should be saved. 6. 2.inkscape.org. Copying. new Topo array.Page 5-37 RELATED TOPICS • • • • • • • • • • • • • • • Using Export Current Topo to SVG (page 5-37) Printing a Wire Frame Atlas (page 5-34) Copying a Wire Frame Atlas (page 5-35) Exporting a 2D Atlas (page 5-35) Atlas Viewer Menu and Tool Bars (page 5-2) Manipulating the Atlas in the Atlas Window (page 5-2) Using the Atlas Parameters Dialog Box (page 5-7) Setting Atlas Parameters . In the Atlas Viewer. use the Atlas Shop to combine the Topo arrays into a single. • 3. BIOQUANT Topographer Handbook: The Atlas Viewer in Detail . Click the OK button to create the file. in the Select Arrays Selected box.Rotation Tab (page 5-25) Using Alternate Display Options (page 5-29) Saving and Loading an Atlas Parameter File (page 5-30) Working With 3D Wire Frame Atlases (page 5-2) Printing. The Save TOPO Array to SVG File Box 4. The default folder for saving Topographer parameter files is BQOSTEO\Topographer or BQLifeScience\Topographer. Firefox. In the Atlas Viewer.Perspective Tab (page 5-7) Setting Atlas Parameters . Do not use the Parameters box to change colors.

Page 5-38 RELATED TOPICS • • • • • • • • • • • • • • • Using Export Current View to BMP (page 5-36) Printing a Wire Frame Atlas (page 5-34) Copying a Wire Frame Atlas (page 5-35) Exporting a 2D Atlas (page 5-35) Atlas Viewer Menu and Tool Bars (page 5-2) Manipulating the Atlas in the Atlas Window (page 5-2) Using the Atlas Parameters Dialog Box (page 5-7) Setting Atlas Parameters .Rotation Tab (page 5-25) Using Alternate Display Options (page 5-29) Saving and Loading an Atlas Parameter File (page 5-30) Working With 3D Wire Frame Atlases (page 5-2) Printing. These are also the arrays that are available for editing in the Atlas Shop when the full Topographer Plug-in program is present. Copying.Colors/Symbols Tab (page 5-10) Setting Atlas Parameters . or Exporting an Atlas (page 5-34) Manipulating Data Arrays and Data Sets in the Atlas Viewer (page 5-38) MANIPULATING DATA ARRAYS AND DATA SETS IN THE ATLAS VIEWER Following are Atlas Viewer features that were not covered in detail elsewhere in this manual. The Select Arrays box can be used to rename arrays.Rotation Tab (page 5-25) Using Alternate Display Options (page 5-29) Saving and Loading an Atlas Parameter File (page 5-30) Working With 3D Wire Frame Atlases (page 5-2) Printing. The Select Arrays box determines which topo arrays are drawn in the Atlas Window.Perspective Tab (page 5-7) Setting Atlas Parameters . BIOQUANT Topographer Handbook: The Atlas Viewer in Detail . or Exporting an Atlas (page 5-34) USING SELECT ARRAYS IN THE ATLAS VIEWER SELECT ARRAYS Select Arrays is available on the Atlas Viewer’s Arrays menu regardless of whether the Atlas Window is closed or open. Copying. Each data set can memorize a group of arrays which is moved collectively into the Selected list. Only Topo arrays can be put in the Selected list. To add and delete arrays. TOPIC CONTENTS Using Select Arrays in the Atlas Viewer (page 5-38) Using List Data in the Atlas Viewer (page 5-40) Using Save Data and Save Data Set (page 5-45) Converting BQ-OS/2 Data to Topo Data (page 5-46) RELATED TOPICS • • • • • • • • • • Atlas Viewer Menu and Tool Bars (page 5-2) Manipulating the Atlas in the Atlas Window (page 5-2) Using the Atlas Parameters Dialog Box (page 5-7) Setting Atlas Parameters . The Available Arrays list shows all the arrays in the data set. The arrays in the Selected list are the arrays used to construct the atlas. The arrays is the selected list are also saved in the Parameter file.Perspective Tab (page 5-7) Setting Atlas Parameters .Colors/Symbols Tab (page 5-10) Setting Atlas Parameters . use the Add/Delete Topo Arrays box that is on the Arrays menu when there is no atlas open.

Choose List to open the List Data window. click an array to display its name in the Name field. The Expanded Select Arrays Box • • Choose Shrink to hide the Name and Comment fields. choose Load Selected List to put the memorized arrays into the Selected list. Both can be edited. 3. 4. 2. From the File menu. Double click an array’s index in the Selected list to remove it from the Selected list. BIOQUANT Topographer Handbook: The Atlas Viewer in Detail . choose Save Selected List to have the system memorize which arrays are in the Selected list. Type a new name for the array into the Name field. Click another array to update the name change. From the Select menu. Click the Shrink menu item to hide the Name and Comment field. From the File menu. In the Available Arrays list. 5. From the Select menu. 1. Choose Expand to show the Name and Comments fields.Page 5-39 The Select Arrays Dialog Box GENERAL SELECT ARRAYS FUNCTIONS • • • • • • • Double click an array name in the Available Arrays list to move it to the Selected list. Click the Expand menu item to display the Name and Comment fields. RENAMING AN ARRAY Arrays can be renamed in the Select Arrays box. choose Select All Arrays to move all arrays to the Selected list. choose Unselect All Arrays to remove all arrays from the selected list.

Perspective Tab (page 5-7) Setting Atlas Parameters . Unlike measurement arrays.Colors/Symbols Tab (page 5-10) Setting Atlas Parameters . This can be done by selecting the Topo array on the Select Arrays dialog box and using the appropriate tools on the List window. If the current data set is password protected (a password was assigned and Password Protection was enabled in Life Science or OSTEO).Page 5-40 RELATED TOPICS • • • • • • • • • • • • • • Using List Data in the Atlas Viewer (page 5-40) Using Save Data and Save Data Set (page 5-45) Converting BQ-OS/2 Data to Topo Data (page 5-46) Atlas Viewer Menu and Tool Bars (page 5-2) Manipulating the Atlas in the Atlas Window (page 5-2) Using the Atlas Parameters Dialog Box (page 5-7) Setting Atlas Parameters . Copying. The only data editing tool that remains is Delete Listed Data . TOPIC CONTENTS Viewing Topo Data (page 5-40) Printing Topo Data (page 5-41) Deleting Data From a Topo Array (page 5-42) Adding and Deleting Topo Arrays (page 5-43) RELATED TOPICS • • • • • • • • • • • • • • • Using Select Arrays in the Atlas Viewer (page 5-38) Using List Data in the Atlas Viewer (page 5-40) Using Save Data and Save Data Set (page 5-45) Converting BQ-OS/2 Data to Topo Data (page 5-46) Atlas Viewer Menu and Tool Bars (page 5-2) Manipulating the Atlas in the Atlas Window (page 5-2) Using the Atlas Parameters Dialog Box (page 5-7) Setting Atlas Parameters .Perspective Tab (page 5-7) Setting Atlas Parameters . or Exporting an Atlas (page 5-34) Manipulating Data Arrays and Data Sets in the Atlas Viewer (page 5-38) USING LIST DATA IN THE ATLAS VIEWER The List Data window shows the data in array(s). or delete the data in a Topo array. The width of the array column can be increased to see BIOQUANT Topographer Handbook: The Atlas Viewer in Detail . or Exporting an Atlas (page 5-34) Manipulating Data Arrays and Data Sets in the Atlas Viewer (page 5-38) VIEWING TOPO DATA Topography data is unique. Y Position. five of the six data editing buttons on the List toolbar become unavailable (grayed out). only one parameter of the last element in the array is visible. Copying.Rotation Tab (page 5-25) Using Alternate Display Options (page 5-29) Saving and Loading an Atlas Parameter File (page 5-30) Working With 3D Wire Frame Atlases (page 5-2) Printing.Colors/Symbols Tab (page 5-10) Setting Atlas Parameters . it may seem necessary or desirable to view. When the List window is first opened.Rotation Tab (page 5-25) Using Alternate Display Options (page 5-29) Saving and Loading an Atlas Parameter File (page 5-30) Working With 3D Wire Frame Atlases (page 5-2) Printing. Z Offset Position. On rare occasions. but each has four parameters: X Position. Every topographic data point is recorded as one element in the Topo array. the data in Topo arrays cannot be edited in the List window. and a color number. the correct password must be entered before Topo data can be deleted on the Atlas Viewer’s List window. print. When a Topo array is selected.

Copying. D2. Some elements are occupied by Start of Section (SOSEC) or Start of Object (SOOB) markers.Perspective Tab (page 5-7) Setting Atlas Parameters .Rotation Tab (page 5-25) Using Alternate Display Options (page 5-29) Saving and Loading an Atlas Parameter File (page 5-30) Working With 3D Wire Frame Atlases (page 5-2) Printing.Colors/Symbols Tab (page 5-10) Setting Atlas Parameters . Fortunately. Use the scroll bar on the right end of the List window to scroll to the first (or any other) element in the array. From the Array menu. so printing topographic data is a time and paper consuming job. On the Select Arrays dialog box.Page 5-41 all four data point parameters. or Exporting an Atlas (page 5-34) Manipulating Data Arrays and Data Sets in the Atlas Viewer (page 5-38) PRINTING TOPO DATA There may be many thousands of data points in a single Topo array.) to widen the data column and reveal all four parameters of the visible element. PROCEDURE 1. select the desired Topo array. 2. The List Window When the List window first opens. and the scroll bar is used to scroll to other elements in the array. Click and drag the right border of the array name field (D1. The List Window The width of the array column is increased to show all four parameters of each data point. but it is possible. BIOQUANT Topographer Handbook: The Atlas Viewer in Detail . etc. 3. RELATED TOPICS • • • • • • • • • • • • • • • • • • Printing Topo Data (page 5-41) Deleting Data From a Topo Array (page 5-42) Adding and Deleting Topo Arrays (page 5-43) Using Select Arrays in the Atlas Viewer (page 5-38) Using List Data in the Atlas Viewer (page 5-40) Using Save Data and Save Data Set (page 5-45) Converting BQ-OS/2 Data to Topo Data (page 5-46) Atlas Viewer Menu and Tool Bars (page 5-2) Manipulating the Atlas in the Atlas Window (page 5-2) Using the Atlas Parameters Dialog Box (page 5-7) Setting Atlas Parameters . only one parameter in the last data point (element) is visible. printing Topo data is rarely necessary. choose List Data to open the List dialog box. 4.

From the Array menu. On the Print Setup dialog box do one or more of the following: • • • To include the array name on the printout. RELATED TOPICS • • • • • • • • • • • • • • • • • • Viewing Topo Data (page 5-40) Deleting Data From a Topo Array (page 5-42) Adding and Deleting Topo Arrays (page 5-43) Using Select Arrays in the Atlas Viewer (page 5-38) Using List Data in the Atlas Viewer (page 5-40) Using Save Data and Save Data Set (page 5-45) Converting BQ-OS/2 Data to Topo Data (page 5-46) Atlas Viewer Menu and Tool Bars (page 5-2) Manipulating the Atlas in the Atlas Window (page 5-2) Using the Atlas Parameters Dialog Box (page 5-7) Setting Atlas Parameters . On the Select Arrays dialog box. The List window’s Print Setup dialog box 4. On the Verify message box. From the Array menu. then click the OK button. delete the existing text. choose List Data to open the List dialog box. click the cursor in the field that is to be edited. 5. 2. Click the OK button to print the data report. 3. button on the List toolbar. and type the desired information.. select the desired Topo array. • • Click the Yes button to continue the delete procedure. Copying.. choose List Data to open the List dialog box.. enter the correct password.Rotation Tab (page 5-25) Using Alternate Display Options (page 5-29) Saving and Loading an Atlas Parameter File (page 5-30) Working With 3D Wire Frame Atlases (page 5-2) Printing. To change the default header (title) information on the printout. 2. click to check the Print Array Names check box. If a Password box opens. select the desired Topo array. Click the No button to cancel the delete command. Click the Delete Listed Data • 4.Colors/Symbols Tab (page 5-10) Setting Atlas Parameters .Perspective Tab (page 5-7) Setting Atlas Parameters . or Exporting an Atlas (page 5-34) Manipulating Data Arrays and Data Sets in the Atlas Viewer (page 5-38) DELETING DATA FROM A TOPO ARRAY PROCEDURE 1.. On the Select Arrays dialog box. BIOQUANT Topographer Handbook: The Atlas Viewer in Detail .Page 5-42 PROCEDURE 1. Click the Print button on the List toolbar to open the Print Setup dialog box. 3. On the Warning message box.

.g. which can be changed to a more descriptive name. In the Arrays list. Click the Close button to close the Add/Delete Topo Array dialog box. RELATED TOPICS • • • • • • • • • • • • • • • • • • Adding and Deleting Topo Arrays (page 5-43) Viewing Topo Data (page 5-40) Printing Topo Data (page 5-41) Using Select Arrays in the Atlas Viewer (page 5-38) Using List Data in the Atlas Viewer (page 5-40) Using Save Data and Save Data Set (page 5-45) Converting BQ-OS/2 Data to Topo Data (page 5-46) Atlas Viewer Menu and Tool Bars (page 5-2) Manipulating the Atlas in the Atlas Window (page 5-2) Using the Atlas Parameters Dialog Box (page 5-7) Setting Atlas Parameters . Click the Add Topo button to add a topo array. As Topo arrays are added. For example. From the Array menu. rename.Perspective Tab (page 5-7) Setting Atlas Parameters . the D4 array must be deleted before the D3 array can be deleted. 1. and remove Topo arrays from the currently open data set.. choose Add/Delete Topo. from the Atlas menu. Copying. 6.Colors/Symbols Tab (page 5-10) Setting Atlas Parameters . 5. they are given the next available index (e. D3). Click the No button to cancel the delete command. 7. choose Close to close it. click on the new topo array to display its name in the Name field. they are given the next available D# index and given the default name “Topo”. The Add/ Delete Topo Array dialog box is used to add. or Exporting an Atlas (page 5-34) Manipulating Data Arrays and Data Sets in the Atlas Viewer (page 5-38) ADDING AND DELETING TOPO ARRAYS Add/Delete Topo is available on the Atlas Viewer’s Array menu only when the Atlas Window is closed. 2. The Add/Delete Topo Array Dialog Box 3. Click the Update button to update the name of the array in the arrays list. Type in a new name for the array. Arrays can only be deleted from the bottom of the index series up. ADDING A TOPO ARRAY When topo arrays are added. 4.Page 5-43 • • Click the Yes button to delete the data in the listed Topo array.Rotation Tab (page 5-25) Using Alternate Display Options (page 5-29) Saving and Loading an Atlas Parameter File (page 5-30) Working With 3D Wire Frame Atlases (page 5-2) Printing. If the Atlas Window is open. BIOQUANT Topographer Handbook: The Atlas Viewer in Detail . to open the Add/Delete Topo Array box.

2. Click the Close button to close the Add/Delete Topo dialog box. from the Atlas menu. Click the cursor in the Name edit field and type in a new name. 2. BIOQUANT Topographer Handbook: The Atlas Viewer in Detail . If the Atlas Window is open. The Add/Delete Topo Dialog Box The name of the highlighted array is displayed in the Name field. choose Add/Delete Topo. Click the Update button to update the name in the array list. the D4 array would have to be deleted before the D3 array could be deleted. 5. 3. 3. (Example: D3 must be deleted before D2.Page 5-44 ADDITIONAL NOTES Arrays can be renamed in the Select Arrays box too. If the Atlas Window is open. choose Close to close it. For example. Its current name will appear in the Name edit field. Repeat from step 3 for each Topo array that needs to be deleted.. 5. From the Array menu. from the Atlas menu. to open the Add/Delete Topo Array box.. 6. From the Array menu. Click the Delete button. DELETING A TOPO ARRAY Arrays can only be deleted from the bottom of the index series up. 4. In the Arrays list. click to highlight the array that is to be renamed. • Click the No button to cancel the delete command. The Add/Delete Topo Dialog Box The name of the highlighted array is displayed in the Name field. choose Close to close it.. If a Delete Failed message appears with the message “Arrays with the same letter in the index must be deleted from the bottom up.)” then the other arrays must be deleted before the currently chosen array can be deleted. RENAMING AN ADDED TOPO ARRAY 1. 4. Click the Close button to close the Add/Delete dialog box. In the Arrays list. A delete Warning message will appear. 1. 6. • Click the Yes button to delete the array. to open the Add/Delete Topo Array box.. choose Add/Delete Topo. click to highlight the name of the array that is to be deleted.

Page 5-45 RELATED TOPICS • • • • • • • • • • • • • • • • • • Viewing Topo Data (page 5-40) Printing Topo Data (page 5-41) Deleting Data From a Topo Array (page 5-42) Using Select Arrays in the Atlas Viewer (page 5-38) Using List Data in the Atlas Viewer (page 5-40) Using Save Data and Save Data Set (page 5-45) Converting BQ-OS/2 Data to Topo Data (page 5-46) Atlas Viewer Menu and Tool Bars (page 5-2) Manipulating the Atlas in the Atlas Window (page 5-2) Using the Atlas Parameters Dialog Box (page 5-7) Setting Atlas Parameters . Save Data is used to permanently record changes in data or array comments in the data set’s existing arrays. choose Close. click the Save Data button on the system tool bar. If the computer should malfunction while the Topographer is open. PROCEDURE: SAVE DATA • After making a change in an array’s data or the notation in an array’s Comment field. RELATED TOPICS • • • • • • • • • • • • • • Using Select Arrays in the Atlas Viewer (page 5-38) Using List Data in the Atlas Viewer (page 5-40) Converting BQ-OS/2 Data to Topo Data (page 5-46) Atlas Viewer Menu and Tool Bars (page 5-2) Manipulating the Atlas in the Atlas Window (page 5-2) Using the Atlas Parameters Dialog Box (page 5-7) Setting Atlas Parameters . any time the Topographer is deliberately closed. If the Atlas Window is open.Colors/Symbols Tab (page 5-10) Setting Atlas Parameters . it is best to save changes immediately after making them. the Save Data button is available on the system tool bar. as well as changes in the data or array comments. Copying.Perspective Tab (page 5-7) Setting Atlas Parameters . When the Atlas Window is closed. or Exporting an Atlas (page 5-34) Manipulating Data Arrays and Data Sets in the Atlas Viewer (page 5-38) USING SAVE DATA AND SAVE DATA SET When an Atlas Window is open. from the Atlas menu.Colors/Symbols Tab (page 5-10) Setting Atlas Parameters . PROCEDURE: SAVE DATA SET 1. Copying.Rotation Tab (page 5-25) Using Alternate Display Options (page 5-29) Saving and Loading an Atlas Parameter File (page 5-30) Working With 3D Wire Frame Atlases (page 5-2) Printing. or Exporting an Atlas (page 5-34) Manipulating Data Arrays and Data Sets in the Atlas Viewer (page 5-38) BIOQUANT Topographer Handbook: The Atlas Viewer in Detail .Rotation Tab (page 5-25) Using Alternate Display Options (page 5-29) Saving and Loading an Atlas Parameter File (page 5-30) Working With 3D Wire Frame Atlases (page 5-2) Printing. 2. From the File menu. choose Save Data Set. when new arrays are added while in the Topographer). unsaved changes would be lost. Save Data Set is available on the File menu to permanently record structural changes in the data set (e.Perspective Tab (page 5-7) Setting Atlas Parameters .g. Although the system performs both of these functions automatically.

Click the Open button. c. Click to highlight the desired data set in the Data Sets list. PROCEDURE 1. then from the Atlas menu. The Open a Data Set Box 3. 7. BIOQUANT Topographer Handbook: The Atlas Viewer in Detail . Click to highlight the desired data volume in the Data Volumes list.. The data sets in the highlighted Volume will be displayed in the Data Sets list. If the desired data volume is not shown in the Data Volume list: a.. Select the directory that contains the desired data volume.Page 5-46 CONVERTING BQ-OS/2 DATA TO TOPO DATA Convert OS/2 Data is available on the Atlas Viewer’s Array menu when the Atlas Window is closed. choose Open Data Set to display the Open a Data Set box. The Convert OS/2 Quickdraw Data to Topo Data 8. it must be converted from the Quickdraw format to the Topographer format. Choose Convert OS/2 Data. 2. choose Close to close the Atlas Window. The Choose BQ Volume Search DIrectory Box b. 5. Before topography collected with the OS/2 BIOQUANT system can be viewed. Click the OK button. If the Atlas Window is open. click the Change Dir button to open the Choose BQ Volume Search Directory box. Click the Add Topo button to add an empty topo array. from the Array menu to open the Convert OS/2 Quickdraw Array to Topo Array box. The arrays of the data set appear in the Select Arrays box. 4. 6. From the File menu.

Rotation Tab (page 5-25) Using Alternate Display Options (page 5-29) Saving and Loading an Atlas Parameter File (page 5-30) Working With 3D Wire Frame Atlases (page 5-2) Printing. RELATED TOPICS • • • • • • • • • • • • • • • Using Select Arrays in the Atlas Viewer (page 5-38) Using List Data in the Atlas Viewer (page 5-40) Using Save Data and Save Data Set (page 5-45) Converting BQ-OS/2 Data to Topo Data (page 5-46) Atlas Viewer Menu and Tool Bars (page 5-2) Manipulating the Atlas in the Atlas Window (page 5-2) Using the Atlas Parameters Dialog Box (page 5-7) Setting Atlas Parameters . Click on the Quickdraw array to be converted in the Select Quickdraw list. 11. 12. Click the Close button. Choose Save from the File menu. Copying. Click the Convert button.Page 5-47 9. or Exporting an Atlas (page 5-34) Manipulating Data Arrays and Data Sets in the Atlas Viewer (page 5-38) BIOQUANT Topographer Handbook: The Atlas Viewer in Detail .Colors/Symbols Tab (page 5-10) Setting Atlas Parameters . the computer beeps when the conversion is done. Click the empty topo array in the Select Destination Topo list. 10.Perspective Tab (page 5-7) Setting Atlas Parameters . 13.

Page 5-48 BIOQUANT Topographer Handbook: The Atlas Viewer in Detail .

Select. The File Menu (page 6-2) The Select Menu (page 6-7) The View Menu (page 6-16) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66) Taking Measurements from an Atlas (page 6-69) The Atlas Shop in Detail . View.BIOQUANT Topographer Handbook The Atlas Shop in Detail This section is a reference guide to the Atlas Shop’s File. Options on the Atlas Shop’s Measure and Tools menu are special procedures that are covered in Section 8. and Edit menus and the tools on both its tool bars.

Page 6-2 ATLAS SHOP INTERFACE The atlas is displayed for editing or measurement on the Atlas Shop’s desktop. TOPIC CONTENTS The File Menu (page 6-2) The Select Menu (page 6-7) The View Menu (page 6-16) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66) THE FILE MENU This section covers the File menu items in the Atlas Shop. TOPIC CONTENTS File > Save (page 6-3) File > Save as (page 6-3) File > Save Selection As (page 6-4) File> Restore Original (page 6-5) File> Exit Atlas Shop (page 6-6) BIOQUANT Topographer Handbook: The Atlas Shop in Detail . The Atlas Shop Desktop The black Perspective panel shows section distribution along the Z axis. A two-axis sketch of the atlas is also shown in a black Perspective panel along the right hand side of the work space.

PROCEDURES • • • Choose Save from the File menu. RELATED TOPICS • • • • • • • • • • • File > Save as (page 6-3) File > Save Selection As (page 6-4) File> Restore Original (page 6-5) File> Exit Atlas Shop (page 6-6) The File Menu (page 6-2) The Select Menu (page 6-7) The View Menu (page 6-16) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66) FILE > SAVE AS Save As on the File menu opens the Save Array As dialog box where the entire atlas may be saved to a new Topo array before editing begins. There are three ways the Save command can be executed. (Press and hold the Control key. It is recommended that data sets be backed up in BIOQUANT’s Data Manager before editing. permanently alter the data. Use Ctrl-Shift-S on the keyboard. the Save option is grayed out and Save As must be used instead. or to save alternate versions of the atlas after editing. Using Save. Certain editing functions (Internal Cut. saves changes made to an atlas into the current atlas Topo array. When these types of edits are made. Use Ctrl-S on the keyboard.) On Exiting the Atlas Shop. then tap the S key. Z Sort. and Resolution) change the topographic data in ways that can only be saved to a new Topo array. (Press and hold the Control and Shift keys. Most types of edits can be saved this way.) BIOQUANT Topographer Handbook: The Atlas Shop in Detail . then tap the S key. WAYS TO OPEN THE SAVE ARRAY AS DIALOG BOX: • • Choose Save As from the File menu. click the YES button on the Save Data message box that asks if the data should be saved.Page 6-3 RELATED TOPICS • • • • • • The Select Menu (page 6-7) The View Menu (page 6-16) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66) FILE > SAVE Edits saved directly into original atlas Topo array(s) using File> Save. Internal Paste. to consolidate the atlas data into a single Topo array.

Page 6-4 The Save Array As Box Save Array As dialog box before (left) and after (right) a new Topo array has been added. because it puts the data being used in the current atlas at risk of being corrupted. Click the Save button to save the atlas to that array. delete the default name and type in a name that identifies the version of the atlas that is being saved. RELATED TOPICS • • • • • • • • • • • File > Save (page 6-3) File > Save Selection As (page 6-4) File> Restore Original (page 6-5) File> Exit Atlas Shop (page 6-6) The File Menu (page 6-2) The Select Menu (page 6-7) The View Menu (page 6-16) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66) FILE > SAVE SELECTION AS Save Selection As is used to save selected portions of the atlas to a new Topo array. If there is an empty topo array. PROCEDURE: 1. In the Array Name text box. Although it is possible to replace data or append data in an existing Topo array. scroll through the Available Arrays list and click to choose the desired destination array. 4. If you are sure that an existing Topo array (listed on the Save Selection As dialog box) does NOT contain data for the current atlas. Use Ctrl-Alt-S on the keyboard. If there is not an empty topo array in the list of arrays. this is not recommended. 3. Open the Save As dialog box using one of the above methods. • • 2. then tap the S key. click the New Array button to add one. (Press and hold the Control and Alternate keys.) BIOQUANT Topographer Handbook: The Atlas Shop in Detail . CAUTION • Replace or append data in an existing Topo array ONLY IF the existing array does NOT contain data for the current atlas. The New Array button on the Save Selection As dialog box is used to add a new Topo array to the data set. its data may be replaced or appended with the selected portion of the current atlas. WAYS TO OPEN THE SAVE SELECTION AS DIALOG BOX: • • Choose Save As from the File menu. Click the Close button to close the Save Array As dialog box.

RELATED TOPICS • • • • • • • • • • • File > Save (page 6-3) File > Save as (page 6-3) File> Restore Original (page 6-5) File> Exit Atlas Shop (page 6-6) The File Menu (page 6-2) The Select Menu (page 6-7) The View Menu (page 6-16) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66) FILE> RESTORE ORIGINAL Any unsaved edits made to the atlas can be cancelled by using the Restore Original option on the File menu. delete the default name from the Destination Array field and type in a new name that identifies the portion of the atlas that is being saved. PROCEDURE 1. To use an existing Topo array. Its name will appear in the Destination Array field. If saving the selected data to a new. Do not select as the destination array any topo array that holds data for the current atlas. click the New Array button. empty array. click the Append button. • • Select the portion of the atlas that is to be saved. click the Replace button. Open the Save Selection As dialog box using one of the methods above. 2. To add a new Topo array to the data set. Click the Close button to close the Save Selection As dialog box. click the Append button. choose Restore Original. scroll through the arrays list and click the Topo array to which the selection will be saved. To rename the destination array.Page 6-5 The Save Selection As Dialog Box Add a new Topo array or select an existing Topo array that does NOT contain data that is being used in the current atlas. PROCEDURE: 1. From the File menu. To append the selected data to the end of existing data in the destination array. • • • • 3. If saving the selected data to over data in a previously used array. BIOQUANT Topographer Handbook: The Atlas Shop in Detail .

Z Sort. SAVE DATA MESSAGE 1 If there are unsaved edits that can be saved to the original Topo array(s).Page 6-6 RELATED TOPICS • • • • • • • • • • • File > Save (page 6-3) File > Save as (page 6-3) File > Save Selection As (page 6-4) File> Exit Atlas Shop (page 6-6) The File Menu (page 6-2) The Select Menu (page 6-7) The View Menu (page 6-16) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66) FILE> EXIT ATLAS SHOP Choosing Exit Atlas Shop from the File menu.) Answer NO if you have already saved an edited version of the atlas using Save As from the File menu or the Save button on the special dialog boxes that appear during editing. BIOQUANT Topographer Handbook: The Atlas Shop in Detail . the following message will appear: The Save Data Box • • • • Answer YES if you want to save the edited version of the atlas to a new array and you have not already done so.) Click Cancel to stay in the Atlas Shop.) Answer NO if you want to discard the changes. If unsaved edits exist. one of two Save Data message boxes will appear. Answer NO if edits are to be discarded. Click Cancel to stay in the Atlas Shop. closes the Atlas Shop and returns the user to the Atlas Viewer. (The Atlas Shop will close. if you want the edits to permanently change the original data in the atlas Topo array(s). depending on the type of edits made. or Internal Paste were used. Internal Copy. Internal Cut. or pressing Alt-X on the keyboard. the following message box will open: The Save Data Box • • • Answer YES. (The Atlas Shop will close. (The Save Array As dialog box will open. SAVE DATA MESSAGE 2 If Resolution.

See “Select Using Rectangle or Polygon” on 6-49.Page 6-7 RELATED TOPICS • • • • • • • • • • • File > Save (page 6-3) File > Save as (page 6-3) File > Save Selection As (page 6-4) File> Restore Original (page 6-5) The File Menu (page 6-2) The Select Menu (page 6-7) The View Menu (page 6-16) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66) THE SELECT MENU This section covers the Select menu items in the Atlas Shop. TOPIC CONTENTS Select> Select Using Rectangle (page 6-7) Select> Select Using Polygon (page 6-8) Select> Select By Color (page 6-8) Select> Select All Sections (page 6-9) Select> Add Interior Objects to Selection (page 6-9) Select> Select None (page 6-10) Select> Section Mode (page 6-10) Select> Object Mode (page 6-11) Select> Point Mode (page 6-11) Select> Select Across Sections (page 6-12) Select> Next (page 6-13) Select> Back (page 6-13) Select> GoTo (page 6-14) RELATED TOPICS • • • • • • The File Menu (page 6-2) The View Menu (page 6-16) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66) SELECT> SELECT USING RECTANGLE Same as clicking the Select Using Rectangle • tool on the Vertical Tool Bar. BIOQUANT Topographer Handbook: The Atlas Shop in Detail .

Page 6-8 RELATED TOPICS • • • • • • • • • • • • • • • • • • • Select> Select Using Polygon (page 6-8) Select> Select By Color (page 6-8) Select> Select All Sections (page 6-9) Select> Add Interior Objects to Selection (page 6-9) Select> Select None (page 6-10) Select> Section Mode (page 6-10) Select> Object Mode (page 6-11) Select> Point Mode (page 6-11) Select> Select Across Sections (page 6-12) Select> Next (page 6-13) Select> Back (page 6-13) Select> GoTo (page 6-14) The File Menu (page 6-2) The Select Menu (page 6-7) The View Menu (page 6-16) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66) SELECT> SELECT USING POLYGON Same as clicking the Select Using Polygon • tool on the Vertical Tool Bar. See “Select Using Rectangle or Polygon” on 6-49. RELATED TOPICS • • • • • • • • • • • • • • • • • • • Select> Select Using Rectangle (page 6-7) Select> Select By Color (page 6-8) Select> Select All Sections (page 6-9) Select> Add Interior Objects to Selection (page 6-9) Select> Select None (page 6-10) Select> Section Mode (page 6-10) Select> Object Mode (page 6-11) Select> Point Mode (page 6-11) Select> Select Across Sections (page 6-12) Select> Next (page 6-13) Select> Back (page 6-13) Select> GoTo (page 6-14) The File Menu (page 6-2) The Select Menu (page 6-7) The View Menu (page 6-16) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66) SELECT> SELECT BY COLOR Same as clicking the Select By Color • See “Select By Color” on 6-52. tool on the Vertical Tool Bar. BIOQUANT Topographer Handbook: The Atlas Shop in Detail .

2.Page 6-9 RELATED TOPICS • • • • • • • • • • • • • • • • • • • Select> Select Using Rectangle (page 6-7) Select> Select Using Polygon (page 6-8) Select> Select All Sections (page 6-9) Select> Add Interior Objects to Selection (page 6-9) Select> Select None (page 6-10) Select> Section Mode (page 6-10) Select> Object Mode (page 6-11) Select> Point Mode (page 6-11) Select> Select Across Sections (page 6-12) Select> Next (page 6-13) Select> Back (page 6-13) Select> GoTo (page 6-14) The File Menu (page 6-2) The Select Menu (page 6-7) The View Menu (page 6-16) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66) SELECT> SELECT ALL SECTIONS • To select every thing in the atlas. RELATED TOPICS • • • • • • • • • • • • • • • • • • • Select> Select Using Rectangle (page 6-7) Select> Select Using Polygon (page 6-8) Select> Select By Color (page 6-8) Select> Add Interior Objects to Selection (page 6-9) Select> Select None (page 6-10) Select> Section Mode (page 6-10) Select> Object Mode (page 6-11) Select> Point Mode (page 6-11) Select> Select Across Sections (page 6-12) Select> Next (page 6-13) Select> Back (page 6-13) Select> GoTo (page 6-14) The File Menu (page 6-2) The Select Menu (page 6-7) The View Menu (page 6-16) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66) SELECT> ADD INTERIOR OBJECTS TO SELECTION Add Interior Objects to Selection is an option than can be used when a currently selected tracing (object) encircles other tracings that need to be added to the selection. BIOQUANT Topographer Handbook: The Atlas Shop in Detail Click to activate Object Mode . . In Section mode interest. select the section that contains the object of . using the most convenient method. Add Interior Object to Selection is used only in Object Mode. PROCEDURE 1. choose Select All Sections from the Select menu.

RELATED TOPICS • • • • • • • • • • • • • • • • • • • Select> Select Using Rectangle (page 6-7) Select> Select Using Polygon (page 6-8) Select> Select By Color (page 6-8) Select> Select All Sections (page 6-9) Select> Add Interior Objects to Selection (page 6-9) Select> Section Mode (page 6-10) Select> Object Mode (page 6-11) Select> Point Mode (page 6-11) Select> Select Across Sections (page 6-12) Select> Next (page 6-13) Select> Back (page 6-13) Select> GoTo (page 6-14) The File Menu (page 6-2) The Select Menu (page 6-7) The View Menu (page 6-16) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66) SELECT> SECTION MODE In Section mode. RELATED TOPICS • • • • • • • • • • • • • • • • • • • Select> Select Using Rectangle (page 6-7) Select> Select Using Polygon (page 6-8) Select> Select By Color (page 6-8) Select> Select All Sections (page 6-9) Select> Select None (page 6-10) Select> Section Mode (page 6-10) Select> Object Mode (page 6-11) Select> Point Mode (page 6-11) Select> Select Across Sections (page 6-12) Select> Next (page 6-13) Select> Back (page 6-13) Select> GoTo (page 6-14) The File Menu (page 6-2) The Select Menu (page 6-7) The View Menu (page 6-16) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66) SELECT> SELECT NONE • To un-select every thing in the atlas. From the Select menu. 4. editing operations are applied to the selected section(s).Page 6-10 3. Using the most convenient method. choose Select None from the Select menu. • To activate Section mode. choose Section Mode from the Select menu or click the Section Mode on the system tool bar. choose Add Interior Objects to Selection. button BIOQUANT Topographer Handbook: The Atlas Shop in Detail . select the tracing (object) that surrounds another set of objects that need to be selected.

each contains two data points with zero distance between them. Objects are individual tracings or markers within a section map. Data points are the individual points within a tracing or object marker. • To activate Object mode. button RELATED TOPICS • • • • • • • • • • • • • • • • • • • Select> Select Using Rectangle (page 6-7) Select> Select Using Polygon (page 6-8) Select> Select By Color (page 6-8) Select> Select All Sections (page 6-9) Select> Add Interior Objects to Selection (page 6-9) Select> Select None (page 6-10) Select> Section Mode (page 6-10) Select> Point Mode (page 6-11) Select> Select Across Sections (page 6-12) Select> Next (page 6-13) Select> Back (page 6-13) Select> GoTo (page 6-14) The File Menu (page 6-2) The Select Menu (page 6-7) The View Menu (page 6-16) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66) SELECT> POINT MODE In Point mode. editing operations are applied to the selected data point(s). Although. choose Object Mode from the Select menu or click the Object Mode on the system tool bar. object markers appear to be single points in the atlas.Page 6-11 RELATED TOPICS • • • • • • • • • • • • • • • • • • • Select> Select Using Rectangle (page 6-7) Select> Select Using Polygon (page 6-8) Select> Select By Color (page 6-8) Select> Select All Sections (page 6-9) Select> Add Interior Objects to Selection (page 6-9) Select> Select None (page 6-10) Select> Object Mode (page 6-11) Select> Point Mode (page 6-11) Select> Select Across Sections (page 6-12) Select> Next (page 6-13) Select> Back (page 6-13) Select> GoTo (page 6-14) The File Menu (page 6-2) The Select Menu (page 6-7) The View Menu (page 6-16) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66) SELECT> OBJECT MODE In Object mode. editing operations are applied to the selected object(s). BIOQUANT Topographer Handbook: The Atlas Shop in Detail .

button on the RELATED TOPICS • • • • • • • • • • • • • • • • • • • Select> Select Using Rectangle (page 6-7) Select> Select Using Polygon (page 6-8) Select> Select By Color (page 6-8) Select> Select All Sections (page 6-9) Select> Add Interior Objects to Selection (page 6-9) Select> Select None (page 6-10) Select> Section Mode (page 6-10) Select> Object Mode (page 6-11) Select> Select Across Sections (page 6-12) Select> Next (page 6-13) Select> Back (page 6-13) Select> GoTo (page 6-14) The File Menu (page 6-2) The Select Menu (page 6-7) The View Menu (page 6-16) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66) SELECT> SELECT ACROSS SECTIONS In Object Mode. When active. choose Point Mode from the Select menu or click the Point Mode system tool bar. the Select Across Sections feature tells the system to select objects on all sections in an area that corresponds to the selection box or polygon that is being created on the current section. In Section Mode select a section map that contains the area of interest. the Select Using Rectangle and Select Using Polygon tools can be made to work across the entire atlas. 3. Click the Object Mode On the Select menu. click to check Select Across Sections. PROCEDURE 1. Select Using Rectangle or Polygon (page 6-49) tool to define the desired selection area on BIOQUANT Topographer Handbook: The Atlas Shop in Detail . 4. Use the Select Using Rectangle or Select Using Polygon the current section. button. 2.Page 6-12 • To activate Point mode.

the next section map in the series is selected. In Section mode. In Object mode. In Section mode. RELATED TOPICS • • • • • • • • • • • • • • • • • • • Select> Select Using Rectangle (page 6-7) Select> Select Using Polygon (page 6-8) Select> Select By Color (page 6-8) Select> Select All Sections (page 6-9) Select> Add Interior Objects to Selection (page 6-9) Select> Select None (page 6-10) Select> Section Mode (page 6-10) Select> Object Mode (page 6-11) Select> Point Mode (page 6-11) Select> Select Across Sections (page 6-12) Select> Back (page 6-13) Select> GoTo (page 6-14) The File Menu (page 6-2) The Select Menu (page 6-7) The View Menu (page 6-16) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66) SELECT> BACK Same as clicking the Select Previous • button on the system tool bar. the previous section map in the series is selected. the next point in the current object is selected. the next tracing or marker in the current section is selected.Page 6-13 RELATED TOPICS • • • • • • • • • • • • • • • • • • • Select> Select Using Rectangle (page 6-7) Select> Select Using Polygon (page 6-8) Select> Select By Color (page 6-8) Select> Select All Sections (page 6-9) Select> Add Interior Objects to Selection (page 6-9) Select> Select None (page 6-10) Select> Section Mode (page 6-10) Select> Object Mode (page 6-11) Select> Point Mode (page 6-11) Select> Next (page 6-13) Select> Back (page 6-13) Select> GoTo (page 6-14) The File Menu (page 6-2) The Select Menu (page 6-7) The View Menu (page 6-16) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66) SELECT> NEXT Same as clicking the Select Next • • • button on the system tool bar. In Point mode. BIOQUANT Topographer Handbook: The Atlas Shop in Detail .

From the Select menu. Click to activate the Section mode button. BIOQUANT Topographer Handbook: The Atlas Shop in Detail . to open the GoTo Section list box. In Point mode. In this case the object list would be very long and possibly tedious to use. unless the current section has dozens or hundreds of cell markers. choose GoTo.Page 6-14 • • In Object mode. SELECT SECTIONS FROM GOTO SECTION LIST 1. RELATED TOPICS • • • • • • • • • • • • • • • • • • • Select> Select Using Rectangle (page 6-7) Select> Select Using Polygon (page 6-8) Select> Select By Color (page 6-8) Select> Select All Sections (page 6-9) Select> Add Interior Objects to Selection (page 6-9) Select> Select None (page 6-10) Select> Section Mode (page 6-10) Select> Object Mode (page 6-11) Select> Point Mode (page 6-11) Select> Select Across Sections (page 6-12) Select> Next (page 6-13) Select> GoTo (page 6-14) The File Menu (page 6-2) The Select Menu (page 6-7) The View Menu (page 6-16) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66) SELECT> GOTO Sections (in Section Mode) and objects (in Object Mode) may be selected from a GoTo list. The GoTo Section list is almost always the fastest way to select multiple sections. click to highlight its entry in the list. the previous tracing or marker in the current section is selected. the previous point in the current object is selected. The GoTo Object list is a quick way to select objects. 2. GoTo Section List With the First Section Selected • To select a single section.

. choose GoTo. press and hold the Shift key. contiguous objects. 3. then click the last section in the series that is to be selected. click the first section. click one object. press and hold the Ctrl key. The list of objects on the right is from a section with dozens of cell markers. To select multiple. click the first object. then click the last object in the series. To select multiple. All objects between and including the first and the last will be selected. then click each additional object that is to be selected. click one section. To select multiple. click to highlight its entry in the list. select the section that contains the objects of . non-contiguous sections. non-contiguous objects. Click to activate Object Mode From the Select menu. • • To select a single object.Page 6-15 • To select multiple. Example GoTo Object Lists The Ctrl key was used to help select non-contiguous objects in the short list on the left. All sections between and including the first and the last will be selected. to open the Go To Object list. then click each additional section that is to be selected. In Section mode interest. press and hold the Shift key. • SELECT OBJECTS FROM GOTO OBJECTS LIST 1. using the most convenient method. 2. • BIOQUANT Topographer Handbook: The Atlas Shop in Detail . contiguous sections. press and hold the Ctrl key.

BIOQUANT Topographer Handbook: The Atlas Shop in Detail button on the . TOPIC CONTENTS View> Resize to Fit (page 6-16) View> Zoom (page 6-17) View> Pan (page 6-17) View> Center (page 6-18) View> Flash Selection (page 6-18) View> Selection Only (page 6-19) View> Show All Sections (page 6-20) View> Overlay Sections (page 6-20) View>Show Start Point (page 6-21) View> Show Landmark (page 6-22) View> Show Data (page 6-22) View> Redraw (page 6-23) View> Auto Redraw (page 6-24) View> Z Perspective (page 6-25) View> Y Perspective (page 6-25) View> X Perspective (page 6-26) RELATED TOPICS • • • • • • The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66) VIEW> RESIZE TO FIT Centers and resizes the atlas to fit the Atlas Shop work space. Same as clicking the Resize to Fit system tool bar.Page 6-16 RELATED TOPICS • • • • • • • • • • • • • • • • • • • Select> Select Using Rectangle (page 6-7) Select> Select Using Polygon (page 6-8) Select> Select By Color (page 6-8) Select> Select All Sections (page 6-9) Select> Add Interior Objects to Selection (page 6-9) Select> Select None (page 6-10) Select> Section Mode (page 6-10) Select> Object Mode (page 6-11) Select> Point Mode (page 6-11) Select> Select Across Sections (page 6-12) Select> Next (page 6-13) Select> Back (page 6-13) The File Menu (page 6-2) The Select Menu (page 6-7) The View Menu (page 6-16) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66) THE VIEW MENU This section covers the View menu items in the Atlas Shop.

See “Pan” on 6-48. Same as clicking the Pan tool. BIOQUANT Topographer Handbook: The Atlas Shop in Detail . Same as clicking the Zoom tool on the Vertical Tool Bar. RELATED TOPICS • • • • • • • • • • • • • • • • • • • • • View> Resize to Fit (page 6-16) View> Pan (page 6-17) View> Center (page 6-18) View> Flash Selection (page 6-18) View> Selection Only (page 6-19) View> Show All Sections (page 6-20) View> Overlay Sections (page 6-20) View>Show Start Point (page 6-21) View> Show Landmark (page 6-22) View> Show Data (page 6-22) View> Redraw (page 6-23) View> Auto Redraw (page 6-24) View> Z Perspective (page 6-25) View> Y Perspective (page 6-25) View> X Perspective (page 6-26) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66) VIEW> PAN Activates the Pan • tool on the Vertical Tool Bar.Page 6-17 RELATED TOPICS • • • • • • • • • • • • • • • • • • • • • View> Zoom (page 6-17) View> Pan (page 6-17) View> Center (page 6-18) View> Flash Selection (page 6-18) View> Selection Only (page 6-19) View> Show All Sections (page 6-20) View> Overlay Sections (page 6-20) View>Show Start Point (page 6-21) View> Show Landmark (page 6-22) View> Show Data (page 6-22) View> Redraw (page 6-23) View> Auto Redraw (page 6-24) View> Z Perspective (page 6-25) View> Y Perspective (page 6-25) View> X Perspective (page 6-26) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66) VIEW> ZOOM Activates the Zoom • tool on the Vertical Tool Bar. See “Zoom” on 6-48.

Page 6-18 RELATED TOPICS • • • • • • • • • • • • • • • • • • • • • View> Resize to Fit (page 6-16) View> Zoom (page 6-17) View> Center (page 6-18) View> Flash Selection (page 6-18) View> Selection Only (page 6-19) View> Show All Sections (page 6-20) View> Overlay Sections (page 6-20) View>Show Start Point (page 6-21) View> Show Landmark (page 6-22) View> Show Data (page 6-22) View> Redraw (page 6-23) View> Auto Redraw (page 6-24) View> Z Perspective (page 6-25) View> Y Perspective (page 6-25) View> X Perspective (page 6-26) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66) VIEW> CENTER Centers the entire atlas in the middle of the Atlas Shop’s work space. Same as clicking the Flash Selection the system tool bar. Same as clicking the Center system tool bar. button on the RELATED TOPICS • • • • • • • • • • • • • • • • • • • • • View> Resize to Fit (page 6-16) View> Zoom (page 6-17) View> Pan (page 6-17) View> Flash Selection (page 6-18) View> Selection Only (page 6-19) View> Show All Sections (page 6-20) View> Overlay Sections (page 6-20) View>Show Start Point (page 6-21) View> Show Landmark (page 6-22) View> Show Data (page 6-22) View> Redraw (page 6-23) View> Auto Redraw (page 6-24) View> Z Perspective (page 6-25) View> Y Perspective (page 6-25) View> X Perspective (page 6-26) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66) VIEW> FLASH SELECTION Causes the currently selected section. or point to flash once. object. BIOQUANT Topographer Handbook: The Atlas Shop in Detail button on .

Page 6-19 RELATED TOPICS • • • • • • • • • • • • • • • • • • • • • View> Resize to Fit (page 6-16) View> Zoom (page 6-17) View> Pan (page 6-17) View> Center (page 6-18) View> Selection Only (page 6-19) View> Show All Sections (page 6-20) View> Overlay Sections (page 6-20) View>Show Start Point (page 6-21) View> Show Landmark (page 6-22) View> Show Data (page 6-22) View> Redraw (page 6-23) View> Auto Redraw (page 6-24) View> Z Perspective (page 6-25) View> Y Perspective (page 6-25) View> X Perspective (page 6-26) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66) VIEW> SELECTION ONLY • • Checking Selection Only on the View menu removes all un-selected tracings or markers from the work space. RELATED TOPICS • • • • • • • • • • • • • • • • • • • • • View> Resize to Fit (page 6-16) View> Zoom (page 6-17) View> Pan (page 6-17) View> Center (page 6-18) View> Flash Selection (page 6-18) View> Show All Sections (page 6-20) View> Overlay Sections (page 6-20) View>Show Start Point (page 6-21) View> Show Landmark (page 6-22) View> Show Data (page 6-22) View> Redraw (page 6-23) View> Auto Redraw (page 6-24) View> Z Perspective (page 6-25) View> Y Perspective (page 6-25) View> X Perspective (page 6-26) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66) BIOQUANT Topographer Handbook: The Atlas Shop in Detail . re-displays un-selected objects in the current section. In Points Mode. In Object Mode. re-displays un-selected section maps. re-displays un-selected points in the current object. leaving only the currently selected items. Un-checking Selection Only on the View menu does the following: • • • In Section Mode.

In Points Mode. In Object Mode. removes all un-selected section maps except those in which objects are currently selected. removes all un-selected section maps from the work space. RELATED TOPICS • • • • • • • • • • • • • • • • • • • • • View> Resize to Fit (page 6-16) View> Zoom (page 6-17) View> Pan (page 6-17) View> Center (page 6-18) View> Flash Selection (page 6-18) View> Selection Only (page 6-19) View> Overlay Sections (page 6-20) View>Show Start Point (page 6-21) View> Show Landmark (page 6-22) View> Show Data (page 6-22) View> Redraw (page 6-23) View> Auto Redraw (page 6-24) View> Z Perspective (page 6-25) View> Y Perspective (page 6-25) View> X Perspective (page 6-26) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66) VIEW> OVERLAY SECTIONS Choosing Overlay Section from the View menu opens the Overlay Section dialog box. The Overlay Section dialog box must remain open during editing. 2. to retain the overlay of designated tracings. removes all un-selected section maps except the one in which points are currently selected. Overlay Section provides a way to display a limited number of non-selected sections for visual reference during editing.Page 6-20 VIEW> SHOW ALL SECTIONS • • Checking Show All Sections on the View menu displays all un-selected parts of the entire atlas. Choose Overlay Section from the View menu to open the Overlay Section dialog box. Un-checking Show All Sections on the View menu does the following: • • • In Section Mode. (those that precede the selected section in the Z plane) a. To overlay a given number of previous sections. This is particularly helpful when lining up sections with translate and rotate. regardless of which selection mode is currently active. The Overlay Sections Dialog Box PROCEDURE: 1. BIOQUANT Topographer Handbook: The Atlas Shop in Detail . Click to check the Overlay previous sections check box.

Click the Apply button 4. 3. To overlay one or more particular sections: a. Type or choose from the drop list the number of sections to overlay. click to highlight the additional sections to be overlaid. b. click to highlight the sections to be overlaid. Designate the number of previous and/or next sections that are to be overlaid. the limits imposed on the overlay are canceled and all non selected sections are redrawn on the atlas. Type or choose from the drop list the number of previous sections to overlay. BIOQUANT Topographer Handbook: The Atlas Shop in Detail .Page 6-21 b. c. Click to check the Overlay These Sections check box. Click to check the Overlay next sections check box. b. RELATED TOPICS • • • • • • • • • • • • • • • • • • • • • View> Resize to Fit (page 6-16) View> Zoom (page 6-17) View> Pan (page 6-17) View> Center (page 6-18) View> Flash Selection (page 6-18) View> Selection Only (page 6-19) View> Show All Sections (page 6-20) View>Show Start Point (page 6-21) View> Show Landmark (page 6-22) View> Show Data (page 6-22) View> Redraw (page 6-23) View> Auto Redraw (page 6-24) View> Z Perspective (page 6-25) View> Y Perspective (page 6-25) View> X Perspective (page 6-26) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66) VIEW>SHOW START POINT Show Start Point places a pink star at the location of the Start Point that was defined when tracing a contour. Click the Apply button. ADDITIONAL NOTES: • When the Overlay Section dialog box is closed. To overlay a given number of next sections (ones that follow the selected section in the Z plane): a. c. b. c. d. and check the Overlay These Sections check box. Click to check one or both of the Overlay previous and Overlay next check boxes. Click to uncheck the Overlay previous sections and Overlay next sections check boxes. c. In the list of sections. To overlay a given number of previous and/or next sections plus one or more particular sections: a. Click the Apply button. Click the Apply button 5. d. In the list of sections.

and the translation is saved to the Topo array. The Atlas Shop initially stacks section maps so that the individual landmarks for each section map are perfectly aligned. That initial point of alignment is the alignment landmark for the entire atlas. that section’s individual landmark is permanently changed to the XY position that matches the atlas’s alignment landmark. If a section map is translated (moved in the XY plane) during editing. RELATED TOPICS • • • • • • • • • • • • • • • • • • • • • View> Resize to Fit (page 6-16) View> Zoom (page 6-17) View> Pan (page 6-17) View> Center (page 6-18) View> Flash Selection (page 6-18) View> Selection Only (page 6-19) View> Show All Sections (page 6-20) View> Overlay Sections (page 6-20) View>Show Start Point (page 6-21) View> Show Data (page 6-22) View> Redraw (page 6-23) View> Auto Redraw (page 6-24) View> Z Perspective (page 6-25) View> Y Perspective (page 6-25) View> X Perspective (page 6-26) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66) VIEW> SHOW DATA Choosing Show Data from the View menu opens the View BIOQUANT Data window and displays the content of the BIOQUANT Topographer Handbook: The Atlas Shop in Detail .Page 6-22 RELATED TOPICS • • • • • • • • • • • • • • • • • • • • • View> Resize to Fit (page 6-16) View> Zoom (page 6-17) View> Pan (page 6-17) View> Center (page 6-18) View> Flash Selection (page 6-18) View> Selection Only (page 6-19) View> Show All Sections (page 6-20) View> Overlay Sections (page 6-20) View> Show Landmark (page 6-22) View> Show Data (page 6-22) View> Redraw (page 6-23) View> Auto Redraw (page 6-24) View> Z Perspective (page 6-25) View> Y Perspective (page 6-25) View> X Perspective (page 6-26) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66) VIEW> SHOW LANDMARK Displays the alignment landmark for the atlas as a green star.

) When the View BIOQUANT Data window first opens. The window’s scroll bar is used to scroll up and down the data point list. The View BIOQUANT Data window will open. Same as clicking the Redraw button on the system BIOQUANT Topographer Handbook: The Atlas Shop in Detail . beginning with Section 0. or points are highlighted in blue. The beginning of each section is preceded by the notation SECTION #. UNDERSTANDING THE TOPO DATA • Each line of data corresponds to a single data point in a measurement tracing. Y Position (3600). Z Position (500). or the default Z Offset value shown in the Change All Z Values To field on the Change Z dialog box. (Example: If the Z Position in the View BIOQUANT Data window is 500. Description of One Data Point • • To determine the Z Offset Value of a section or object of interest. click to choose Show Data. objects. the Z Offset Value is 50. • • • RELATED TOPICS • • • • • • • • • • • • • • • • • • • • • View> Resize to Fit (page 6-16) View> Zoom (page 6-17) View> Pan (page 6-17) View> Center (page 6-18) View> Flash Selection (page 6-18) View> Selection Only (page 6-19) View> Show All Sections (page 6-20) View> Overlay Sections (page 6-20) View>Show Start Point (page 6-21) View> Show Landmark (page 6-22) View> Redraw (page 6-23) View> Auto Redraw (page 6-24) View> Z Perspective (page 6-25) View> Y Perspective (page 6-25) View> X Perspective (page 6-26) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66) VIEW> REDRAW Refreshes the atlas tracings in the Atlas Shop’s work space. The beginning of each object is preceded by the notation Start of Object. divide the Z Position value of its data points by 10. The non existent distance between the two data points confirms to the computer that it should be drawn as a single point. will have two identical data points. Each entry beneath a Start of Object notation describes a single data point within that object. X Position (4067). To close the View BIOQUANT Data window. where the pound sign (#) identifies the section. Sections are always numbered sequentially. 2. the data points for the currently selected sections. IMPORTANT: The Z Position displayed in the View BIOQUANT Data window is always 10 times greater than the Z Offset value that was used during measurement. Color # (4). click the X button in the window’s upper right corner. Single point objects (such as those generated when an Object Count array is used). PROCEDURE: OPENING AND CLOSING THE VIEW BIOQUANT DATA WINDOW 1.Page 6-23 Topo arrays that make up the current atlas. From the View menu. Data points are identified by five parameters (as in the example below): Data Point # (20).

Page 6-24 tool bar. RELATED TOPICS • • • • • • • • • • • • • • • • • • • • • View> Resize to Fit (page 6-16) View> Zoom (page 6-17) View> Pan (page 6-17) View> Center (page 6-18) View> Flash Selection (page 6-18) View> Selection Only (page 6-19) View> Show All Sections (page 6-20) View> Overlay Sections (page 6-20) View>Show Start Point (page 6-21) View> Show Landmark (page 6-22) View> Show Data (page 6-22) View> Auto Redraw (page 6-24) View> Z Perspective (page 6-25) View> Y Perspective (page 6-25) View> X Perspective (page 6-26) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66) VIEW> AUTO REDRAW When Auto Redraw is checked on the View menu. Usually the automatic refresh happens so quickly that is it hardly noticed. the refresh is more apparent. With extremely large atlases. however. click to uncheck Auto Redraw on the View menu. • • To discontinue the auto refresh. the system automatically refreshes the atlas display any time a dialog box is moved in the Atlas Shop. click to check Auto Redraw on the View menu. To reactivate auto refresh. RELATED TOPICS • • • • • • • • • • • • • • • • • • • • • View> Resize to Fit (page 6-16) View> Zoom (page 6-17) View> Pan (page 6-17) View> Center (page 6-18) View> Flash Selection (page 6-18) View> Selection Only (page 6-19) View> Show All Sections (page 6-20) View> Overlay Sections (page 6-20) View>Show Start Point (page 6-21) View> Show Landmark (page 6-22) View> Show Data (page 6-22) View> Redraw (page 6-23) View> Z Perspective (page 6-25) View> Y Perspective (page 6-25) View> X Perspective (page 6-26) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66) BIOQUANT Topographer Handbook: The Atlas Shop in Detail .

RELATED TOPICS • • • • • • • • • • • • • • • • • • • • • View> Resize to Fit (page 6-16) View> Zoom (page 6-17) View> Pan (page 6-17) View> Center (page 6-18) View> Flash Selection (page 6-18) View> Selection Only (page 6-19) View> Show All Sections (page 6-20) View> Overlay Sections (page 6-20) View>Show Start Point (page 6-21) View> Show Landmark (page 6-22) View> Show Data (page 6-22) View> Redraw (page 6-23) View> Auto Redraw (page 6-24) View> Y Perspective (page 6-25) View> X Perspective (page 6-26) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66) VIEW> Y PERSPECTIVE Activates Y Perspective in the black Perspective panel.Page 6-25 VIEW> Z PERSPECTIVE Activates Z Perspective in the black Perspective panel. Same as clicking the Z Perspective button on the system tool bar. • See “Y Perspective” on 6-46. BIOQUANT Topographer Handbook: The Atlas Shop in Detail . • See “Z Perspective” on 6-46. Same as clicking the Y Perspective button on the system tool bar.

Same as clicking the X Perspective button on the system tool bar. RELATED TOPICS • • • • • • • • • • • • • • • • • • • • • View> Resize to Fit (page 6-16) View> Zoom (page 6-17) View> Pan (page 6-17) View> Center (page 6-18) View> Flash Selection (page 6-18) View> Selection Only (page 6-19) View> Show All Sections (page 6-20) View> Overlay Sections (page 6-20) View>Show Start Point (page 6-21) View> Show Landmark (page 6-22) View> Show Data (page 6-22) View> Redraw (page 6-23) View> Auto Redraw (page 6-24) View> Z Perspective (page 6-25) View> Y Perspective (page 6-25) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66) BIOQUANT Topographer Handbook: The Atlas Shop in Detail .Page 6-26 RELATED TOPICS • • • • • • • • • • • • • • • • • • • • • View> Resize to Fit (page 6-16) View> Zoom (page 6-17) View> Pan (page 6-17) View> Center (page 6-18) View> Flash Selection (page 6-18) View> Selection Only (page 6-19) View> Show All Sections (page 6-20) View> Overlay Sections (page 6-20) View>Show Start Point (page 6-21) View> Show Landmark (page 6-22) View> Show Data (page 6-22) View> Redraw (page 6-23) View> Auto Redraw (page 6-24) View> Z Perspective (page 6-25) View> X Perspective (page 6-26) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66) VIEW> X PERSPECTIVE Activates X Perspective in the black Perspective panel. • See “X Perspective” on 6-46.

Choosing Undo on the Edit menu is the same as clicking the Undo button on the Vertical Tool Bar. & Internal Paste (page 6-28) Edit> Translate (page 6-32) Edit> Rotate (page 6-33) Edit> Resize (page 6-33) Edit> Change Color (page 6-34) Edit> Change Z (page 6-35) Edit> Align Sections (page 6-35) Edit> Resolution (page 6-36) Edit> Z Sort (page 6-37) Edit > Open Polygon (page 6-39) Edit> Close Polygon (page 6-40) Edit> Numeric Transform (page 6-41) RELATED TOPICS • • • • • • The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66) EDIT> UNDO Undo on the Edit menu reverses the most recent editing change. PROCEDURES • • From the Edit menu. Internal Copy.Page 6-27 THE EDIT MENU This section covers the Edit menu items in the Atlas Shop. then tap Z). There is only one level of undo. tap Ctrl-Z (press and hold the control key. TOPIC CONTENTS Edit> Undo (page 6-27) Edit> Internal Cut. However. On the keyboard. choose Undo. BIOQUANT Topographer Handbook: The Atlas Shop in Detail . Restore Original on the File menu restores the atlas to the way it looked when it was last saved.

Internal Copy. it is sometimes quicker to cut out problem sections rather than edit them. In an atlas with many sections. TOPIC CONTENTS Eliminate a Problem Section (page 6-29) Create a new Topographic Section From an Object Within a Section (page 6-30) Duplicate A Section (page 6-31) RELATED TOPICS • • • • • • • • • • • • • • • • • • • File> Restore Original (page 6-5) Edit> Undo (page 6-27) Edit> Translate (page 6-32) Edit> Rotate (page 6-33) Edit> Resize (page 6-33) Edit> Change Color (page 6-34) Edit> Change Z (page 6-35) Edit> Align Sections (page 6-35) Edit> Resolution (page 6-36) Edit> Z Sort (page 6-37) Edit > Open Polygon (page 6-39) Edit> Close Polygon (page 6-40) Edit> Numeric Transform (page 6-41) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66) BIOQUANT Topographer Handbook: The Atlas Shop in Detail . INTERNAL COPY. to create a new topographic section. & Internal Paste (page 6-28) Edit> Translate (page 6-32) Edit> Rotate (page 6-33) Edit> Resize (page 6-33) Edit> Change Color (page 6-34) Edit> Change Z (page 6-35) Edit> Align Sections (page 6-35) Edit> Resolution (page 6-36) Edit> Z Sort (page 6-37) Edit > Open Polygon (page 6-39) Edit> Close Polygon (page 6-40) Edit> Numeric Transform (page 6-41) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66) EDIT> INTERNAL CUT. After Internal cut is used the edited version of the atlas must be saved to a new Topo array. & INTERNAL PASTE Internal Cut may be used to eliminate problem sections.Page 6-28 RELATED TOPICS • • • • • • • • • • • • • • • • • • • File> Restore Original (page 6-5) Edit> Internal Cut. and paste it. Internal Cut and Internal Copy may be used with Internal Paste to cut or copy an object from a topographic section.

Choose Exit Atlas Shop from the File menu. c. 4. do the following: a.) Click the Select Next button on the system tool bar to select one of the uncut sections. On the Warning message box click OK to acknowledge the warning and cut the selected section. & Internal Paste (page 6-28) Edit> Translate (page 6-32) Edit> Rotate (page 6-33) Edit> Resize (page 6-33) Edit> Change Color (page 6-34) Edit> Change Z (page 6-35) Edit> Align Sections (page 6-35) Edit> Resolution (page 6-36) Edit> Z Sort (page 6-37) Edit > Open Polygon (page 6-39) Edit> Close Polygon (page 6-40) Edit> Numeric Transform (page 6-41) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66) BIOQUANT Topographer Handbook: The Atlas Shop in Detail . To display or make additional edits in the changed version of the atlas. 5. 6. 7. click Redraw on the system tool bar. On the Select Arrays dialog box. (The data in the original atlas Topo array will remain unchanged. (Or.” on 6-63. In the Array Name field. click Cancel to cancel the Internal Cut command. click YES to indicate that the changed atlas is to be saved. b. Internal Copy. RELATED TOPICS • • • • • • • • • • • • • • • • • • • • • • Create a new Topographic Section From an Object Within a Section (page 6-30) Duplicate A Section (page 6-31) File> Restore Original (page 6-5) Edit> Undo (page 6-27) Edit> Internal Cut. click the Atlas Shop button to reopen the Atlas Shop. The Save Array As dialog box will open. To continue editing. To display the revised version of the atlas. type a name that indicates that this is a revised version of the atlas. 3. At this point you will probably want to use Change Z to evenly distribute the remaining sections along the Z axis. See “Evenly Distribute Topographic Sections Along the Z Axis. A Save Data message will appear. On the Save Data message.Page 6-29 ELIMINATE A PROBLEM SECTION PROCEDURE 1. Click the New Array button to add a new Topo array to the data set. Click the Save button to record the cut version of the atlas in the new array.) Click the Close button to close the Atlas Shop and reopen the Atlas Viewer. A Warning box will open to remind you that the altered atlas must be saved to a new array. d. On the Save Array As dialog box do the following: a. 2. b. deselect the original atlas array(s) and select the Topo array that holds the revised version of the atlas. 8. or to adjust the Z Offsets of adjacent sections to prevent a gap in the reconstructed atlas. In Section mode select the problem section. in the Atlas Viewer. Choose Internal Cut from the Edit menu.

on the Select Arrays dialog box. A Warning box will open to inform you that the Z sorted atlas must be saved to a new array. The tracing will still appear in its proper place within the reconstructed atlas. click Redraw on the system tool bar. if its Z Offset is correct. (The chosen Topo array cannot be one of the current atlas arrays. For display purposes. (Clicking Cancel will cancel the Internal Cut command. click NO (since the changed version of the atlas has already been saved). Internal Cut and Internal Paste may be used to cut objects comprising a physical section and paste them as a new topographic section.) In the Z Sort Options area. ADDITIONAL NOTE • Keyboard shortcut: Control-X is the same as choosing Cut Selection from the Edit menu. A Save Data message will appear. In Section mode select the topographic section that contains the object(s) of interest. b. do the following: a. c. c. In the Atlas Viewer. then add a New Array. 4. If the chosen array is not new.) Click Close. To display the revised version of the atlas.) Choose Internal Paste from the Edit menu. button and select the Object(s) that need(s) to be changed into a new Click the Object mode topographic section. and asks if you want to add a new array. Click the Apply button to record the edited version of the atlas to the array in the Destination Array field. On the Sort Sections By Z Value dialog box. d. (Or. the fact that the tracing is a topographic object instead of a topographic section may be of little consequence. click the OK button on the Warning box that says existing data will be overwritten. 8. choose Exit Atlas Shop. PROCEDURE 1. 7. If another object or set of objects also needs to be cut and pasted as a new section. BIOQUANT Topographer Handbook: The Atlas Shop in Detail . click to choose the Ascending or Descending radio button. it may be important to select and manipulate the tracing as a separate topographic section. d.Page 6-30 CREATE A NEW TOPOGRAPHIC SECTION FROM AN OBJECT WITHIN A SECTION Tracings for more then one physical tissue section may show up in a single topographic section when neither Set Landmark nor New Section were chosen prior to the measurement of a new tissue section. For editing purposes. click Cancel. repeat steps 1 through 4. From the File menu. choose Z Sort. Click the New Array button to add a new Topo array. or to continue editing. you must do the following: a.) Click OK to acknowledge the notice. From the Edit menu. 3. Choose Internal Cut from the Edit menu. 2. deselect the original atlas array(s) and select the Topo array that holds the revised version of the atlas. 6. The Atlas Shop closes and the Atlas Viewer reopens. A Warning box will open to remind you that the altered atlas must be saved to a new array. In this case. click the Atlas Shop button to reopen the Atlas Shop. Click the YES button to open the Sort Sections By Z Value dialog box. (In this case the last array will be the new Topo array that is going to be added in step 6. On the Save Data message. A message box appears to let you know that Elements will be pasted as a new section in the last array. b. 5. Click OK to acknowledge the warning and cut the selected object(s) from the displayed atlas. Consequently the tracing of the new physical section became an object within a topographic section. or click the down arrow in the Destination Array field and choose an existing Topo array from the drop list. In order to display or continue editing the changed version of the atlas.

select a different section to duplicate and repeat steps 2 and 3. In Section mode select a section that approximates the size and shape of the missing section. 6. click the OK button on the Warning box that says existing data will be overwritten. (Clicking Cancel will cancel the Internal Copy command. 2. Click the Apply button to record the edited version of the atlas to the array in the Destination Array field. Click the New Array button to add a new Topo array. c. click to choose the Ascending or Descending radio button. then add a New Array. A Notice box appears to let you know that Elements will be pasted as a new section in the last array. 5. On the Sort Sections By Z Value dialog box.) BIOQUANT Topographer Handbook: The Atlas Shop in Detail 3. 4. (Or. do the following: a. (The chosen Topo array cannot be one of the current atlas arrays. and asks if you want to add a new array. PROCEDURE 1.Page 6-31 RELATED TOPICS • • • • • • • • • • • • • • • • • • • • • • Eliminate a Problem Section (page 6-29) Duplicate A Section (page 6-31) File> Restore Original (page 6-5) Edit> Undo (page 6-27) Edit> Internal Cut. If more than one duplicate of the selected tracing is needed. . & Internal Paste (page 6-28) Edit> Translate (page 6-32) Edit> Rotate (page 6-33) Edit> Resize (page 6-33) Edit> Change Color (page 6-34) Edit> Change Z (page 6-35) Edit> Align Sections (page 6-35) Edit> Resolution (page 6-36) Edit> Z Sort (page 6-37) Edit > Open Polygon (page 6-39) Edit> Close Polygon (page 6-40) Edit> Numeric Transform (page 6-41) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66) DUPLICATE A SECTION Occasionally one or more tissue sections in a series is lost or damaged during tissue processing and the absence of those sections is obvious in the reconstructed atlas. A Warning box will open to remind you that the altered atlas must be saved to a new array. choose Internal Paste. From the Edit menu. choose Internal Copy. choose Internal Paste again for each additional tracing that is needed. Missing sections may be filled with duplicates made from near by sections. If the chosen array is not new. Internal Copy. click Cancel. Click the YES button to open the Sort Sections By Z Value dialog box. b. (In this case the last array will be the new array that will be added in step 6. choose Z Sort.) Click OK to acknowledge the notice. Click OK to acknowledge the Warning and copy the selected section. or click the down arrow in the Destination Array field and choose an existing Topo array from the drop list.) In the Z Sort Options area. (Alternately.) From the Edit menu.) From the Edit menu. A Warning box will open to inform you that the Z sorted atlas must be saved to a new array.

ADDITIONAL NOTE • • Keyboard shortcut: Control-C is the same as choosing Internal Cut from the Edit menu. Keyboard shortcut: Control-V is the same as choosing Internal Paste from the Edit menu. Click Close. choose Exit Atlas Shop. click Redraw on the system tool bar. g. f. deselect the original atlas array and select the Topo array that holds the revised version of the atlas. From the File menu. click the Atlas Shop button. In order to display or continue editing the changed version of the atlas. on the Select Arrays dialog box. BIOQUANT Topographer Handbook: The Atlas Shop in Detail . See “Translate Selected Parts of the Atlas” on 6-54. A Save Data message will appear.Page 6-32 d. & Internal Paste (page 6-28) Edit> Translate (page 6-32) Edit> Rotate (page 6-33) Edit> Resize (page 6-33) Edit> Change Color (page 6-34) Edit> Change Z (page 6-35) Edit> Align Sections (page 6-35) Edit> Resolution (page 6-36) Edit> Z Sort (page 6-37) Edit > Open Polygon (page 6-39) Edit> Close Polygon (page 6-40) Edit> Numeric Transform (page 6-41) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66) EDIT> TRANSLATE Activates the Translate • tool on the Vertical Tool Bar. you must do the following: e. RELATED TOPICS • • • • • • • • • • • • • • • • • • • • • • Eliminate a Problem Section (page 6-29) Create a new Topographic Section From an Object Within a Section (page 6-30) File> Restore Original (page 6-5) Edit> Undo (page 6-27) Edit> Internal Cut. The Atlas Shop closes and the Atlas Viewer reopens. To display the revised version of the atlas. 7. or to continue editing. Same as clicking the Translate tool. On the Save Data message. In the Atlas Viewer. Internal Copy. click NO (since the changed version of the atlas has already been saved).

Same as clicking the Rotate tool. RELATED TOPICS • • • • • • • • • • • • • • • • • • • • • • Eliminate a Problem Section (page 6-29) Create a new Topographic Section From an Object Within a Section (page 6-30) Duplicate A Section (page 6-31) File> Restore Original (page 6-5) Edit> Undo (page 6-27) Edit> Internal Cut. See “Rotate Selected Parts of the Atlas” on 6-53. & Internal Paste (page 6-28) Edit> Rotate (page 6-33) Edit> Resize (page 6-33) Edit> Change Color (page 6-34) Edit> Change Z (page 6-35) Edit> Align Sections (page 6-35) Edit> Resolution (page 6-36) Edit> Z Sort (page 6-37) Edit > Open Polygon (page 6-39) Edit> Close Polygon (page 6-40) Edit> Numeric Transform (page 6-41) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66) EDIT> ROTATE Activates the Rotate • tool on the Vertical Tool Bar. Internal Copy.Page 6-33 RELATED TOPICS • • • • • • • • • • • • • • • • • • • • • • Eliminate a Problem Section (page 6-29) Create a new Topographic Section From an Object Within a Section (page 6-30) Duplicate A Section (page 6-31) File> Restore Original (page 6-5) Edit> Undo (page 6-27) Edit> Internal Cut. Same as clicking the Resize tool. Internal Copy. & Internal Paste (page 6-28) Edit> Translate (page 6-32) Edit> Resize (page 6-33) Edit> Change Color (page 6-34) Edit> Change Z (page 6-35) Edit> Align Sections (page 6-35) Edit> Resolution (page 6-36) Edit> Z Sort (page 6-37) Edit > Open Polygon (page 6-39) Edit> Close Polygon (page 6-40) Edit> Numeric Transform (page 6-41) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66) EDIT> RESIZE Activates the Resize tool on the Vertical Tool Bar. BIOQUANT Topographer Handbook: The Atlas Shop in Detail .

& Internal Paste (page 6-28) Edit> Translate (page 6-32) Edit> Rotate (page 6-33) Edit> Resize (page 6-33) Edit> Change Z (page 6-35) Edit> Align Sections (page 6-35) Edit> Resolution (page 6-36) Edit> Z Sort (page 6-37) Edit > Open Polygon (page 6-39) Edit> Close Polygon (page 6-40) Edit> Numeric Transform (page 6-41) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66) BIOQUANT Topographer Handbook: The Atlas Shop in Detail .Page 6-34 • See “Resize the Selected Parts of the Atlas” on 6-55. RELATED TOPICS • • • • • • • • • • • • • • • • • • • • • • Eliminate a Problem Section (page 6-29) Create a new Topographic Section From an Object Within a Section (page 6-30) Duplicate A Section (page 6-31) File> Restore Original (page 6-5) Edit> Undo (page 6-27) Edit> Internal Cut. See “Change Color of the Selected Parts of the Atlas” on 6-57. Internal Copy. Internal Copy. Same as clicking the Change Color tool. & Internal Paste (page 6-28) Edit> Translate (page 6-32) Edit> Rotate (page 6-33) Edit> Change Color (page 6-34) Edit> Change Z (page 6-35) Edit> Align Sections (page 6-35) Edit> Resolution (page 6-36) Edit> Z Sort (page 6-37) Edit > Open Polygon (page 6-39) Edit> Close Polygon (page 6-40) Edit> Numeric Transform (page 6-41) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66) EDIT> CHANGE COLOR Activates the Change Color • button on the Vertical Tool Bar. RELATED TOPICS • • • • • • • • • • • • • • • • • • • • • • Eliminate a Problem Section (page 6-29) Create a new Topographic Section From an Object Within a Section (page 6-30) Duplicate A Section (page 6-31) File> Restore Original (page 6-5) Edit> Undo (page 6-27) Edit> Internal Cut.

MANUAL ALIGNMENT TOOLS Rotate Selected Parts of the Atlas (page 6-53) Translate Selected Parts of the Atlas (page 6-54) Resize the Selected Parts of the Atlas (page 6-55) Edit> Numeric Transform (page 6-41) BIOQUANT Topographer Handbook: The Atlas Shop in Detail . 2. or Point) that is currently active. Serial sections that do not have these dual alignment points can be manually rotated when needed. Choose Align Sections from the Edit menu. & Internal Paste (page 6-28) Edit> Translate (page 6-32) Edit> Rotate (page 6-33) Edit> Resize (page 6-33) Edit> Change Z (page 6-35) Edit> Align Sections (page 6-35) Edit> Resolution (page 6-36) Edit> Z Sort (page 6-37) Edit > Open Polygon (page 6-39) Edit> Close Polygon (page 6-40) Edit> Numeric Transform (page 6-41) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66) EDIT> ALIGN SECTIONS Serial sections that were measured with consistent landmarks and tracing start points may be automatically rotated to correct for differences in orientation of sections on slides. tool on the Vertical Tool Bar. TO AUTOMATICALLY ALIGN SERIAL SECTIONS THAT HAVE DUAL ALIGNMENT POINTS: 1. refine the alignment of particular sections using the manual alignment tools listed below. Internal Copy.Page 6-35 EDIT> CHANGE Z Opens the Change Z dialog box. Align Sections on the Edit menu operates on all sections in the atlas. without regard for the selection mode (Section. If needed. RELATED TOPICS • • • • • • • • • • • • • • • • • • • • • • Eliminate a Problem Section (page 6-29) Create a new Topographic Section From an Object Within a Section (page 6-30) Duplicate A Section (page 6-31) File> Restore Original (page 6-5) Edit> Undo (page 6-27) Edit> Internal Cut. Same as clicking the Change Z • See “Change Z” on 6-63. Object.

Page 6-36 RELATED TOPICS
• • • • • • • • • • • • • • • • • • • • • • Eliminate a Problem Section (page 6-29) Create a new Topographic Section From an Object Within a Section (page 6-30) Duplicate A Section (page 6-31) File> Restore Original (page 6-5) Edit> Undo (page 6-27) Edit> Internal Cut, Internal Copy, & Internal Paste (page 6-28) Edit> Translate (page 6-32) Edit> Rotate (page 6-33) Edit> Resize (page 6-33) Edit> Change Color (page 6-34) Edit> Change Z (page 6-35) Edit> Resolution (page 6-36) Edit> Z Sort (page 6-37) Edit > Open Polygon (page 6-39) Edit> Close Polygon (page 6-40) Edit> Numeric Transform (page 6-41) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66)

EDIT> RESOLUTION
When the atlas is displayed in the Atlas Modeler, if it takes a long time to render the surface or redraw the model after it has been moved in the Model Window, the resolution of the surface tracings should be reduced. CAUTION: Do not attempt to change the resolution of an entire atlas. To do so may corrupt the data, especially in larger atlases. When resolution is changed, the edited version of the atlas must be saved to a new Topo array. The original resolution was set by the smoothing limit in BIOQUANT Life Science or BIOQUANT OSTEO (the lower the Smoothing Limit the higher the resolution).

PROCEDURE:
1. Select a limited number of objects) (e.g. all section outlines) for which the resolution needs to be changed. Hint: If all section outlines (or other objects of interest) are of the same unique color, these may be selected quickly using Select by Color. See “Select By Color” on 6-52. Choose Resolution from the Edit menu to open the Set Image Resolution dialog box. When asked if you want to add a new Topo array, click Yes, unless you think the data set already contains an empty Topo array that can be used. Set Image Resolution

2.

3.

On the Set Image Resolution dialog box, if a new Topo array was added in step 2, it will already be selected in the Destination Array field. Otherwise, click the down arrow in the Destination Array field and click to choose the desired empty Topo array from the drop list. If there is not an empty Topo array, do the following: a. b. Click the Add Topo button. The New Array dialog box opens. In the Array Name field, edit the name of the Topo array to indicate that this is a lower resolution version of the atlas.

BIOQUANT Topographer Handbook: The Atlas Shop in Detail

Page 6-37
c. 4. 5. Click the OK button to close the New Array dialog box.

In the Resolution Distance field, increase the micron value between data points (to decrease the resolution), by doubling or tripling the initial default value in the Resolution Distance field. Click the Apply button to generate the lower resolution atlas in the selected Topo array. A warning will appear to remind you that any data in the selected array will be overwritten. Verify that the intended Destination Array is selected, then click OK. IMPORTANT: If a single Smoothing Limit was not maintained during data collection for the selected outlines, read the following carefully, then, if it seems necessary, repeat steps 4 and 5. a. b. The initial default value in the Resolution Distance field is the minimum distance the system found between any two data points in the selected portion of the atlas. The change in resolution, (the new micron distance) is only applied between pairs of data points in the selected outlines, for which the original distance matched the minimum (initial) value in the Resolution Distance field. If a single smoothing limit was maintained during measurement, the distance between all data points will match the minimum value, and all will be increased simultaneously to the new value. (Excess data points are discarded to maintain the original size of the tracings). In this case, simply doubling or tripling the default Resolution Distance and clicking the Apply button once, is usually enough to produce the desired effect. However, if the smoothing limit was changed during data collection, the number of data set pairs that are separated by the minimum distance may be small. In this case, it may be necessary to repeat steps 4 and 5 several times before the desired effect would be apparent in a surface rendered model.

c.

d.

6. 7.

Click the Close button to close the Set Image Resolution dialog box. To display or edit the new resolution atlas, exit the Atlas Shop. In the Atlas Viewer, on the Select Arrays dialog box, remove the original Topo arrays from the Selected list, and select the Topo array that contains the lower resolution version of the atlas. The lower resolution atlas is now ready to be displayed in the Atlas Viewer, Atlas Modeler, or Atlas Shop.

RELATED TOPICS
• • • • • • • • • • • • • • • • • • • • • • Eliminate a Problem Section (page 6-29) Create a new Topographic Section From an Object Within a Section (page 6-30) Duplicate A Section (page 6-31) File> Restore Original (page 6-5) Edit> Undo (page 6-27) Edit> Internal Cut, Internal Copy, & Internal Paste (page 6-28) Edit> Translate (page 6-32) Edit> Rotate (page 6-33) Edit> Resize (page 6-33) Edit> Change Color (page 6-34) Edit> Change Z (page 6-35) Edit> Align Sections (page 6-35) Edit> Z Sort (page 6-37) Edit > Open Polygon (page 6-39) Edit> Close Polygon (page 6-40) Edit> Numeric Transform (page 6-41) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66)

EDIT> Z SORT
Topographer draws topographic units (sections or objects) in the atlas window and the black Axis Perspective panel in the order their data appear in the atlas topo array. So an item with a Z Offset Value of 100 that has been appended BIOQUANT Topographer Handbook: The Atlas Shop in Detail

Page 6-38
(pasted) to the end of the Topo array, will draw below an item that has a Z Offset Value of zero (0). This can lead to some strange looking atlas displays and may cause confusion during editing procedures. Z Sort generates an atlas in which all the topographic units are sorted by Z position, in either ascending or descending order. The Z sorted atlas must be saved to a new Topo array.

PROCEDURE:
1. From the Edit menu, choose Z Sort. A message box will open to inform you that the Z sorted atlas must be saved to a new array, and asks if you want to add a new array. Do one of the following: • • Click the YES button if you want the system to automatically add a Topo array named Z Sorted Topo. This default name cannot be edited. Click the NO button if you prefer to give the new Topo array a different name, or if the data set already contains a suitable Topo array (one that is empty or one that you wish to overwrite).

Sort Sections by Z Value dialog box

2.

If you choose NO in step 1, do one of the following: • • Click the New Array button to add a new Topo array, rename the new array on the New Array dialog box, and click the OK button to close the New Array box. Click the down arrow in the Destination Array field and choose an existing Topo array from the drop list. (The chosen Topo array cannot be one of the current atlas arrays.)

3. 4.

In the Z Sort Options area, click to choose the Ascending or Descending radio button. Click the Apply button to record the edited version of the atlas to the array in the Destination Array field. If the chosen array is not new, click the OK button on the Warning box that says existing data will be overwritten. (Or, click Cancel, then add a New Array.) Click Close. In order to display or continue editing the changed version of the atlas, you must do the following: a. b. c. From the File menu, choose Exit Atlas Shop. A Save Data message will appear. On the Save Data message, click NO (since the changed version of the atlas has already been saved). The Atlas Shop closes and the Atlas Viewer reopens. In the Atlas Viewer, on the Select Arrays dialog box, deselect the original atlas array and select the Topo array that holds the Z Sorted version of the atlas. To display the revised version of the atlas, click Redraw on the system tool bar, or to continue editing, click the Atlas Shop button.

5. 6.

BIOQUANT Topographer Handbook: The Atlas Shop in Detail

Page 6-39 RELATED TOPICS
• • • • • • • • • • • • • • • • • • • • • • Eliminate a Problem Section (page 6-29) Create a new Topographic Section From an Object Within a Section (page 6-30) Duplicate A Section (page 6-31) File> Restore Original (page 6-5) Edit> Undo (page 6-27) Edit> Internal Cut, Internal Copy, & Internal Paste (page 6-28) Edit> Translate (page 6-32) Edit> Rotate (page 6-33) Edit> Resize (page 6-33) Edit> Change Color (page 6-34) Edit> Change Z (page 6-35) Edit> Align Sections (page 6-35) Edit> Resolution (page 6-36) Edit > Open Polygon (page 6-39) Edit> Close Polygon (page 6-40) Edit> Numeric Transform (page 6-41) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66)

EDIT > OPEN POLYGON
Choosing Open Polygon from the Edit menu inserts a small disconnecting gap in the selected polygonal tracing (closed object). Open Polygon is used to create an open object that will not fill with color when the Fill option is used in the Atlas Viewer program. Open Polygon is only available in Object Mode.

PROCEDURE
1. 2. 3. In Section Mode select the section that contains the object of interest. button on the system tool bar, then select the polygonal tracing that is to be

Click the Object Mode opened.

Choose Open Polygon from the Edit menu.

BIOQUANT Topographer Handbook: The Atlas Shop in Detail

Page 6-40 RELATED TOPICS
• • • • • • • • • • • • • • • • • • • • • • Eliminate a Problem Section (page 6-29) Create a new Topographic Section From an Object Within a Section (page 6-30) Duplicate A Section (page 6-31) File> Restore Original (page 6-5) Edit> Undo (page 6-27) Edit> Internal Cut, Internal Copy, & Internal Paste (page 6-28) Edit> Translate (page 6-32) Edit> Rotate (page 6-33) Edit> Resize (page 6-33) Edit> Change Color (page 6-34) Edit> Change Z (page 6-35) Edit> Align Sections (page 6-35) Edit> Resolution (page 6-36) Edit> Z Sort (page 6-37) Edit> Close Polygon (page 6-40) Edit> Numeric Transform (page 6-41) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66)

EDIT> CLOSE POLYGON
Choosing Close Polygon from the Edit menu connects the loose ends of the selected tracing (open object) to change it into a closed polygon. Close Polygon is used to create a closed object that will fill with color when the Fill option is used in the Atlas Viewer program. Close Polygon is only available in Object Mode.

PROCEDURE
1. 2. 3. In Section Mode select the section that contains the object of interest. button on the system tool bar, then select the open object that is to be closed.

Click the Object Mode

Choose Close Polygon from the Edit menu.

BIOQUANT Topographer Handbook: The Atlas Shop in Detail

Page 6-41 RELATED TOPICS
• • • • • • • • • • • • • • • • • • • • • • Eliminate a Problem Section (page 6-29) Create a new Topographic Section From an Object Within a Section (page 6-30) Duplicate A Section (page 6-31) File> Restore Original (page 6-5) Edit> Undo (page 6-27) Edit> Internal Cut, Internal Copy, & Internal Paste (page 6-28) Edit> Translate (page 6-32) Edit> Rotate (page 6-33) Edit> Resize (page 6-33) Edit> Change Color (page 6-34) Edit> Change Z (page 6-35) Edit> Align Sections (page 6-35) Edit> Resolution (page 6-36) Edit> Z Sort (page 6-37) Edit > Open Polygon (page 6-39) Edit> Numeric Transform (page 6-41) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66)

EDIT> NUMERIC TRANSFORM
Numeric Transform translates, rotates, or resizes the selected parts of the atlas by a known amount.

PROCEDURE: SETUP
1. Select the section(s) or objects) or point(s) of interest. 2. From the Atlas Shop Edit menu, choose Numeric Transform to open the Numeric Transform dialog box. Numeric Transform Dialog Box

CHOOSE FROM THE FOLLOWING
Translate by Numeric Transform (page 6-42) Resize by Numeric Transform (page 6-43) Rotate by Numeric Transform (page 6-44)

BIOQUANT Topographer Handbook: The Atlas Shop in Detail

Left: In the X field.) • If Relative is checked. click to check the Translate check box. Up: In the Y field.Page 6-42 RELATED TOPICS • • • • • • • • • • • • • • • • • • • • • • • Eliminate a Problem Section (page 6-29) Create a new Topographic Section From an Object Within a Section (page 6-30) Duplicate A Section (page 6-31) File> Restore Original (page 6-5) Edit> Undo (page 6-27) Edit> Internal Cut. enter a negative micron distance (the selection will be moved this distance upwards. In the Y field. Decide whether or not the Relative check box should be checked.0 Offset) position of the current coordinate system. Internal Copy. However. Down: In the Y field. the values that are typed into the X and Y fields designate the micron distance that the selection is to be moved relative to its current position in the atlas. (All other points in the selection will be moved to maintain their positional relationship to the first point. 2. it should be noted that the XY plane of the coordinate system used by the Windows operating system is unconventional. enter a positive micron distance (the selection will be moved this distance to the right). enter a negative micron distance (the selection will be moved this distance to the left). the atlas landmark always occupies the XYZ(0. • If Relative is not checked.0. type the positive or negative Y coordinate to which the first point in the first object should be moved. the values that are typed into the X and Y fields designate actual X and Y coordinates to which the first point in the selection is to be moved. to move the first point of the first object in the selection to a specific XY location… a. The X and Y signs (x. b. If Relative is not checked. type the positive or negative X coordinate to which the first point in the first object should be moved.: • • If Relative is checked.y) in the various quadrants are given below: BIOQUANT Topographer Handbook: The Atlas Shop in Detail . In the X field. & Internal Paste (page 6-28) Edit> Translate (page 6-32) Edit> Rotate (page 6-33) Edit> Resize (page 6-33) Edit> Change Color (page 6-34) Edit> Change Z (page 6-35) Edit> Align Sections (page 6-35) Edit> Resolution (page 6-36) Edit> Z Sort (page 6-37) Edit > Open Polygon (page 6-39) Edit> Close Polygon (page 6-40) Edit> Numeric Transform (page 6-41) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66) TRANSLATE BY NUMERIC TRANSFORM PROCEDURE 1. On the Numeric Transform dialog box. Helpful Hint: As expected. to move the selected item(s) … • • • • Right: In the X field. enter a positive micron distance (the selection will be moved this distance downwards).

if the atlas is saved using Save on the File menu. Internal Copy. in the Width or/and Height field(s) enter a percentage value that is less than 100. +) Upper Left Quadrant (. If it is unchecked..Page 6-43 • • • • 3. NOTE: If subsequent resizing is done. SAVING THE EDIT After Numeric Transform is used. To increase the size of the selected item(s). or by responding YES to the Save Data message when exiting the Atlas Shop. RELATED TOPICS • • • • • • • • • • • • • • • • • • • • • • Resize by Numeric Transform (page 6-43) Rotate by Numeric Transform (page 6-44) File> Restore Original (page 6-5) Edit> Undo (page 6-27) Edit> Internal Cut. 2. On the Numeric Transform dialog box. -) Click the Apply button. The selected item(s) are shown at the new size in the Atlas Window. The current size of the selection is designated 100%. If desirable. when a value is entered in either the Height or Width field. click to check the Resize check box. click to uncheck the Maintain Aspect Ratio check box. If the Maintain Aspect Ratio check box is checked. to save the edited version of the atlas to a new Topo array. +) Upper Right Quadrant (+ . Height and Width resizing are independent of each other. • • 3. the data in the original atlas Topo array(s) are permanently changed. Save As on the File menu may be used instead. BIOQUANT Topographer Handbook: The Atlas Shop in Detail .. Lower Right Quadrant (+ . If desirable. -) Lower Left Quadrant (. the other field automatically updates to the same value. To decrease the size of the selected item(s). & Internal Paste (page 6-28) Edit> Translate (page 6-32) Edit> Rotate (page 6-33) Edit> Resize (page 6-33) Edit> Change Color (page 6-34) Edit> Change Z (page 6-35) Edit> Align Sections (page 6-35) Edit> Resolution (page 6-36) Edit> Z Sort (page 6-37) Edit > Open Polygon (page 6-39) Edit> Close Polygon (page 6-40) Edit> Numeric Transform (page 6-41) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66) RESIZE BY NUMERIC TRANSFORM PROCEDURE 1. Click the Apply button. in the Width or/and Height field(s) type a percentage value that is greater than 100. the new size just applied is now the current size and is considered the 100% value for the selected item(s).

if the atlas is saved using Save on the File menu. Internal Copy. Save As on the File menu may be used instead. Save As on the File menu may be used instead. the data in the original atlas Topo array(s) are permanently changed. to save the edited version of the atlas to a new Topo array. Click the Apply button. in the Angle field type the number of degrees the selected item(s) should be rotated. SAVING THE EDIT After Numeric Transform is used. or by responding YES to the Save Data message when exiting the Atlas Shop. or by responding YES to the Save Data message when exiting the Atlas Shop. click to check the Rotate check box. To rotate counter-clockwise. if the atlas is saved using Save on the File menu. To rotate clockwise. BIOQUANT Topographer Handbook: The Atlas Shop in Detail . & Internal Paste (page 6-28) Edit> Translate (page 6-32) Edit> Rotate (page 6-33) Edit> Resize (page 6-33) Edit> Change Color (page 6-34) Edit> Change Z (page 6-35) Edit> Align Sections (page 6-35) Edit> Resolution (page 6-36) Edit> Z Sort (page 6-37) Edit > Open Polygon (page 6-39) Edit> Close Polygon (page 6-40) Edit> Numeric Transform (page 6-41) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66) ROTATE BY NUMERIC TRANSFORM PROCEDURE 1. RELATED TOPICS • • • • • • • • • • • • • • • • • • • • • • Translate by Numeric Transform (page 6-42) Rotate by Numeric Transform (page 6-44) File> Restore Original (page 6-5) Edit> Undo (page 6-27) Edit> Internal Cut. On the Numeric Transform dialog box. to save the edited version of the atlas to a new Topo array. in the Angle field type the negative number of degrees the selected item(s) should be rotated. • • 2. If desirable. If desirable. the data in the original atlas Topo array(s) are permanently changed.Page 6-44 SAVING THE EDIT After Numeric Transform is used.

Page 6-45 RELATED TOPICS
• • • • • • • • • • • • • • • • • • • • • • Translate by Numeric Transform (page 6-42) Resize by Numeric Transform (page 6-43) File> Restore Original (page 6-5) Edit> Undo (page 6-27) Edit> Internal Cut, Internal Copy, & Internal Paste (page 6-28) Edit> Translate (page 6-32) Edit> Rotate (page 6-33) Edit> Resize (page 6-33) Edit> Change Color (page 6-34) Edit> Change Z (page 6-35) Edit> Align Sections (page 6-35) Edit> Resolution (page 6-36) Edit> Z Sort (page 6-37) Edit > Open Polygon (page 6-39) Edit> Close Polygon (page 6-40) Edit> Numeric Transform (page 6-41) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66)

TOOLS ON THE SYSTEM TOOL BAR
SECTION MODE
Activates Section mode. Same as choosing Section Mode from the Select menu.

OBJECT MODE
Activates Object mode. Same as choosing Object Mode from the Select menu.

POINT MODE
Activates Point mode. Same as choosing Point Mode from the Select menu.

SELECT PREVIOUS
• • • In Section mode, selects the previous section map in the series. In Object mode, selects the previous object (tracing or marker) in the current section. In Point mode, selects the previous data point in the current object.

SELECT NEXT
• • • In Section mode, selects the next section map in the series. In Object mode, selects the next object (tracing or marker) in the current section. In Point mode, selects the next data point in the current object.

CENTER
Centers the atlas in the Atlas Shop work space. Same as choosing Center from the View menu.

FLASH SELECTION
Causes the currently selected section, object, or data point to flash. Same as choosing Flash Selection from the View menu.

VIEW > REDRAW
Refreshes the atlas drawing in the Atlas Shop’s work space. Same as choosing Redraw from the View menu. BIOQUANT Topographer Handbook: The Atlas Shop in Detail

Page 6-46 VIEW > RESIZE TO FIT
Resizes and centers the atlas to fit the Atlas Shop’s work space. Same as choosing Resize To Fit from the View Menu.

CAP OBJECT
Formats the selected end tracings of an atlas to fill with color when the atlas is surface rendered in the Atlas Modeler. • See “Cap Object” on 6-68.

END OF OBJECT/LEAVE OPEN
Formats three or more selected tracings in the atlas to be excluded from surface rendering when the atlas is moved into the Atlas Modeler, thus creating an open window through which interior structures in the model may be visible. • See “End of Object/Leave Open” on 6-68.

MIDDLE OF OBJECT
Removes special formatting (Cap Object or End of Object/Leave Open) from the selected tracing(s). • See “Middle of Object” on 6-69.

Z PERSPECTIVE
Causes the vertical line in the black Perspective panel to represent the Z axis, while the X axis of the atlas becomes the panel’s central horizontal line. Section maps appear as horizontal lines distributed along the vertical Z axis. Same as choosing Z Perspective from the View menu. Z Perspective

Y PERSPECTIVE
Causes the vertical line in the black Perspective panel to represent the Y axis, while the Z axis of the atlas becomes the panel’s central horizontal line. Section maps appear as shorter vertical lines adjacent to the vertical Y axis. Same as choosing Y Perspective from the View menu. Y Perspective

X PERSPECTIVE
Causes the vertical line in the black Perspective panel to represent the X axis, while the Z axis of the atlas points toward the viewer. Section maps create a miniature sketch of the atlas as it appears in the Atlas Shop’s work space. Same as choosing X Perspective from the View menu.

BIOQUANT Topographer Handbook: The Atlas Shop in Detail

Page 6-47
X Perspective

HELP> HOW DO I
Opens the Atlas Shop’s “How Do I...” help window. The “How Do I...” help window provides links to comprehensive system help files for the features and special procedures that are covered in this manual.

THE COLOR PALETTE
The Color Palette

When the Select By Color tool on the Vertical Tool bar is active, clicking a square on the Color Palette selects all objects in the atlas of that color. tool on the Vertical Tool Bar is active, clicking a square on the Color Palette When the Change Color changes the currently selected sections, objects, or points to that color. The colored “button” at the left end of the Color Palette shows the color that was last chosen on the palette.

• •

RELATED TOPICS
• • • • • The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66)

TOOLS ON THE VERTICAL TOOL BAR
This section covers tools of the vertical toolbar in the Atlas Shop.

TOPIC CONTENTS
Zoom & Pan Tools (page 6-48) Select Tools (page 6-49) Align & Change Color Tools (page 6-52) Line Edit Tools (page 6-58) Change Z (page 6-63) Undo Tool (page 6-66)

BIOQUANT Topographer Handbook: The Atlas Shop in Detail

Page 6-48 RELATED TOPICS
• • • • • • The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66)

ZOOM & PAN TOOLS
The Zoom and Pan tools on the Vertical Tool Bar operate on the entire atlas, regardless of which Selection mode is currently active. An atlas can be independently zoomed or panned, or it may be simultaneously zoomed and panned. Zoom and Pan Tools

ZOOM
1. 2. 3. • Click the Zoom tool on the Vertical Tool Bar.

Position the cursor anywhere in the work space, and click the left mouse button once. Repeat as needed to increase the zoom level. To return to a less-zoomed state, verify that the Zoom tool is active, position the cursor anywhere in the work space, and click the right mouse button once. Repeat if needed to return the atlas to fully un-zoomed state.

PAN
1. 2. 3. Click the Pan tool on the Vertical Tool bar

Using the left mouse button, click and drag the atlas to the desired location. Repeat step 2 as need until the atlas is in the desired position.

SIMULTANEOUSLY ZOOM AND PAN
1. 2. 3. On the vertical tool bar, click the Zoom tool.

With the cursor positioned over the objects of interest, using the left mouse button, click and drag the objects of interest toward the center of the work space. Release the cursor button. Repeat step 2 as needed until the objects of interest are sufficiently enlarged and are in the center of the work space.

RELATED TOPICS
• • • • • • • • • • • Select Tools (page 6-49) Align & Change Color Tools (page 6-52) Line Edit Tools (page 6-58) Change Z (page 6-63) Undo Tool (page 6-66) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66)

BIOQUANT Topographer Handbook: The Atlas Shop in Detail

Page 6-49

SELECT TOOLS
The Select By Rectangle, Select By Polygon, and Select By Color tools are used to select individual parts of the atlas for editing. The action of each select tool depends on the selection mode that is currently active. Vertical Tool Bar Select Tools

TOPIC CONTENTS
Select Using Rectangle or Polygon (page 6-49) Select By Color (page 6-52)

RELATED TOPICS
• • • • • • • • • • • Select Tools (page 6-49) Align & Change Color Tools (page 6-52) Line Edit Tools (page 6-58) Change Z (page 6-63) Undo Tool (page 6-66) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66)

SELECT USING RECTANGLE OR POLYGON
The Select Using Rectangle and Select Using Polygon tools on the Vertical Tool Bar can be used to select one or more sections (in Section Mode), one or more objects (in Object Mode), or one or more data points (in Point Mode). If even one data point of a section or object falls within the selection box or polygon, the whole section or object will be selected.

PROCEDURE: SELECT SECTIONS
1. 2. Click to activate Section Mode . tool or the Select Using Polygon tool,

On the Vertical Tool Bar, click either the Select Using Rectangle then do the following: •

If Select Using Rectangle is active, click and hold the left mouse button while dragging the cursor diagonally to form a small selection box that crosses the outline of the section(s) that you want to select. If Select Using Polygon is active, click a series of points to create a selection polygon of any shape that crosses the outline of the section(s) you want to select.

BIOQUANT Topographer Handbook: The Atlas Shop in Detail

Page 6-50
Selecting Sections Using the Select With Rectangle or Polygon Tool

On the left is a selection rectangle across the outlines of three sections. In the middle is a selection polygon across the same outlines. The result is shown on the right: All tracings and markers within those three sections are selected. A selection polygon can be any shape.

ADDITIONAL INFORMATION
If even one data point of a section falls within the rectangle or polygon, all tracings and markers within that section are selected.

PROCEDURE: SELECT OBJECTS
An “object” is any individual tracing or cell marker. To work with objects, a section must first be selected in Section mode, then Object mode is activated. In Object mode, the Select Using Rectangle and Select Using Polygon tools operate only on the current section, unless a special feature called Select Across Sections is turned on. The Select Across Sections feature works only in Object mode and tells the system to select objects on all sections in an area that corresponds to the selection box or polygon that is being created on the current section. 1. 2. 3. 4. In Section mode , using the most convenient method, select the section of interest. .

Click to activate Object Mode

If you want the system to select objects on all sections that correspond to the objects you intend to select on this section, on the Select menu, click to check Select Across Sections. If the objects of interest are small and need to be magnified to make selection easier, you may simultaneously zoom and pan them to the middle of the work space by doing the following: a. b. On the vertical tool bar, click the Zoom tool. With the cursor positioned over the objects of interest, using the left mouse button, click and drag the objects of interest toward the center of the work space. Release the cursor button. Repeat as needed. tool or the Select Using Polygon tool,

5.

On the Vertical Tool Bar, click either the Select Using Rectangle then do the following: • •

If Select Using Rectangle is active, click and hold the left mouse button while dragging the cursor diagonally to form a small selection box that encloses or touches all the objects you want to select. If Select Using Polygon is active, click a series of points to create a selection polygon of any shape that encloses or touches all the objects you want to select.

BIOQUANT Topographer Handbook: The Atlas Shop in Detail

while still in Object mode. cells of interest are selected with the Select Using Rectangle tool (upper right) or the Select Using Polygon tool (lower right). you may simultaneously zoom and pan the selected object(s) to the middle of the work space by doing the following: a. If Select Using Polygon is active. then the object within that section that contains the data points of interest. click the Points Mode On the Vertical Tool Bar. PROCEDURE: SELECT DATA POINTS 1. click either the Select Using Rectangle then do the following: • • If Select Using Rectangle is active. button. RELATED TOPICS • • • • • • • • • • • • Select By Color (page 6-52) Select Tools (page 6-49) Align & Change Color Tools (page 6-52) Line Edit Tools (page 6-58) Change Z (page 6-63) Undo Tool (page 6-66) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66) BIOQUANT Topographer Handbook: The Atlas Shop in Detail . tool or the Select Using Polygon tool. On the system tool bar. select first the section map.Page 6-51 Selecting Zoomed Objects with Select Using Rectangle or Select Using Polygon The illustrated section has small cell markers in the middle that need to be selected. With the cursor positioned over the selected object(s). click and drag the object(s) toward the center of the work space. Using the most convenient method. Release the cursor button. 4. click the Zoom tool. b. Repeat as needed. click and hold the left mouse button while dragging the cursor diagonally to form a small selection box that encloses all the data points you want to select. On the vertical tool bar. 3. 2. After the atlas is zoomed. click a series of points to create a selection polygon of any shape that encloses all of the data points you want to select. using the left mouse button. If the data points of interest need to be magnified to make selection easier.

It simply selects all tracings and/or markers of the same color. PROCEDURE 1. throughout the entire atlas. and Change Color Tools TOPIC CONTENTS Rotate Selected Parts of the Atlas (page 6-53) Translate Selected Parts of the Atlas (page 6-54) Resize the Selected Parts of the Atlas (page 6-55) Change Color of the Selected Parts of the Atlas (page 6-57) BIOQUANT Topographer Handbook: The Atlas Shop in Detail . Translate. click the color that matches the color of the objects that need to be selected. Rotate. Resize) and the Change Color tool operate only on the currently selected parts of the atlas. RELATED TOPICS • • • • • • • • • • • • Select Using Rectangle or Polygon (page 6-49) Select Tools (page 6-49) Align & Change Color Tools (page 6-52) Line Edit Tools (page 6-58) Change Z (page 6-63) Undo Tool (page 6-66) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66) ALIGN & CHANGE COLOR TOOLS The three manual alignment tools (Rotate. Resize. System Tool Bar With Color Palette When the Select By Color tool on the Vertical Tool Bar is active. 2. Translate. click the Select By Color button On the system tool bar’s color palette. regardless of which Selection Mode is currently active.Page 6-52 SELECT BY COLOR Select By Color operates across the entire atlas. On the Vertical Tool Bar. clicking a colored square on the system tool bar’s Color Palette selects all objects in the atlas of that color.

BIOQUANT Topographer Handbook: The Atlas Shop in Detail . then click and drag the cursor straight down. The section will rotate around this marker. 3. 2. click and drag the red marker to a different location on the object. choose Show All Sections from the View menu. Click the Rotate button on the vertical tool bar. or choose Overlay Sections from the View menu and select the particular sections to be overlaid. PROCEDURE: ROTATE A SECTION 1. then click and drag the cursor straight up. place the cursor anywhere in the atlas window. A red marker will appear on the selected object. or choose Overlay Sections from the View menu and select the particular sections to be overlaid. 5. If desirable. 6. 4. A red marker will appear on the section. 2. place the cursor any where in the atlas window. select the object of interest. then click and drag the cursor straight up. Click the Rotate button on the vertical tool bar. PROCEDURE: ROTATE AN OBJECT 1. If other section tracings are needed for reference and are not currently being displayed. To rotate the object clockwise. To rotate the object counter-clockwise. If desirable. choose Show All Sections from the View menu. If other section tracings are needed for reference and are not currently being displayed. To rotate the section counter-clockwise. In Section mode In Object mode select the section that contains the object of interest.Page 6-53 RELATED TOPICS • • • • • • • • • • • Select Tools (page 6-49) Align & Change Color Tools (page 6-52) Line Edit Tools (page 6-58) Change Z (page 6-63) Undo Tool (page 6-66) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66) ROTATE SELECTED PARTS OF THE ATLAS Sections or objects can be manually rotated to improve alignment with other sections or objects. place the cursor anywhere in the atlas window. then click and drag the cursor straight down. 5. To rotate the section clockwise. 3. 4. In Section mode select the section to be rotated. The object will rotate around this marker. click and drag the red marker to a different location. place the cursor any where in the atlas window.

From the View menu. Click the Apply button. Overlay Section Dialog Box b. the simplest is to superimpose only the previous section. On the Overlay Section dialog box. Overlay at least one adjacent section map for visual reference by doing the following: a. In Section mode . type 1 in the previous section edit field and verify that there is a check mark next to it. If desirable. The Undo button on the vertical tool bar will undo the last rotation. Save As on the File menu may be used instead. click and drag the Overlay Section dialog box to the back Perspective Panel. if the atlas is saved using Save on the File menu. ii. With the cursor on its title bar. 3. choose Overlay Sections to open the Overlay Section dialog box. 2. tool. This will keep the dialog box from obscuring the atlas during the edit procedure. select a section map that needs to be moved in the same XY plane to a new location. the data in the original atlas Topo array(s) are permanently changed. BIOQUANT Topographer Handbook: The Atlas Shop in Detail . To use the simplest approach. click the Translate The cursor takes the shape of crossed arrows. or by responding YES to the Save Data message when exiting the Atlas Shop. Although various combinations of reference maps may be used.Page 6-54 ADDITIONAL INFORMATION • After Rotate is used. On the Vertical Tool Bar. to save the edited version of the atlas to a new Topo array. • • RELATED TOPICS • • • • • • • • • • • • • • Translate Selected Parts of the Atlas (page 6-54) Resize the Selected Parts of the Atlas (page 6-55) Change Color of the Selected Parts of the Atlas (page 6-57) Select Tools (page 6-49) Align & Change Color Tools (page 6-52) Line Edit Tools (page 6-58) Change Z (page 6-63) Undo Tool (page 6-66) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66) TRANSLATE SELECTED PARTS OF THE ATLAS PROCEDURE: TRANSLATE A SECTION MAP 1. do the following: i. Choosing Restore Original from the File menu will undo all unsaved changes to the atlas.

2. To learn more about Overly Section options see: View> Overlay Sections (page 6-20) Choosing Save on the File menu permanently saves the edit in the current atlas Topo array. When the cursor button is released. Place the cursor over the selected object(s). If needed. RELATED TOPICS • • • • • • • • • • • • • • Rotate Selected Parts of the Atlas (page 6-53) Resize the Selected Parts of the Atlas (page 6-55) Change Color of the Selected Parts of the Atlas (page 6-57) Select Tools (page 6-49) Align & Change Color Tools (page 6-52) Line Edit Tools (page 6-58) Change Z (page 6-63) Undo Tool (page 6-66) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66) RESIZE THE SELECTED PARTS OF THE ATLAS PROCEDURE: RESIZE A SECTION MAP 1. In Object Mode select the object or objects that needs to be moved. click and drag the selected object(s) to the desired location. 6. choose Save from the File menu to permanently change the object’s location. 5. choose Save from the File menu to permanently change the object’s location. When the cursor button is released. On the Vertical Tool Bar. 5. the moved tracing will settle into its new position. then using the left mouse button. PROCEDURE: TRANSLATE AN OBJECT 1. If needed. See “Edit> Numeric Transform” on 6-41. click the Translate The cursor takes the shape of crossed arrows. If satisfied with the translation. repeat step 4 to refine the placement. click and drag the section map so that its tracings are better aligned with the reference (gray) section.Page 6-55 4. 3. repeat step 4 to refine the placement. Place the cursor over the selected section. BIOQUANT Topographer Handbook: The Atlas Shop in Detail . tool. In Section Mode select a section that contains an object that needs to be moved. 4. 6. ALTERNATE PROCEDURE • Sections may also be moved a known micron distance using Numeric Transform. In Section mode select the section that is to be resized. close the Overlay Section dialog box. If satisfied with the translation. the moved tracing will settle into its new position. ADDITIONAL INFORMATION • • • To remove the overlaid tracings. then using the left mouse button.

See “View> Overlay Sections” on 6-20. To narrow or widen the object while maintaining its current height. click and drag the resize control point on the top or bottom of the resize box. ADDITIONAL INFORMATION • After Resize is used. 5. If other section tracings are needed for reference and are not currently being displayed. To increase or decrease the height of the object while maintaining its current width. Do one of the following to resize the selected object: • • • To expand or shrink the object while maintaining its current height and width ratio. or choose Show All Sections from the View menu to display all un-selected section maps. If desirable. A resizing box will appear around the selected section. click and drag the resize control point on the top or bottom of the resize box. Do one of the following to resize the selected section: • • • To expand or shrink the section map while maintaining its current height and width ratio. to save the edited version of the atlas to a new Topo array. ADDITIONAL INFORMATION Sections and objects may also be resized using Numeric Transform. choose Show All Sections from the View menu. 4. 2. When resizing is finished for the currently selected item. Edit> Numeric Transform (page 6-41) • • • BIOQUANT Topographer Handbook: The Atlas Shop in Detail .Page 6-56 2. 4. A resizing box will appear around the selected object. To increase or decrease the height of the section while maintaining its current width. Choosing Restore Original from the File menu will undo all unsaved edits. if the atlas is saved using Save on the File menu. or by responding YES to the Save Data message when exiting the Atlas Shop. In Section mode In Object mode select the section that contains the object of interest. Save As on the File menu may be used instead. Click the Resize button on the vertical tool bar. To narrow or widen the section map while maintaining its current height. click and drag the resize control point on either side of the resize box. See “Edit> Numeric Transform” on 6-41. 3. select the object of interest. click and drag the resize control point on either side of the resize box. See “View> Show All Sections” on 6-20. click an alternate tool on the vertical tool bar. click and drag the resize control point in any corner of the resize box. PROCEDURE: RESIZE AN OBJECT 1. choose Overlay Sections from the View menu and select the particular sections to be overlaid. The selection may be resized without maintaining the height to width ratio using Numeric Transform. Clicking the Undo button on the vertical tool bar will undo the last resizing. To remove the resize box from the atlas. or choose Overlay Sections from the View menu and select the particular sections to be overlaid. the data in the original atlas Topo array(s) are permanently changed. sequencing to the Select Next button will cause the resize box to automatically adjust to fit the size of the new selection. Click the Resize button on the vertical tool bar. click and drag the resize control point in any corner of the resize box. If other section tracings are needed for reference and are not currently being displayed. 3.

the data in the original atlas Topo array(s) are permanently changed. Select the section(s). PROCEDURE 1. if the atlas is saved using Save on the File menu or saved when exiting the Atlas Shop. Save As on the File menu may be used instead.Page 6-57 RELATED TOPICS • • • • • • • • • • • • • • Rotate Selected Parts of the Atlas (page 6-53) Translate Selected Parts of the Atlas (page 6-54) Change Color of the Selected Parts of the Atlas (page 6-57) Select Tools (page 6-49) Align & Change Color Tools (page 6-52) Line Edit Tools (page 6-58) Change Z (page 6-63) Undo Tool (page 6-66) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66) CHANGE COLOR OF THE SELECTED PARTS OF THE ATLAS Choosing Change Color from the Edit menu or clicking the Change Color tool on the vertical tool bar readies the cursor to choose a new color for the selected parts of the atlas. ADDITIONAL INFORMATION • After Change Color is used. or point(s) for which the color is to be changed. Colors may be changed simply to improve the appearance of the atlas. The Undo button on the vertical tool bar will undo the last color change. Click the Change Color button on the vertical tool bar or choose Change Color from the Edit menu. or by responding YES to the Save Data message when exiting the Atlas Shop. object(s). if the atlas is saved using Save on the File menu. the default color for the selected objects is permanently changed in the original Topo array. to save the edited version of the atlas to a new Topo array. If desirable. 2. IMPORTANT: After using Change Color. Choosing Restore Original from the File menu will undo all unsaved changes to the atlas. • • • BIOQUANT Topographer Handbook: The Atlas Shop in Detail . all objects of the same color may be manipulated as a group. When displaying or editing an atlas. click to choose a new color. All currently selected items will change to the new color. 3. or to group items differently. On the system tool bar’s color palette.

The Line Editing Tools on the Vertical Toolbar From top to bottom the tools are “Straighten Edge.” “Delete”.” “Combine Two Objects.” “Redefine Edge. Line Edit tools are only used after an object (tracing) of interest has been selected in Object mode.” “Separate Two Objects.Page 6-58 RELATED TOPICS • • • • • • • • • • • • • • • Rotate Selected Parts of the Atlas (page 6-53) Translate Selected Parts of the Atlas (page 6-54) Resize the Selected Parts of the Atlas (page 6-55) Change Color of the Selected Parts of the Atlas (page 6-57) Select Tools (page 6-49) Align & Change Color Tools (page 6-52) Line Edit Tools (page 6-58) Change Z (page 6-63) Undo Tool (page 6-66) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66) LINE EDIT TOOLS The line editing tools on the Vertical Tool Bar correct tracing errors made when the topographic data was collected in the measurement software. TOPIC CONTENTS Straighten Edge (page 6-59) Combine Two Objects (page 6-59) Separate Two Objects (page 6-60) Redefining an Object’s Edge (page 6-61) Deleting Objects (page 6-62) RELATED TOPICS • • • • • • • • • • • Select Tools (page 6-49) Align & Change Color Tools (page 6-52) Line Edit Tools (page 6-58) Change Z (page 6-63) Undo Tool (page 6-66) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66) BIOQUANT Topographer Handbook: The Atlas Shop in Detail .

Click the undo button to undo the last edit. On the vertical. Select the tracing that needs to be Line edited. 3. Click the one end of the segment to be straightened. 1. The Combine Two Objects tool on the vertical tool bar connects two objects with straight lines which are defined by mouse clicks. 4. Click where one end of the connecting line should be on object A. BIOQUANT Topographer Handbook: The Atlas Shop in Detail . 3. Click the other end of the segment.Page 6-59 STRAIGHTEN EDGE PROCEDURE The new straight line segment will be constructed counterclockwise from the first point to the second point. Click the Combine Objects button. Combine Objects Example Clicking in the order shown will connect these two objects 1. 2. This procedure corrects this. 2. RELATED TOPICS • • • • • • • • • • • • • • • Combine Two Objects (page 6-59) Separate Two Objects (page 6-60) Redefining an Object’s Edge (page 6-61) Deleting Objects (page 6-62) Select Tools (page 6-49) Align & Change Color Tools (page 6-52) Line Edit Tools (page 6-58) Change Z (page 6-63) Undo Tool (page 6-66) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66) COMBINE TWO OBJECTS Sometimes a single object will be thresholded and traced as two separate halves. ADDITIONAL NOTES • • Click the right mouse button to cancel after the first click. Select the objects that are to be combined. click the Straighten Edge button.

Click one side of the single tracing. Click where the other end of the connecting line should be on object B.Page 6-60 4. ADDITIONAL NOTES • • Click the right mouse button after the first click to cancel the separation. Select the objects that need to be separated. 5. Click the Separate Two Objects button on the vertical tool bar. BIOQUANT Topographer Handbook: The Atlas Shop in Detail . A dividing gap will appear. 2. RELATED TOPICS • • • • • • • • • • • • • • • Straighten Edge (page 6-59) Separate Two Objects (page 6-60) Redefining an Object’s Edge (page 6-61) Deleting Objects (page 6-62) Select Tools (page 6-49) Align & Change Color Tools (page 6-52) Line Edit Tools (page 6-58) Change Z (page 6-63) Undo Tool (page 6-66) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66) SEPARATE TWO OBJECTS Sometimes. Click where one end of the second connecting line should be on object B. then click the opposite side. Click the button to undo the last edit. Click the undo button to undo the separation. 6. 3. creating two separate tracings. two objects are traced as one. Clicking two points defines the location for a gap that will separate the object into two. This procedure corrects this. Click where the other end of the connecting line should be on object A. PROCEDURE 1. ADDITIONAL NOTES • • Click the right mouse button to cancel before the series of 4 clicks is finished.

3. BIOQUANT Topographer Handbook: The Atlas Shop in Detail . Click to mark the other end of the segment. This tool is recommended (instead of the Straighten Edge tool) when editing atlases that are to be surface rendered or any other time that a significant portion of an object’s tracing needs to be altered.Page 6-61 RELATED TOPICS • • • • • • • • • • • • • • • Straighten Edge (page 6-59) Combine Two Objects (page 6-59) Redefining an Object’s Edge (page 6-61) Deleting Objects (page 6-62) Select Tools (page 6-49) Align & Change Color Tools (page 6-52) Line Edit Tools (page 6-58) Change Z (page 6-63) Undo Tool (page 6-66) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66) REDEFINING AN OBJECT’S EDGE A segment of an object’s contour tracing can be redrawn with the Redefine Edge tool. click a series of data points to define the new contour. If desirable. if the atlas is saved using Save on the File menu. Click the undo button to undo the redefinition of the contour. click the series of data points fairly close together. Click to mark one end of the segment that is to be redefined. 5. Save As on the File menu may be used instead. 2. the data in the original atlas Topo array(s) are permanently changed. 4. If the atlas is to be surface rendered. Starting from the first point. to save the edited version of the atlas to a new Topo array. PROCEDURE: 1. ADDITIONAL NOTES: • • Click the Undo button on the vertical tool bar to undo the redefinition of the contour. SAVING THE EDIT After Redefine Edge is used. or by responding YES to the Save Data message when exiting the Atlas Shop. Click the right mouse button to end the construction of the new edge. Click the Redefine Edge tool on the vertical tool bar.

RELATED TOPICS • • • • • • • • • • • • • • • Straighten Edge (page 6-59) Combine Two Objects (page 6-59) Separate Two Objects (page 6-60) Redefining an Object’s Edge (page 6-61) Select Tools (page 6-49) Align & Change Color Tools (page 6-52) Line Edit Tools (page 6-58) Change Z (page 6-63) Undo Tool (page 6-66) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66) BIOQUANT Topographer Handbook: The Atlas Shop in Detail . ADDITIONAL NOTES: • • The most recent unsaved deletion may be canceled by clicking the Undo tool bar. PROCEDURE: 1. button on the vertical All unsaved edits may be canceled by choosing Restore Original from the File menu. Note: The removed data is temporarily stored in the Topographer’s backup buffer and the delete does not become permanent until the data is saved using Save on the File menu or by responding YES to the Save Data message on exiting the Atlas Shop. 2. Click on the tracing of the object to be deleted. The object immediately disappears from the atlas window. Click the Delete Object tool on the vertical tool bar.Page 6-62 RELATED TOPICS • • • • • • • • • • • • • • • Straighten Edge (page 6-59) Combine Two Objects (page 6-59) Separate Two Objects (page 6-60) Deleting Objects (page 6-62) Select Tools (page 6-49) Align & Change Color Tools (page 6-52) Line Edit Tools (page 6-58) Change Z (page 6-63) Undo Tool (page 6-66) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66) DELETING OBJECTS The Delete tool on the vertical tool bar is used to permanently remove the data of a chosen object from the original Topo array.

or points.Page 6-63 CHANGE Z Change Z is used to change the Z Offset value of section maps. objects within section maps. PROCEDURE: 1. click the Change All Sections radio button. Reasons the default Z value may need to be changed: • • • Items were measured or counted using the wrong Z Offset on the Parameters dialog box. or points within objects. or points may be repositioned along the Z axis. objects. Change All Sections on the Change Z dialog box may be used to distribute sections evenly along the Z axis. The initial (default) Z position of everything in the atlas is based on the Z Offset value that was displayed during measurement on the Parameters dialog box in BIOQUANT Life Science or BIOQUANT OSTEO. Click the Section Mode button on the system tool bar to activate Section Mode. 2. A section has been duplicated using Internal Copy or Cut and Internal Paste. Change Z Tool Choosing Change Z from the Edit menu or clicking the Change Z tool on the vertical tool bar opens the Change Z dialog box. The Z Offset was changed by mistake. Click the Change Z tool on the vertical tool bar or choose Change Z from the Edit menu to open the Change Z dialog box. On the Change Z dialog box. Now the Z-Offset in the new section needs to be changed to properly position it on the Z axis. TOPIC CONTENTS Evenly Distribute Topographic Sections Along the Z Axis. Change Z With Change All Sections Mode Active In this example the first section’s Z Offset is 0. before all measurements for one physical tissue section were complete. So part of the tissue section displays at one Z level. BIOQUANT Topographer Handbook: The Atlas Shop in Detail . The other sections will be evenly distributed along the Z axis with 20 microns between each. so that sections. Change Z can operate on all sections at once or only on selected sections. 3. objects. (page 6-63) Relocate Selected Items to a Specific Z Offset Position (page 6-64) Shift Selected Items a Specific Micron Distance from Current Position (page 6-65) RELATED TOPICS • • • • • • • • Line Edit Tools (page 6-58) Undo Tool (page 6-66) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66) EVENLY DISTRIBUTE TOPOGRAPHIC SECTIONS ALONG THE Z AXIS. the rest at another.

enter the Z value for the very first section in the atlas. • • BIOQUANT Topographer Handbook: The Atlas Shop in Detail . PROCEDURE 1. 2. Verify that the Change Selected Section(s) radio button is active. RELATED TOPICS • • • • • • • • • • • Relocate Selected Items to a Specific Z Offset Position (page 6-64) Shift Selected Items a Specific Micron Distance from Current Position (page 6-65) Line Edit Tools (page 6-58) Change Z (page 6-63) Undo Tool (page 6-66) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66) RELOCATE SELECTED ITEMS TO A SPECIFIC Z OFFSET POSITION One or more sections. objects. All selected items will be relocated to the Z Offset position specified by the new Z value. If the default value is not the desired Z Offset for all selected items. If only one item is selected. Click the Close button to dismiss the Change Z dialog box. or points may be relocated to a specific. Click the Apply button. (Often this value will be zero. In the Z Value of First Section field. If multiple items are selected. 3. all will be relocated to the same point on the Z axis. 5. do the following: a. type the micron distance that is to separate each section from the proceeding one. the Change All Z Value To field holds the current Z value of the first selected item.Page 6-64 4. the default value in the Change All Z Value To field is the current Z Offset value for that item. b. Delete the current value in the Change All Z Value To field and type in the desired new Z value. Click the Apply button. or point(s) for which the Z value is to be changed. known Z Offset. object(s). 6. Select the section(s). If multiple items are selected. If the default value in the Change All Z Value To field is the desired Z Offset for all of the selected items.) In the Z Offset Between Sections field. 7. Change Z With Change Selected Sections Active In this example all selected items will be reset to a Z Offset of 70. Click the Change Z button on the vertical tool bar or choose Change Z from the Edit menu to open the Change Z dialog box. click the Apply button.

Click the Close button to close the Change Z dialog box. If multiple items are selected. the default value in the Change All Z Value To field is the current Z Offset value for that item. In the Raise/Lower Z Value To field. 2. 5. -10).g.g.Page 6-65 4. RELATED TOPICS • • • • • • • • • • • Evenly Distribute Topographic Sections Along the Z Axis. Select the section(s). Click the Apply button. Change Z With Change Selected Sections Active Each selected section will be moved upward 10 microns from its current position. Positive values raise the selected parts. The micron distance will be added to (or subtracted from) the default value in the Change All Z Value To field. BIOQUANT Topographer Handbook: The Atlas Shop in Detail . and negative values lower the selected parts. Click the Close button to close the Change Z dialog box. PROCEDURE 1. this procedure preserves the relative distances between. 6. Click the Change Z button on the vertical tool bar or choose Change Z from the Edit menu to open the Change Z dialog box. the Change All Z Value To field holds the current Z value of the first selected item. 4. and all selected items will be shifted up (or down) from their current positions on the Z axis by the specified micron distance. To lower the Z value. (page 6-63) Shift Selected Items a Specific Micron Distance from Current Position (page 6-65) Line Edit Tools (page 6-58) Change Z (page 6-63) Undo Tool (page 6-66) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66) SHIFT SELECTED ITEMS A SPECIFIC MICRON DISTANCE FROM CURRENT POSITION If multiple items are selected. In the Raise/Lower All Z Values by field. object(s). type a negative micron distance (e. 10). or point(s) that are to be shifted up or down the Z axis. 3. type a positive micron distance (e. the value that is entered is the number of microns that the selected items should be moved up or down. Verify that the Change Selected Section(s) radio button is active If only one item is selected. do one of the following: • • To raise the Z value.

its Z Position value in the View BIOQUANT Data window will be 1500. (Example: If the default Z Value for a selected item is 150 on the Change Z dialog box. it is best that these be done prior to adding special surface rendering formats. After editing is finished. COMMON ADJUSTMENTS THAT ENHANCE SURFACE RENDERING • Change Resolution . Save As on the File menu may be used instead. click the Undo button. (page 6-63) Relocate Selected Items to a Specific Z Offset Position (page 6-64) Line Edit Tools (page 6-58) Change Z (page 6-63) Undo Tool (page 6-66) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66) UNDO TOOL The Undo tool on the Vertical Tool Bar performs the same function as the Undo option on the Edit menu. Undo Tool PROCEDURE • On the Vertical Tool Bar. Both undo the last unsaved edit made in the atlas. such as aligning sections and correcting errors in Z positioning. Edit> Resolution (page 6-36) BIOQUANT Topographer Handbook: The Atlas Shop in Detail .) • RELATED TOPICS • • • • • • • • • • • Evenly Distribute Topographic Sections Along the Z Axis. To preserve the original data. to save the edited version of the atlas to a new Topo array. or by responding YES to the Save Data message when exiting the Atlas Shop. If corrective edits. RELATED TOPICS • • • • • • • • File> Restore Original (page 6-5) Undo Tool (page 6-66) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66) SPECIAL EDITS TO ENHANCE SURFACE RENDERING Particular editing and formatting tools in the Topographer’s Atlas Shop help improve the quality of a surface rendered model. are needed. the edited atlas is opened again in the Atlas Modeler. The following procedures are all done in the Atlas Shop. The current Z Positions for data viewed in the View BIOQUANT Data window.Page 6-66 ADDITIONAL INFORMATION • After Change Z is used. the change may be saved to permanently alter the original data in the atlas array using Save on the File menu.The resolution (number of data points) in large atlases may be decreased to speed the process of surface rendering. are exactly ten times greater than the Z Offset value of that same data.

button on the vertical tool bar or choose Change Color from the Edit menu. Repeat steps 2 through 5 to select and change the color of all outlines that define this branch of the structure. Save As on the File menu may be used instead. 3. the defining surface outline breaks into two sets of outlines and the system must deal with the sudden appearance of “too many points” that do not correspond. Click to activate Section Mode then select the first (or next) topographic section that contains a surface defining outline for the shortest branch of the Y or V shaped structure.The “cap” or “open” markers on a tracing may be removed to return the tracing to its original “Middle of Object” default status. BIOQUANT Topographer Handbook: The Atlas Shop in Detail . if the atlas is saved using Save on the File menu. The “shortest” branch of the structure is the branch that is defined by the fewest tracings. through which interior objects may be viewed. Middle of Object (page 6-69) • • • RELATED TOPICS • • • • • • • File> Restore Original (page 6-5) Undo Tool (page 6-66) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) CHANGE COLOR IN BRANCHED STRUCTURES The system creates surfaces by looking for corresponding points of the same color on adjacent sections. click to choose a new color.Y or V shaped structures in an atlas surface render more accurately if one of the “branches” of the Y or V is a different color. If the outline is one of several objects within the selected topographic section. Making the “shortest” leg or branch of the Y or V shaped structure a different color. End of Object/Leave Open (page 6-68) Middle of Object . make initial corrective edits to the atlas. If desirable. Cap Object (page 6-68) End of Object/Leave Open .A number of tracings in the atlas may be marked as “open” to create a transparent window in a surface rendered model. For branched (Y or V shaped) structures. without reducing the opacity of the entire model. The selected outline will change to the new color. PROCEDURE 1. 2. 5. SAVING THE EDIT: After Change Color is used. On the system tool bar’s color palette.The first and last contour tracings in an atlas can be marked as “caps” that will cover the open ends of a surface rendered model. Change Color in Branched structures (page 6-67) Cap Object . the data in the original atlas Topo array(s) are permanently changed. eliminates the confusion. 6. If needed.Page 6-67 • Change Colors in a Branched Structure . such as aligning sections and correcting errors in Z positioning that may have been made during data collection. then use the Select Next 4. or by responding YES to the Save Data message when exiting the Atlas Shop. to save the edited version of the atlas to a new Topo array. Click the Change Color button until only the correct outline is selected. using the same new color for each outline. click the Object Mode button.

all but the first and last outlines marked “Leave Open” will automatically be constructed as a diffused linear cloud. But. 3. and there is no outline before the first tracing or after the last. by simply decreasing the opacity of the entire outer surface. 1. 5. through which interior objects may be viewed. use the Select Next button on the system tool bar to cycle through the objects in the selected section. but not always. even though the color of the “open” lines is identical to the rest of the surface. End of Object/Leave Open. without reducing the opacity of the entire model. 2. Click the Section Mode button on the system tool bar to activate Section Mode. are actually End of Object markers that allow the system to recognize the intervening outlines as a separate object. These holes may be closed using the Cap Object tool in the Atlas Shop. Click the Section Mode button on the system tool bar to activate Section Mode. Select the topographic section that contains the first (or next) outline that is to be marked with Leave Open. When the atlas is opened in the Atlas Modeler. 2. The inner structures of a surface rendered model may be revealed while in the Atlas Modeler program. The very first and last outlines in a marked series. leaving open holes at the top and bottom of the rendered model.Page 6-68 RELATED TOPICS • • • • • • • • • • Format Contour Lines (page 6-68) Edit> Resolution (page 6-36) File> Restore Original (page 6-5) Undo Tool (page 6-66) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66) FORMAT CONTOUR LINES The Cap Object. The tool is used to mark a series of surface defining outlines that are to be “left open”. 6. Click the Object Mode button to activate Object Mode. the resultant loss of surface details across the entire model may not be desirable. the rendered surface stops abruptly. Because surface rendering connects points of the same color on adjacent surface defining outlines (usually section outlines). Select the topographic section that contains the first or last surface defining outline for the model. 1. Repeat steps 1 through 5 to mark (as a cap) the tracing at the opposite end of the model. BIOQUANT Topographer Handbook: The Atlas Shop in Detail . If necessary. Surface Render Formatting Tools CAP OBJECT The Cap Object tool is used to tag the first and last outlines in the model as surface rendering caps. until the correct contour outline is selected. NOTE: For the bottom cap this is usually. rather than a solid line. and Middle of Object buttons on the system tool bar add special formatting to an atlas that is to be surface rendered. The End of Object/Leave Open tool in the Atlas Shop makes it possible to create a limited transparent window without reducing the opacity of the rest of the model’s surface. An outline that is tagged as a cap will automatically fill with the surface color when the atlas is opened in the Atlas Modeler. END OF OBJECT/LEAVE OPEN A number of tracings in the atlas may be marked as “open” to create a transparent window in a surface rendered model. Click the Cap Object button on the system tool bar to mark the selected tracing as a “cap”. Section 0. 4.

Click the Object Mode button to activate Object Mode. tool button on the system tool bar to mark the selected tracing as 5. 6. until only the correct contour outline is selected. MIDDLE OF OBJECT The “cap” or “open” markers on a tracing may be removed to return a tracing to its original “Middle of Object” default status. Repeat steps 1 through 5 to mark (as Leave Open) all the tracings that are to be part of the transparent window. The Middle of Object tool on the system tool bar removes the special formatting that was applied to a tracing using the Cap Object or End of Object/Leave Open tools 1. all tracings in an atlas are termed Middle of Object. areas. Select the topographic section that contains the outline for which the Cap or End of Object/Leave Open formatting is to be removed. TOPIC CONTENTS Measure Volume (page 6-70) Measure Region Of Interest Area (page 6-71) Measure Area of An Object (page 6-72) Count Objects (page 6-74) Measure Distance (page 6-76) BIOQUANT Topographer Handbook: The Atlas Shop in Detail . Click the Object Mode button to activate Object Mode. 4. and distances within an atlas. 2. use the Select Next button on the system tool bar to cycle through the objects in the selected section. Click the Middle of Object button on the system tool bar to remove the special formatting and restore the tracing’s default Middle of Object status. 4. until only the specially formatted outline is selected. Before special formatting is added. If necessary.Page 6-69 3. Click the End of Object/Leave Open “Leave Open”. counts. 3. Click the Section Mode button on the system tool bar to activate Section Mode. RELATED TOPICS • • • • • • • • • • Change Color in Branched structures (page 6-67) Edit> Resolution (page 6-36) File> Restore Original (page 6-5) Undo Tool (page 6-66) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66) TAKING MEASUREMENTS FROM AN ATLAS Options on the Measure menu in the Atlas Shop are used to determine volumes. use the Select Next button on the system tool bar to cycle through the objects in the selected section. 5. If necessary.

the micron distance between the selected contour tracings. PROCEDURE 1. activate Section Mode Select by Color • . In the Atlas Shop. or less than half. click the cursor in the Destination array field and type the desired name. the Precision value (on the Volume tab of the Calculate/Measure dialog box) can be set to half.Page 6-70 RELATED TOPICS • • • • • • • • • • Change Color in Branched structures (page 6-67) Edit> Resolution (page 6-36) File> Restore Original (page 6-5) Undo Tool (page 6-66) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66) MEASURE VOLUME Topographer determines the volume of a structure by interpolating a 3D space from selected polygonal tracings. d. To edit the name of the new array. c. If the micron distance (Z Offset) between the selected tracings is rather large. IMPORTANT: Be sure that only the contour outlines of the three dimensional structure are selected. To save the volume to an array. smaller stair-steps in the implied surface of the structure. activate Object Mode the needed tracings (objects) from the GoTo Object list or by selecting corresponding objects across sections. the system creates virtual sections between the selected tracings that provide additional. On the Save Value to Array dialog box. Choose Volume from the Measure menu. 3. When this is the case. click the Append button. otherwise the volume measurement will be that of the whole structure plus the volumes of any selected internal structures. and use and select If the tracings that define the volume are not of a unique color. b. change the Precision micron value to half the distance between tracings. Click the Close button on the Save Value to Array dialog box. To increase the accuracy of interpolation. The Calculate/Measure dialog box opens with the volume in cubic microns displayed. 4. BIOQUANT Topographer Handbook: The Atlas Shop in Detail . Calculate/Measure: Volume 2. select the tracings that define the volume • If all the tracings that define the volume are the same unique color. a. click the Save button on the Calculate/Measure dialog box. To record the volume in the destination array. click the New Array button to add a Volume array. and click the Measure button to create virtual sections and update the measurement to a more precise volume.

click the Append button. If all of the objects are the same unique color. Determine and save the volume of the structure using the above procedure. button and select the section that contains the region On the View menu. Frequently the structure of interest is the entire atlas and the objects of interest are cell markers or cell area tracings that are all the same unique color.Page 6-71 ADDITIONAL INFORMATION Should it be needed. click the Section Mode of interest. If multiple sections exist. button on the vertical tool bar. Select the internal objects that are to be counted. click the cursor in the Destination array field and type the desired name. click to uncheck it. 2. The number of objects in the measured region is simultaneously recorded and may be saved to an array to determine count per area. click the New Array button to add an Attribute array. (The system automatically renames the Attribute array to reflect the type of measurement being saved. Click the Object mode button on the system tool bar. 1. Click To measure a polygonal area. use the Select By Color tool. 3. Click successive points to define the ROI area. If it is. a. c. click the Select With Polygon button on the vertical tool bar. determining the number of objects in that volume provides a count per volume. verify that Selection Only is not checked. the number of tracings that were used to determine the volume are recorded on the Count tab of the Calculate/Measure dialog box. the rectangle or polygon selection tools are used to define a region of interest (ROI) that is to be measured. Simply click the Count tab to reveal the tracing count. 4. To record the object count in the destination array. Click the right mouse button to close the area. click the Select With Rectangle and drag diagonally to define the ROI area. Construct the Region of Interest (ROI) • • To measure a rectangular area. DETERMINE COUNTS PER VOLUME Once the volume of a structure has been determined and saved to an array. On the Save Value to Array dialog box. tool can be used to RELATED TOPICS • • • • • • • • • • Measure Region Of Interest Area (page 6-71) Measure Area of An Object (page 6-72) Count Objects (page 6-74) Measure Distance (page 6-76) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66) MEASURE REGION OF INTEREST AREA In Object mode. The Calculate/Measure dialog box opens and the Count result is displayed. When this is the case.) To edit the name of the new array. 3. 4. BIOQUANT Topographer Handbook: The Atlas Shop in Detail . the Select By Color simultaneously select all cells in the atlas. From the Measure menu choose Count. 2. PROCEDURE 1. b. To save the count to an array click the Save button on the Calculate/Measure dialog box.

To save the count to an array click the Save button on the Calculate/Measure dialog box. Calculate/Measure: Selected Area ROI 6. d. a. click the cursor in the Destination array field and type the desired name. click the New Array button to add an Attribute array. click the name of the array in the list to make it the Destination Array before clicking the Append button. To record the count in the destination array. (The system automatically renames the Attribute array to reflect the type of measurement being saved. RELATED TOPICS • • • • • • • • • • Measure Volume (page 6-70) Measure Area of An Object (page 6-72) Count Objects (page 6-74) Measure Distance (page 6-76) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66) MEASURE AREA OF AN OBJECT The area of a selected object tracing may be measured. To save the ROI Area to an array. Click the Close button on the Save Value to Array dialog box. 2. Choose ROI Area from the Measure menu. click the cursor in the Destination array field and type the desired name. click the Save button on the Calculate/Measure dialog box. The Calculate/Measure dialog box opens on the Selection Area ROI tab with the ROI area reported in square microns. Click the Count tab on the Calculate/Measure dialog box. On the Save Value to Array dialog box. click the Append button. On the Save Value to Array dialog box.) To edit the name of the new array. a. c. the number of individual objects within the larger tracing may also be determined. The number of objects in the measured area is displayed. If the object contains internal structures.Page 6-72 5. c. In order for an object to be included in the count. (The system automatically renames the Attribute array to reflect the type of measurement being saved. click the New Array button to add an Attribute array. click the Append button. DETERMINE OBJECT COUNT FOR THIS ROI AREA 1. b.) To edit the name of the new array. b. ADDITIONAL INFORMATION • • To append the current area measurement or object count a new element in an existing array. at least one of its data points must lie within or under the defining borders of the ROI. To record the ROI Area in the destination array. BIOQUANT Topographer Handbook: The Atlas Shop in Detail . To over write the datum in an existing Area or Object Count array click the name of the array in the list to make it the Destination Array and click the Replace button instead of the Append button.

If multiple sections exist. BIOQUANT Topographer Handbook: The Atlas Shop in Detail . If the object has smaller Click the Object Mode objects within it.) To edit the name of the new array. 4. click the Measure button to update the count. b. click the cursor in the Destination array field and type the desired name. At this point the Count will be 1. (The system automatically renames the Attribute array to reflect the type of measurement being saved. 3. 2. button and select the Object that is to be measured. in Section Mode select the section that contains the object of interest. click the Save button on the Calculate/Measure dialog box. From the Select menu. click the cursor in the Destination array field and type the desired name. To record the count in the destination array. at this time select only the contour outline of the primary object. DETERMINE NUMBER OF OBJECTS WITHIN AN OBJECT AREA 1. On the Calculate/Measure dialog box. To over write the datum in an existing array click the name of the array in the list to make it the Destination Array and click the Replace button instead of the Append button. Click the Count tab on the Calculate/Measure dialog box. 3. click the New Array button to add an Attribute array. Count will now be the number of objects inside the larger object’s tracing plus 1 for the tracing of the larger object. c. To record the Object Area in the destination array. choose Add Interior Objects to Selection. a. click the Append button.Page 6-73 PROCEDURE 1. click the New Array button to add an Attribute array. click the Append button. ADDITIONAL INFORMATION • • To append the current measurement to the data in an existing array. Calculate/Measure: Object Area 4.) To edit the name of the new array. 2. On the Save Value to Array dialog box. To save the object area to an array. b. To save the count to an array click the Save button on the Calculate/Measure dialog box. The Calculate/Measure dialog box opens with the Object Area in square microns displayed. Click the Close button on the Save Value to Array dialog box. d. c. On the Save Value to Array dialog box. Choose Object Area from the Measure menu. a. The number of selected objects included in the area measured is displayed. (The system automatically renames the Attribute array to reflect the type of measurement being saved. click the name of the array in the list to make it the Destination Array before clicking the Append button.

the count reported is exactly the number of objects that In Object mode are selected on the GoTo Object list. (Area of the section is not simultaneously recorded. Click the Select menu and. 2. using the GoTo Object list.) . Because there are advantages and disadvantages to each approach.) Exception: If Select Across Sections is checked on the Select menu.Page 6-74 RELATED TOPICS • • • • • • • • • • Measure Region Of Interest Area (page 6-71) Measure Volume (page 6-70) Count Objects (page 6-74) Measure Distance (page 6-76) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66) COUNT OBJECTS The number of objects within an area or volume may be automatically determined using Count on the Measure menu. using Select by Color . review the scenarios below before performing the procedures. (Area or volume is simultaneously recorded. then select the section that contains the objects of interest. at least one of its data points must lie within or under the defining borders of the ROI. on all sections.) In Section mode. click to uncheck Select Across Sections. not the number of objects. Count is most useful for determining the number of single point objects (e. the area of the section may be determined in a separate Object Area measurement by selecting only the section’s contour outline. 3. the count reported is the number of interior objects plus 1. to activate Object mode. the count reported is exactly the number of objects of In Object mode that color in the currently selected section. All objects. . (Neither area nor volume is simultaneously recorded. if checked. the count reported is exactly the number of objects that lie in the defined area or volume.) If a count per area is needed. cells) in a given area or volume. the value reported is the number of objects of that color in the entire atlas (just as if Section mode were active. If a count per volume is needed.g. Select Across Sections must be checked on the Select menu. Click the Section mode Click the Object mode button. the count reported is exactly the number of objects of that color in the entire atlas.) In order for an object to be included in the count. Use one of the following methods to select the objects that are to be counted: BIOQUANT Topographer Handbook: The Atlas Shop in Detail . button. In Object mode. The larger object is the extra one. if the count is to be taken from a volume. using Select by Color .) • • • COUNT OBJECTS IN AN AREA PROCEDURE 1. 4. . (Area is not simultaneously recorded. It is important to be aware that the number of objects reported by the system is influenced by both the selection mode and the selection method used. selecting smaller objects inside a larger one using Add Interior Objects on the In Object mode Select menu. with at least one data point in or under the defined borders of the ROI will be counted. MODE & METHODS FOR COUNT ONLY • In Section mode . if any other selection method is used. MODE & METHOD FOR COUNT PLUS AREA OR VOLUME • In Object mode using one of the ROI selection tools (Rectangle or Polygon). the volume of the atlas may be determined in a separate volume measurement. the reported value will be the number of selected sections. (Volume of the atlas is not simultaneously recorded.

(Area is not simultaneously recorded. b.) If the objects are a unique color. f. On the Save Value to Array dialog box. 7. (The system automatically renames the Attribute array to reflect the type of measurement being saved. c. Calculate/Measure: Count 6. (The system automatically renames the Attribute array to reflect the type of measurement being saved. If objects were selected using either the Rectangle or Polygon tool. click the Append button.. then click the color on the color palette that matches the objects. Click the Section mode button. Click the Append button to record the area. first select the larger object. d. i. On the Save Value to Array dialog box. c. Click the Close button on the Save Value to Array dialog box. click the cursor in the Destination array field and type the desired name. then click the color on the color palette that matches the objects of interest. ii. the area from which the count was taken may also be saved to an array as follows: a.) If a larger object contains the objects that are to be counted. (With this selection method. Click the Save button on the Calculate/Measure dialog box. Click the Select Using Polygon tool. COUNT OBJECTS IN A VOLUME PROCEDURE 1. then choose Add Interior Objects from the Select menu.) • If the color of the objects is not unique. click the cursor in the Destination array field and type the desired name. The count may be saved to an array by doing the following: a. Click the Select by Color tool on the vertical tool bar.) To edit the name of the new array. The Calculate/Measure dialog box opens with the count of objects displayed. then click and drag a rectangular ROI around the objects.) 5. e. Click the Close button on the Save Value to Array dialog box. To record the Count in the destination array. (Area is not simultaneously recorded.. then click a series of points to define an ROI around the objects.) tool.) To edit the name of the new array. Click the Selection Area ROI tab to display the square micron area in which the objects were counted. Choose Count from the Measure menu. (Area is simultaneously recorded. d. you may. Click the Save button on the Calculate/Measure dialog box. click the New Array button to add an Attribute array to the data set.Page 6-75 • • • • Click the Select Using Rectangle (Area is simultaneously recorded. a volume will not be simultaneously recorded. BIOQUANT Topographer Handbook: The Atlas Shop in Detail . Use one of the following methods to select the objects of interest: • If the objects are a unique color. e. Click the left mouse button to close the polygon. click the Select by Color tool on the vertical tool bar. The resultant count will include the larger object as 1. click the New Array button to add an Attribute array.. b.. or if a simultaneous volume measurement is desired.

iii. e. On the Save Value to Array dialog box. tool on the vertical tool bar. Click the Append button to record the area. Click the Object mode button. click the Append button. Click the Close button on the Save Value to Array dialog box. d. click the New Array button to add an Attribute array.Page 6-76 i. Choose Count from the Measure menu to open the Calculate/Measure dialog box with the number of objects displayed. c. On the Save Value to Array dialog box. 2. Calculate/Measure: Count 3. b. Click either the Select Using Rectangle or Select Using Polygon then construct an ROI around the objects. e. click the cursor in the Destination array field and type the desired name. b. Click the Close button on the Save Value to Array dialog box. or between two arbitrary points any where in the atlas window. between points on two different sections. Click the Save button on the Calculate/Measure dialog box. click the New Array button to add an Attribute array to the data set. f. Click the Save button on the Calculate/Measure dialog box. The count may be saved to an array by doing the following: a. If objects were selected using either the Rectangle or Polygon tool. c. The Snap to Point option must be checked BIOQUANT Topographer Handbook: The Atlas Shop in Detail .) To edit the name of the new array. (The system automatically renames the Attribute array to reflect the type of measurement being saved. Click the Volume tab to display the cubic micron volume in which the objects were counted. (The system automatically renames the Attribute array to reflect the type of measurement being saved.) To edit the name of the new array. 4. distances can be measured between two points on the same section. RELATED TOPICS • • • • • • • • • Measure Region Of Interest Area (page 6-71) Measure Volume (page 6-70) Measure Distance (page 6-76) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66) MEASURE DISTANCE In Section mode. To record the Count in the destination array. click the cursor in the Destination array field and type the desired name. From the Select menu choose Select Across Sections (to place a check mark next to this option). ii. the volume from which the count was taken may also be saved to an array as follows: a. d.

2. Choose Distance from the Measure menu to open the Calculate/Measure dialog box. Calculate/Measure: Distance 3. or choose Section from the Select menu. Click the Section mode button on the tool bar. On the Calculate/Measure dialog box. see the Save the Distance to a Array procedure below.Page 6-77 for specimen related distances and unchecked for arbitrary distances. On the Calculate/Measure dialog box. The distance between the points will be displayed in microns. Click two points on the Atlas. TOPIC CONTENTS Measure a Distance on One Section (page 6-77) Measure a Distance Between Sections (page 6-78) Measure an Arbitrary Distance in the Atlas Window (page 6-79) Measure a Distance on One Object (page 6-79) Save the Distance to an Array (page 6-80) RELATED TOPICS • • • • • • • • • • Measure Region Of Interest Area (page 6-71) Measure Volume (page 6-70) Count Objects (page 6-74) Measure Distance (page 6-76) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66) MEASURE A DISTANCE ON ONE SECTION PROCEDURE 1. In Object mode. 5. 4. 6. click the Measure button. BIOQUANT Topographer Handbook: The Atlas Shop in Detail . the only distance that can be measured is between two points on one selected object. click to check the Snap to Point check box. To save the distance value to an array.

9. On the Calculate/Measure dialog box. Select the section on which the measurement will end. Select the section from which the measurement will begin. see the Save the Distance to a Array procedure below. 7. 3. If not already open. To save the distance value to an array. 4.Page 6-78 RELATED TOPICS • • • • • • • • • • • • • • Measure a Distance Between Sections (page 6-78) Measure an Arbitrary Distance in the Atlas Window (page 6-79) Measure a Distance on One Object (page 6-79) Save the Distance to an Array (page 6-80) Measure Region Of Interest Area (page 6-71) Measure Volume (page 6-70) Count Objects (page 6-74) Measure Distance (page 6-76) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66) MEASURE A DISTANCE BETWEEN SECTIONS PROCEDURE 1. Click the point on the selected section at which the measurement is to begin. The distance between the points will be displayed in microns. 2. On the Calculate/Measure dialog box. Click the point on the selected section at which the measurement ends. Click the Section mode button on the tool bar. 6. click the Measure button. 8. click to check the Snap to Point check box. RELATED TOPICS • • • • • • • • • • • • • • Measure a Distance on One Section (page 6-77) Measure an Arbitrary Distance in the Atlas Window (page 6-79) Measure a Distance on One Object (page 6-79) Save the Distance to an Array (page 6-80) Measure Region Of Interest Area (page 6-71) Measure Volume (page 6-70) Count Objects (page 6-74) Measure Distance (page 6-76) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66) BIOQUANT Topographer Handbook: The Atlas Shop in Detail . or choose Section from the Select menu. choose Distance from the Measure menu to open the Calculate/Measure dialog box. 5.

If not already open. 3. then click the Object mode 2. Click the Section mode button on the tool bar. click the Measure button. see the Save the Distance to a Array procedure below. button and select the object. Click the Section mode button on the tool bar. click to un-check the Snap to Point check box. To save the distance value to an array. 4. Click two points on one selected object. or choose Section from the Select menu. click to check the Snap to Point check box. 4. choose Distance from the Measure menu to open the Calculate/Measure dialog box. On the Calculate/Measure dialog box. On the Calculate/Measure dialog box. 6. 5. click the Measure button. see the Save the Distance to a Array procedure below. RELATED TOPICS • • • • • • • • • • • • • • Measure a Distance on One Section (page 6-77) Measure a Distance Between Sections (page 6-78) Measure a Distance on One Object (page 6-79) Save the Distance to an Array (page 6-80) Measure Region Of Interest Area (page 6-71) Measure Volume (page 6-70) Count Objects (page 6-74) Measure Distance (page 6-76) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66) MEASURE A DISTANCE ON ONE OBJECT PROCEDURE 1. 2. select the section that contains the object of interest. The distance between the points will be displayed in microns. 6. Choose Distance from the Measure menu to open the Calculate/Measure dialog box. 3. Click two points on the Atlas window. The distance between the points will be displayed in microns. 5. On the Calculate/Measure dialog box. BIOQUANT Topographer Handbook: The Atlas Shop in Detail .Page 6-79 MEASURE AN ARBITRARY DISTANCE IN THE ATLAS WINDOW PROCEDURE 1. To save the distance value to an array. On the Calculate/Measure dialog box.

To over write the datum in an existing array click the name of the array in the list to make it the Destination Array and click the Replace button instead of the Append button. To edit the destination array’s name. ADDITIONAL INFORMATION • • • To append the current measurement to the data in an existing array. 3. click the cursor in the Destination Array field and type the desired name.Page 6-80 RELATED TOPICS • • • • • • • • • • • • • • Measure a Distance on One Section (page 6-77) Measure a Distance Between Sections (page 6-78) Measure an Arbitrary Distance in the Atlas Window (page 6-79) Save the Distance to an Array (page 6-80) Measure Region Of Interest Area (page 6-71) Measure Volume (page 6-70) Count Objects (page 6-74) Measure Distance (page 6-76) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66) SAVE THE DISTANCE TO AN ARRAY PROCEDURE 1. click the Append button. On the Save Value to Array dialog box. or choose an existing distance array from the drop down list that opens when the down arrow in the Destination Array field is clicked. To record the distance value in the destination array. click the name of the array in the list to make it the Destination Array before clicking the Append button. click the New Array button to add a Distance array. Click the Save button on the Calculate/Measure dialog box. 2. RELATED TOPICS • • • • • • • • • • • • • • Measure a Distance on One Section (page 6-77) Measure a Distance Between Sections (page 6-78) Measure an Arbitrary Distance in the Atlas Window (page 6-79) Measure a Distance on One Object (page 6-79) Measure Region Of Interest Area (page 6-71) Measure Volume (page 6-70) Count Objects (page 6-74) Measure Distance (page 6-76) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66) BIOQUANT Topographer Handbook: The Atlas Shop in Detail . Arrays added to the data set on the Save Value to Array dialog box are Attribute arrays that are named by default to reflect the current calculation or measurement. 4.

see instructions in the Life Science help or manual in the Topographer Data Collection chapter.BIOQUANT Topographer Handbook Planar & Contour Conversion This section covers planar and contour conversion in the Topographer. To collect data for planar or contour conversion. Understanding the Basics of Planar and Contour Conversion (page 7-2) Planar Conversion (page 7-4) Displaying and Modifying the Planar Histogram (page 717) Contour Conversion (page 7-25) Displaying and Modifying the Contour Converted Atlas (page 7-37) Planar & Contour Conversion .

See the Topographer Data Collection section of the BIOQUANT Life Science help or manual. tracings may be manually rotated. Also in the Atlas Viewer. For Planar or Contour Conversion. but consistent Start Points were not maintained during data collection. or structures within sections. a unique Z Offset value. The result is a Planar Histogram. section contour tracings retain their original configuration. therefore the Landmark should be placed at a similar point on all sections. one by one. each section’s contour tracing is broken at a defined point and stretched into a vertical line. Each is described below. the process pulls cell markers within the section to the nearest point on the section’s contour tracing. The Z Offset value for the first section is commonly designated as zero (0). a section’s Z Offset value assigned during data collection dictates its position on the Z axis. using the Topographer’s Rotate tool. The system is not able to join multiple length measurements into a single length measurement. In both types of conversion. the Start Points of all contour tracings must be deliberately placed by the user. Contour tracings are constructed using either a Length array or Area array. • In the Topographer program. Every physical tissue section in a series will have a single Landmark point. The Z Offset value for every other section reflects its micron distance from the first section. The number of cells at each point are represented by proportionally sized symbols. • • • • BIOQUANT Topographer Handbook: Planar & Contour Conversion . if rotational alignment is desirable. although similar orientation of tracings can be visually helpful to the user. using the topographic tracings that were recorded in BIOQUANT during measurement. With Contour Conversion. Planar Conversion does not require that section tracings have rotational alignment. • • Contour tracings are of whole tissue sections. With Planar Conversion. RELATED TOPICS • • • • Planar Conversion (page 7-4) Displaying and Modifying the Planar Histogram (page 7-17) Contour Conversion (page 7-25) Displaying and Modifying the Contour Converted Atlas (page 7-37) GENERAL GUIDELINES Topographic data for Contour or Planar Conversion consist only of contour tracings and cell markers. In the Topographer program. ideally at a similar point on all sections. section Landmarks are automatically aligned when the tracings are “stacked” along the Z axis. the Topographer’s Align Sections feature may be used to automatically reorient (rotate) tracings from all sections so they match. There are five different data collection strategies that may be used.Page 7-2 UNDERSTANDING THE BASICS OF PLANAR AND CONTOUR CONVERSION Both Planar Conversion and Contour Conversion quantitatively map deferentially labeled cell populations across serial brain sections. display parameters for Converted atlases or Planar Histograms may be modified. When Start Points are deliberately placed at a similar point on all sections. Alternately. Actual data collection for Planar or Contour Conversion is done in BIOQUANT Life Science. TOPIC CONTENTS General Guidelines (page 7-2) Data Collecting Strategies (page 7-3) DATA COLLECTION NOTE This section just provides a general overview of the basics of planar and contour conversion. There should be one length or area measurement per contour. and a known Start Point for its contour tracing. Cell location markers are generated using an Object Count array. A Contour Converted atlas or Planar Histogram is displayed and may be printed in the Topographer’s Atlas Viewer. return to this section for instruction on how to use the Topographer’s planar and contour conversion tools. Once the data has been collected. for each section.

otherwise user’s choice. Multiple sections can be stored in a single Topo array. Structures that cannot be thresholded. STRATEGY 1: RECOMMENDED FOR SMALL STUDIES • • • • Number of Topo arrays required = 1 Use only one Topo array for all outlines and all cell counts.RECOMMENDED FOR MOST STUDIES • • Number of Topo arrays required = less than the number of sections. if there are hundreds of sections. if sections are large and have many cells. For instance. as long as both the contour tracing and cells for all sections are included. Structures that can be thresholded are usually automatically traced or counted. TOPO ARRAY STRATEGY The contour tracing and cells for a section should be in the same Topo array. you may want to store the data for up to ten sections in each Topo array. This strategy is most appropriate when the number of tissue sections is relatively small and the number of cells per section is expected to be no more than a few hundred. Automatic Align Sections may be used with this method. RELATED TOPICS • • • • • General Guidelines (page 7-2) Planar Conversion (page 7-4) Displaying and Modifying the Planar Histogram (page 7-17) Contour Conversion (page 7-25) Displaying and Modifying the Contour Converted Atlas (page 7-37) BIOQUANT Topographer Handbook: Planar & Contour Conversion . Use one Topo array for all of the data for several sections.Page 7-3 • Data collection may be automatic or manual. On the other hand. Record both the contour tracing and the cell counts in the Topo array designated for each section. must be manually traced or counted. you may want to limit the number of sections per Topo array to five or less.RECOMMENDED FOR STUDIES WITH A LARGE NUMBER OF CELLS TO BE COUNTED • • • • Number of Topo arrays required = number of sections Use one Topo array for each serial section. Automatic Align Sections may be used with this method. Record both contour tracings and cell counts for a limited number of tissue sections in one Topo array. Automatic Align Sections may be used with this method. This guarantees that the cells remain associated with the Contour. STRATEGY 2 . The number of cells per section may be numerous or few. • STRATEGY 3 . RELATED TOPICS • • • • • Data Collecting Strategies (page 7-3) Planar Conversion (page 7-4) Displaying and Modifying the Planar Histogram (page 7-17) Contour Conversion (page 7-25) Displaying and Modifying the Contour Converted Atlas (page 7-37) DATA COLLECTING STRATEGIES The most important point to note about saving Topo data for Planar or Contour Conversion is that the contour and cells for a section should be in the same Topo array. depending on how many sections are to be analyzed. This strategy is employed when the number of sections in the study is relatively small.

return to this section for instruction on how to use the Topographer’s planar and contour conversion tools. Click the Open Atlas Click the Resize To Fit button on the system tool bar (or choose Open from the Atlas menu).Page 7-4 PLANAR CONVERSION Planar Conversion in the Topographer’s Atlas Shop is used to convert Topo data to a Planar Histogram format. Actual data collection for Planar or Contour Conversion is done in BIOQUANT Life Science. button on the system tool bar. Once the data has been collected. At this point only Topo arrays should be selected. See the Topographer Data Collection section of the BIOQUANT Life Science help or manual. DATA COLLECTION NOTE This section just provides a protocol for using Planar Conversion after data has been correctly collected in BIOQUANT Life Science. The Topo arrays selected will be used to create special DTI and Line arrays to display Planar data. 3. The Planar Histogram is displayed in the Topographer’s Atlas Viewer. click Topographer to execute the BIOQUANT Topographer program. TOPIC CONTENTS Step 1: Selecting the Topo Arrays and Opening the Atlas Shop (page 7-4) Step 2: Backing Up the Raw Topo Array(s) (page 7-6) Step 3: Setting up for Conversion (page 7-7) Step 4: Customizing the DTI Array Parameters (page 7-8) Step 5: Defining Fiduciary Points (page 7-10) Step 6: Setting a Shift Value (page 7-14) Step 7: Choosing the Aligning Fiduciary (page 7-15) Step 8: Converting to Planar Data (page 7-16) Step 9: Exiting the Atlas Shop (page 7-17) RELATED TOPICS • • • • General Guidelines (page 7-2) Displaying and Modifying the Planar Histogram (page 7-17) Contour Conversion (page 7-25) Displaying and Modifying the Contour Converted Atlas (page 7-37) STEP 1: SELECTING THE TOPO ARRAYS AND OPENING THE ATLAS SHOP 1. On the Select Arrays dialog box. 4. select the one or more Topo arrays that contain data to be converted. The Topographer opens into the Atlas Viewer. BIOQUANT Topographer Handbook: Planar & Contour Conversion . 2. On BIOQUANT Life Science’s or BIOQUANT OSTEO’s system menu bar.

Page 7-5 Atlas Window Resize to Fit centers the topographic map. Click the Atlas Shop button (or choose Atlas Shop from the Tools menu). The Atlas Shop will open with Section Mode active. 5. Atlas Shop BIOQUANT Topographer Handbook: Planar & Contour Conversion .

rename the new Topo array to “Master Raw Topo Data. At this point there should not be any arrays selected. We will perform the Planar and Contour Conversion on the new Topo array to preserve the integrity of the raw Topo arrays. choose Exit Atlas Shop. “Master Raw Topo Data” to move it to the Selected list. PROCEDURE 1. from the Select menu. BIOQUANT Topographer Handbook: Planar & Contour Conversion . choose Save As.Page 7-6 6. Click the Atlas Shop button (or choose Atlas Shop from the Tools menu). 2. In the Atlas Shop.” Click the Save button. 8. click the New Array button to add a new Topo array to the data set. in the Available Arrays list. Continue with Step 2: Backing Up the Raw Topo Array(s) (page 7-6). In the Array Name edit file. choose Unselect All Arrays. You are returned to the Atlas Viewer. In the Atlas Viewer. PLANAR CONVERSION PROCEDURE Step 1: Selecting the Topo Arrays and Opening the Atlas Shop (page 7-4) Step 2: Backing Up the Raw Topo Array(s) (page 7-6) Step 3: Setting up for Conversion (page 7-7) Step 4: Customizing the DTI Array Parameters (page 7-8) Step 5: Defining Fiduciary Points (page 7-10) Step 6: Setting a Shift Value (page 7-14) Step 7: Choosing the Aligning Fiduciary (page 7-15) Step 8: Converting to Planar Data (page 7-16) Step 9: Exiting the Atlas Shop (page 7-17) RELATED TOPICS • • • • • General Guidelines (page 7-2) Planar Conversion (page 7-4) Displaying and Modifying the Planar Histogram (page 7-17) Contour Conversion (page 7-25) Displaying and Modifying the Contour Converted Atlas (page 7-37) STEP 2: BACKING UP THE RAW TOPO ARRAY(S) Before we go further we will copy the data from the selected Topo array(s) into a new Topo array. In the Atlas Shop. 6. 9. On the Save Array As dialog box. 7. 5. from the File menu. The map drawn should equal the map generated from the raw Topo data. 4. In this way we can always make a new copy of the raw Topo arrays in the future. double click Topo array we just added. 3. On Select Arrays. on Select Arrays. The Atlas Shop will open with Section Mode active. Click the Resize To Fit button on the system tool bar. from the File menu.

choose Planar Conversion to open the Planar dialog box. If necessary.Page 7-7 10. From the File menu. 2. (Optional) Align the rotation of all the sections by doing the following: a. choose Save. choose Select All Sections. From the Tools menu. d. From the Edit menu. click the Resize to Fit work space. The sections rotate so that the start points on all sections are aligned. b. Planar One DTI array is automatically displayed for each cell type that was counted. button on the system tool bar to scale the atlas to the size of the From the Select menu. choose Align Sections. the atlas contains two cell types. c. BIOQUANT Topographer Handbook: Planar & Contour Conversion . Continue with Step 3: Setting up for Conversion (page 7-7). In this illustration. PLANAR CONVERSION PROCEDURE Step 1: Selecting the Topo Arrays and Opening the Atlas Shop (page 7-4) Step 2: Backing Up the Raw Topo Array(s) (page 7-6) Step 3: Setting up for Conversion (page 7-7) Step 4: Customizing the DTI Array Parameters (page 7-8) Step 5: Defining Fiduciary Points (page 7-10) Step 6: Setting a Shift Value (page 7-14) Step 7: Choosing the Aligning Fiduciary (page 7-15) Step 8: Converting to Planar Data (page 7-16) Step 9: Exiting the Atlas Shop (page 7-17) RELATED TOPICS • • • • • General Guidelines (page 7-2) Planar Conversion (page 7-4) Displaying and Modifying the Planar Histogram (page 7-17) Contour Conversion (page 7-25) Displaying and Modifying the Contour Converted Atlas (page 7-37) STEP 3: SETTING UP FOR CONVERSION 1.

placement. Symbol parameters that are changed from the default are automatically saved to the corresponding DTI array’s comment. In the DTI Array(s) box. Ellipse S2. BIOQUANT Topographer Handbook: Planar & Contour Conversion . The rectangle defaults to a height and width of 1. magnitude. PROCEDURE: CUSTOMIZING DTI PARAMETERS 1. The default shape is Line. Shape: DTI Array Comment: Line Default . • Ellipse: Represent the cell type using an ellipse. Cell types are identified by color. The shape. and color parameters of the symbol are customizable. Rectangle: Represent the cell type using a rectangle. click to highlight the first DTI array. height to width ratio. The Ellipse defaults to a height and width of 1. color. Cell data in this case is point data collected with an Object Count array. The height of the Line is always 1. PLANAR CONVERSION PROCEDURE Step 1: Selecting the Topo Arrays and Opening the Atlas Shop (page 7-4) Step 2: Backing Up the Raw Topo Array(s) (page 7-6) Step 3: Setting up for Conversion (page 7-7) Step 4: Customizing the DTI Array Parameters (page 7-8) Step 5: Defining Fiduciary Points (page 7-10) Step 6: Setting a Shift Value (page 7-14) Step 7: Choosing the Aligning Fiduciary (page 7-15) Step 8: Converting to Planar Data (page 7-16) Step 9: Exiting the Atlas Shop (page 7-17) RELATED TOPICS • • • • • General Guidelines (page 7-2) Planar Conversion (page 7-4) Displaying and Modifying the Planar Histogram (page 7-17) Contour Conversion (page 7-25) Displaying and Modifying the Contour Converted Atlas (page 7-37) STEP 4: CUSTOMIZING THE DTI ARRAY PARAMETERS DTI ARRAY EXPLANATION When the Planar dialog box opens. 2. The shape in the preview box changes to match the symbol type chosen. Continue with Step 4: Customizing the DTI Array Parameters (page 7-8). choose one of the following shapes: • • Line: Represents the cell type using a line. In the Symbol Shape region.Page 7-8 3. A symbol is used to represent the cell population at each data point along the specimen contour line.No comment Rectangle S1. one DTI array is listed (and added to the current data set) for each cell type in the selected Topo arrays.

The color numbers increment by one for each remaining color in the palette. If you have a small number of cells. reading left to right. it might be useful to type in a Mag that is less than 1. 8.500000 1 Default . The Mag can also be changed at a later point. Fill is not available for the Line symbol. The color numbers increment by one for each remaining color in the palette.No comment 2 M2. Moving the slider to the right increases the ratio. The Ratio determines the symbol’s height to width ratio. 3 M3. Light Blue F5. the Fill color of the symbol defaults to the original cell type measurement color. In the Position region.05 M0.No Comment 2/1 R2. Center. Moving the slider to the left decreases the height to width ratio. choose either Left. Pink F3. Color: DTI Array Comment: Blue No comment Red C2. In the Symbol Shape region. Mag: DTI Array Comment: 0. It is important to have the same Mag for all DTI arrays in a study. The ratio range available with the slider is between 0.No comment Right P1. the Outline color of the symbol defaults to the original cell type measurement color. move the Ratio slider to the desired position.4. . or Right to indicate the orientation of the symbol to the line. The default ratio is 1. Pink C3.6. then click the desired color. The height is the Y distance from the vertical line. 3/5 R0. 2/5 R0.3 and 3.Page 7-9 3. 1/1 Default . 5. The default position is Center. The width is the X distance along the vertical line.000000. In the Symbol Shape region.050000.3. Position: DTI Array Comment: Left P2.000000. Light Green F4. To change the fill color of the symbol for this cell type. Repeat from step 1 for each DTI array in the DTI array(s) box. Ratio: DTI Array Comment: (Height/Width) 3/10 R0.0. The position of the shape to the contour line in the preview box changes to match the position chosen. type the desired magnitude. Light Blue C5. Center Default . The height and width of the symbol are multiplied by the Magnitude. Light Green C4. reading left to right. 3/1 R3. To change the outline color of the symbol for this cell type. Color: DTI Array Comment: Blue No comment Red F2. 1/2 R0. In the Color region.5. 0.5 M0. Ratios less than 1 do not affect the Line shape because the Line’s height is always 1. In the Color region. it might be useful to increase the Mag. first click the Outline radio button. 7. If you have an extremely large number of cell counts. first click the Fill radio button. in the Mag edit box.0. BIOQUANT Topographer Handbook: Planar & Contour Conversion 4. then click the desired color. 6.

The DTI parameters can also be changed at a later point. this procedure is more complicated. especially from the middle of a contour. The user adds fiduciary points on the specimen contour where each lobule begins. The Line Array holds the information needed to stretch the specimen contour line into a straight vertical line. The system represents each lobule by a different colored segment on the straight vertical line. manually type the desired parameter into the comment of the DTI array. The BIOQUANT Topographer Handbook: Planar & Contour Conversion . If all sections have all lobules. It is important to have the same Mag for all DTI arrays in a study. If some lobules are missing. Continue with Step 5: Defining Fiduciary Points (page 7-10).Page 7-10 ADDITIONAL NOTES • • • 9. then this procedure is straight-forward. PLANAR CONVERSION PROCEDURE Step 1: Selecting the Topo Arrays and Opening the Atlas Shop (page 7-4) Step 2: Backing Up the Raw Topo Array(s) (page 7-6) Step 3: Setting up for Conversion (page 7-7) Step 4: Customizing the DTI Array Parameters (page 7-8) Step 5: Defining Fiduciary Points (page 7-10) Step 6: Setting a Shift Value (page 7-14) Step 7: Choosing the Aligning Fiduciary (page 7-15) Step 8: Converting to Planar Data (page 7-16) Step 9: Exiting the Atlas Shop (page 7-17) RELATED TOPICS • • • • • General Guidelines (page 7-2) Planar Conversion (page 7-4) Displaying and Modifying the Planar Histogram (page 7-17) Contour Conversion (page 7-25) Displaying and Modifying the Contour Converted Atlas (page 7-37) STEP 5: DEFINING FIDUCIARY POINTS LINE ARRAY EXPLANATION A Line Array is created when Topo data are converted to Planar data. If the ratio parameters offered do not meet requirements. TOPIC CONTENTS Procedure ONE: Defining Fiduciary Points (page 7-11) Procedure TWO: Going to the Next Outline (page 7-13) Then continue with Step 6: Setting a Shift Value (page 7-14) IMPORTANT NOTE It is important to sequence through your sections before this procedure and become familiar with how the lobules are organized within the sections.

Page 7-11 goal is to make it so that the color coded lobules are the same lobules in each section. On the specimen contour for the first section click once at the beginning of the lobule that you want to be the starting point of the Planar Histogram. PLANAR CONVERSION PROCEDURE Step 1: Selecting the Topo Arrays and Opening the Atlas Shop (page 7-4) Step 2: Backing Up the Raw Topo Array(s) (page 7-6) Step 3: Setting up for Conversion (page 7-7) Step 4: Customizing the DTI Array Parameters (page 7-8) Step 5: Defining Fiduciary Points (page 7-10) Step 6: Setting a Shift Value (page 7-14) Step 7: Choosing the Aligning Fiduciary (page 7-15) Step 8: Converting to Planar Data (page 7-16) Step 9: Exiting the Atlas Shop (page 7-17) RELATED TOPICS • • • • • General Guidelines (page 7-2) Planar Conversion (page 7-4) Displaying and Modifying the Planar Histogram (page 7-17) Contour Conversion (page 7-25) Displaying and Modifying the Contour Converted Atlas (page 7-37) PROCEDURE ONE: DEFINING FIDUCIARY POINTS 1. click the Add Fiduciary Points button. click once at the beginning of each lobule. Then. The pointer changes to the Add Fiduciary cursor. in a counter-clockwise direction. BIOQUANT Topographer Handbook: Planar & Contour Conversion . using the following pointers. choose Add Fiduciaries. On the Planar dialog box. If the sections in the background decrease the visibility of the current section. check Selection Only to display only the current section. Add a fiduciary marker at the beginning of each lobule. or from the Edit menu. Atlas Shop 2. from the View menu.

then if you turn on Connect Fiduciary Points later there will be a line connecting the bottom of the histogram. click the right mouse button to exit Delete Fiduciary mode. After unwanted fiduciary points have been deleted. take care that the lobule color assignment matches corresponding lobules on other sections.Page 7-12 POINTERS • • • A fiduciary marker is placed on the specimen contour at each location clicked. starting at the same location. choose • • iii. do the following. To delete fiduciary points. Then click the specimen contour at the location the fiduciary point should be. You need to add fiduciary points in the same order. After misplaced fiduciary points have been moved. choose iii. or from the Edit menu. do the following: i. To move a fiduciary point along the contour. It this is not required. If the color coding gets messed up. button. The pointer changes to the Move Fiduciary cursor. then it may be deleted by itself. There are special rules for deleting fiduciary points. click the Add Fiduciary Points button. Moving a fiduciary point will not mess up the color assignment of the lobule. then all the fiduciary points must be deleted on the contour. After all fiduciary points have been defined for this section. Click the right mouse button to exit the Add Fiduciary Point mode. Click the right mouse button to exit the Add Fiduciary Point mode. i. On the Planar dialog box. as long as you do not move it before a preceding fiduciary point or after a following fiduciary points. If a lobule in the middle of a contour does not exist for a particular section. If more fiduciary points need to be added. If the point is NOT THE LAST on the contour. You want the lobules that do exist to show up in the correct sequenced segment color for comparison to other sections. BIOQUANT Topographer Handbook: Planar & Contour Conversion . 3. ii. or from the Edit menu. On the specimen contour for the current section click once on the fiduciary to be deleted. If the point to be deleted IS THE LAST on the contour. • If more fiduciary points need to be added. In this case use Add Fiduciary Points to redefine the points. On the specimen contour for the current section click once at on the fiduciary to be moved to make it disappear. click the Move Fiduciary Point Move Fiduciary. ii. click the Add Fiduciary Points button. On the Planar dialog box. v. If the fiduciary point is not the last on the contour. click the right mouse button to exit Move Fiduciary mode. button. If you need to re-arrange the order of the fiduciary points. Repeat for all fiduciary points to be moved. iv. click two fiduciary points very close together to skip that color. The fiduciary marker disappears. If you set a fiduciary point at the end of the last lobule. then repeat to delete all fiduciary points on the current section. click the right mouse button to exit Add Fiduciary Point mode. v. This prevents the lobule color assignment from messing up. iv. The markers sequence through the colors on the color palette. The pointer changes to the Delete Fiduciary cursor. click the Delete Fiduciary Point Delete Fiduciary. for each section to avoid confusion caused by different colored markers. delete all the fiduciary points for the section and start over.

choose Next Outline. If you want to return to edit DTI array parameters at a later point. Continue with Procedure TWO: Going to the Next Outline (page 7-13). do the following: 1. or if you want to do a Contour Conversion at a later point. choose Save Fiduciary(s). you will not need to re-define the fiduciary points. from the Planar dialog box File menu. they show up as larger points. When all Fiduciary Points have been set. 3. BIOQUANT Topographer Handbook: Planar & Contour Conversion .Page 7-13 4. 2. Follow the procedure to set fiduciary points as previously described in “Procedure ONE: Defining Fiduciary Points” on page 7-11. or from the Edit menu. This saves the positions of the fiduciary points to the array. click the Next Outline button. Atlas Shop When you sequence back to the a section that already has fiduciary markers defined. On the Planar dialog box. PLANAR CONVERSION PROCEDURE Step 1: Selecting the Topo Arrays and Opening the Atlas Shop (page 7-4) Step 2: Backing Up the Raw Topo Array(s) (page 7-6) Step 3: Setting up for Conversion (page 7-7) Step 4: Customizing the DTI Array Parameters (page 7-8) Step 5: Defining Fiduciary Points (page 7-10) Step 6: Setting a Shift Value (page 7-14) Step 7: Choosing the Aligning Fiduciary (page 7-15) Step 8: Converting to Planar Data (page 7-16) Step 9: Exiting the Atlas Shop (page 7-17) RELATED TOPICS • • • • • General Guidelines (page 7-2) Planar Conversion (page 7-4) Displaying and Modifying the Planar Histogram (page 7-17) Contour Conversion (page 7-25) Displaying and Modifying the Contour Converted Atlas (page 7-37) PROCEDURE TWO: GOING TO THE NEXT OUTLINE After the Fiduciary Points are in the correct locations on the first contour outline.

Shift: Line Array Comment: 1 Default . PROCEDURE: ENTERING A SHIFT VALUE 1. If the sections in the background decrease the visibility of the current section. by adding or modifying the Line Array Comment. 3 S=3. The default Shift value is 1. the markers are drawn larger to indicate that the section has already been marked. Shift In this example. If the Shift value is changed from the default. To refresh existing fiduciary points. When an outline is reached that already has fiduciary points. from the Tools menu. The Shift can be modified later. in the Shift edit box. BIOQUANT Topographer Handbook: Planar & Contour Conversion . a shift of 5 has been entered. 2. Continue with Step 6: Setting a Shift Value (page 7-14). On the Shift dialog box. To refresh the display. type the desired value. choose Define Shift to open the Planar Shift dialog box. click the RD button on the tool bar. On Planar dialog box. click the Add Fiduciary Points button. PLANAR CONVERSION PROCEDURE Step 1: Selecting the Topo Arrays and Opening the Atlas Shop (page 7-4) Step 2: Backing Up the Raw Topo Array(s) (page 7-6) Step 3: Setting up for Conversion (page 7-7) Step 4: Customizing the DTI Array Parameters (page 7-8) Step 5: Defining Fiduciary Points (page 7-10) Step 6: Setting a Shift Value (page 7-14) Step 7: Choosing the Aligning Fiduciary (page 7-15) Step 8: Converting to Planar Data (page 7-16) Step 9: Exiting the Atlas Shop (page 7-17) RELATED TOPICS • • • • • General Guidelines (page 7-2) Planar Conversion (page 7-4) Displaying and Modifying the Planar Histogram (page 7-17) Contour Conversion (page 7-25) Displaying and Modifying the Contour Converted Atlas (page 7-37) STEP 6: SETTING A SHIFT VALUE SHIFT EXPLANATION The Shift determines the distance between the vertical lines used to represent the specimen contour. from the View menu.No comment 2 S=2. check Selection Only to display only the active section.Page 7-14 ADDITIONAL INFORMATION • • • • 4. it adds a S=#. comment to the Line array. Shift multiplies the Z value by the number entered.

3. Set Alignment In this example. Continue with Step 7: Choosing the Aligning Fiduciary (page 7-15). PLANAR CONVERSION PROCEDURE Step 1: Selecting the Topo Arrays and Opening the Atlas Shop (page 7-4) Step 2: Backing Up the Raw Topo Array(s) (page 7-6) Step 3: Setting up for Conversion (page 7-7) Step 4: Customizing the DTI Array Parameters (page 7-8) Step 5: Defining Fiduciary Points (page 7-10) Step 6: Setting a Shift Value (page 7-14) Step 7: Choosing the Aligning Fiduciary (page 7-15) Step 8: Converting to Planar Data (page 7-16) Step 9: Exiting the Atlas Shop (page 7-17) RELATED TOPICS • • • • • General Guidelines (page 7-2) Planar Conversion (page 7-4) Displaying and Modifying the Planar Histogram (page 7-17) Contour Conversion (page 7-25) Displaying and Modifying the Contour Converted Atlas (page 7-37) STEP 7: CHOOSING THE ALIGNING FIDUCIARY ALIGNMENT EXPLANATION After converting the specimen contours to a straight vertical line with each lobule represented by a different color on the line. Lobule 3 has been selected as the aligning lobule. button. click the Select Aligning Fiduciary Point Alignment to open the Set Alignment dialog box. BIOQUANT Topographer Handbook: Planar & Contour Conversion . choose Define In the Lobule list. or Tools menu. click to highlight the lobule with which all other will be aligned. Click the OK button. PROCEDURE: CHOOSING THE ALIGNING FIDUCIARY 1. On the Planar dialog box. 2. the system aligns the straight line contours of all section based on the user designated aligning fiduciary.Page 7-15 3. Be sure the chosen lobule is present on all sections.

position. you do not need to re-convert the Line Array. It creates the Line Array from the Contour topo data and fills the DTI Arrays with cell references to the Line Array from the Cell topo data. PROCEDURE: CONVERTING TO PLANAR DATA 1. 2. or from the Tools menu.Page 7-16 4. choose Perform 3. or if the Line Array shift parameter is changed at a later point. click the Perform Conversion Conversion to convert the data to the Line Array. Before converting make sure that the DTI Array parameters have been defined and that the fiduciary points have been set. Continue with Step 8: Converting to Planar Data (page 7-16). or color parameters are changed at a later point. Continue with Step 9: Exiting the Atlas Shop (page 7-17). This step may take awhile. If the DTI Array symbol shape. PLANAR CONVERSION PROCEDURE Step 1: Selecting the Topo Arrays and Opening the Atlas Shop (page 7-4) Step 2: Backing Up the Raw Topo Array(s) (page 7-6) Step 3: Setting up for Conversion (page 7-7) Step 4: Customizing the DTI Array Parameters (page 7-8) Step 5: Defining Fiduciary Points (page 7-10) Step 6: Setting a Shift Value (page 7-14) Step 7: Choosing the Aligning Fiduciary (page 7-15) Step 8: Converting to Planar Data (page 7-16) Step 9: Exiting the Atlas Shop (page 7-17) RELATED TOPICS • • • • • General Guidelines (page 7-2) Planar Conversion (page 7-4) Displaying and Modifying the Planar Histogram (page 7-17) Contour Conversion (page 7-25) Displaying and Modifying the Contour Converted Atlas (page 7-37) STEP 8: CONVERTING TO PLANAR DATA CONVERTING EXPLANATION Converting redefines the Topo data as Planar data. The parameter changes made will be automatically updated. button. Be patient. On Planar dialog box. PLANAR CONVERSION PROCEDURE Step 1: Selecting the Topo Arrays and Opening the Atlas Shop (page 7-4) Step 2: Backing Up the Raw Topo Array(s) (page 7-6) Step 3: Setting up for Conversion (page 7-7) Step 4: Customizing the DTI Array Parameters (page 7-8) Step 5: Defining Fiduciary Points (page 7-10) Step 6: Setting a Shift Value (page 7-14) Step 7: Choosing the Aligning Fiduciary (page 7-15) Step 8: Converting to Planar Data (page 7-16) Step 9: Exiting the Atlas Shop (page 7-17) RELATED TOPICS • • • • • General Guidelines (page 7-2) Planar Conversion (page 7-4) Displaying and Modifying the Planar Histogram (page 7-17) Contour Conversion (page 7-25) Displaying and Modifying the Contour Converted Atlas (page 7-37) BIOQUANT Topographer Handbook: Planar & Contour Conversion .

choose Unselect All Arrays. The # references the original Topo data arrays used to create the Line array. See “Planar Conversion” on 7-4. 2. double click the Line=D# Array(s) to move it (or them) to the Selected box. On the system tool bar. On the Select Arrays dialog box. click the Close button. BIOQUANT Topographer Handbook: Planar & Contour Conversion . choose Exit Atlas Shop. button to center the histogram and resize it to fit the Atlas 3. On the Select Arrays dialog box. from the Select menu. in the Available Arrays box. 3. From the File menu. You should be in the Atlas Viewer. TOPIC CONTENTS Step 1: Displaying the Planar Histogram (page 7-17) Step 2: Changing the DTI Array or Line Array Parameters (page 7-20) Step 3: Saving the Planar Display to a Parameters File (page 7-24) Step 4: Retrieving the Planar Display from a Parameters File (page 7-24) RELATED TOPICS • • • • General Guidelines (page 7-2) Planar Conversion (page 7-4) Displaying and Modifying the Planar Histogram (page 7-17) Contour Conversion (page 7-25) STEP 1: DISPLAYING THE PLANAR HISTOGRAM 1. On the Planar dialog box.Page 7-17 STEP 9: EXITING THE ATLAS SHOP 1. click the Resize to Fit window. Continue with Displaying and Modifying the Planar Histogram (page 7-17). 2. PLANAR CONVERSION PROCEDURE Step 1: Selecting the Topo Arrays and Opening the Atlas Shop (page 7-4) Step 2: Backing Up the Raw Topo Array(s) (page 7-6) Step 3: Setting up for Conversion (page 7-7) Step 4: Customizing the DTI Array Parameters (page 7-8) Step 5: Defining Fiduciary Points (page 7-10) Step 6: Setting a Shift Value (page 7-14) Step 7: Choosing the Aligning Fiduciary (page 7-15) Step 8: Converting to Planar Data (page 7-16) Step 9: Exiting the Atlas Shop (page 7-17) RELATED TOPICS • • • • • General Guidelines (page 7-2) Planar Conversion (page 7-4) Displaying and Modifying the Planar Histogram (page 7-17) Contour Conversion (page 7-25) Displaying and Modifying the Contour Converted Atlas (page 7-37) DISPLAYING AND MODIFYING THE PLANAR HISTOGRAM At this point you should have already followed the Planar Conversion procedure.

Connect corresponding fiduciary points with a line. • • Choose Black Background from the Atlas menu. represented by light yellow and light green lines. 4. Examine the planar histogram in the Atlas window and decide if any of the following changes would be beneficial: • • Display the histogram on a black background. BIOQUANT Topographer Handbook: Planar & Contour Conversion .Page 7-18 Planar Histogram In this illustration there are two cell types. Choose Connect Fiduciaries from the Atlas menu.

To change vertical line spacing while in the Atlas Viewer . magnitude. left. or fill color. Move the vertical lines closer or further apart. outline color.See “Procedure: Modify a Symbol” on 720. • • Fill the space between lines with the colors assigned to the individual lobules. center).See “Modify Parameters in the Atlas Shop” on 723. To change cell symbol attributes in the Atlas Shop .Page 7-19 Planar Histogram In this illustration Connect Fiduciaries has been activated. position relative to the vertical line (right. height to width ratio. • Change any of the following cell symbol attributes: shape.See “Modify Parameters in the Atlas Shop” on 723. 5. check Fill.See “Procedure: Modify Distance Between Vertical Lines” on 7-22. Continue with Step 2: Changing the DTI Array or Line Array Parameters (page 7-20). • • To change cell symbol attributes while in the Atlas Viewer . BIOQUANT Topographer Handbook: Planar & Contour Conversion . To change vertical line spacing in the Atlas Shop . Note that the aligning fiduciary is more visible (pink line). • • • From the Atlas Menu.

position. or. magnitude. PROCEDURE: MODIFY A SYMBOL 1. outline color. The original Topo arrays can be re-selected. while still in the Atlas Viewer. TOPIC CONTENTS Modify Parameters in the Atlas Viewer (page 7-20) Modify Parameters in the Atlas Shop (page 7-23) Then continue with Step 2: Changing the DTI Array or Line Array Parameters (page 7-20).Page 7-20 DISPLAYING AND MODIFYING THE PLANAR HISTOGRAM CONTENTS Step 1: Displaying the Planar Histogram (page 7-17) Step 2: Changing the DTI Array or Line Array Parameters (page 7-20) Step 3: Saving the Planar Display to a Parameters File (page 7-24) Step 4: Retrieving the Planar Display from a Parameters File (page 7-24) RELATED TOPICS • • • • • General Guidelines (page 7-2) Planar Conversion (page 7-4) Displaying and Modifying the Planar Histogram (page 7-17) Contour Conversion (page 7-25) Displaying and Modifying the Contour Converted Atlas (page 7-37) STEP 2: CHANGING THE DTI ARRAY OR LINE ARRAY PARAMETERS The DTI and LINE array parameters can be changed in two ways. the DTI and LINE Array comments can be modified on the Select Arrays dialog box. height to width ratio. a symbol’s shape. the Atlas Shop opened. and the distance between vertical lines may be adjusted. and different DTI Array Parameters assigned. or fill color may be changed. Many people prefer to remain in the Atlas Viewer and manually edit DTI and LINE array comments. DISPLAYING AND MODIFYING THE PLANAR HISTOGRAM CONTENTS Step 1: Displaying the Planar Histogram (page 7-17) Step 2: Changing the DTI Array or Line Array Parameters (page 7-20) Step 3: Saving the Planar Display to a Parameters File (page 7-24) Step 4: Retrieving the Planar Display from a Parameters File (page 7-24) RELATED TOPICS • • • • • General Guidelines (page 7-2) Planar Conversion (page 7-4) Displaying and Modifying the Planar Histogram (page 7-17) Contour Conversion (page 7-25) Displaying and Modifying the Contour Converted Atlas (page 7-37) MODIFY PARAMETERS IN THE ATLAS VIEWER While in the Atlas Viewer. Do the following to determine the DTI array to be edited: BIOQUANT Topographer Handbook: Planar & Contour Conversion .

b. Then from the Atlas menu. On Select Arrays. Note that D4 and D5 are referenced as the DTI arrays.No comment Rectangle S1. R0. Select Arrays The D4 DTI array is highlighted with its Name and Comment displayed. On Select Arrays. These entries reference the DTI arrays used in the Planar display. On Select Arrays. a. click the Expand menu to display the Name and Comment fields. DTI Array Comment Table: Shape: DTI Array Comment: Line Default . modify the comment of the symbol parameter.3.4. BIOQUANT Topographer Handbook: Planar & Contour Conversion .Page 7-21 Select Arrays The D6 Line=D1 array is highlighted with its Name and Comment displayed.5.0. choose Redraw to update the display. R3. 3. in the Comment Field for the DTI Array. R0.0. 2. Ellipse S2 Ratio: (Height/Width) 3/10 2/5 1/2 3/5 1/1 2/1 3/1 DTI Array Comment: R0.No Comment R2. Default . R0.6. The D# part of the Line array’s name references the raw data array from which it was created. click the Expand menu. with the Line =D# array highlighted. In the Comment note any DTI=D# entries.

5 M0. F9. in the Comment Field for the Line=D# Array. Position: Left Center Right Color: Blue Red Pink Light Green Light Blue Light Yellow Dark Grey Dark Blue Brown Dark Purple Dark Green Teal Black Light Grey DTI Array Comment: P2. in the Available Arrays box. it might be useful to increase the Mag. C8. F7. comment does not exist. F6. C9.000000. C5. On Select Arrays. C3.No comment P1. C4. Fill Color No comment F2.No comment 2 M2. 2. If you have an extremely large number of cell counts. Plus any user customized magnitude. click the Expand menu to display the Name and Comment fields. F8. Shift: Line Array Comment: BIOQUANT Topographer Handbook: Planar & Contour Conversion . If the S=#. C12. 3. add it.05 M0. comment. F5. Decrease the number to decrease the distance between the lines. C6. If you have a small number of cells. C7. 0. DTI Array Comment: Outline Color No comment C2. Select Arrays The D6 Line array is highlighted and its Name and Comment. The Mag can also be changed at a later point. 3 M3. F14. On Select Arrays.500000 1 Default . F4. Mag: DTI Array Comment: 0. Increase the number to increase the distance between the lines. F13. F10. F11.Page 7-22 Magnitude: DTI Array Comment: The height and width of the symbol are multiplied by the Magnitude. C10. modify the S=#. C14. On Select Arrays.000000. it might be useful to type in a Mag that is less than 1. C11. click to highlight the Line Array. F12. Default . PROCEDURE: MODIFY DISTANCE BETWEEN VERTICAL LINES 1.050000. F3. C13. It is important to have the same Mag for all DTI arrays in a study.

de-select the LINE array(s). 4. from the Tools menu. button to update the histogram display with the Continue with Step 3: Saving the Planar Display to a Parameters File (page 7-24). 1.No comment 2 S=2. 8. then select the Master Raw Topo array we created earlier. 5. c. 6. From the File menu. The Atlas Shop will open with In the Atlas Shop. Close the Planar dialog box when finished. BIOQUANT Topographer Handbook: Planar & Contour Conversion . Click the Atlas Shop Section Mode active. 4. b.Page 7-23 1 Default . 7. Plus any user customized shift value. DISPLAYING AND MODIFYING THE PLANAR HISTOGRAM CONTENTS Step 1: Displaying the Planar Histogram (page 7-17) Step 2: Changing the DTI Array or Line Array Parameters (page 7-20) Step 3: Saving the Planar Display to a Parameters File (page 7-24) Step 4: Retrieving the Planar Display from a Parameters File (page 7-24) RELATED TOPICS • • • • • General Guidelines (page 7-2) Planar Conversion (page 7-4) Displaying and Modifying the Planar Histogram (page 7-17) Contour Conversion (page 7-25) Displaying and Modifying the Contour Converted Atlas (page 7-37) MODIFY PARAMETERS IN THE ATLAS SHOP DTI cell and LINE parameters may be modified by returning to the Atlas Shop and choosing different parameters on the DTI Array Parameters dialog box. 3 S=3. d. In the Atlas Viewer. button to update the Atlas window with the 2. click the Redraw new parameters. 3. choose Exit Atlas Shop. 5. a. Parameters in the Symbol Shape region Parameters in the Position region Parameters in the Color region The Shift value from the Tools>Shift menu. click the Redraw original atlas. On the Atlas Viewer’s system tool bar. On the Atlas Viewer’s system tool bar. Change any of the following parameters for the DTI Arrays: DO NOT Add Fiduciary Points again or convert data. button (or choose File> Atlas Shop on the menu bar). Continue with Step 3: Saving the Planar Display to a Parameters File (page 7-24). The original DTI arrays with previous parameters are listed. choose Planar Conversion to open the Planar dialog box. on the Select Arrays dialog box.

Note: If you were saving a parameters file for the original Section data. For ease of finding the parameters file again. Note: The parameters files can also be used to quickly load and center the original Section Topo data using the same procedure. choose Load Parameters to open the Open Parameter File box. 6. orientation. 2. PROCEDURE 1. Make sure that the Line Array is selected and the Planar Display is that way you want it in the Atlas window. These files allow one atlas to have many views quickly accessed by loading parameter files. it is recommended that you create a subdirectory in the Topographer folder that is named the same as your Data Volume and Data Set. as well as the selected array list. 5. any Parameter file for it can be loaded. BIOQUANT Topographer Handbook: Planar & Contour Conversion . Parameters file automatically selects the arrays and sets the zoom. From the File menu. the Topo Section Z# arrays would be selected and displayed in the Atlas window at this step. choose Save Parameters open the Save Parameter file dialog box. 3. 4.Page 7-24 DISPLAYING AND MODIFYING THE PLANAR HISTOGRAM CONTENTS Step 1: Displaying the Planar Histogram (page 7-17) Step 2: Changing the DTI Array or Line Array Parameters (page 7-20) Step 3: Saving the Planar Display to a Parameters File (page 7-24) Step 4: Retrieving the Planar Display from a Parameters File (page 7-24) RELATED TOPICS • • • • • General Guidelines (page 7-2) Planar Conversion (page 7-4) Displaying and Modifying the Planar Histogram (page 7-17) Contour Conversion (page 7-25) Displaying and Modifying the Contour Converted Atlas (page 7-37) STEP 3: SAVING THE PLANAR DISPLAY TO A PARAMETERS FILE The Planar Display can be saved to a Parameters file. From the File menu. 1. Parameter files save the zoom. The Parameters file is a *. Click the OK button to save the Parameters file. pan. Continue with Step 4: Retrieving the Planar Display from a Parameters File (page 7-24). Type a file name into the File Name: text box. and rotation of an atlas. DISPLAYING AND MODIFYING THE PLANAR HISTOGRAM CONTENTS Step 1: Displaying the Planar Histogram (page 7-17) Step 2: Changing the DTI Array or Line Array Parameters (page 7-20) Step 3: Saving the Planar Display to a Parameters File (page 7-24) Step 4: Retrieving the Planar Display from a Parameters File (page 7-24) RELATED TOPICS • • • • • General Guidelines (page 7-2) Planar Conversion (page 7-4) Displaying and Modifying the Planar Histogram (page 7-17) Contour Conversion (page 7-25) Displaying and Modifying the Contour Converted Atlas (page 7-37) STEP 4: RETRIEVING THE PLANAR DISPLAY FROM A PARAMETERS FILE Once a data set is opened. The default Save in location is BQOSTEO\Topographer or BQLifescience\Topographer. and orientation settings for an Atlas.set file type. Then when you later need to find and open the parameter files for a particular Data Set you can easily navigate to them. pan.

The default location for saving parameter files is BQOSTEO\Topographer. TOPIC CONTENTS Step 1: Selecting the Topo Arrays and Opening the Atlas Shop (page 7-26) Step 2: Backing Up the Raw Topo Array(s) (page 7-27) Step 3: Setting up for Conversion (page 7-28) Step 4: Customizing the DTI Array Parameters (page 7-29) Step 5: Defining Fiduciary Points (page 7-31) Step 6: Setting a Shift Value (page 7-35) Step 7: Converting to Contour Data (page 7-36) Step 8: Exiting the Atlas Shop (page 7-36) RELATED TOPICS • • • • • General Guidelines (page 7-2) Planar Conversion (page 7-4) Displaying and Modifying the Planar Histogram (page 7-17) Contour Conversion (page 7-25) Displaying and Modifying the Contour Converted Atlas (page 7-37) BIOQUANT Topographer Handbook: Planar & Contour Conversion . Navigate to the folder that contains the Parameter file for the current data set. The Contour Converted atlas is displayed in the Topographer’s Atlas Viewer. DISPLAYING AND MODIFYING THE PLANAR HISTOGRAM CONTENTS Step 1: Displaying the Planar Histogram (page 7-17) Step 2: Changing the DTI Array or Line Array Parameters (page 7-20) Step 3: Saving the Planar Display to a Parameters File (page 7-24) Step 4: Retrieving the Planar Display from a Parameters File (page 7-24) ADDITIONAL OUTPUT NOTES The Planar Display can also be printed and saved as a Bitmap or Metafile. Click on the Parameter file to be opened. Once the data has been collected. See the Topographer Data Collection section of the BIOQUANT Life Science help or manual. it will be listed here. RELATED TOPICS • • • • • General Guidelines (page 7-2) Planar Conversion (page 7-4) Displaying and Modifying the Planar Histogram (page 7-17) Contour Conversion (page 7-25) Displaying and Modifying the Contour Converted Atlas (page 7-37) CONTOUR CONVERSION Contour Conversion in the Topographer’s Atlas Shop converts Topo data so that cell populations are represented by symbols that appear along section outline tracings. If you created a subdirectory associated with your Data Volume and Data Set as recommended in the Save Parameters procedure. return to this section for instruction on how to use the Topographer’s planar and contour conversion tools. Actual data collection for Planar or Contour Conversion is done in BIOQUANT Life Science. 4. DATA COLLECTION NOTE This section just provides a protocol for using Contour Conversion after data has been correctly collected in BIOQUANT Life Science. or Exporting an Atlas” on page 5-34. Copying. The atlas will change to reflect the loaded parameters 3. Click the OK button.Page 7-25 2. See “Printing.

3. 2. On the Select Arrays dialog box. button on the system tool bar. The Topo arrays selected will be used to create special DTI and Contour arrays to display converted data. Click the Atlas Shop button (or choose Atlas Shop from the Tools menu). The Topographer opens into the Atlas Viewer. BIOQUANT Topographer Handbook: Planar & Contour Conversion . At this point only Topo arrays should be selected. Atlas Window Resize to Fit centers the topographic map. click Topographer to execute the BIOQUANT Topographer program. On BIOQUANT Life Science’s or BIOQUANT OSTEO’s system menu bar. Click the Open Atlas Click the Resize To Fit button on the system tool bar (or choose Open from the Atlas menu). 4. The Atlas Shop will open with Section Mode active. 5.Page 7-26 STEP 1: SELECTING THE TOPO ARRAYS AND OPENING THE ATLAS SHOP 1. select the one or more Topo arrays that contain data to be converted.

click the New Array button to add a new Topo array to the data set. Continue with Step 2: Backing Up the Raw Topo Array(s) (page 7-27). On the Save Array As dialog box. choose Save As. TOPIC CONTENTS Step 1: Selecting the Topo Arrays and Opening the Atlas Shop (page 7-26) Step 2: Backing Up the Raw Topo Array(s) (page 7-27) Step 3: Setting up for Conversion (page 7-28) Step 4: Customizing the DTI Array Parameters (page 7-29) Step 5: Defining Fiduciary Points (page 7-31) Step 6: Setting a Shift Value (page 7-35) Step 7: Converting to Contour Data (page 7-36) Step 8: Exiting the Atlas Shop (page 7-36) RELATED TOPICS • • • • • General Guidelines (page 7-2) Planar Conversion (page 7-4) Displaying and Modifying the Planar Histogram (page 7-17) Contour Conversion (page 7-25) Displaying and Modifying the Contour Converted Atlas (page 7-37) STEP 2: BACKING UP THE RAW TOPO ARRAY(S) Before we go further we will copy the data from the selected Topo array(s) into a new Topo array. We will perform the Contour Conversion on the new Topo array to preserve the integrity of the raw Topo arrays. from the File menu. In the Array Name edit file. 3.Page 7-27 Atlas Shop 6. 2. BIOQUANT Topographer Handbook: Planar & Contour Conversion . In the Atlas Shop. In this way we can always make a new copy of the raw Topo arrays in the future. PROCEDURE 1. 4. rename the new Topo array to “Master Raw Topo Data.” Click the Save button.

in the Available Arrays list. c. choose Save. button on the system tool bar to scale the atlas to the size of the From the Select menu.Page 7-28 5. on Select Arrays. 9. choose Select All Sections. TOPIC CONTENTS Step 1: Selecting the Topo Arrays and Opening the Atlas Shop (page 7-26) Step 2: Backing Up the Raw Topo Array(s) (page 7-27) Step 3: Setting up for Conversion (page 7-28) Step 4: Customizing the DTI Array Parameters (page 7-29) Step 5: Defining Fiduciary Points (page 7-31) Step 6: Setting a Shift Value (page 7-35) Step 7: Converting to Contour Data (page 7-36) Step 8: Exiting the Atlas Shop (page 7-36) RELATED TOPICS • • • • • General Guidelines (page 7-2) Planar Conversion (page 7-4) Displaying and Modifying the Planar Histogram (page 7-17) Contour Conversion (page 7-25) Displaying and Modifying the Contour Converted Atlas (page 7-37) STEP 3: SETTING UP FOR CONVERSION 1. From the File menu. Continue with Step 3: Setting up for Conversion (page 7-28). click the Resize to Fit work space. In the Atlas Viewer. choose Align Sections. The Atlas Shop will open with Section Mode active. BIOQUANT Topographer Handbook: Planar & Contour Conversion . 7. choose Unselect All Arrays. At this point there should not be any arrays selected. The map drawn should equal the map generated from the raw Topo data. Click the Resize To Fit button on the system tool bar. 6. Click the Atlas Shop button (or choose Atlas Shop from the Tools menu). 8. “Master Raw Topo Data” to move it to the Selected list. d. On Select Arrays. The sections rotate so that the start points on all sections are aligned. b. from the File menu. 2. From the Edit menu. From the Tools menu. choose Contour Conversion to open the Contour dialog box. (Optional) Align the rotation of all the sections by doing the following: a. double click Topo array we just added. 10. In the Atlas Shop. If necessary. choose Exit Atlas Shop. from the Select menu. You are returned to the Atlas Viewer.

The height of the Line is always 1. magnitude. Continue with Step 4: Customizing the DTI Array Parameters (page 7-29). PROCEDURE: CUSTOMIZING DTI PARAMETERS 1. Cell types are identified by color. placement. one DTI array is listed (and added to the current data set) for each cell type in the selected Topo arrays. height to width ratio. In the DTI Array(s) box.Page 7-29 Contour One DTI array is automatically displayed for each cell type that was counted. and color parameters of the symbol are customizable. Symbol parameters that are changed from the default are automatically saved to the corresponding DTI array’s comment. BIOQUANT Topographer Handbook: Planar & Contour Conversion . color. The shape. 2. In this illustration. Cell data in this case is point data collected with an Object Count array. 3. the atlas contains two cell types. TOPIC CONTENTS Step 1: Selecting the Topo Arrays and Opening the Atlas Shop (page 7-26) Step 2: Backing Up the Raw Topo Array(s) (page 7-27) Step 3: Setting up for Conversion (page 7-28) Step 4: Customizing the DTI Array Parameters (page 7-29) Step 5: Defining Fiduciary Points (page 7-31) Step 6: Setting a Shift Value (page 7-35) Step 7: Converting to Contour Data (page 7-36) Step 8: Exiting the Atlas Shop (page 7-36) RELATED TOPICS • • • • • General Guidelines (page 7-2) Planar Conversion (page 7-4) Displaying and Modifying the Planar Histogram (page 7-17) Contour Conversion (page 7-25) Displaying and Modifying the Contour Converted Atlas (page 7-37) STEP 4: CUSTOMIZING THE DTI ARRAY PARAMETERS DTI ARRAY EXPLANATION When the Planar dialog box opens. A symbol is used to represent the cell population at each data point along the specimen contour line. In the Symbol Shape region. choose one of the following shapes: • Line: Represents the cell type using a line. click to highlight the first DTI array.

No Comment 2/1 R2. Moving the slider to the right increases the ratio. Ratios less than 1 do not affect the Line shape because the Line’s height is always 1. Position: DTI Array Comment: Left P2.0. Shape: DTI Array Comment: Line Default . move the Ratio slider to the desired position. The default shape is Line. Moving the slider to the left decreases the height to width ratio. 3. 3/5 R0.No comment Rectangle S1. Mag: DTI Array Comment: 0. The rectangle defaults to a height and width of 1. It is important to have the same Mag for all DTI arrays in a study.4. Pink C3. 2/5 R0. The ratio range available with the slider is between 0. Ellipse S2. If you have an extremely large number of cell counts. BIOQUANT Topographer Handbook: Planar & Contour Conversion . The position of the shape to the contour line in the preview box changes to match the position chosen.000000. choose either Left.0. Color: DTI Array Comment: Blue No comment Red C2. first click the Outline radio button. The height and width of the symbol are multiplied by the Magnitude. In the Color region. If you have a small number of cells. Light Blue C5. The Mag can also be changed at a later point. 1/1 Default . in the Mag edit box. 6. The shape in the preview box changes to match the symbol type chosen. The height is the Y distance from the vertical line.000000. 3 M3.05 M0.6. 0.Page 7-30 • Rectangle: Represent the cell type using a rectangle. type the desired magnitude. it might be useful to type in a Mag that is less than 1.No comment Right P1. The Ratio determines the symbol’s height to width ratio. • Ellipse: Represent the cell type using an ellipse.500000 1 Default . 1/2 R0.3 and 3. Center Default . To change the outline color of the symbol for this cell type. 3/1 R3. reading left to right. The default position is Center.5 M0. The Ellipse defaults to a height and width of 1. In the Symbol Shape region. The width is the X distance along the vertical line. Ratio: DTI Array Comment: (Height/Width) 3/10 R0.No comment 2 M2. The color numbers increment by one for each remaining color in the palette. or Right to indicate the orientation of the symbol to the line. The default ratio is 1. 4. then click the desired color.5. the Outline color of the symbol defaults to the original cell type measurement color.3. In the Symbol Shape region. it might be useful to increase the Mag.050000. 5. Light Green C4. In the Position region. Center.

The Contour Array holds the information needed to display the specimen contour’s lobules in different colors. this procedure is more complicated. Repeat from step 1 for each DTI array in the DTI array(s) box. ADDITIONAL NOTES • • • 9. reading left to right. first click the Fill radio button. TOPIC CONTENTS Step 1: Selecting the Topo Arrays and Opening the Atlas Shop (page 7-26) Step 2: Backing Up the Raw Topo Array(s) (page 7-27) Step 3: Setting up for Conversion (page 7-28) Step 4: Customizing the DTI Array Parameters (page 7-29) Step 5: Defining Fiduciary Points (page 7-31) Step 6: Setting a Shift Value (page 7-35) Step 7: Converting to Contour Data (page 7-36) Step 8: Exiting the Atlas Shop (page 7-36) RELATED TOPICS • • • • • General Guidelines (page 7-2) Planar Conversion (page 7-4) Displaying and Modifying the Planar Histogram (page 7-17) Contour Conversion (page 7-25) Displaying and Modifying the Contour Converted Atlas (page 7-37) STEP 5: DEFINING FIDUCIARY POINTS CONTOUR ARRAY EXPLANATION A Contour Array is created when Topo data are converted to Contour data. The BIOQUANT Topographer Handbook: Planar & Contour Conversion . the Fill color of the symbol defaults to the original cell type measurement color. The user adds fiduciary points on the specimen contour where each lobule begins. Light Green F4. The color numbers increment by one for each remaining color in the palette. Color: DTI Array Comment: Blue No comment Red F2. If all sections have all lobules. The DTI parameters can also be changed at a later point. Pink F3. manually type the desired parameter into the comment of the DTI array. To change the fill color of the symbol for this cell type. In the Color region. Continue with Step 5: Defining Fiduciary Points (page 7-31). Fill is not available for the Line symbol. TOPIC CONTENTS Procedure ONE: Defining Fiduciary Points (page 7-32) Procedure TWO: Going to the Next Outline (page 7-34) Then continue with Step 6: Setting a Shift Value (page 7-35) IMPORTANT NOTE It is important to sequence through your sections before this procedure and become familiar with how the lobules are organized within the sections. then click the desired color. If some lobules are missing. It is important to have the same Mag for all DTI arrays in a study. Light Blue F5. 8.Page 7-31 7. especially from the middle of a contour. If the ratio parameters offered do not meet requirements. then this procedure is straight-forward. The system represents each lobule by a different colored segment.

check Selection Only to display only the current section. or from the Edit menu.Page 7-32 goal is to make it so that the color coded lobules are the same lobules in each section. click the Add Fiduciary Points button. click once at the beginning of each lobule. using the following pointers. BIOQUANT Topographer Handbook: Planar & Contour Conversion . On the Contour dialog box. Then. choose Add Fiduciaries. On the specimen contour for the first section click once at the beginning of the lobule that you want to be the starting point. Atlas Shop 2. in a counter-clockwise direction. If the sections in the background decrease the visibility of the current section. Add a fiduciary marker at the beginning of each lobule. from the View menu. The pointer changes to the Add Fiduciary cursor. TOPIC CONTENTS Step 1: Selecting the Topo Arrays and Opening the Atlas Shop (page 7-26) Step 2: Backing Up the Raw Topo Array(s) (page 7-27) Step 3: Setting up for Conversion (page 7-28) Step 4: Customizing the DTI Array Parameters (page 7-29) Step 5: Defining Fiduciary Points (page 7-31) Step 6: Setting a Shift Value (page 7-35) Step 7: Converting to Contour Data (page 7-36) Step 8: Exiting the Atlas Shop (page 7-36) RELATED TOPICS • • • • • General Guidelines (page 7-2) Planar Conversion (page 7-4) Displaying and Modifying the Planar Histogram (page 7-17) Contour Conversion (page 7-25) Displaying and Modifying the Contour Converted Atlas (page 7-37) PROCEDURE ONE: DEFINING FIDUCIARY POINTS 1.

The fiduciary marker disappears. take care that the lobule color assignment matches corresponding lobules on other sections. click the right mouse button to exit Add Fiduciary Point mode. You want the lobules that do exist to show up in the correct sequenced segment color for comparison to other sections. then repeat to delete all fiduciary points on the current section. click the Delete Fiduciary Point Delete Fiduciary. In this case use Add Fiduciary Points to redefine the points. v. The pointer changes to the Delete Fiduciary cursor. After misplaced fiduciary points have been moved. delete all the fiduciary points for the section and start over. or from the Edit menu. choose iii. button. click the Move Fiduciary Point Move Fiduciary. v. click the right mouse button to exit Delete Fiduciary mode. choose • iii. On the Planar dialog box. click the Add Fiduciary Points button. If you need to re-arrange the order of the fiduciary points. After all fiduciary points have been defined for this section. 3. click two fiduciary points very close together to skip that color. If a lobule in the middle of a contour does not exist for a particular section. If the color coding gets messed up. BIOQUANT Topographer Handbook: Planar & Contour Conversion . You need to add fiduciary points in the same order. button. There are special rules for deleting fiduciary points. iv. On the specimen contour for the current section click once on the fiduciary to be deleted. On the specimen contour for the current section click once at on the fiduciary to be moved to make it disappear. On the Planar dialog box. as long as you do not move it before a preceding fiduciary point or after a following fiduciary points. do the following Moving a fiduciary point will not mess up the color assignment of the lobule. After unwanted fiduciary points have been deleted. This prevents the lobule color assignment from messing up. ii. do the following: i. Click the right mouse button to exit the Add Fiduciary Point mode. then it may be deleted by itself. click the right mouse button to exit Move Fiduciary mode. If the point is NOT THE LAST on the contour. iv. The pointer changes to the Move Fiduciary cursor. ii. Repeat for all fiduciary points to be moved. To move a fiduciary point along the contour. Then click the specimen contour at the location the fiduciary point should be. click the Add Fiduciary Points button. starting at the same location. The markers sequence through the colors on the color palette. for each section to avoid confusion caused by different colored markers. • If more fiduciary points need to be added. If more fiduciary points need to be added. If the fiduciary point is not the last on the contour. i. then all the fiduciary points must be deleted on the contour. Click the right mouse button to exit the Add Fiduciary Point mode.Page 7-33 POINTERS • • • A fiduciary marker is placed on the specimen contour at each location clicked. or from the Edit menu. To delete fiduciary points. If the point to be deleted IS THE LAST on the contour.

Follow the procedure to set fiduciary points as previously described in “Procedure ONE: Defining Fiduciary Points” on page 7-11. 2.Page 7-34 4. Atlas Shop When you sequence back to the a section that already has fiduciary markers defined. they show up as larger points. TOPIC CONTENTS Step 1: Selecting the Topo Arrays and Opening the Atlas Shop (page 7-26) Step 2: Backing Up the Raw Topo Array(s) (page 7-27) Step 3: Setting up for Conversion (page 7-28) Step 4: Customizing the DTI Array Parameters (page 7-29) Step 5: Defining Fiduciary Points (page 7-31) Step 6: Setting a Shift Value (page 7-35) Step 7: Converting to Contour Data (page 7-36) Step 8: Exiting the Atlas Shop (page 7-36) RELATED TOPICS • • • • • General Guidelines (page 7-2) Planar Conversion (page 7-4) Displaying and Modifying the Planar Histogram (page 7-17) Contour Conversion (page 7-25) Displaying and Modifying the Contour Converted Atlas (page 7-37) PROCEDURE TWO: GOING TO THE NEXT OUTLINE After the Fiduciary Points are in the correct locations on the first contour outline. When all Fiduciary Points have been set. or from the Edit menu. BIOQUANT Topographer Handbook: Planar & Contour Conversion . choose Next Outline. Continue with Step 6: Setting a Shift Value (page 7-35). If you want to return to edit DTI array parameters at a later point. do the following: 1. you will not need to re-define the fiduciary points. This saves the positions of the fiduciary points to the array. from the Contour dialog box File menu. click the Next Outline button. 3. On the Contour dialog box. or if you want to do a Planar Conversion at a later point. choose Save Fiduciary(s).

On Planar dialog box. type the desired value. On the Shift dialog box.No comment 2 S=2.Page 7-35 ADDITIONAL INFORMATION • • • • 4. from the View menu. Shift: Line Array Comment: 1 Default . 3 S=3. 2. PROCEDURE: ENTERING A SHIFT VALUE 1. choose Define Shift to open the Planar Shift dialog box. Shift multiplies the Z value by the number entered. Shift In this example. BIOQUANT Topographer Handbook: Planar & Contour Conversion . The Shift can be modified later. To refresh existing fiduciary points. a shift of 5 has been entered. If the Shift value is changed from the default. click the RD button on the tool bar. check Selection Only to display only the active section. When an outline is reached that already has fiduciary points. from the Tools menu. To refresh the display. the markers are drawn larger to indicate that the section has already been marked. by adding or modifying the Line Array Comment. If the sections in the background decrease the visibility of the current section. in the Shift edit box. it adds a S=#. The default Shift value is 1. comment to the Line array. Continue with Step 6: Setting a Shift Value (page 7-35). TOPIC CONTENTS Step 1: Selecting the Topo Arrays and Opening the Atlas Shop (page 7-26) Step 2: Backing Up the Raw Topo Array(s) (page 7-27) Step 3: Setting up for Conversion (page 7-28) Step 4: Customizing the DTI Array Parameters (page 7-29) Step 5: Defining Fiduciary Points (page 7-31) Step 6: Setting a Shift Value (page 7-35) Step 7: Converting to Contour Data (page 7-36) Step 8: Exiting the Atlas Shop (page 7-36) RELATED TOPICS • • • • • General Guidelines (page 7-2) Planar Conversion (page 7-4) Displaying and Modifying the Planar Histogram (page 7-17) Contour Conversion (page 7-25) Displaying and Modifying the Contour Converted Atlas (page 7-37) STEP 6: SETTING A SHIFT VALUE SHIFT EXPLANATION The Shift determines the distance between the vertical lines used to represent the specimen contour. click the Add Fiduciary Points button.

Before converting make sure that the DTI Array parameters have been defined and that the fiduciary points have been set. PROCEDURE: CONVERTING TO PLANAR DATA 1. or color parameters are changed at a later point. It creates the Contour Array from the raw topo data and fills the DTI Arrays with cell references to the Contour Array from the Cell topo data. choose Perform 3. If the DTI Array symbol shape. TOPIC CONTENTS Step 1: Selecting the Topo Arrays and Opening the Atlas Shop (page 7-26) Step 2: Backing Up the Raw Topo Array(s) (page 7-27) Step 3: Setting up for Conversion (page 7-28) Step 4: Customizing the DTI Array Parameters (page 7-29) Step 5: Defining Fiduciary Points (page 7-31) Step 6: Setting a Shift Value (page 7-35) Step 7: Converting to Contour Data (page 7-36) Step 8: Exiting the Atlas Shop (page 7-36) RELATED TOPICS • • • • • General Guidelines (page 7-2) Planar Conversion (page 7-4) Displaying and Modifying the Planar Histogram (page 7-17) Contour Conversion (page 7-25) Displaying and Modifying the Contour Converted Atlas (page 7-37) STEP 8: EXITING THE ATLAS SHOP 1. or if the Contour Array shift parameter is changed at a later point. BIOQUANT Topographer Handbook: Planar & Contour Conversion . click the Perform Conversion Conversion to convert the data to the Contour Array. Be patient. you do not need to re-convert the Contour Array. position. TOPIC CONTENTS Step 1: Selecting the Topo Arrays and Opening the Atlas Shop (page 7-26) Step 2: Backing Up the Raw Topo Array(s) (page 7-27) Step 3: Setting up for Conversion (page 7-28) Step 4: Customizing the DTI Array Parameters (page 7-29) Step 5: Defining Fiduciary Points (page 7-31) Step 6: Setting a Shift Value (page 7-35) Step 7: Converting to Contour Data (page 7-36) Step 8: Exiting the Atlas Shop (page 7-36) RELATED TOPICS • • • • • General Guidelines (page 7-2) Planar Conversion (page 7-4) Displaying and Modifying the Planar Histogram (page 7-17) Contour Conversion (page 7-25) Displaying and Modifying the Contour Converted Atlas (page 7-37) STEP 7: CONVERTING TO CONTOUR DATA CONVERTING EXPLANATION Converting redefines the Topo data as Contour data.Page 7-36 3. On Contour dialog box. The parameter changes made will be automatically updated. or from the Tools menu. On the Contour dialog box. 2. click the Close button. This step may take awhile. Continue with Step 8: Exiting the Atlas Shop (page 7-36). button. Continue with Step 7: Converting to Contour Data (page 7-36).

(Optional) From the Atlas menu. NOTE: The names of DTI arrays also include the word “Contour.” but DTI array names do NOT include an equal (=) sign. Continue with Displaying and Modifying the Contour Converted Atlas (page 7-37). then the Resize to Fit button. to center and resize the 3. in the Available Arrays list. click the Redraw converted atlas in the Atlas window.Page 7-37 2. 4. 2. choose Black Background. On the system tool bar. BIOQUANT Topographer Handbook: Planar & Contour Conversion . choose Unselect All Arrays. double click the Contour=D# array to move it to the Selected list. choose Exit Atlas Shop. 3. button. From the File menu. On the Select Arrays dialog box. On the Select Arrays dialog box. TOPIC CONTENTS Step 1: Selecting the Topo Arrays and Opening the Atlas Shop (page 7-26) Step 2: Backing Up the Raw Topo Array(s) (page 7-27) Step 3: Setting up for Conversion (page 7-28) Step 4: Customizing the DTI Array Parameters (page 7-29) Step 5: Defining Fiduciary Points (page 7-31) Step 6: Setting a Shift Value (page 7-35) Step 7: Converting to Contour Data (page 7-36) Step 8: Exiting the Atlas Shop (page 7-36) RELATED TOPICS • • • • • General Guidelines (page 7-2) Planar Conversion (page 7-4) Displaying and Modifying the Planar Histogram (page 7-17) Contour Conversion (page 7-25) Displaying and Modifying the Contour Converted Atlas (page 7-37) DISPLAYING AND MODIFYING THE CONTOUR CONVERTED ATLAS TOPIC CONTENTS Step 1: Displaying the Converted Atlas (page 7-37) Step 2: Changing the DTI or Contour Array Parameters (page 7-39) Step 3: Saving a Parameters File (page 7-42) Step 4: Loading a Parameters File (page 7-43) RELATED TOPICS • • • • • General Guidelines (page 7-2) Planar Conversion (page 7-4) Displaying and Modifying the Planar Histogram (page 7-17) Contour Conversion (page 7-25) Displaying and Modifying the Contour Converted Atlas (page 7-37) STEP 1: DISPLAYING THE CONVERTED ATLAS 1. from the Select menu.

DISPLAYING AND MODIFYING THE CONTOUR CONVERSION PROTOCOL: Step 1: Displaying the Converted Atlas (page 7-37) Step 2: Changing the DTI or Contour Array Parameters (page 7-39) Step 3: Saving a Parameters File (page 7-42) Step 4: Loading a Parameters File (page 7-43) RELATED TOPICS • • • • • General Guidelines (page 7-2) Planar Conversion (page 7-4) Displaying and Modifying the Planar Histogram (page 7-17) Contour Conversion (page 7-25) Displaying and Modifying the Contour Converted Atlas (page 7-37) BIOQUANT Topographer Handbook: Planar & Contour Conversion . position relative to the contour outline (right. one represented by red squares and the other represented by blue circles.See “Modify Converted Atlas Parameters in the Atlas Viewer” on 7-39.Page 7-38 Contour Converted Atlas In this illustration there are two different types of cells. height to width ratio. or fill color. magnitude. • • • To change cell symbol attributes while in the Atlas Viewer . 6. Continue with Step 2: Changing the DTI or Contour Array Parameters (page 7-39). To change cell symbol attributes in the Atlas Shop . Increase the Shift value so contour tracings are not stacked so closely on top of each other. center).See “Modify Converted Atlas Parameters in the Atlas Shop” on 7-41. Examine the Contour Converted atlas and decide if any of the following changes would be beneficial: • • Display the atlas on an alternate colored background. left. 5. Change any of the following cell symbol attributes: shape. • Check or uncheck Black Background on the Atlas menu.

a symbol’s shape. with the Contour =D# array highlighted. On Select Arrays. 2. On Select Arrays. do the following: Select Arrays The D16 Contour=D1 array is highlighted with its Name and Comment displayed. Many people prefer to remain in the Atlas Viewer and manually edit DTI and Contour array comments. the DTI and Contour array comments can be modified on the Select Arrays dialog box.Page 7-39 STEP 2: CHANGING THE DTI OR CONTOUR ARRAY PARAMETERS The DTI and Contour array parameters can be changed in two ways. click to highlight one of the DTI=D#:Contour D# array that was referenced in the Contour array to edit it. Note that D8 and D9 are referenced as the DTI arrays. The original Master Raw Topo array can be reselected. TOPIC CONTENTS Modify Converted Atlas Parameters in the Atlas Viewer (page 7-39) Modify Converted Atlas Parameters in the Atlas Shop (page 7-41) Then continue with Step 3: Saving a Parameters File (page 7-42). On Select Arrays. BIOQUANT Topographer Handbook: Planar & Contour Conversion . click the Expand menu to display the Name and Comment fields. height to width ratio. magnitude. These entries reference the DTI arrays used in the Contour display. The D# part of the Contour array’s name references the raw data array from which it was created. To determine the DTI arrays associated with the Contour array. or. or fill color may be changed. click the Expand menu. position. and the distance between vertical lines may be adjusted. outline color. and different DTI Array Parameters assigned. a. b. in the Available Arrays box. the Atlas Shop opened. PROCEDURE: MODIFY A SYMBOL 1. In the Comment note any DTI=D# entries. while still in the Atlas Viewer. The Contour D# portion of this arrays name references the raw data array from which it was created. DISPLAYING AND MODIFYING THE CONTOUR CONVERSION PROTOCOL: Step 1: Displaying the Converted Atlas (page 7-37) Step 2: Changing the DTI or Contour Array Parameters (page 7-39) Step 3: Saving a Parameters File (page 7-42) Step 4: Loading a Parameters File (page 7-43) RELATED TOPICS • • • • • General Guidelines (page 7-2) Planar Conversion (page 7-4) Displaying and Modifying the Planar Histogram (page 7-17) Contour Conversion (page 7-25) Displaying and Modifying the Contour Converted Atlas (page 7-37) MODIFY CONVERTED ATLAS PARAMETERS IN THE ATLAS VIEWER While in the Atlas Viewer. 3.

It is important to have the same Mag for all DTI arrays in a study. R0. DTI Array Comment: The height and width of the symbol are multiplied by the Magnitude.6.Page 7-40 Select Arrays The D8 DTI:Contour array is highlighted with its Name and Comment displayed. Then from the Atlas menu. Position: Left Center Right DTI Array Comment: P2. R0. 0. Ellipse S2 Ratio: (Height/Width) 3/10 2/5 1/2 3/5 1/1 2/1 3/1 Magnitude: DTI Array Comment: R0. R3.5. in the Comment Field for the DTI Array. The Mag can also be changed at a later point. Mag: DTI Array Comment: 0. Default .0.000000. 4. DTI Array Comment Table: Shape: DTI Array Comment: Line Default . If you have an extremely large number of cell counts. modify the comment of the symbol parameter.500000 1 Default .3. it might be useful to type in a Mag that is less than 1. BIOQUANT Topographer Handbook: Planar & Contour Conversion . Plus any user customized magnitude.5 M0.4.050000.No comment Rectangle S1.No comment 2 M2.0.No Comment R2. R0. If you have a small number of cells. Default .000000. On Select Arrays.No comment P1. 3 M3.05 M0. it might be useful to increase the Mag. choose Redraw to update the display.

F12. in the Comment Field for the Contour=D# Array. F11. On Select Arrays. F4. C5. in the Available Arrays box. F8. on the Select Arrays dialog box. Shift: Line Array Comment: 1 Default . comment. de-select the Contour=D# array. the greater the shift. The greater the number. comment does not exist. BIOQUANT Topographer Handbook: Planar & Contour Conversion . 3 S=3. 5. C12. click to highlight the Contour=D# array. 1. Fill Color No comment F2. DISPLAYING AND MODIFYING THE CONTOUR CONVERSION PROTOCOL: Step 1: Displaying the Converted Atlas (page 7-37) Step 2: Changing the DTI or Contour Array Parameters (page 7-39) Step 3: Saving a Parameters File (page 7-42) Step 4: Loading a Parameters File (page 7-43) RELATED TOPICS • • • • • General Guidelines (page 7-2) Planar Conversion (page 7-4) Displaying and Modifying the Planar Histogram (page 7-17) Contour Conversion (page 7-25) Displaying and Modifying the Contour Converted Atlas (page 7-37) MODIFY CONVERTED ATLAS PARAMETERS IN THE ATLAS SHOP DTI cell and Contour array parameters may be modified by returning to the Atlas Shop and choosing different parameters on the Contour Conversion dialog box. On Select Arrays. C3. F3. If the S=#. button to update the converted atlas display Continue with Step 3: Saving a Parameters File (page 7-42). C7. then select the original raw data Topo array. C4. add it. DTI Array Comment: Outline Color No comment C2. C8. PROCEDURE: MODIFY SHIFT DISTANCE BETWEEN CONTOUR OUTLINES On Select Arrays. Increase the number to increase the distance between the contour outlines. click the Redraw with the new parameters. F10. F5. F9. F14. On the Atlas Viewer’s system tool bar. C11. F7. Plus any user defined shift value. F13. 4. C13. C6.Page 7-41 Color: Blue Red Pink Light Green Light Blue Light Yellow Dark Grey Dark Blue Brown Dark Purple Dark Green Teal Black Light Grey 1. In the Atlas Viewer. C14. 2. modify the S=#. 3. F6. click the Expand menu to display the Name and Comment fields. Decrease the number to decrease the distance between the contour outlines. C10. C9.No comment 2 S=2.

4. the display parameters can be saved to a Parameters file. as well as the selected array list. Close the Contour dialog box (without resetting fiduciary markers or re-converting the atlas). For ease of finding the parameters file again. Choose an alternate Symbol Shape. button to update the Atlas window with the button (or choose File> Atlas Shop on the menu bar). 4. Click the Atlas Shop Section Mode active. click the Redraw original atlas. from the Tools menu. right). d. Click the OK button to save the Parameters file. center. 8. Change any of the following parameters: DO NOT reset fiduciary markers or re-convert data. 5. The default Save in location is BQOSTEO\Topographer or BQLifescience\Topographer. c. From the File menu. and rotation of an atlas. BIOQUANT Topographer Handbook: Planar & Contour Conversion . choose Exit Atlas Shop to return to the Atlas Viewer to see the results of the changes. choose Save Parameters to open the Save Parameter file dialog box. Change the Shift value (Tools>Shift menu). orientation. choose Contour Conversion to open the Contour dialog box. Type a file name into the File Name: text box. Parameter files save the zoom. the way the converted atlas looks in the Atlas window can be adjusted using options on Atlas Viewer’s Parameters dialog box. 3. The Atlas Shop will open with In the Atlas Shop. After an ideal view of the atlas is established. Then when you later need to find and open the parameter files for a particular Data Set you can easily navigate to them. The Parameters file is a *. pan. 2. 3. Continue with Step 4: Loading a Parameters File (page 7-43). b. 5.Page 7-42 2. On the Atlas Viewer’s system tool bar.set file type. it is recommended that you create a subdirectory in the Topographer folder that is named the same as your Data Volume and Data Set. DISPLAYING AND MODIFYING THE CONTOUR CONVERSION PROTOCOL: Step 1: Displaying the Converted Atlas (page 7-37) Step 2: Changing the DTI or Contour Array Parameters (page 7-39) Step 3: Saving a Parameters File (page 7-42) Step 4: Loading a Parameters File (page 7-43) RELATED TOPICS • • • • • General Guidelines (page 7-2) Planar Conversion (page 7-4) Displaying and Modifying the Planar Histogram (page 7-17) Contour Conversion (page 7-25) Displaying and Modifying the Contour Converted Atlas (page 7-37) STEP 3: SAVING A PARAMETERS FILE After the conversion parameters have been set or adjusted to produce a satisfactory atlas. 7. PROCEDURE 1. 6. 6. Make sure that the Contour=D# array is selected and that the currently displayed view of the atlas is the one you wish to save. Choose an alternate Position (left. From the File menu. Choose a different Fill color. a. Continue with Step 3: Saving a Parameters File (page 7-42). The previously generated DTI arrays are listed.

From the File menu. The view of the atlas will change to reflect the loaded parameters 3.Page 7-43 DISPLAYING AND MODIFYING THE CONTOUR CONVERSION PROTOCOL: Step 1: Displaying the Converted Atlas (page 7-37) Step 2: Changing the DTI or Contour Array Parameters (page 7-39) Step 3: Saving a Parameters File (page 7-42) Step 4: Loading a Parameters File (page 7-43) RELATED TOPICS • • • • • General Guidelines (page 7-2) Planar Conversion (page 7-4) Displaying and Modifying the Planar Histogram (page 7-17) Contour Conversion (page 7-25) Displaying and Modifying the Contour Converted Atlas (page 7-37) STEP 4: LOADING A PARAMETERS FILE Once a data set is opened. pan. 2. 4. The default location for saving parameter files is BQOSTEO\Topographer or BQLifescience\Topographer. any Parameter file for it can be loaded. 1. Copying. DISPLAYING AND MODIFYING THE CONTOUR CONVERSION PROTOCOL: Step 1: Displaying the Converted Atlas (page 7-37) Step 2: Changing the DTI or Contour Array Parameters (page 7-39) Step 3: Saving a Parameters File (page 7-42) Step 4: Loading a Parameters File (page 7-43) RELATED TOPICS • • • • • General Guidelines (page 7-2) Planar Conversion (page 7-4) Displaying and Modifying the Planar Histogram (page 7-17) Contour Conversion (page 7-25) Displaying and Modifying the Contour Converted Atlas (page 7-37) BIOQUANT Topographer Handbook: Planar & Contour Conversion . Click the OK button. and orientation settings for an Atlas. If you created a subdirectory associated with your Data Volume and Data Set as recommended in the Save Parameters procedure. See “Printing. or Exporting an Atlas” on 5-34. it will be listed there. Navigate to the folder that contains the Parameter file for the current data set. The Parameter file automatically selects the arrays and sets the zoom. ADDITIONAL OUTPUT NOTES The Converted Atlas Display can also be printed and/or saved as a Bitmap or Metafile. Click to highlight the Parameter file to be opened. choose Load Parameters to open the Open Parameter File box.

Page 7-44 BIOQUANT Topographer Handbook: Planar & Contour Conversion .

6-68 Index . 3-24 numeric transform 3-54. 6-41 open polygon 6-39 overlay sections 6-20 redefine edge 2-34 resolution 6-36 rotate section or object 6-53 straighten edge 2-31 undo 6-27 z sort 6-37 Atlas Viewer add/delete topo arrays 5-43 center atlas 5-6 open data set 3-2 play AVI movie 5-28 record AVI movie 5-27 redraw 5-6 resize to fit 5-4 rotate atlas continuously 5-26 rotate xyz perspectives 5-9 save atlas parameters file 5-31 set atlas parameters 5-7 show control bar 5-2 symbols 5-20 thick tracings 5-30 zoom 5-4 auto movie rotate 4-13 auto redraw in Atlas Shop 6-24 auto rotate model 4-13 AV_F1_SAVE_DATA_SET 5-45 AVI movie play in Atlas Viewer 5-28 record and play in Atlas Modeler 4-14 record in Atlas Viewer 5-27 B background color change in Atlas Modeler 4-5 change in Atlas Viewer 5-29 backup original 2D map data 2-19 Bitmap Export 5-36 BMP Export 5-36 bounding box 4-15 branched structures changing color of one branch 3-30 closing gap after color change 3-31 identifying 3-11 improve surface rendering of 3-11 C cap object 6-46. correcting 3-9 Atlas Modeler auto rotate 4-13 load model parameters file 4-18 pan model 4-5 print model 4-23 record and play AVI movie 4-14 rotate model 4-5 save model parameters file 4-18 set color parameters 4-7 set lighting parameters 4-9 set movie parameters 4-11 use ideal forms to set lighting 4-6 view surface as points 4-3 view surface as solid 4-2 view surface as wire frame 4-2 atlas parameters colors/symbols tab 5-10 perspective tab 5-7 rotation tab 5-25 Atlas Shop align sections 6-35 Atlas Shop interface 6-2 auto redraw 6-24 close polygon 6-40 combine two objects 2-32 delete objects 2-34 internal copy 6-28 internal cut 6-28 internal paste 6-28 line editing tools 2-30.Page index--i Index A add interior object to selection 6-9 add/delete topo arrays in Atlas Viewer 5-43 align sections automatically 3-33 manually 3-33 Aligning Fiduciary Planar Conversion 7-15 alignment problems.

dealing with 3-42 Connect Fiduciaries 7-18 Contour Conversion 7-25 backing up raw topo data 7-27 Color 7-30 Converting 7-36 customizing DTI arrays 7-29 data collection strategies 7-3 define Fiduciaries 7-31 delete Fiduciaries 7-33 displaying in Topographer 7-37 Fill 7-31 guidelines for data set 7-2 Loading a Parameters file 7-43 Mag 7-30 modifying the DTI using Select Arrays 7-39 move Fiduciaries 7-33 opening Atlas Shop 7-26 Position 7-30 Ratio 7-30 Saving a Parameters file 7-42 Shift Value 7-35 symbol shape 7-29 understanding the basics 7-2 Index convert OS/2 data 5-46 copy to clipboard surface rendered model 4-24 D data deleting from topo array 5-42 list in Atlas Viewer 5-40 OS/2 convert 5-46 print in Atlas Viewer 5-41 save 5-45 save data set 5-45 understand topo data 6-23 view in Atlas Shop 6-22 view in Atlas Viewer 5-40 data set open in Atlas Viewer 3-2 delete objects in Atlas Shop 2-34 DTI Array parameters 7-8 dual label color in Atlas Viewer 5-14 duplicate a section map 6-31 E end of object 6-46. 6-45 in Atlas Viewer 5-6 change color of background in Atlas Modeler 4-5 of background in Atlas Viewer 5-29 of branched structure 3-30. 6-67 of section. correcting 3-8 combine two objects 2-32 conjoint sections. 6-68 Export to BMP 5-36 Export to SVG 5-37 F Fiduciaries Defining for Planar Conversion 7-10 Fill Contour Conversion 7-31 Planar Conversion 7-9 fill color in Atlas Viewer 5-14 flash section 6-18.Page index--ii center in Atlas Shop 6-18. or points 6-57 of tracings or symbols 5-13 wire frame fill color 5-16 change resolution to speed rendering 6-36 change z offset 6-63 close atlas window in Atlas Viewer 5-3 close ends of rendered model 6-46. object. 6-68 close polygon 6-40 Color Contour Conversion 7-30 Planar Conversion 7-9 color index verses color shown 4-8 color palette 6-47 color parameters of model hide objects of particular color 4-8 make surface transparent 4-8 color problems. 6-45 format rendered model cap ends 3-51 create transparent window 3-51 remove format 3-52 H help files 6-47 how do I? 6-47 I internal copy 6-28 .

6-68 lighting parameters of model global ambient light 4-10 set first on ideal test forms 4-6 spotlight on camera 4-10 surrounding light 4-10 line edit tools combine two objects 3-25.Page index--iii internal cut 6-28 internal paste 6-28 O object mode 6-11. 6-62 redefine edge (tracing) 3-25. 6-59 delete object 3-26. 6-45 open atlas window in Atlas Viewer 5-3 open data set in Topographer 3-2 open polygon 6-39 open window in model 6-46 orientation of atlas in Atlas Viewer 5-7 overlay sections for reference 6-20 L landmark show in Atlas Shop 6-22 leave open 6-46. 6-59 list data 5-40 P pan in Atlas Modeler 4-5 in Atlas Shop 6-17. 6-45 Position Contour Conversion 7-30 Planar Conversion 7-9 print rendered model 4-23 topo data 5-41 Index M Mag Contour Conversion 7-30 Planar Conversion 7-9 measuring the atlas area of object 6-72 count objects in area 6-74 count objects in volume 6-75 counts per volume 6-71 distance 6-76 region of interest area 6-71 volume 6-70 messages to save data 6-6 middle of object 6-46. 6-60 straighten edge 3-24. 6-69 movie parameters auto movie rotate 4-13 bounding box 4-15 video compression 4-15 N Numeric Transform resize 3-56 rotate 3-57 translate 3-55 numeric transform 6-41 . 6-61 separate two objects 3-25. 6-48 in Atlas Viewer 5-5 perspective tab 5-7 Planar Conversion Aligning Fiduciary 7-15 backing-up raw topos 7-6 Color 7-9 Connect Fiduciaries 7-18 Converting 7-16 data collection strategies 7-3 Define Fiduciaries 7-10 Delete Fiduciary 7-12 displaying the Planar histogram 7-17 DTI Array parameters 7-8 edit DTI using comments 7-21 Fill 7-9 guidelines for data set 7-2 Mag 7-9 Move Fiduciary 7-12 Opening the Atlas Shop 7-4 Position 7-9 Ratio 7-9 retrieving parameters file 7-24 saving parameters file 7-24 setting up for conversion 7-7 Shift Value 7-14 Symbol 7-8 Topographer Procedure 7-4 understanding the basics 7-2 point mode 6-11.

Page index--iv problem section map. 6-45 select arrays in Atlas Viewer 5-38 select objects in Atlas Shop all section maps in atlas 6-9 Index by adding interior objects 6-9 by color 6-8. 6-49 Shift Value Contour Conversion 7-35 Planar Conversion 7-14 show aligning landmark in Atlas Shop 6-22 all sections in Atlas Shop 6-20 data in Atlas Shop 6-22 data in Atlas Viewer 5-40 larger objects as symbols 5-21 only selected items in Atlas Shop 6-19 small objects as symbols 5-20 Show Start Point 6-21 sort sections by z offset 3-40 Start Point 6-21 straighten edge tool in Atlas Shop 2-31 surface render enhancements cap open ends of model 3-51 create transparent window 3-51 remove 3-52 surface rendered model special formatting options 4-19 surface rendering parameters file 4-17 SVG Export 5-37 Symbol Planar Conversion 7-8 symbol Contour Conversion 7-29 symbols change shape 5-22 change size 5-23 fill some. continuously 5-26 wire frame. eliminate 6-29 R Ratio Contour Conversion 7-30 Planar Conversion 7-9 redefine edge (tracing) 2-34 redraw in Atlas Shop 6-23. 6-45 in Atlas Viewer 5-6 remove surface format 6-46. show others 5-18 reduce number of 5-24 show larger objects as 5-21 show small objects as 5-20 T test isohedron 4-6 test plane 4-6 test sphere 4-6 . deselect all 6-10 using polygon tool 6-8. 6-49 using rectangle tool 6-7. 6-45 from goto list 6-14 in same area on all sections 6-12 select none. continuously 4-13 section or object in Atlas Shop 6-53 specify "rotate around" point 5-10 wire frame. 6-46 in Atlas Viewer 5-4 resolution of atlas surface 6-36 restore color and symbol defaults 5-17 rotate by numeric transform 6-44 model perspective 4-5 model. do not fill others 5-19 hide some. 6-45 by selecting previous 6-13. xyz perspectives 5-9 S sample maps and models 1-5 save atlas parameters in Atlas Shop 5-12 atlas to new topo array 3-6 edits in Atlas Shop 6-2 save data 5-45 save data messages 6-6 save data set 5-45 saving Atlas Shop edits save 6-3 save as 6-3 save selection as 6-4 Scalable Vector Graphic (SVG) Export 5-37 section mode 6-10. 6-52 by selecting next 6-13. 6-69 rename an array 5-39 resize section or object with numeric transform 6-43 with resize tool 6-55 resize to fit in Atlas Shop 6-16.

6-46 z shift for wire frame atlas 5-9 z sort 3-40.Page index--v thick tracings in Atlas Viewer 5-30 topo arrays adding in Atlas Viewer 5-43 deleting from data set 5-44 print data 5-41 show data in Atlas Shop 6-22 show data in Atlas Viewer 5-40 tracings change color 5-10 make thicker 5-30 translate by numeric transform 6-42 translate section or object 6-54 transparent window in model 6-46. 6-68 U undo last atlas edit 6-27. correcting 3-9 z offset change 3-38. 6-66 W Windows Media Player 4-15 X x perspective 6-26. 6-35. 6-46 Z z axis spacing problems. 6-46 xyz rotation of wire frame 5-9 Y y perspective 6-25. 6-37 zoom in Atlas Shop 6-17. 6-63 z perspective 6-25. 6-48 in Atlas Viewer 5-4 zoom factor 5-8 Index .

Page index--vi Index .

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