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Acknowledgements

“I am going to start my dissertation in respect of God, Who is gracious and
Merciful.”
Successfully completing any task gives us satisfaction as well as internal strength for future
problems but the person alone has never existed. He is truly accompanied by few people. They use to
give the person support as well as suggestion to successfully complete his work. So I am pleasured in
thanking all such people who motivates me and provides there kind support at all stages of my research
work.
Firstly, I would like to honor my institute “Ideal Institute of Technology –Ghaziabad”. Here I
have been provided with a workplace to learn recent techniques and conceptual background to
strengthen my programming and professional skills.
I am very much grateful to Dr. S.K. Chaudhrai , (Director) and Dr. Yaduvir Singh (Associate
Professor & Head of Department of Computer Science &

Engineering)

Ideal Institute of

Technology, Ghaziabad, for his helpful attitude and encouragement in time to time to excel in our
studies.
I would like to express my sincere heartfelt gratitude to my honourable, esteemed supervisor Ms.
Anjali Goel (Assistant professor), Department of Computer Science and Engineering for her kind and
valuable guidance for the successful completion of the presentation work. I am glad to work under his
supervision.
Furthermore, I am thankful to, all faculty members for motivating me and to the Staffs of computer
labs in the department for providing excellent valuable facility as well as issuing me a computer system
of good configuration and providing regular maintenance.
I would like to extend special thanks to all my batch mates for their love, encouragement and
constant support.
Last but not least I would like to thank my parents for supporting me to complete my presentation
report in all ways.
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ABSTRACT

3D-DOCTOR Software is used to extract information from image files to
create 3D model. It was developed using object-oriented technology and provides efficient tools to
process and analyze 3D images, object boundaries, 3D models and other associated data items in an
easy-to-use environment. It does 3D image segmentation, 3D surface modeling, rendering, volume
rendering, 3D image processing, disconsolation, registration, automatic alignment, measurements, and
many other functions.3D-DOCTOR supports both grayscale and color images stored in DICOM, TIFF,
Interfile, GIF, JPEG, PNG, BMP, PGM, RAW or other image file formats. 3D-DOCTOR creates 3D
surface models and volume rendering from 2D cross-section images in real time on your PC. Leading
hospitals, medical schools and research organizations around the world are currently using 3DDOCTOR.

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Table of Contents
Certificate
Acknowledgement ……………………………………………………………... 1
Abstract …………………………………………………………………………...2
Table of Contents………………………………………………………………...3
Lists of Figures…………………………………………………………………..5

Chapter 1 : Introduction

6

Chapter 2 : 3d doctor basics

8

Chapter 3 : steps to create 3d rendering from 2d image slices

10

3.1

Image formats that 3D-DOCTOR support and which can be

10

3.2

used:
6 C System

11

Chapter 4 : 3d formats ,handling and reslicing

12

4.1

Introduction

12

4.2

Big data lake

14

4.3

Storing , Selecting & Processing Data

15

4.3.1 Storing

15

4.3.2 Selecting Big Data stores

16

4.3.3 Processing Big Data

16

Chapter 5 : 3d surface rendering
5.1

17

Standard size for Big Data

17

5.1.1 Need of Big Data Growth

18

Chapter 6 : able software upgrades 3d doctor
Chapter 7 : measurement done by 3d doctor

19
20

7.1

Data Generation Points

20

7.2

Big Data Analytics

21

Chapter 8 : 3d measurements
8.1

22

Tools

22
3

8.2 Examples
Chapter 9 : advance 3d image processing
9.1

23
24

Government

25

9.1.1

USA

25

9.1.2

India

25

9.1.3

UK

26

9.2 International Development
9.3 Manufacturing

26
27

9.4 Media
9.5 Technology

28
28

9.6 Private Sector

29

9.6.1

Retail

30

9.6.2

Retail Banking

30

9.6.3

Retail Estate

30

9.7 Science

30

9.8 Science & Research

31

Chapter 10 : advance 3d image processing

32

10.1

Leading Technology Vendors

32

10.1.1

Examples

32

10.1.2

Commodity

32

Chapter 11 : 3d image fusion

33

Chapter 12 : platforms 3d doctor runs

34

12.1

Big Data Impact on IT

34

12.1.1

Potential value of Big Data

34

12.1.2

India – Big Data

34

12.2

Future of Big Data

35

Chapter 13 : Conclusion

36

Chapter 14 : References

37

4

...2 Big Data analytics…………. 21 5 .……………….1 Traditional data v/s Big Data…... 20 7.. 10 14 16 5.... Title Page No.…………………….. Brainstorming Big Data Architecture.List of Figures Figure No....1 Standard table size for Big Data………………….....1 4.. 19 7..3 3 V’s Characteristics…………………..1 4.………....………… Processing Big Data……………………………….1 Big Data Sources…………………………………. 17 6... 3.

HANDLING. AND RESLICING  3D SURFACE RENDERING  ABLE SOFTWARE UPGRADES 3D DOCTOR  MEASUREMENTS DONE BY 3D DOCTOR  3D MEASUREMENTS  ADVANCE 3D IMAGE PROCESSING  3D IMAGE FUSION  PLATFORMS 3D DOCTOR RUNS  CONCLUSION  REFERENCES 6 .CONTENTS  INTRODUCTION  3D DOCTOR BASICS  STEPS TO CREATE 3D RENDERING FROM 2D IMAGE SLICES  3D FORMATS.

JPEG. These formats include DICOM. 3D surface modeling. quantitative analysis and rapid prototyping applications. volume resizing. IGES. BMP. deconvolution. PNG and RAW. 3D image processing. scientific. BMP. automatic alignment. Interfile. image processing and measurement software for MRI. TIFF. 3D imaging software developed by Able Software Corp. and many other functions. microscopy. OBJ.CHAPTER 1 INTRODUCTION 3D-DOCTOR is an advanced. RAW or other image file formats. registration. CT. You can calculate 3D volume and make other 3D measurements for quantitative analysis. 3D-DOCTOR supports a variety of image formats in both 2D and 3D.3D CT/MRI images can be re-sliced easily along an arbitrary axis. 3D-DOCTOR's vector-based tools support easy image data handling. Multi-modality images can be registered to create image fusions.It is an advanced 3D modeling. rendering. Other image processing functions include template-based film cropping. PGM. measurement. simulation. image reslicing to correct slices of uneven thickness. VRML. volume rendering. Interfile. GIF. PET. DXF.This software does 3D image segmentation. and industrial imaging applications. TIFF. You can export the polygonal mesh models to STL. JPEG. and analysis. 3DDOCTOR creates 3D surface models and volume rendering from 2D cross-section images in real time on your PC. Other non-standard image formats 7 .The 3DBasic scripting tool makes it easy to create Basic-like sophisticated 3D imaging programs. and image rotation. 3DS. XYZ and other formats for surgical planning. PNG. GIF. 3D-Doctor supports both grayscale and color images stored in DICOM. Misaligned slices can be automatically or semi-automatically aligned using 3D-DOCTOR's image alignment functions. measurements.

bit depth per pixel. little endian or big endian. 8 . and the size of file header. 3D-DOCTOR is currently being used by leading hospitals. but only with known dimensions (number of columns. medical schools and research organizations around the world.are also supported. rows and planes).

3D Studio. VRML. MRI. ➢ Works with both grayscale and color images (color classification and separation) ➢ Supports CT.images such as CT.CHAPTER 2 3D. image resizing. microscopy. GIF. ➢ 3D Output Formats: STL (ASCII and Binary). image fusion. Interfile and RAW (vendor proprietary formats). It has been used to process images with over 2000 slices on a PC with only 256MB RAM. boundary slices. IGES. scanned film images. ➢ Write your own programs with 3DBasic script to automated frequently used steps. BMP. etc. DXF. PNG. The following lists some of the main differences between 3D-DOCTOR and other packages: DOCTOR uses its unique vector-based technologies to create better 3D models from volumetric ➢ Unique vector-based technologies for better 3D model creation and easy editing. PET. ➢ High End 3D Image Processing Functions: image registration for multi-modality application. MRI and microscopy images. ➢ Smart memory management with no limit for the number of slices to be used. image reslicing. 9 . JPEG. ➢ ➢ Single command volume calculation and quantitative analysis report Handles DICOM and other image formats. such as TIFF.DOCTOR BASICS 3D. ➢ Surface model uses smaller number of triangles while maintaining all details for high quality rapid prototyping applications. industrial CT. slice data and XYZ points.

Wavefront OBJ and more. ➢ Software Reliability: No known bugs in our products because we fix them right away once they are reported. 10 . ➢ Reasonably priced.

6.Or the File/Open command if the slices are already in a list or a single image file. The boundary data will be used by the following steps. Edit/Object Settings to add new object groups for holding the boundary data. Click on the animation tool bar to fly through the slices. Edit/Calibrations to enter image spatial/spectral resolution. When the 3D surface models are displayed. Use the 3D Rendering/Volume Rendering to create 3D volume rendering for 3D visualization. File/New Stack to add the slices to the stack list and open it.CHAPTER 3 STEPS TO CREATE 3D RENDERING FROM 2D IMAGE SLICES The following lists the main 3D-DOCTOR functions and steps youcan use to create 3D rendering from your 2D image slices: 1. 11 . etc. Function Keys F2 and F3 to zoom in and out. use View/Object to change the transparency and color properties and functions under Tools submenu for further analysis. 5. F5 and F6 to switch to the previous and next image slice. 2. 3. Use 3D Rendering/Auto Segment and define the number of objects to be segmented for fast automatic segmentation. 4. 7. Use the 3D Rendering/Surface Rendering commands to create 3D surface models. You can ase the 3D Rendering/Interactive Segment or Edit/Boundary Editor to trace object boundaries automatically or manually. View/Image Contrast to adjust display contrast.

8. Use Edit/Object Report and Boundary Report to get quantitative analysis of your image 12 .

and the size of file header. PNG and RAW. bit depth per pixel. 13 . 8. TIFF. 3D contours. Other non-standard image formats are also supported. and 8 and 24 bit color images. industrial CT. These formats include DICOM. Images can be obtained from medical imaging devices or scanned from films or other image sources. but only with known dimensions (number of columns.CHAPTER 4 3D Formats. little endian or big endian. rows and planes). 3D-DOCTOR supports TWAIN-compatible imaging devices and functions for cropping medical film images. and 3D cloud points. MRI (magnetic resonance imaging). seismic wave data. 1-bit black/white images. and Reslicing Image formats that 3D-DOCTOR support and which can be used: 3D-DOCTOR supports a variety of image formats in both 2D and 3D. Interfile. Handling.3D-DOCTOR supports grayscale images in 4. including CT (computed tomography). microscopy. GIF.3D-DOCTOR can process a wide variety of images. scientific volume data. 12 and 16 bits. JPEG. BMP.

VRML. including IGES. You can read an image file directly from a server where the image is stored when direct network access is available. IGES. 256MB RAM should be a reasonable point for most 3D medical images. and 3D-DOCTOR's own binary format. not NURB (non-uniform rational B-splines) models.It is always recommended to add more memory (RAM) to reduce disk swapping an erformance.3D formats that 3D-DOCTOR support: 3D surface models created using the surface rendering commands can be saved as AutoCAD DXF. raw triangles. The models are saved in the form of surface polygons and triangles when exported to the above formats. instead it only keeps what's needed in memory to get the best performance. Wavefront OBJ. CD. If direct access is not available. STL (ASCII and Binary). Images are brought into 3D-DOCTOR by file. or tape) and then move the data file to the system where 3D-DOCTOR is 14 . 3D-DOCTOR does not load an entire 3D volume into memory for processing. 3D Studio 3DS. There are also software tools available to convert a polygonal model to a NURB modeI Limit on image size 3D-DOCTOR can handle very large 3D volume images thanks to the efficient memory management implementation. Many NURB based CAD software supports polygonal model and have functions to import them as surface body. you can copy the image file to a removable storage media (ZIP disk.3D models created by 3D-DOCTOR are polygonal models. solid body or graphics model. 3D-DOCTOR is designed to handle image sizes way above what today's scanners can produce.

Can convert color images to grayscale using the Image/Conversion function. Acquisition of transverse CT.. The Visible Human Project is the creation of complete. Color images can be processed using 3D-DOCTOR.If your image is on multiple films where each film has a matrix of slices. anatomically detailed.installed. MR and cryosection images of representative male and female cadavers has been completed. threedimensional representations of the normal male and female human bodies. It supports both 24-bit and 8-bit color images. Import raw image files from the Visible Human Project: 3D-DOCTOR can import the raw images files from the Visible Human Project for 3D rendering and modeling. use the "File/Raw Image File Import/Multiple Files" command. Color images can also be used in 3D Volume Rendering. You can also use the Image/Processing/Color Classification function to group the colors and then extract boundaries using the segmentation function. The male was sectioned at one millimeter intervals. To import the files. finite element analysis and other applications. Many 3D-DOCTOR users have successfully used the datasets to create anatomical model for research. education. Add the raw data 15 . the female at one-third of a millimeter intervals. product design. Read the image file into 3D-DOCTOR and start from there. Bring the scanned images into 3D-DOCTOR and then use the template based Crop Film command to separate the slices for 3D visualization with just a few simple mouse clicks. then simply scan the films using a regular image scanner with a transparency kit or a film scanner. The 3D Rendering/Segment Object function lets you segment both color and grayscale images to get object boundaries.

33mm.TXT file in the image file folder).files to the list and enter the image size information (described in the README. For example. Z = 1 mm Here is a screen shot of the color image imported into 3D-DOCTOR and models created 16 . if you are importing the color raw image files. the parameters will be entered like this: Number of Columns: 2048 Number of Rows: 1216 Bits Per Pixel: 8 Number of Bytes to Skip: 0 Photometric Display: RGB Color Little Endian: checked For the Calibration: X. Y are 0.

one is a Fast Nearest Neighbor deconvolution and the other is an iterative Maximum Entropy deconvolution method. as well as noise due to electronic and photometric sources. 17 .Deconvolution Image deconvolution is used to remove or reduce degradations caused in the imaging process. 3D-DOCTOR provides two types of deconvolution to restore degraded 3D images. These include the blurring introduced by optical systems and by image motion.

This can be adjusted easily by using the Edit/Calibrations command. you can enter them in the Image Calibration Parameters dialog box. Y. enter the values for X. The 3D surface model consists of triangle faces. At the dialog box. The simple surface rendering uses a proprietary algorithm to create smooth and simpler surface models. 18 . With 3D-DOCTOR. Multiple objects can be combined together using 3D surface rendering. 3D-DOCTOR assumes the slice thickness (or distance between slices) is the same as the pixel size in the XY plane (column and row).There are 2 surface rendering commands in 3DDOCTOR: Simple Surface Rendering and Complex Surface Rendering. This method is slow but robust. This method is fast and the models are better suited for rapid prototyping and volume calculation applications. you can select the proper rendering method for an object and mix multiple objects created using different rendering methods for 3D display. Y. Z) of my 3D rendering When you create a 3D rendering with only a few slices. They both create 3D surface model but use different algorithms and are suitable for different objects. The complex surface rendering uses a triangulation algorithm. How to adjust the scale (X. enter a larger value for Z so its scale will be adjusted automatically in the 3D rendering.CHAPTER 5 3D SURFACE RENDERING: D-DOCTOR's. The Z value is the slice thickness plus the distance or gap between slices. The X and Y are the size of a pixel within a slice. and Z. If you know the size in all dimensions and the physical unit. the 3D rendering may appear as a very thin object because. by default. If you need to increase the slice thickness. 3D surface rendering commands create 3D surface models from object boundary lines or contours. and is better for rendering objects with complicated branches and topologies.

Step 3. Use the File/Boundary/Export Boundary command to save the boundary data to a file. If you need to render only part of an object. You can also create a volume rendering using the 3D Rendering/Volume Rendering command. Move the cursor to the ending location and click the left 19 . Step 2. Now you can create a 3D surface rendering using the 3D Rendering/Surface Rendering commands. Activate the image plane window where the object boundary is displayed. Step 1. Step 4. the correct scaling will be applied when making measurements and calculating 3D volume and surface area. The cursor will change to a cross. Open the 3D image using the File/Open Image command. Select the 3D Rendering/Split Object command. Move the cursor to the starting location of the cutting line and click the left mouse button. Segment the image using one of the segmentation commands to generate boundaries for an object.and surface area. Edit the boundary lines using the Edit/Boundary Editor. Now you'll see a rubber band line which connects the cursor to the starting location. you can use the 3D Rendering/Split Object command to split the object along an arbitrary axis. Creating 3D surface model from images The following steps explain the process of creating a 3D surface model from images. Split or Cut objects for 3D rendering With 3D-DOCTOR. if necessary. The following are the steps required for cutting or splitting objects: Step 1. an object defined by object boundaries can be cut or split into smaller objects.

Interactive Segmentation Step 3. Once the new object boundaries are cut. 20 .mouse to define the line. A 3D mesh model can be created from a CT image in 3 main steps Step 1. A CT image normally has different pixel intensity range for tissues such as bones. Now select a 3D rendering (surface or volume) command to create the 3D rendering of the split object 3D DOCTOR Software has been one of the tremendous analysis software that I use on a regular bases to extract information from image files to create 3D model. Step 2. Step 1. Open Image Step 2. use the "New Stack" command. A dialog box appears to let you select the range of image slices to be cut. organs and other tissues. Open the CT image. If the image slices come in as separate files. Select the option "Only keep object on the right" to keep the split object on the right side of the cutting line or uncheck it to keep objects on both side. The threshold-based "Interactive Segmentation" provides an easy way to segment a CT image for 3D modeling. use Edit/Object Settings to turn off objects that are not to be used for 3D rendering. Creating 3D Model Computed tomography (CT) is an imaging technique that uses special x-ray equipment to obtain crosssectional images of the body.

Step 2. STL (ASCII and Binary). rapid prototyping . Create 3D mesh models using the surface rendering command. Step 3. OBJ. DXF. PLY and other formats for 3D measurement. 3DS. the manual tracing method can also be used. Use the "Interactive Segmentation" to generate object boundaries. Boundaries can be edited using the boundary editor. The models can be exported . treatment planning and other applications 21 . VRML. For small size soft tissues. simulation.

microscopy and volumetric images. A control point based registration function is also available for multi-modality 3D image registration and fusion. MRI and PET. modeling and measurement of CT (computed tomography). an interactive 3D image registration function is implemented to register images of different modalities. such as CT. microscopy and volumetric image features an enhanced modeling algorithm for quicker rendering and higher quality models. color and grayscale are supported. modeling and measurement software for CT. ABLE released a new version of 3D-DOCTOR ABLE Software has released a new version of 3D-DOCTOR. polygon-based mesh models are created from CT/MRI images in DICOM (Digital Imaging and Communications in Medicine). In this new version. the new 'smooth shading' volume rendering can be used for real-time 3D image visualization. has announced a new version of its 3D-DOCTOR software for vectorbased 3D imaging. The 3D surface modeling algorithm has been enhanced to provide faster rendering and 22 .CHAPTER 6 ABLE Software upgrades 3D-DOCTOR ABLE Software Corp. MRI (magnetic resonance images). and new boundary tracing functions have been developed to speed and ease object boundary definition using a touch screen or a tablet. MRI. The registration function displays both the source and the target image in 3D and interactively adjusts (rotate. move and stretch) the source image until it fits the target the image. the vector-based 3D imaging. the company..

ultrasonic and other volumetric data). a portion defined by regions of interest (ROI). Objects can be moved. wire frame or with texture map during the animation. The volume rendering uses either the entire image volume. surgical simulation. opaque. or a portion defined by the user interactively. quickly extract object boundaries using both fully automatic and interactive 3D image segmentation. and 3D rapid prototyping applications. you can visualize 3D image data (CT. 23 . scaled. industrial. 3D models are used for 3D measurement. create both 3D surface and volume rendering. It supports both color and grayscale rendering using either opaque or transparent voxels. 3D-DOCTOR is an advanced 3D imaging software for researchers doing medical. Right from your desktop PC. surgical and treatment planning. The upgraded volume rendering function creates real-time 3D image visualization. MRI. hidden or made visible in the animation process.generate high quality 3D mesh models from CT/MRI scans. Tissues with different density can be included or excluded in the rendering by changing their opacity property. engineering and other imaging applications. volume calculation. in just few easy steps. The tissue display properties can be set as transparent. A new animation function is implemented to create movies and 3D simulations from 3D rendering. microscopy.

3D-DOCTORÆs restoration functions are the solution to de-blur and restore the 3D image to its original quality with either fast nearest neighbor or maximum entropy deconvolution. When the surface model window is displayed. thickness. For image measurement. 24 . and image region histogram. including distance. you can register or geometrically correct a 3D image by giving 4 or more control points. surface and volume. 3D-DOCTOR lets you measure angles using the Angle Measurement tool. 3D-DOCTOR allows you to measure distance. 3D volumes of 3D surface models can be calculated easily. easily combine two registered images using one of 8 available methods to create a fusion image. volume.CHAPTER 7 Measurements Done By 3D DOCTOR 3D-DOCTOR can make a variety of image measurements. With 3D-DOCTOR. It is a complex mathematical problem. 3D-DOCTORÆs image registration function. you not only have a number of different ways to visualize your 3D image in 2D. but also the tools necessary to do accurate quantitative analyses for your applications. montage. area. 3D. image density profile and image histogram of a region in any shape. surface area. profile. volume. surface area. but 3D-DOCTOR makes it easy to solve. area of a region. use the Process/Calculate Volumes command.

IGES. such as DXF. there are many 25 . This example shows a skull model printed using a 3D printer from the STL file generated by 3DDOCTOR. The 3D models can be exported to AutoCAD DXF. and VRML for viewing on the Internet by others. the scaling parameters should be entered using the Edit/Calibration command before rendering is done. 3DS for 3DStudio. as well as DXF for AutoCAD. Once you have created 3D mesh models in 3D-DOCTOR. If you do not have access to a 3D printer. This command computes both volume and surface area.. 3D-DOCTOR exports 3D models to STL (both ASCII and Binary) for rapid prototyping machines. Wavefront OBJ. To adjust the scale and unit for volume calculation. etc. STL for rapid prototyping. you can print them out using a 3D printer and a rapid prototyping machine.If you have your 3D model saved in a format supported by 3D-DOCTOR. STL. you can use File/Open Model to read the 3D model into 3D-DOCTOR and then calculate the volume 3D Printing and Rapid Prototyping for Surgical Simulation and Treatment Planning Applications 3D solid and surface models can be created from any types of volumetric images for modeling and rapid prototyping applications. raw triangle.The 3D volume of 3D surface model The volume of a 3D surface model can be calculated easily using the Process/Calculate Volume command within the surface model window. Magnetic resonance imaging (MRI) produces high quality images of the human body. OBJ and 3DS for 3D animation.

the 3D volume and surface area of an object can be easily calculated with just a single command.service bureaus that can provide printing service. Thanks to the vector-based architecture. 3D Model Examples 3D Mesh Model Generated by 3D-DOCTOR 3D Output from a 3D Printer 3D Volume Calculation. measurement and quantitative report. 26 . Measurements and Quantitative Analysis 3D-DOCTOR provides an extensive set of tools for 3D volume calculation.

If you have a surface model display window open. use the View/Image Planes command to turn on the image plane 27 .CHAPTER 8 3D Measurements: ➢ Object volume ➢ Object surface area ➢ Length on 3D object ➢ Digitize 3D points ➢ Crop 3D object ➢ Cut 3D object Object Measurements: ➢ Total pixel density ➢ Average pixel density ➢ Area and volume ➢ Number of objects ➢ Min and max pixel density ➢ Calibrated density ➢ Variance and standard deviation ➢ Histogram data Display image slices together with 3D models 3D-DOCTOR can easily displays the image slices together with your 3D models.

28 . You can use the View/Image Settings command to change the transparent and opaque properties and individual plane display status.display.

and color classification can all be performed on your 3D images. background removal. 3D image filtering. Turn your x-ray machine into a full CT system using 3D-DOCTOR.CHAPTER 9 Advanced 3D Image Processing 3D Computed Tomography: Create parallel cross-section. volume resizing. Other image processing functions include: template-based scanned film cropping. 29 . image mosaic. pattern recognition. 3D Image Restoration by Deconvolution: 3D-DOCTOR provides two highly efficient deconvolution methods for 3D image restoration and reconstruction. orientation adjustment. Image rotation. contrast adjustment. segmentation. image combination. a fast nearest neighbor algorithm and an iterative maximum entropy algorithm. linear feature extraction. volume images using x-ray images taken at angles around an object. 3DBasic scripting language will let you create your own Basic-like sophisticated programs using 3D-DOCTOR's advanced imaging and rendering functions quickly.

Open a 3D image. The main steps to create 3D models and volume rendering from a 2D slice images (CT. The following explains each step and commands used: Step 1. If your 3D image is stored in a series of DICOM files or in a format that's directly supported (DICOM. This Figure shows an opened CT pelvis image: 30 . MRI. PNG. TIFF. microscopy): 1) Open the 3D image. JPG. which is displayed by a single plane window and a montage window with all slices. 2) Define objects and create object boundaries for each object.HDR). BMP. you can use the File/New Stack command to put the files into a stack list and open it. object boundaries. 3D models and other associated data items in an easy-to-use environment. raw image data with a header *.Deconvolution of an image from Hubble Space Telescope THE BASICS 3D-DOCTOR was developed using object-oriented technology and provides efficient tools to process and analyze 3D images. 3) 3D surface rendering and volume rendering.

use the File/Raw Image File Import command to add a header or multiple header files and then open the image data files.If the image format is not directly supported. Step 2. If your image is on a film. Volume Rendering: If you need to do a 3D volume rendering. All slices must be cropped to the same size so they can be put together as a 3D image for further processing. Use the Interactive Segment command to trace object boundaries interactively or the Auto Segment for fully automatic object boundary detection. for example. go back to the image display. you can use the "3D Rendering/Volume Rendering/Smooth Rendering" command now. If you want to render different tissue range. Once you have the image files. you can scan the film using a scanner and then use the Image/Crop Image/Crop Region command to crop each slice and save a separate file using the File/Save/Save Image As command. one film has 12 slices. 31 . then use the File/New Stack command to create the 3D stack list. Define objects and create boundary lines for each object. adjust the contrast and then do a volume rendering again.

Interactive Segmentation: Once the interactive segmentation starts. you can click the “Segment Plane” button to extract the boundaries for the current image plane. you can click on the “Segment All” button to extract 32 . the image plane display is refreshed to apply color to pixels that fall within the threshold range specified by the Min and Max values. If the threshold values are applicable to all slices. When pixels that belong to the intended object are displayed in color. The display of the image slice is updated in real-time according to the current threshold selection. Use the slider bar to adjust the Min and Max values. Use the “Next Plane” or “Prev Plane” button to go through other planes to segment them individually.

Boundary lines are organized by object groups for more effective management and more flexible use by the rendering functions.boundaries for all image slices. including the background. Click “Finish” to leave the interactive segmentation function. You can use the Object Report to get 33 . you will need to use the Edit/Object Settings command to turn off some of the objects that are not of interest before surface rendering or volume rendering is performed. Auto Segmentation: This figure shows the image segmented using the Auto Segment command with the number of objects defined as 2. Boundary lines can be edited using the Boundary Editor under the Edit menu or processed using the boundary line processing functions under the Edit/Boundary Process menu. Since Auto Segment command segments the entire image.

PET and other cross-sectional images in DICOM. MRI. When boundary lines are generated. MRI and other Images Input Image: CT. GIF. Raw Image Data. Image files in various vendor specific formats can be easily read using 3D-DOCTOR's universal image configuration and 34 . JPEG. rapid prototyping. PNG. Step 3.we can also calculate the volume using the Tools/Calculate Volume command and the Tools/Measure to make 3D measurements on the model. Interfile. use 3D surface rendering to create 3D surface models or 3D volume rendering. The 3D models can be exported to many 3D formats for simulation. PGM. TIFF. quantitative analysis and other applications. 3D Mesh Modeling from CT.detailed quantitative analysis of the objects. This figure shows the model created for the bone structure. and other uncompressed image formats. animation. BMP.

3D Model Export: STL (ASCII and Binary). and other 3D graphics file formats for rapid prototyping. 3D printing. IGES. VRML. raw triangles. Wavefront OBJ. animation and visualization applications Once object boundaries are generated from segmentation. 3D mesh models are created in using one of the surface rendering 35 . finite element analysis. PLY. 3D Studio (3DS). Scanned CT/MRI films can easily be cropped using the template-based function for 3D imaging applications. the region-based Object Segmentation and the easy-to-use polygon-based manual tracing. Both grayscale (8-bit and 16-bit) and color images are supported.input function. Head MR Image with Brain Tumor Pelvis CT Image Segmentation Tools: the fully automatic texture-based segmentation for grayscale and color images. AutoCAD DXF. the thresholding-based Interactive Segmention for CT images.

A.functions. 2) Focus Fusion: eliminates the problems of limited depth of field by automatically capturing the in-focus regions from a range of focal planes and combining them into a single fullyfocused. Transparent. AND. 3) Fusion: combines two images with one of the mathematical operators: Add. or maximum method.) Image Fusion of CT and MRI Images The color image window on the left is the fusion result created from the CT liver image and the MRI liver image. 4) Plane Fusion: combines image slices into a single slice image by using the average. green. Unlimited number of objects representing different tissues are supported . There are 3 types of image fusion functions: 1) Color Fusion: uses each image source as a color component (red. The CT image is used as the red color component and the MRI image as the green color component. high resolution image. XOR. MAX. OR. MIN. etc. and blue) and creates a full color image as the result. CHAPTER 11 3D IMAGE FUSION 3D-DOCTOR provides several powerful image fusion functions to combine multi-modality images together for analysis and visualization. A third image may also be used as the blue color component if available 36 . minimum. Subtract. 1) Color Fusion The following shows some color image fusion examples using multi-modality image sources.

B. The image in the middle is a PET image. The image on the right is the fused image by using the CT as the background and the PET image as the blue color.) Image Fusion of CT and PET Images The image on the left is a CT image. 37 .

high resolution image. This picture shows how the fusion command is used. 38 . Much more information can be visualized in the combined image than from the individual ones. 3) Fusion Two registered images can be combined to create a fusion image. This is often used to combine two images acquired differently but from a single source to enhance the display of various materials or tissues. For example.2) Focus fusion Focus Fusion uses a proprietary image processing algorithm developed by Able Software to eliminate the problems of limited depth of field by automatically capturing the in-focus regions from a range of focal planes and combining them into a single fully-focused. No knowledge with your image acquisition system is required for this processing. a CT image and an MRI image from the same patient can be combined to show both bones and fat clearly in a single image.

viewing them from any angle. heart disease and breast lumps. average and maximum.➢ Plane Fusion: You can combine multiple image slices into a single slice image using one of the methods: minimum. The following example shows the fusion image of a MRI knee image. The window on the right is the fusion image by taking average of all slices. 39 . US-based Superscape have produced a 3D virtual reality browser which allows visitors to their site to watch. The window on the left is the original image slices Virtual doctor trains patients in 3D The latest 3D web technology is being used to allow women to look out for problems such as osteoporosis. or even interact with informative presentations .

Virtual reality has already been used to help doctors learn the skills of brain surgery by offering a 3D image of a patient's head which can be operated on with a "software scalpel". 40 .then see a 3D representation of the results.this provides the ability for concerned people to check out some of the basics. allowing viewing to take place from any angle." He is hopeful that the technology could eventually be used in hospitals to guide patients through exactly what is going to happen during their operation. and perhaps even to help train medical students. So a smoker who admits to having a poor diet and taking little exercise might see a heart artery pumping slowly because it is clogged with fatty deposits. Visitors to the site will have to download the browser and should be running at least a 133 MHz Pentium processor. And someone who does not drink enough milk. whether good or bad. Ben Green said: "The information we are conveying is already available to the general public through leaflets .Personal details taken The sections of the site devoted to heart disease and osteoporosis allow the visitor to enter personal health details . might be depicted as a stooping figure because of the effects of osteoporosis. The site aims to teach women how to carry out their own breast examinations. to go and see a doctor. Superscape are well known for their innovative 3D virtual reality software .in the past. and if they're still concerned after that. or a young person who diets too much. they have produced 3D shopping malls. a virtual medieval garden and even a virtual graveyard.

a badly defined face with an open trimming loop will be displayed as curves The solution 3D DOCTOR is the most productive tool in the market that allows the automatic correction of some of the flaws you may encounter. Bezier. B-spline. This will enable a greater number of functions and modelers to accept the validity the definition of objects without changing their geometry. cylinder.…) and geometric entities (circles. shells. 41 .g. and even the different functions of the same modeler. There exists today a consensus around the STEP standard for the exchange of topological entities (solids.3D DOCTOR Connecting Engineers The problem B-rep modeling (boundary representation) is presently the most efficient tool for the representation of 3D CAD objects (solids or surfaces). cones. The different modelers.…). faces. have different tolerance values regarding "defective definition". fill up holes or delete some trimming curves. For instance. but there is no accepted standard to check if a definition is valid or not. n't be shown in solid mode. Nurbs. And more 3D DOCTOR offers also some operations to complete or modify the definition e.

you can do the following if you have the available budget: ➢ Add more RAM (128MB or more recommended for processing large size volume images and renderings) ➢ Faster CPU ➢ Faster video display board with built-in OpenGL support ➢ Faster and larger hard disk drive 42 . Windows NT/2000/XP. The current version does not run directly on a Linux system. No native MAC (Macintosh system)version yet. The only requirement is setting up your display to high color (16-bit or higher). including Windows 9x.CHAPTER 12 Platforms (Operating Systems) does 3D-DOCTOR runs on 3D-DOCTOR runs on PC running Windows. We are looking into the possibility of creating a Linux version for a future release. or newer versions of Windows. 3D-DOCTOR run on a Unix systems not directly however. 3D-DOCTOR can pretty much run on any PC in use today.It could work on a Unix machine if a Windows binary emulator is installed. Windows ME. The ideal hardware set up to run 3D DOCTOR To get the best performance. There are Windows binary emulators available but we have not tested them for compatibility.

Accumulatively.CHAPTER 13 CONCLUSION 3D-DOCTOR Software has been one of the tremendous analysis software that is use to extract information from image files to create 3D model. It provide engineering team more accurate analysis for internal human parts and also create visual models for complex blood vessel such as coronary artery. sort out the anatomy and present 3D model to project team to see first hand the anatomy before making next decision. assist in making initial decision to choose a case and help analyze the case before creating visual models for device deployment/testing in the lab. the 3D-DOCTOR software help save time. we can quickly load up image file. With 3D-DOCTOR. 43 . aorta and superficial femoral artery (SFA) in a much faster turnaround time.

CHAPTER 14 REFERENCES 123seminarsonly.com 44 .