UserGuideVisHab r9626 PDF

User Guide
BioSonics, Inc. | Seattle, WA USA | 206.782.2211

www.biosonicsinc.com | support@biosonicsinc.com
User Guide
TABLE OF CONTENTS
END-USER LICENSE AGREEMENT .................................................................................................... 3

INTRODUCTION ............................................................................................................................... 8
GETTING STARTED .......................................................................................................................... 9
INSTALLING VISUAL HABITAT ...................................................................................................... 9
COMPUTER SPECIFICATIONS ...................................................................................................... 9
WHAT'S NEW IN THIS RELEASE (2.0) ......................................................................................... 10
STEP-BY-STEP GUIDE ..................................................................................................................... 11
STEP 1 – LAUNCH VISUAL HABITAT........................................................................................... 11
STEP 2 – SELECT FILES TO ANALYZE .......................................................................................... 11
STEP 3 – PERFORM YOUR ANALYSIS ......................................................................................... 20
Overview ............................................................................................................................... 20
Visualize the Acoustic Data ................................................................................................... 20
Determining Bottom Depth .................................................................................................. 21
Manual Editing Tools ............................................................................................................ 25
Determining SAV Location and Coverage ............................................................................. 26
Identifying Plants on the Echogram ...................................................................................... 28
Bottom Type Analysis ........................................................................................................... 30
STEP 4: MAP CREATION AND DATA EXPORT ........................................................................... 35
Map Properties ..................................................................................................................... 35
Data Export ........................................................................................................................... 40
GRIDDING DATA ............................................................................................................................ 43
Method 1 – Triangulated Linear ............................................................................................... 43
Method 2 – Inverse Distance Weighting .................................................................................. 52
Method 3 – Kriging.................................................................................................................... 61
GLOSSARY OF FUNCTIONS ............................................................................................................ 66
FILE VIEW FUNCTIONS .............................................................................................................. 66
MAP VIEW FUNCTIONS ............................................................................................................. 69
Drop-Down Menu - Map ....................................................................................................... 69
Drop-Down Menu – Grid Tools ............................................................................................. 73
Drop-Down Menu – View ..................................................................................................... 75
DATA VIEW FUNCTIONS ............................................................................................................ 75
Drop-Down Menu – File ........................................................................................................ 75
Drop-Down Menu – Edit ....................................................................................................... 76
Drop-Down Menu – View ..................................................................................................... 78
Drop-Down Menu – Chart..................................................................................................... 82
Drop-Down Menu – Window ................................................................................................ 84
APPENDIX A: INTERMEDIATE FILE DESCRIPTIONS ....................................................................... 86
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END-USER LICENSE AGREEMENT
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INTRODUCTION
BioSonics lines of scientific echosounder systems are designed to collect high quality
hydroacoustic data that can be used to describe the bathymetry, submerged aquatic vegetation
(SAV), and seabed classification of your survey area. The systems produce geo-referenced files
suitable for import into various mapping software applications in addition to interpolated map
making capabilities.
For habitat assessment, BioSonics echosounders are typically used to collect data along a series
of predefined transects chosen to determine the location and quantity of aquatic habitat
features. Data is collected and stored using BioSonics Visual Acquisition software for later
analysis using a variety of post-processing techniques and programs. This manual demonstrates
how to analyze and visualize your data for habitat assessment using BioSonics Visual Habitat
Software.
This User Guide is divided into two main sections. The first section is a step-by-step tutorial
explaining the analysis and mapping process from start to finish. The second section is a
glossary explaining each menu item found in each of the three primary views found in Visual
Habitat; File View, Data View, and Map View. Visual Habitat is a Windows-based program that
allows for viewing a file in multiple Views simultaneously, and the resizing of each View
window. One of the most exciting features within Visual Habitat is the ability to view a file in
different aspects at the same time. Users can simultaneously view a file as an echogram using
the Data View (cross-section) and as a transect using the Map View (plan).
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GETTING STARTED
INSTALLING VISUAL HABITAT
A Visual Habitat software license key is included with your purchase of a BioSonics MX Aquatic
Echosounder.
Visual Habitat is also available for sale for post processing and visualization of habitat data
collected with a BioSonics DT-X Echosounder. Contact our sales team for product information
and pricing – call us at 206-782-2211 or email us at info@biosonicsinc.com.
You can also visit the Visual Habitat product page on our website for more information:
http://www.biosonicsinc.com/product-software-visual-habitat.asp.
A Visual Habitat license key allows for activation on three devices. Your license to use a fully
functional version of Visual Habitat begins when you activate the software using your License
Key.
You can install Visual Habitat software using the software installation media found in the
accessory pouch included with your shipment, or for the most current version, you can install
via download from any computer connected to the Internet. Register or Login to download
software and check for updates here: http://www.biosonicsinc.com/clientaccess/signup.cfm.
Our Technical Support team is always available to answer any questions you may have:
By email: support@biosonicsinc.com
Or call (206)782-2211, and ask for Support
COMPUTER SPECIFICATIONS
Operating System: Windows 10; Windows 8; Windows 7 Service Pack 1; Windows XP Service
Pack 3; Vista Service Pack 2
Computer Specifications:
Memory: Minimum of 512MB; 1 GB or more recommended
Hard Drive: Minimum of 120GB hard drive
Display Resolution: Minimum of 1024 x 768
CPU: Pentium 4 class chip or better
Communication: Internet is required to load dynamic
base map imagery
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A ruggedized Toughbook class computer with anti-glare, anti-reflective sunlight viewable

display is highly recommended for data collection/field work.1
Software Prerequisites: .NET Framework is required. The required versions of .NET are
available on the Microsoft website and through Windows updates.
 For Windows Vista or newer, you must have .NET 4.5.2 or higher installed - this is
available through Windows Update as an important update.
 For Windows XP, you must have .NET 4 installed (not the Client Profile, but the full
framework)
Additional Software Requirements: PDF reader (to view the User Guides)
WHAT'S NEW IN THIS RELEASE (2.0)

 Interpolate data points to form gridded data using the following methods:
o Triangulated Linear Interpolation
o Inverse Distance Weighting
o Ordinary Kriging
 Create full color maps with bathymetry contours
 Define survey region by manually drawing or importing from shapefile
 Automatically compute grid statistics including: area, water volume, min/max/avg.
depth
 Export results as KML, shapefile, or image files for use in Google Earth or ArcGIS
 Map measure tool
 Adjust opacity of data points, gridded data and contours
 Choose projection option UTM, Geographic, or Web Mercator
 Choose from Google, Bing, or Open Street Map imagery
 Export Bottom Type intermediate results to CSV or MATLAB file
 Compute plant area and volume
 AND MUCH MORE!
1
BioSonics recommends the Panasonic Toughbook for rugged, reliable performance in harsh field conditions.
BioSonics is a reseller of the Panasonic Toughbook.
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STEP-BY-STEP GUIDE
STEP 1 – LAUNCH VISUAL HABITAT
Visual Habitat may be launched using the desktop shortcut that was created
during the software installation. Alternatively, you may open Windows Explorer,
browse to the software’s installation folder (C:\BioSonics\VisualHabitat), and
double-click on the file name (VisualHabitat.exe).
STEP 2 – SELECT FILES TO ANALYZE
Figure 1. Visual Habitat File View data file window
The File View screen will launch with recently used or demo files visible (see Figure 1). To create
a new dataset, click ‘File > New Dataset’, otherwise load a previous dataset by clicking ‘File >
Load Dataset...’
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To load the files into your new dataset for analysis, go to ‘File > Add File(s).’ You may also click
on the button in the upper left corner to call up the ‘Select BioSonics Data File(s)’ window.
Choose one or more files by holding the ‘CTRL’ or ‘SHIFT’ keys while selecting the desired file
names. In the example above, all but the first two files have been selected for analysis.
After you have selected your files, click ‘Open.’ The selected files will appear in the Visual
Habitat ‘File View’ screen (see Figure 2).
Figure 2. File View window in Visual Habitat
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If you are using DT4 files that have more than one channel (DT-X ONLY), you can use the drop-
down ‘Filter’ bar to select which channel of data to use for editing (see Figure 3). If you need to
select different channels for some files (i.e. channel 1 for a file, and channel 2 for another file,
etc.) then click on the ‘Edit Filters...’ button. This opens a dialogue box where you can choose a
specific channel to be displayed for each individual file (see Figure 4).
Figure 3. If your DT4 file consists of more than one channel, you can use the channel filter to select which
channel to use
Figure 4. You can select which channel of data to display for each individual file in your dataset
Confirm these are the files that you want to analyze by checking for their survey positions. Click
on ‘View > Show Map View.’ The ‘Map View’ window will pop up and display the GPS
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coordinates of the data files that were selected (see Figure 5). The color of transects alternates
from file to file so that close-together transects may be differentiated more easily. Double-
clicking on any transect opens that file in the ‘Data View’ window. Transects drawn in RED are
from the file that is shown in the ‘Data View.’
Figure 5. Map View window (overlaid on File View window)
To view transects in a geographic context, you can add background images from multiple
sources.
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Select Base Map Properties’
Figure 6. Base Map Properties window
You can choose to either display the position information in either decimal degrees or degrees
and decimal minutes.
Optional “Scale Bar” and “North Arrow” when selected allows you to position the symbols in
any quadrant on the map.
The Max Tile Level only needs to be adjusted if the server you are getting images from does not
have imagery at the appropriate level of zoom. In this situation some servers return images
that are blank or have an icon indicating no imagery is available. If you see this in your
background image you may need to reduce the Max Tile Level number.
Clicking on ‘Map Image: Select’ brings up mapping options.
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Figure 7. Base Map Configuration and Map Type windows
Double Clicking on your preferred map type brings up additional mapping options (Figure 7
right).
The “Image File” option supports many georeferenced image file formats using the GDAL open
source library. In most cases the geo-referencing information for an image will be read
automatically, but if not you can manually set it.
The plus symbol allows you to import images from servers that support the WMS or
WMTS protocol (Figure 8).
Figure 8. Web Map Server Configuration Window
Clicking on ‘Set’ will import your background image.
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Projection: Select the map projection option you want from the Coordinate Reference System
options. If this selection is changed after gridding, the data must be re-gridded with the new
projection (Figure 9).
Figure 9. Coordinate Reference System window
Once you’ve made your selection, click OK to close the window.
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Figure 10. Map View Window showing imported image
If the track plots shown correspond to the positions of transects that you surveyed, you have
successfully loaded the correct files (Figure 10). This is a good time to delete any undesired
transects that you do not wish to be processed (Figure 11). To permanently remove stray
transect(s) from your analysis dataset, you may double-click to highlight them, and remove by
clicking the button. Check the ‘Map View’ one last time before you begin data analysis.
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Figure 11. Map View with stray transects (circled)
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STEP 3 – PERFORM YOUR ANALYSIS
Overview
Figure 12 below shows each row containing information corresponding to the files loaded.
Analysis of these files involves displaying each file individually and viewing the performance of
the desired analysis algorithm: bathymetry, feature extraction, bottom typing, and plant
measurement. After the analysis of all files and map creation is completed, the final task is to
export the results to an output file. The following steps are required to analyze a file. Repeat
the same steps for each subsequent file(s).
Visualize the Acoustic Data

In this example, we will click on the second row to select that data file (Figure 12).
Figure 12. File View (with second file highlighted)
Click on the ‘Playback’ control to display the ‘Data View’ of the second file in echogram
format: X axis = ping number, Y axis = depth (see Figure 12). You can also double-click on any of
the files to open the ‘Data View,’ or select it from the ‘View’ menu.
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Figure 13. Echogram of selected data file in 'Data View' (ping number along X-axis and range along Y-axis)
Observe that a brown line has been painted just above the bottom echo in Figure 13. Bottom
depths were determined by the data collection software when the file was created. The bottom
values are rarely 100% satisfactory, and thus we will re-analyze the file for bottom depth and
over-ride the values determined before.
Determining Bottom Depth

In Visual Habitat, we have two methods to change the bottom depth measured during data
collection. We may reconfigure the analysis and re-process the data to fine tune the algorithm
to pick a more accurate bottom line. In addition we can manually edit the bottom line.
Click on the ‘Configure Analysis’ button and select ‘Bottom Detection’ to configure the
bottom picking algorithm (see Figure 14).
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Figure 14. Analysis Parameters are editable (including Bottom Detection Parameters)
The Domain refers to what level of Time Varied Gain (TVG) is applied to the echogram. For
bottom typing, 30LogR is the appropriate value to use.
The Rising Edge Method

The Rising Edge Method is the default setting used for bottom detection. The Rising Edge
Threshold (dB) value picks the first signal that is higher than the specified value as the
candidate for the bottom echo. Its width is then tested against the Rising Edge Length Criterion
(cm) and the Rising Edge Search Window (cm) values. If the bottom echo is not located after
the number of pings specified in ‘Reset Search Window after’, then the bottom locating
algorithm looks throughout the entire range to locate the bottom. The minimum and maximum
bottom detection ranges are also set in this window.
The Trailing Edge Method

For areas with dense plants, check the box titled ‘Use Trailing Edge method to select bottom’ to
obtain optimal results.
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The Trailing Edge Offset (pulse length)

Adjust this value to raise the brown “bottom line” from the lower limit of the displayed data
view to the appropriate position indicating the true bottom.
The default values for analysis parameters (shown in Figure 14) should work well for many
surveys. Adjust the rising edge threshold (dB) for varying degrees of bottom “hardness”. To re-
analyze the bottom depth using different parameters, change the desired parameters in the
window shown above. Usually this requires either raising or lowering the Rising Edge Threshold
value. Once the Bottom Detection parameters are reconfigured, click the ‘OK’ button. Next,
click the ‘Run Analysis’ button to start. The ‘Run Analysis’ window will open (see Figure 15).
Figure 15. Run Analysis window
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To determine bottom depth, make sure that the ‘Bottom Detection’ check box is checked (as
shown) and click the ‘Start’ button. Once the data analysis is complete, you can ‘Close’ the
analysis box. To examine the results of the bottom detection analysis we just ran, click on the
Playback button .
NOTE 1: In Figure 15, a single file is analyzed for bottom depth. Typically one may analyze
multiple files by selecting them from the “Available” list and then clicking the right arrow to
move the files to the “Selected” list.
NOTE 2: It is possible to configure analysis parameters for several processes (bottom detection,
plant detection, feature extraction, and/or bottom typing) before running the analysis.
However, the first step of locating the bottom echo must be completed before running any
further analysis.
Figure 16. The bottom picking algorithm failed where plants were the densest. This can be corrected by
manually drawing the bottom line.
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In the echogram shown above (Figure 16), the bottom depth algorithm failed where the rooted
plants were extremely dense. Because the plants have modified the reflectivity of the bottom,
we will have to manually repair the sections where the bottom detection analysis failed.
Manual Editing Tools

The ‘Use Edit Tool’ helps you to manually edit either the bottom or the plant canopy line in
one of three ways:
1. The Raw mode allows the user to draw a section of line one pixel at a time.
2. The linear mode allows the operator to draw a straight line by left-clicking on start and
end points on the line, and right-clicking to accept the new line. (Recommended for
beginners.)
3. The Bezier creates a line segment the same way as the linear mode, but then allows the
line to be stretched up or down into a curved section.
Figure 17. Before, during and after manually editing the bottom line.
In the first panel of Figure 17, the drawing marker tip is placed at the point where the linear
section is to begin, and the left mouse button is clicked. The marker is moved to the end point
of the linear section, which is shown by a scarlet line (center panel). By clicking the right mouse
button, the scarlet section is replaced by the new manually drawn bottom line (final panel). If
you want to draw multiple linear sections, just click the left button at the start and end of each
section, and click the right mouse button at the end of the final linear section. The bottom
depth will be determined from the brown bottom line, which may be composed of
automatically and manually drawn segments. Once you are done editing the bottom line, you
can close the ‘Data View’ screen – it automatically saves any changes that have been made.
Observe that in the ‘File View’ screen now indicates that the Bottom Depth field for this file has
been analyzed and contains ‘Manual Edits.’ At this point, we can analyze additional files for
bottom depth, export the analysis of bottom depth for this file, or we can complete further
analysis of this and other files before exporting.
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Determining SAV Location and Coverage

Once the bottom depth has been determined for the selected file, we are ready to analyze the
acoustic file to determine the characteristics of any submerged plants. Access the ‘Analysis
Parameters’ window and select ‘Plant Detection.’
Figure 18. Analysis Parameters window for plant detection.
Figure 18 shows a list and description of the plant detection parameters that can be adjusted by
the user.
Other parameters shown include:
Domain: The Domain refers to what level of Time Varied Gain (TVG) the algorithm uses for
finding the top of the plant canopy. For plant detection, 30LogR is the appropriate value to use.
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Plant Detection Threshold (dB): This value should equal the signal level at which background
noise transitions to the plant canopy. It’s used to establish the top of the plant feature. We
recommend leaving it set to the default value for most data sets.
Set to Start Range When Lost: Activate this function when plants are “topping out” and filling
the majority of the water column. This will track and map the plants to the surface as the plant
detection threshold criteria will not be exceeded in these conditions.
Plant Detection Length Criterion (cm) – This is the minimum number of centimeters above the
initial plant detection threshold that the signal strength must not exceed to be classified as the
plant top. In the case of a -70dB threshold and a 10 cm length criterion, the signal strength
must not exceed -70dB for 10 cm above the initial -70 threshold point.
Maximum expected plant depth (m) – Set this to the maximum expected plant depth (if
known). The algorithm will not look for plants deeper than this value.
We suggest that you always start by using the default parameter values. Click OK, followed by
‘Run Analysis’ . Inside the ‘Run Analysis’ window, click on the ‘Plant Detection’ check box,
then click ‘Start.’ When analysis is complete, click on ‘Close,’ then click on ‘Data View’ . The
plant detection algorithm draws a dark green line over the outer canopy of the plants.
Please note that the bottom depth must be established first.
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Identifying Plants on the Echogram
Plants on an echogram appear as a patch of lower intensity signals extending from the bottom
upwards. Figure 19 shows a typical presentation of what an underwater plant looks like
growing from the bottom in an echogram. Figures 16 and 17 also show plants growing from the
bottom (the peaked mounds above the brown bottom line from ping 1-120).
One echogram characteristic of plants growing from the bottom is that directly below the plant
canopy signal, and below the bottom line is a visible “beard” of noise (see Figure 19). This is the
result of the plants scattering and delaying the echosounder signal slightly, so that it returns to
the transducer just after the actual plant signal. This secondary signal is a good indication that
you are indeed seeing plants in your echogram.
Figure 19. Example of plants, noise "beard,” and microbubbles from boat wake in a typical echogram.
The visible patch of noise around ping 300 looks similar to the plant signal, but is actually
microbubbles from a boat wake. If unattached/floating plants are present in your survey area,
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they may present themselves similar to the boat wake. Visual Habitat is designed to analyze
only anchored plants.
If the plant canopy is dense enough, it may block the echosounder signal so that the bottom
signal is hard to see. Using the ‘Trailing Edge Method’ bottom detection algorithm can
calculate bottom depth even when the bottom signal is partially obscured by plants.
The plant canopy line may now be manually edited if necessary, in a similar manner to the
bottom line (see Figure 20).
Figure 20. Edit the plant canopy line just like you edited the bottom line
In the center list box, select ‘Plant Canopy.’ Now, use the drawing tools to modify the line.
When complete, observe that on the ‘File View’ screen, the ‘Plant’ field for the selected file
now says either ‘Analyzed’ or ‘Manual Edit.’
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Bottom Type Analysis

Analyzing hydroacoustic data in Visual Habitat for bottom or substrate types is a two-step
process. In step 1, the software extracts features from the bottom echo signal. In step 2, the
software determines the number of types by clustering the features extracted in step 1.
To conduct bottom typing analysis, start by clicking on the ‘Configure Analysis’ button , and
select ‘Feature Extraction’ (see Figure 21).
User definable analysis parameters for Bottom Feature Extraction:
Bottom Echo – First Part: Defines where the algorithm starts extracting features for bottom
classification from the first part of the bottom echo – the units are whole number multiples of
the pulse length. It is recommended to leave this set at the default value of 1.
Bottom Echo – Second Part: Defines where the algorithm starts extracting features for bottom
classification from the second part of the bottom echo – the units are whole number multiples
of the pulse length. It is recommended to leave this set at the default value of 3.
Enable Depth Normalization (checkbox): Allows the feature extraction algorithm to compensate
for the effect that depth has on the shape of the bottom echo envelope by normalizing it to a
user selectable reference depth.
Reference Depth (m): Set to the median depth of your survey area, it is used to normalize the
bottom echo envelope (if enabled).
Only normalize if deeper than reference depth (checkbox): Used to normalize the bottom echo
if the depth is deeper than reference depth. It is recommended to leave this option checked by
default.
Fractal Dimension Threshold (dB): Sets the lower threshold at which the algorithm stops
computing the fractal dimension number. This should be set to the echo level of the trailing
edge of the bottom signal – values may range from -60 to -40 dB.
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After the ‘Bottom Feature Extraction’ parameters have been selected, click on the ‘Bottom
Type’ in the left panel to access the Bottom Type Parameters (see Figure 21 ).
Figure 21. 'Bottom Type' Analysis Parameters in the 'Configure' File View drop-down menu
User definable Bottom Type Parameters:
Energy Filter width (# pings): Sets the number of pings that the energy filter will process at one
time. This value should match the report interval (# pings) selected on the map properties
window to prevent unclassified bottom type reports.
Energy Filter threshold (percent): The minimum energy a ping must have to be reported, and
calculated as a percentage of the maximum energy present in the energy filter width. Values of
60-75% are typical – the higher the percentage, the more discriminating the filtering action will
be.
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Omit pings with manually edited bottom pick (checkbox): This option omits areas where the
bottom line was manually edited from being included in the bottom typing analysis step.
Manual editing of the bottom line is more likely to happen in areas of heavy plant growth or
other phenomena where the bottom signal can be potentially corrupted and the user may elect
to exclude that data from the bottom typing results.
Number of clusters: Informs the algorithm how many bottom types to sort the data into. Visual
Habitat requires that you provide an initial estimate of the expected number of distinct
substrate types in your survey area. If you are not certain, make your best estimation with the
understanding that you can re-analyze if your results suggest more or fewer types are present.
For example, if in your survey area you were expecting areas of soft mud, firm clay, and gravel,
enter ‘3’ for number of clusters.
The number of clusters found will depend on the characteristics of the survey area. We suggest
beginning with the default values for the two Principal Components Analysis algorithms.
Intermediate Files (Advanced): Selecting “Write MAT Files” and “Write CSV Files” creates files
containing intermediate results that can be used for custom analysis (see Appendix A:
Intermediate File Descriptions for further details).
Click on the ‘Run Analysis’ button to initiate analysis. Select ‘Feature Extraction’ and ‘Bottom
Typing’ then ‘Start.’
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Figure 22. PCA View showing the clusters and percentages for each cluster type
In this example (Figure 22), we analyzed with 3 clusters. If there is a bottom type that has an
unrealistically small percentage you may want to reduce the number of clusters and reanalyze.
Conversely you may want to increase the starting number of clusters to test for reasonable
class percentages.
Show PCA Plots: Clicking on “Show PCA Plots” will open a window to visualize
the first 3 Principal Components (see Figure 23).
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Figure 23. Bottom type results displaying the first 3 principal components
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STEP 4: MAP CREATION AND DATA EXPORT
Map Properties
Figure 24. Map Properties' window is displayed when 'Configure' is selected from the ‘Map’ drop-down menu in
Map View
Map Properties Data
Figure 25. Report Interval setting (pings)
Report Interval: Selects number of pings to be averaged and displayed on the map. This also
controls how many pings will be averaged and included per report when the final analysis
results are exported.
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For example, if a DT4 file contained 500 pings and you set the ‘Report Interval’ to 1 and had the
’Map View Data Type’set to Bottom Depth, the map would display the depth of all 500 pings
with no averaging. If you set the ‘Report Interval’ to 5 for that same 500 ping file, the map
would show only 100 data points, each one of them equal to the average bottom depth of 5
pings worth of data.
Figure 26. Plant Height Threshold setting
Report Plant Height Threshold: Controls the minimum plant height that will be displayed on the
map, as well as what will be included in the exported analysis report (Figure 26). Plant height is
equal to the distance between the brown bottom line and the green plant canopy line.
For example, if the bottom line was at 3.00 m and the plant canopy line was at 2.80 m, the
resulting plant height would be 0.20 m. If the ‘Report Plant Height Threshold’ was set to 0.10 m,
then any ping with a plant height greater than 0.10 m would be reported.
Plant height data is one of the data types that is subject to the averaging effect caused by
having a ‘Report Interval’ greater than 1.
Figure 27. Map View Data Type selection
‘Map View Data Type:’ Select the data type to be displayed in the ‘Map View’. If you choose a
type of data for which you haven’t done any analysis for AND you have the ‘Omit Invalid Data
from map view display’ box checked, the map will not display any data. If the ‘Omit Invalid Data
from map view display’ is unchecked, invalid data will be displayed in the color defined by the
palette used for invalid data (default is white – see next section).
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Figure 28. Color scale and palette options window
‘Map View’ Color Palette: Customize how each data type (with the exception of GPS Fix data,
which colors cannot be changed by the user) is displayed using pre-defined color palettes or
user-defined custom palettes.
The pre-defined color palettes automatically adjust to the minimum and maximum limits you
enter and the desired number of colors.
For example if you wanted to display bottom depth on your map, and the shallowest was 2 m,
the deepest part was 20 m, to display 2 m increments, the settings should be:
Color scale minimum value: 2

Color scale maximum value: 20
Color palette: Rainbow (or your pre-defined palette of choice)
Number of colors: 9
A good way to determine the number of colors to use is to divide the maximum value, in the
case of bottom depth (which is the minimum subtracted from the maximum), divided by the
increment you want to show, in this case every 2 meters. So that is 20-2 = 18 /2 = 9 colors. To
create your own color palette(s), check the ‘Use Custom Palette’ box, and then click the ‘Edit
Palette’ button – this will bring up the ‘Custom Palette’ window (see Figure 29).
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Map View Custom Palette Window
Figure 29. The Custom Palette is used for displaying data in Map View and in KML files
To create a ‘Custom Palette,’ first enter a name for your new palette in the ‘Palette Name’ –
you can also ‘Load’ a previously created custom palette to edit. The next step is to select the
‘Beginning Color’ of ‘Color Gradient 1’ by clicking on the symbol to bring up the standard
Windows color editing window. Select your desired color, then ‘OK’, and then repeat the same
steps to choose the ending color. Now you need to choose the number of colors that will be
generated between the two colors you selected. The logic behind choosing the appropriate
number of colors is the same as in the previous example – for instance if you wanted to display
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bottom depth that covered a total of 18 m and have each color represent 2 m, you would enter
‘9’ as your ‘Number of Colors’.
For more color palette options, you can add a third color, or ‘Color Gradient 2’ to your custom
made color gradient you just created – it will be added to the end of ‘Color Gradient 1’. So if
‘Color Gradient 1’ went blue to green with 9 intermediate colors, and the ending ‘Color
Gradient 2’ was set to red with ‘Number of Colors’ set to 9, it would result in a gradient that
looks like this:
There are 9 colors from blue to green, then 9 more colors from green to red for a grand total of
18 colors. This palette would show our 18 meter maximum depth bathymetry data as one color
per meter. The colors are applied so that the data minimum is represented by the first color of
the palette (farthest left) and the maximum data value is represented by the last color (farthest
right) of the palette. Once you have picked the beginning and ending colors and the desired
number of color steps, click the ‘Generate’ button to see the resulting palette. Click on
individual colors to replace with another color. If you like it, ‘Save and Use’ the palette –
otherwise cancel and keep editing until you get your perfect colors.
The ‘Color for Data Below Minimum’, ‘Color for Data Above Maximum’, and ‘Color for Invalid
Data’ parameters are used to display data outside of the ranges intended for the map.
Depending on the type of data you are displaying (bottom type, bottom depth, plant height, or
plant coverage), the units for the minimum and maximum data values may change, but any
data that falls outside of the user defined range will be assigned these colors.
The ‘Color for Invalid Data’ is applied to data that has either not been analyzed, or:
 Bottom typing data: has a ‘type’ of 0 (zero)
 Bottom depth data: A portion of the detected bottom line is invalid (not
detected)
The best way to learn about map making with Visual Habitat is to practice, so have fun and
experiment with different color variations. It’s easy to create full color maps that highlight the
information most relevant and important for your project.
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Data Export
After analysis is complete, the resulting values have been stored in the computer memory. To
export these results, click on the ‘Export Results” from the File drop-down menu to bring up the
Data Export window (see Figure 30).
Figure 30. Data Export window allows you to select the type of analysis to export for each file
You may control the files from which you will export analyzed results and select which type of
analytical results to export. Only files listed in the ‘Selected’ box (upper right) will be exported.
Move one or more ‘Available’ files to ‘Selected’ by highlighting them and clicking on the arrow
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pointing to the right. You may also remove files from the ‘Selected’ box by highlighting them
and clicking on the arrow pointing to the left.
You may export results from all files to a single CSV (Comma Separated Values) file for editing
using a spreadsheet program like Microsoft Excel. To do so, click on the selected export type
(Bathymetry, Plants, or Bottom Type) and provide an export file name in the ‘Filename’ box
provided in the CSV export section. The CSV file can be imported into various GIS software to
create detailed and accurate aquatic habitat maps.
You may also export multiple types of analysis into a KML file (for Google Map) by clicking on
the radio button symbol and entering the file name in the ‘Filename’ box provided in the KML
export section.
Finally, enter a name for your survey.
The ‘Report Window’ box (see Figure 31) will show the CSV output after the export has been
accomplished in Visual Habitat. Click on the column headings to sort all of the data by value in
ascending order – click on it again to sort in descending order.
When the export format and analysis types are selected, click the ‘Start’ button. A progress bar
shows the progress of the export process. The ‘Report Window’ is shown below (Figure 31).
Figure 31. Report Window allows you to see the data after it has been exported
In the ‘Data Export’ window, we selected 15 of our sample files and exported a KML file of plant
coverage (see Figure 32). In the Map View we set the “Plant Height Threshold for Percent
Coverage (m)” to 0.3 m. This value was selected because the bottom line and the plant canopy
line are created by different algorithm, and the resulting depth values when no plants are
present sometimes vary slightly. By setting a threshold value greater than 0 m, differences due
to algorithms are not interpreted as plant detections. For this example, we chose the “Number
of Colors” value at 2 (green and brown in a custom palette), and our two colors represent
regions with plants and regions with no plants. This choice may seem somewhat unusual as we
are using “Plant Percent Coverage” as a presence/absence indicator. In this example, we are
dealing with discrete milfoil beds. The plants were visually observed, and within the limits of
the milfoil patches, plant coverage was essentially continuous.
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Figure 32. KML file showing plant presence (green) and absence (brown) exported directly from Visual Habitat
The plant beds are shown by the green colored dots, while the brown dots indicate an absence
of plants. This data set is shown overlaid on a Google Map image, and reveals that the plant
beds are positioned along either side of the dredged channel (see Figure 32).
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GRIDDING DATA
Gridding your data is the final step in habitat analysis using Visual Habitat. While it is not a
necessary step, it can enhance your ability to describe and interpret your hydroacoustic survey.
Gridding takes scattered individual data points (such as those from your hydroacoustic data)
and creates a regular grid of new, calculated intermediate values based on the original data
points in a user defined cell size and, for some methods, in a “search neighborhood”. Once the
data has been gridded, contour lines can be generated to highlight regions of similar values and
are overlaid on top of the base map.
Visual Habitat offers three methods of gridding, and in order of increasing complexity, they are:
Triangulated Linear, Inverse Distance Weighting, and (ordinary) Kriging.
First a note on order of operation - gridding your data is the FINAL step in your Visual Habitat
analysis. This means that before you attempt to grid your data, you must first:
1) Conduct the analyses for whichever type(s) of results to be gridded (bathymetry, plant
canopy and or bottom classification)
2) Choose the Report Interval number of “pings” in the Map View configure – the fewer
number of pings per report you choose, the longer some of the gridding techniques
(especially kriging) will take. We recommend beginning with 10 pings per report.
3) If analyzing plants, choose your Report Plant Height Threshold.
4) Choose your map projection.
5) Choose a color palette – we recommend one color per major unit. For example if your
bathymetry data has a maximum depth of 12 meters, choose a 12 color palette.
Once the above steps have been completed, you are ready to grid your data.
REMEMBER – IF YOU REDO OR CHANGE STEPS 1, 2, 3, OR 4 ABOVE, YOU MUST

RE-GRID YOUR DATA!
Gridding Data Using Each of the Three Methods.
Method 1 – Triangulated Linear
Gridding your data using the triangulated linear method is the simplest and most
straightforward method.
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Step 1) Set a survey region over your base map. This is an optional step. You can define the
boundaries of the gridding results by drawing a survey region polygon using the “Set Survey
Region” tool. You can also load a previously made survey region made in Visual Habitat, or
*.SHP (shape) file made outside of Visual Habitat.
Figure 33. Drawing survey region around data to bound gridding results
To draw a survey region polygon, select the “Add Polygon” tool and left click anywhere you
would like the boundary of the polygon to be. While you are drawing the polygon, the area will
be highlighted in translucent red (see Figure 33). Once you’re happy with your polygon, right
click to set the polygon – the polygon will change to green (Figure 34). If you want to remove
part of the polygon, select the “Remove Polygon” tool and left click anywhere to remove part of
the polygon you had previously made. Once you’re happy with your selection to be removed,
right click to remove the highlighted area. You can now save the survey region polygon, or
undo, or resetting to no survey region. The areal and volumetric statistics (viewable from the
Grid Tools > Grid Report Info drop-down menu) that are calculated during the gridding are
based on the survey region that you set. If you do not set a survey region, the resulting gridding
data will extend out to its natural boundary, which is the search neighborhood for the method.
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Figure 34. Completed survey region - gridding results will only cover the green survey region
Step 2) Now that the survey region is set, the next step is to select the gridding method from
the Grid Tools > Gridding/Contouring drop-down menu. Selecting Gridding/Contouring brings
up the Gridding/Contouring window (see Figure 35).
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Figure 35. Gridding / Contouring dialog box for selecting interpolation method
Create Grids: Here you select which data type(s) will be used to create the grid. The following
example explains gridding of bottom depth, but you can also select plant height, coverage and
bottom type. You can grid more than one type of data at a time.
Grid cell size (m): Enter the grid cell size in meters. Smaller grid cell sizes will display more
detail in your map, but will take longer to compute, especially with the kriging method.
Conversely, a larger grid cell size will display less detail in your resulting map, but the processing
speed will be faster.
Method: This is where you select one of the three gridding methods from the drop-down list in
order of complexity– Triangulated Linear, Inverse Distance Weighting, and (ordinary) Kriging.
The following example will be using the Triangulated Linear method.
Settings: This is where you enter the selected gridding parameters – each gridding method will
have its own unique set of parameters. The Triangular Linear method has no parameters.
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Create Contours From Grids: Select contours for each gridded type. You can select to grid
more than one type of data at a time. Contours are generated by linear interpolation between
adjacent grid cells. Contours are not available for bottom typing.
Contour Interval: This value sets the interval between contours. This value can be set to a
decimal fraction of a meter, although the most useful contour interval tends to match the
number of colors in the map data palette. We recommend setting the contour interval to the
same value as the map’s major interval. For example, if your bathymetry data has a maximum
depth of 12 meters, and you choose a 12 color palette, set your contour interval to 1 m so each
color in the palette gets its own contour interval.
Step 3) Hit the Start button – the “Running” message will pop up on the lower left as well as a
progress bar in the lower right showing how much of the data has been processed. Once the
gridding is done, the “Analysis Complete” message will pop up in the lower left corner.
Figure 36. Data before gridding (left) and after gridding/contouring with 1 m cell size (right)
Step 4) Once the data has been gridded, you can select the opacity of the original data points,
gridded data and contours over the base map image separately using the Layer Opacity (Figure
36) window (Grid Tools > Set Opacity). The left image in Figure 36 was created with the data
points set to 100%, while the gridded data and contours were set to 0%. The right image was
created by reversing the previous opacity levels. The opacity has no bearing on the exported
results – it only affects the visual presentation of the map.
Step 5) To explore the gridded data results, you can choose the Show GridCell Values tool (Grid
Tools > Show GridCell Values...) from the Grid Tools drop-down menu.
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Figure 37. The Show GridCell Values tool shows you information about a single grid cell
When you mouse over on the gridded data, the grid cell information box will show you the X
and Y index numbers, as well as the value of the underlying cell. Figure 37 shows the gridded
bottom depth value for cell (406, 185) to be 4.76 m. The search neighborhood fields are not
filled in because the triangulated linear algorithm does not use search neighborhoods. These
fields will be explained below when we describe the Inverse Distance Weighting algorithm.
Step 6) To further explore the gridded data, you can examine the Grid Report Information (Grid
Tools > Grid Report Info...). This box (see Figure 38) shows statistics about the gridded data
defined by the survey region boundaries. Each data type and grid method will have different
statistics calculated, but much of the information is common to all the data and methods. This,
along with all of the other grid data can be exported in the next step.
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Figure 38. The Grid Report shows various statistics and parameter settings used to calculate gridded data
Step 7) The next and final step is to export the gridded data to be used or viewed outside of
Visual Habitat. Gridding results are exported separately from the data analysis outputs, and
because of this have their own Grid Export window (see Figure 39) available from the Grid Tools
drop-down menu (Grid Tools > Export Grid Results).
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Figure 39. The Grid Export window allows you to choose data types and formats to export
Select Data Types: Select the data types to export, making sure you have previously completed
the associated type of data analysis.
Raster Export: Select the image format in which to export map images – you can select from
PNG, JPG, TIF, or BMP. You can also select image features to export. If you select Map View, this
image will mirror your Map View page and will include visible data points, grid cells, and
contours. If you select gridded data image, it will only export the gridded data without any
other features. To save a screenshot of the entire Map View including axes, and colorbars, use
the Save As from the Map drop-down menu.
Vector Export: Select the desired output formats and associated types for export. Choose from
KML (data points, grid cells, and contour lines), shapefile (data points, grid cells, and contour
lines), and CSV (data points, and grid cells only) formats. KML files are most commonly opened
in Google Earth, while shapefiles are normally opened in GIS software (ArcGIS, Surfer). You can
also export an image of the gridded data in multiple georeferenced formats.
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Shapefile/CSV Spatial Coordinates: You can choose to export the shape and CSV files using
either Latitude and Longitude, or XY Projected coordinates. For XY Projected coordinates to be
exported, the base map must not be using the Geographic Projection.
Grid Statistics Report: The grid statistics report is a text file containing all of the computed
statistics that are shown in the Grid Report we saw in Step 6.
Output File Name: Here you have the option to enter a file prefix name for all of the exported
outputs. Each file name will start with the prefix entered, followed by the data type, output
type, and file extension.
Once your choices have been made, click the “Start” button. A pop-up progress bar will display
the time remaining until the outputs are ready.
The following free software packages can be used to display the exported files in georeferenced
form:
 Google Earth - displays KML files
 Google Earth Pro - displays exported files except for the CSV option.
 ArcGIS Explorer Desktop - displays all exported files except for the CSV option.
 QGIS - displays all exported files except for the CSV option.
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Method 2 – Inverse Distance Weighting
Gridding your data using the Inverse Distance Weighting method is slightly more complicated
than the triangulated linear method, but many of the steps are the same.
Step 1) Set a survey region over your base map. This optional step is the same as for the
previous gridding method.
Step 2) Select the Inverse Distance Weighting (IDW) gridding method from the Grid Tools >
Gridding/Contouring drop-down menu (see Figure 40) and enter in appropriate settings.
Figure 40. Gridding / Contouring window showing settings for Inverse Distance Weighting
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Choosing Parameters for Gridding via the Inverse Distance Weighting Method
Grid Cell Size: Enter the grid cell size in meters. A smaller grid cell size will display more detail in
your map, but will take longer to compute. Conversely, a larger grid cell size will display less
detail in your resulting map, but the processing speed will be faster. In this example we will
choose a 1 m cell size.
Power (≥0): Data weights are proportional to the inverse distance raised to the “Power” value
p. As a result, as the distance increases, the weights decrease rapidly. How fast the weights
decrease is dependent on the value for p – we recommend starting with a p value of 2.
Choosing a higher power emphasizes the closest data points, whereas choosing a lower power
gives data points farther away more weight.
Smoothing Factor: The smoothing factor s reduces the likelihood that any one sample value will
overly influence an estimated value for a given interpolation location. We recommend using
some smoothing – try starting with a value of 2. Too much smoothing can cause you to lose
detail on the map.
Search Neighborhood Shape and Transect Analysis
The Search Neighborhood determines which data points are used to compute each interpolated
value in your gridded data. The Search Neighborhood is a circle or ellipse centered around each
grid cell. You specify the size and shape of that ellipse, and how many data points must be in
the ellipse for an interpolated value to be computed for each cell.
When you add hydroacoustic files to a dataset, the files are automatically analyzed to compute
two statistics used in the gridding process – Minimum Suggested Semi-Major Axis Length (m),
and the Suggested Minor Axis Direction (deg) (see Figure 41). These statistics can be used to
help determine Search Neighborhood Shape parameter settings. Note that these values can be
misleading if your data does not conform to the standard of parallel transects, one transect per
file.
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Figure 41. Transect Analysis statistics are circled in red - use these to determine the search neighborhood shape
Semi-Major Axis Length (m, >0): This setting controls the length of the semi-major axis of the
search neighborhood. If your search neighborhood shape is round (Axis Ratio = 1), the semi-
major axis length is equal to the radius of the circle. If your search neighborhood shape is an
ellipse (Axis Ratio >1), the semi-major axis length runs from the edge of the ellipse to the center
along the “longer” axis. Two example search neighborhood shapes have the semi-major axis
length shown in red in Figure 42. This value should be set to a length as long as, and in most
cases slightly longer than, the minimum recommended semi-major axis length shown in the
transect analysis to avoid gaps in the resulting gridded data. The following example will use a
value of 35.
Figure 42. The semi-major axis length are shown as the red segments of the search neighborhood shapes
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Minor Axis Direction (deg): This should be set to the recommended minor axis direction shown
in the transect analysis. The angle is measured in degrees clockwise from vertical. In Figure 43 a
negative angle would be in the counter-clockwise direction, while a positive angle would be a
clockwise rotation. This allows the search neighborhood to be orientated so it best lines up with
the orientation of the transects in your data set. This example will use a minor axis direction of
0.4 degrees.
Figure 43. The minor axis direction is shown in red - both neighborhood search shapes are show with a 20
degree minor axis direction angle
Axis Ratio (≥1): This parameter sets the ratio value of the major axis over the minor value axis. A
ratio of 1 gives you a circular search neighborhood. A circular neighborhood is best for data
points that are randomly distributed. If your data points have directional autocorrelation,
choosing an axis ratio that will result in an elliptical search neighborhood shape (>1) that is
parallel to the directional component. This example will use an axis ratio value of 2 for an
ellipse shape.
To summarize: if your data has a well-defined along-transect direction and a consistent spacing
between transects, the search neighborhood should be an ellipse with the minor axis in the
along-transect direction and the major axis in the across-transect direction. The size of the
ellipse should be large enough that when interpolating in the middle of two transects, the
ellipse intersects both transects. In other words, the semi-major axis length should be at least
half of the transect spacing. If your data does not have a well-defined along-transect direction,
then the search neighborhood should be circular (axis ratio 1, minor axis direction doesn’t
matter), and large enough that places where you want interpolated data to be computed have
enough data points close enough to be in the search neighborhood.
Advanced Search Parameters
As the heading suggests, these advanced search parameters will be most useful for experienced
data “gridders”. For beginner and intermediate users, we recommend using the default
settings, however please feel free to experiment with them.
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Number of Sectors (>0): You can divide the search neighborhood into multiple sectors – the
default (and the number of sectors in this example) is 1 sector. Dividing the search
neighborhood into sectors is particularly useful when the data points have been collected on
transects or a grid. It allows you to restrict gridding from happening in areas “outside” your
data points. Figure 44 shows the effects of having more than one search sector on data
interpolation. On the left hand side, we have a search neighborhood with one sector, centered
on a grid cell to the left of all the data points. Even if the minimum number of points required
is 3, an interpolated value will be created for this grid cell even though it is “outside” the data
points. On the right, we have a search neighborhood with four sectors centered at the same
place. Here an interpolated value will NOT be created because the two sectors on the left don’t
have any data points.
Figure 44. The search neighborhood on the left has 1 sector, and the one on the right has 4 sectors
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Sector Offset Angle (deg): This angle offsets the sector angle independently of the minor axis
direction (see Figure 45). This parameter only has an effect if the number of sectors is >1.
Usually you will want to use a value of 0 here.
Figure 45. The search neighborhood on the left has 0 offset angle and a 45 degree offset angle on the right
Number of Points Required per Sector (>0): This setting allows you to increase the number of
points that must be present in each sector for an interpolated value to be created – the default
setting is 1. If this value is set too high, your gridded data may have holes where there were not
enough points in each sector. This example is using a value of 2.
Once all of the settings have been set, click OK to close the window.
gridded data, and contours over the base map image separately using the Layer Opacity (Figure
46) window (Grid Tools > Set Opacity) as described in the section on the Triangulated Linear
algorithm.
Figure 46. Data before gridding (left) and after IDW gridding/contouring with 1 m cell size (right)
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The left image in Figure 46 was created with the data points and base map set to 100%, while
the gridded data and contours were set to 0%. The right image was made by reversing the
previous opacity levels (except for base map). The opacity has no bearing on the exported
tabular results – it only affects the visual presentation of the map.
Step 5) To explore the gridded data results, you can choose Show GridCell Values (Grid Tools >
Show GridCell Values...) from the Grid Tools drop-down menu to bring up the Grid Cell
Information window (see Figure 47).
Figure 47. How GridCell Values brings up Grid Cell Information window
Figure 48. The Show GridCell Values tool shows you information about a single grid cell
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When you mouse over on the gridded data, the grid cell information box will show you the X
and Y index numbers, as well as the value of the underlying cell. Figure 48 shows the gridded
bottom depth value for cell (205, 230) to be 2.43 m. It also highlights and lists the number of
valid data points in search neighborhood (17), and the minimum semi-major axis length
required for the search neighborhood to contain a valid data point (17.97 m). The cursor is also
highlighting the search neighborhood over the map (ellipse shape with the cursor in the middle
of it) – this assists you in visualizing how your search neighborhood shape fits your data. You
can either check the box to have the search neighborhood shown or turn it off by unchecking
the box.
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Step 6) To further explore the gridded data, you can examine the Grid Report Information (Grid
Tools > Grid Report Info...). This box (see Figure 49) shows many statistics about the IDW
gridded data defined by the survey region boundaries. Each data type and grid method will
have different statistics calculated for it, but a lot of the information is common to all the data
and methods. This, along with all of the other grid data can be exported in the next step.
Figure 49. The Grid Report shows various statistics generated from the IDW gridded data
Step 7) The next and final step, once you are happy with your gridding results, is to export the
gridding data to be used or viewed outside of Visual Habitat. This can be done in the same way
as was described for the Triangulated Linear algorithm.
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Method 3 – Kriging
Gridding your data using the Kriging method is slightly more complex than with the IDW
method, but many of the steps are the same.
Step 1) Set a survey region over your base map. This optional step is the same as for the
previous gridding methods.
Step 2) Select the Kriging gridding method from the Grid Tools > Gridding/Contouring drop-
down menu (see Figure 50) and enter in appropriate settings.
Figure 50. Gridding / Contouring window displays settings for Kriging
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There are a few more parameters we need to address for the kriging method of gridding. It is
important to note that this User Guide provides a basic introduction with sufficient detail to be
successful using the kriging method in Visual Habitat software. This User Guide is NOT a how-to
course for learning kriging with no prior experience.
Kriging requires that you create a model of how your data varies with distance. This is called the
variogram. To do this, you first calculate the “empirical variogram”, which is an indication of
how your actual data values vary compared with the distance between data points. Then, you
define a mathematical curve that fits the shape of your empirical variogram as well as possible.
The mathematical curve is the model used in the computation of the interpolated values.
When you grid plant data, you are actually gridding plant height and plant coverage
independently at the same time. You need to do the variogram process twice, once for each
variable. When you grid bottom type data that was created with N clusters, you are actually
gridding N variables independently at the same time. These variables are the fuzzy cluster
membership values, for each cluster, that come out of the fuzzy C-means clustering algorithm.
Because of this, you must do the variogram process N times, once for each variable. The
bottom type assigned to each grid cell is determined by picking the cluster with the maximum
interpolated membership value at that grid cell.
Grid Cell Size: Enter the grid cell size in meters. As in the Triagulated Linear and IDW methods, a
smaller grid cell size will display more detail in your map, but will take longer to compute,
especially with the kriging method. Conversely, a larger grid cell size will display less detail in
your resulting map, but the processing speed will be faster. In this example we will choose a 2
m cell size.
Search Neighborhood Shape and Transect Analysis

The Search Neighborhood is specified as with Inverse Distance Weighting method, but there is
one additional advanced parameter:
Maximum Number of Points to Use per Sector (0 to -> no limit): This setting allows you to limit
the number of points to use per sector in the case of densely populated data point areas to
minimize processing time.
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Empirical Variogram
The variogram describes how the data are correlated with distance. This is an intermediate
model that is used in the gridding process. While we have highly automated the process, there
are a few parameters that the user needs to set.
Distance Bin Size (m, >0): This sets the lag size, or size of each distance bin, between pairs of
data points used in the variogram. This value should be larger than the shortest distance
between data points. The smaller the bin size, the more noise your variogram will tend to have
in it, along with more error, but may capture more detail. The larger the bin, the less noise your
variogram will tend to have in it, along with less error, but may capture less detail. You should
experiment with this value – starting with 1, then doubling it to 2, then 4, then 8, and so on
until you get a variogram that best fits your data with the lowest error. In this example we will
use 4. Once you’ve picked your bin, click “Compute” to see the variogram chart.
Variogram Modeling: There are four model types available, which are useful for fitting to
empirical variograms with different shapes. The available model types are Linear, Spherical,
Exponential and Gaussian. Each model is controlled by three numerical parameters:
Sill s: Limit of the variogram Y value as the distance becomes large. For Linear and Spherical
models this is simply the maximum value.
Range r: The distance at which the difference of the variogram Y value from the sill becomes
negligible. For Linear and Spherical models, this is the distance where the variogram becomes
flat. For Exponential and Gaussian models, this is taken to be the distance where the y value
first reaches 95% of the sill.
Nugget: Value at which the variogram model intercepts the Y-axis.
You can set these parameters manually by typing values in the boxes, or use the automated
optimization tools:
Automatically Optimize Nugget and Sill Option: This feature is

checked by default and allows users to automatically optimize Nugget and Sill whenever the
Range or Type is changed.
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Figure 51. Kriging parameters window
Automatic Optimization: Select “Range, Nugget, Sill” (this keeps the type you have selected) or
“Type, Range, Nugget, Sill” (this tries all four types) for automatic optimization. In this case the
Gaussian Model provided the lowest error.
You can also set the range by clicking in the plot area. This sets the Range based on the X
position of your click.
Once all of the settings have been set, click OK to close the window.
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gridded data, and contours over the base map image separately using the Layer Opacity (Figure
46) window (Grid Tools > Set Opacity). You can also view the Grid Report, and export the
results, as described in the Triangulated Linear algorithm description.
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GLOSSARY OF FUNCTIONS
FILE VIEW FUNCTIONS
Figure 52. 'File' drop-down menu in File View
The File View ‘File’ drop-down menu command buttons have the same function as the File View
toolbar buttons.
New Dataset: Creates a new dataset for analysis. Click to name and store the new dataset in an
appropriate location on your computer. Clicking ‘Save’ will bring up an empty File View screen
where you will add files for analysis.
Add Files: Select which files to add to your dataset.
Remove Files: Remove highlighted files from your dataset.
Load Dataset: Loads a previously saved dataset – see ‘Save Dataset As…’
Save Dataset As…: Allows you to save and name your dataset. The dataset contains all of your
analysis results, display settings, and preferences – everything but the raw acoustic data files (it
does remember where they were stored).
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Playback: Opens the selected DT4 file in the ‘Data View’ window for viewing and editing.
File Information: Opens the ‘Data File Properties’ window for the highlighted DT4. It shows all
of the collection parameters the file was recorded with in Visual Acquisition. It is a read-only
view – no changes can be made.
Edit Calibration: Specify the sound velocity and/or absorption fields by entering those values
directly; OR let Visual Habitat calculate those fields by entering the environmental parameters.
The default behavior is to use the values calculated in Visual Acquisition during data acquisition.
Configure Analysis: Opens the ‘Analysis Parameters’ dialog window and allows you to change
the parameters for Bottom Detection, Plant Detection, Feature Extraction, and Bottom Typing.
You can also save or load a previously created set of ‘Analysis Parameters’.
Run Analysis: Opens the ‘Run Analysis’ dialog window and allows you to select which file(s) you
want to analyze, and what type(s) of analysis you want to perform. Making your selections and
clicking ‘Start’ begins the analysis.
Delete Results: Opens the ‘Discard Analysis Results’ dialog window and allows you to select
which analysis result(s) you want to discard from which file(s). This discards analysis results only
for certain files and DOES NOT do anything to the acoustic files themselves.
Export Results: Opens the ‘Data Export’ dialog window and allows you to select which analysis
result(s) from which file(s). You can specify the filename and location for each result type and
the specific location for each of the results to be saved to. You can also specify a survey name
for the ‘KML Export’ analysis exports. The name you enter will be the display title of the color
legend when opened in Google Map. Checking the ‘Report Window’ displays the selected CSV
results inside the ‘File View’ – you can sort the data by field type by clicking on the field
heading.
Message Center (F9): Opens the ‘Message Window’ for Visual Habitat. It lists any notifications,
actions, and errors generated by the program.
Exit: Closes all of the active Visual Habitat windows and closes the program. Visual Habitat’s
default behavior is to start up with the last dataset that was open.
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Figure 53. 'View' drop-down menu in File View
Show Data View (Ctrl+D): Opens the ‘Data View’ window that was previously displayed. Using
the ‘Ctrl+D’ keyboard shortcut allows you to quickly switch to ‘Data View’ from any other view.
Show Map View (Ctrl+M): Opens the ‘Map View’ window that was previously displayed. Using
the ‘Ctrl+M’ keyboard shortcut allows you to quickly switch to ‘Map View’ from any other view.
Figure 54. 'Help' drop-down menu in File View
About Visual Habitat: Displays the Visual Habitat version number, copyright information,
BioSonics Inc. contact information, and a pretty picture.
User’s Guide: Opens a PDF version of Visual Habitat’s users guide – you must have Adobe
Acrobat installed to view.
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MAP VIEW FUNCTIONS
Drop-Down Menu - Map
Figure 55. 'Map' drop-down menu in Map View
Save As...: Save your map image as one of 9 different formats.
Print... (CTRL+P): Print your map straight from Visual Habitat.
Configure: Opens the ‘Map Properties’ window where you enter in the parameters that affect
how the ‘Map View’ is displayed. The ‘Map Properties’ are explained below.
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Map Properties
Map Properties Data
Figure 56. ‘Map Properties’ window is displayed when ‘Configure’ is selected from the ‘Map’ drop-down menu
in Map View – both “Data’ and ‘Image’ tabs are shown above
Figure 57. Report Interval setting (pings)
Report Interval: Controls how many pings will be averaged and displayed on the map. This also
controls how many pings will be averaged and included per report when the final analysis
results are exported.
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For example, if a DT4 file contained 500 pings and you set the ‘Report Interval’ to 1 and had the
’Map View Data Type’set to Bottom Depth, the map would display the depth of all 500 pings
with no averaging. If you set the ‘Report Interval’ to 5 for that same 500 ping file, the map
would show only 100 data points, each one of them equal to the average bottom depth of 5
pings worth of data.
Figure 58. Plant Height Threshold setting
Report Plant Height Threshold: Controls the minimum plant height that will be displayed on the
map, as well as what will be included in the exported analysis report. Plant height is equal to
the distance between the brown bottom line and the green plant canopy line.
Plant height data is one of the data types that is subject to the averaging effect caused by
having a ‘Report Interval’ greater than 1.
Figure 59. Map View Data Type selection
‘Map View Data Type:’ Select which data type will be displayed in the ‘Map View’. If you choose
a type of data for which you haven’t done any analysis for AND you have the ‘Omit Invalid Data
from map view display’ box checked, the map will not display any data. If the ‘Omit Invalid Data
from map view display’ is unchecked, invalid data will be displayed in the color defined by the
palette used for invalid data (default is white – see next section).
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Figure 60. Color scale and palette options window
‘Map View’ Color Palette: Customize how each data type (with the exception of GPS Fix data,
which colors cannot be changed by the user) is displayed using pre-defined color palettes or
user-defined custom palettes.
Base Map Properties:
Axis Units: Display your position coordinates in either ‘Decimal Degrees’ (ie
-122.28500) or ‘Degree, Decimal Minutes’ (ie 122° 17.100W).
Options: Add a scale bar and north arrow to your base map. Check the appropriate box, then
click on where you would like the scale bar and north arrow to appear on the base map.
Map Image: Choose from several base map providers, or choose your own image server.
The plus symbol allows you to import images from servers that support the WMS or
WMTS protocol.
Clicking on ‘Set’ will import your background image.
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Projection: This is where you select the map projection you would like to use.
Max.Tile Level: The Max Tile Level only needs to be adjusted if the server you are getting
images from does not have imagery at the appropriate level of zoom.
GPS Viewer: This allows you to look at the raw data contained in each GPS fix centered in the
crosshair cursor for the highlighted data file.
Zoom In: Each click zooms in on the ‘Map View’ by 25%.
Zoom Out: Each click zoom out of the ‘Map View’ by 25%.
Select Zoom: Draw a box on the map (by left-clicking and dragging) and then zoom in by either
clicking inside of the box OR by clicking on the button.
Select Pan: Turns the mouse cursor into a hand icon which allows you to grab the map (by left-
clicking) and drag to reposition the map. This is especially useful when zoomed in.
Select Measure: A multifunctional measuring tool that has two measure modes: Line and Area,
and your choice of unit – metric and feet/acre.
Reset: Undoes all the zooms and map movements and returns the map to the original size and
centered position…in case you zoom in too much or zoom out too far.
It also resets the opacity so all data layers are visible.
Drop-Down Menu – Grid Tools
Figure 61. Grid Tools drop-down menu
Gridding/Contouring...: Select which data types to grid and generate contour plots. There are
three gridding methods available – Triangulated Linear, Inverse Distance Weighting, and for
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advanced users, Kriging (Ordinary). These different gridding methods are discussed in further
detail in the gridding examples earlier in the manual.
Set Survey Region...: Create, edit, load, and save a survey region polygon. This polygon is used
to set a boundary limit for your gridded data. You can load standard *.SHP polygon files or
BioSonics *.VHXR files. You can save the survey region as a *.VHXR file.
Set Opacity...: Define the map overlay opacity (0-100%) for data points, gridded data, and
contour layers that are displayed over your base map. You can also choose to show or hide data
that falls outside of your survey region.
Show GridCell Values...: With the Grid Cell Information window open, the gridded data point
values (X Index, Y Index, Bottom Depth) are displayed as you mouse over the gridded data on
the map. It also shows the number of valid data points in the search neighborhood, as well as
the minimum semimajor axis length required for the search neighborhood to contain a valid
data point. You can display a highlighted Search Neighborhood shape to help you trouble shoot
gridding issues related to search neighborhoods.
Grid Report Info...: Opens the grid results for the currently displayed gridded data in Map View.
It shows statistics such as the computed survey surface area, volume, and the gridding method
and settings used to generate the gridded data. The information in the grid report changes
depending on the type of data that has been gridded.
Export Grid Results: Opens the Grid Export window. This allows you to select the data type(s),
raster map image type(s), and vector data types such as KML, shapefile, and CSV files. You can
specify the coordinate system (Lat. & Long., and XY Projected) for the shapefile and CSV output
files. You can also select to export the grid statistics report which contains the surface area,
volume, and the depth portions of the grid report in a variety of units.
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Drop-Down Menu – View
Figure 62. 'View' drop-down menu in Map View
Show File View (Ctrl+F): Opens the ‘File View’ window that was previously displayed. Using the
‘Ctrl+F’ keyboard shortcut allows you to quickly switch to ‘File View’ from any other view.
Show Data View (Ctrl+D): Opens the ‘Data View’ window that was previously displayed. Using
the ‘Ctrl+D’ keyboard shortcut allows you to quickly switch to ‘Data View’ from any other view.
DATA VIEW FUNCTIONS
Drop-Down Menu – File
Figure 63. 'File’ drop-down-menu in Data View
Message Center (F9): View notifications from Visual Habitat about the status of the software
and any issues that might need to be resolved.
Close: Closes the ‘Data View’ window, saving any changes that were made to the bottom and
plant lines.
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Drop-Down Menu – Edit
Figure 64. 'Edit' drop-down in Data View
Use Edit Tool: Changes the cursor to the edit pen – brown for bottom edit and green for plant
canopy edit (only green if you have already ran the plant canopy detection algorithm).
Undo Edit: Undoes an unlimited number (one edit per click) of previous unsaved edit(s). Saved
edits cannot be undone, and all edits are saved when you close the Data View window.
Redo Edit: Use this to redo an unlimited number of previously unsaved and undone edit(s).
Saved changes to edits cannot be redone.
Bottom: Causes the bottom line to become the active line for editing. Only a single line type can
be active for editing at any one time.
Plant Canopy: Causes the plant canopy line to become the active line for editing. Only a single
line type can be active for editing at any one time.
Raw: Editing mode that allows the user to edit/draw a section of line one pixel at a time. This
editing method requires a steady hand and is best use for precise adjustments.
Linear: Editing mode that allows the operator to edit/draw a straight line by left-clicking on
start and end points on the line, and right-clicking to accept the new line. We recommend using
this line editing mode to start with.
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Bezier: Editing mode that draws a line segment the same way as the linear mode, but then
allows the line to be stretched up or down into a smooth, curved shape. This method is best
when looks are more important than accuracy.
Suppress Tracks: Shows only the line selected for editing on the echogram, hiding the line NOT
being edited. It can make line editing a bit easier by reducing interference from multiple data
type lines.
Grey Echogram: Changes the echogram from the regular DT4 palette to one composed of
shades of grey. It can be useful in helping differentiating the different types of edited data lines
from the rest of the echogram.
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Drop-Down Menu – View
Figure 65. ‘View’ drop-down menu in Data View
Show File View (Ctrl+F): Opens the ‘File View’ window that was previously displayed. Using the
‘Ctrl+F’ keyboard shortcut allows you to quickly switch to ‘File View’ from any other view.
Show Map View (Ctrl+M): Opens the ‘Map View’ window that was previously displayed. Using
the ‘Ctrl+M’ keyboard shortcut allows you to quickly switch to ‘Map View’ from any other view.
Run Analysis (Ctrl+A): Opens the ‘Run Analysis’ dialog window so you can select which files and
what type of analysis to run directly from the Data View.
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Bottom Depth Display (F6): Opens a panel showing the value of the bottom depth line and
speed over ground (SOG) from the GPS fix for wherever the cursor is.
Event Marker Listings… (Shift+F7): Displays any event marks in the displayed file that were
created while collecting data with Visual Acquisition.
Increase Display Threshold (F3): Applies a higher (user selectable steps – see preferences)
viewing threshold to the data that is shown on the Data View echogram. Increasing display
threshold means that you see less data on the screen – only the stronger acoustic returns make
it past the display threshold filter.
Decrease Display Threshold (Shift+F3): Applies a reduced (user selectable steps – see
preferences) viewing threshold to the data that is shown on the Data View echogram.
Decreasing display thresholding means that you see more data on the screen – weaker returns
make it past the display threshold filter.
Increase Color Sensitivity (F4): Increases the color sensitivity by reducing the highest signal
strength that can be displayed – any level higher will be colored grey. You can think of this
control as the “threshold” for the top of the color scale – increasing color sensitivity lowers the
highest signal color level.
Decrease Color Sensitivity (Shift+F4): Decreases the color sensitivity by increasing the highest
signal strength that can be displayed. You can think of this control as the “threshold” for the top
of the color scale – decreasing color sensitivity raises the highest signal color level.
Zoom In: Each click zooms in on the Data View echogram by 25%.
Zoom Out: Each click zooms out of the Data View echogram by 25%.
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Figure 66. 'Enter Scale Limits' window in Data View
Enter Scale Limits…: Opens the ‘Enter Scale Limits’ window (Figure 66). You can enter the
minimum and maximum ranges for the echogram to display. If the ‘Invert Range Axis’ is
checked, 0 (zero or the minimum range) will be at the top of the echogram and the maximum
range will be at the bottom. You can also set a minimum (like a threshold) and maximum (like
color sensitivity) amplitude level that will be displayed on the echogram.
Figure 67. 'View Preferences' window in Data View
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Preferences…: Opens the ‘View Preferences’ window (see Figure 67).
 Chart Color: Toggles for whether chart color settings are adjusted for nighttime
viewing. The settings are Standard (day time), Night, and Auto, which changes
the colors based on the color of your windows theme (if you switch your theme
to a dark color, then the Night settings will be selected).
 Color Shift Delta (dB): The amount the color axis shifts up or down when
adjusting Display Color Sensitivity or Display Threshold. The range is from 1 to 20
dB.
 Roll Scroll Limit: Sets the percentage of data limits for capping range axis
scrolling. The range is 0 to 1; 0 = stop scrolling at data limits, 1 = allow scrolling
completely beyond data limits.
 Range Scroll Amount: Sets the percentage of data limits to scroll for range axis
up/down. The range is 0 to 1; 0 = scroll by smallest amount, 1 = scroll by largest
amount.
 Frame Scroll Amount: Sets the percentage of echogram to scroll for

previous/next frame. The range is 0 to 1; 0 = scroll single ping, 1 = scroll all pings.
Show Chart Toolbar: Shows or hides the toolbar buttons at the top of the Data View window
(see Figure 68).
Figure 68. Toolbar in Data View
Undo Action (Ctrl+Z): Undoes the previous Data View action (if applicable). Visual Habitat
maintains an unlimited undo stack.
Redo Action (Ctrl+Y): Redoes a previously undone Data View action (if applicable).
Reset To Defaults (All Charts) (Ctrl+R): Resets Data View window to default viewing settings.
Page Back (Page Up): Regress echogram back one frame by the amount that is set in the ‘View
Preferences’ dialog window.
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Page Forward (Page Down): Advance echogram forward one frame by the amount that is set in
the ‘View Preferences’ dialog window.
Previous Ping (Left Arrow): Regress echogram back one ping.
Next Ping (Right Arrow): Advance echogram forward one ping.
Goto First Ping (Home): Returns cursor to and displays first ping of the echogram.
Goto Last Ping (End): Returns cursor to and displays last ping of the echogram.
Goto Ping Number…(Ctrl+G): Sends the cursor to and displays a user specified ping in the
currently displayed echogram.
Drop-Down Menu – Chart
Figure 69. 'Chart' drop-down menu in Data View
Echogram Options: Opens a selection box for echogram viewing options in Data View.
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 Show Report Strip: This strip displays the value for each ping corresponding to
the type of data currently being displayed on the map, using the color palette
being used by the map (see Figure 70).
Figure 70. Bottom Type 'Report Strip' visible at bottom of Data View echogram – each colored vertical line
shows what the corresponding ping was classified as for bottom type.
 Bottom Lock: This viewing option aligns every ping so it’s centered on the
bottom line.
 Invert Range Axis: When selected, it displays the charts with the maximum range
at the bottom (default). If this is turned off, the maximum range is displayed at
the top of the chart.
 Echo Level 40LogR: Applies a 40LogR correction for spreading loss to the data for
viewing purposes only. The main purpose of this display mode is to view the
calibration sphere when performing a field calibration.
 Bottom Type 30LogR: Applies a 30LogR correction for spreading loss to the data
for viewing purposes only. This is the most appropriate mode for viewing the
bottom signal and plant canopy – this is the default display mode.
 Analyzed Bottom Echo: Displays the portion of the bottom that is used in the
feature extraction and bottom classification analysis. It shows from the bottom
line down to the bottom of the echo envelope and is useful for closely
scrutinizing the bottom signal.
Echogram: Raw Data/Tracks/Both (F5): Allows you to toggle through three Data View display
modes – a raw acoustic echogram, the same echogram overlaid with the detected bottom and
plant canopy lines, and just the bottom and plant canopy lines.
Echogram Overview: This viewing mode forces the entire data file to fit onto a one screen
echogram. For data files that are larger than can be shown on one screen, this mode
subsamples the pings to fit everything onto a one screen echogram.
Echogram Full Resolution: This viewing mode shows every ping for the selected data file. For
viewing data files that are larger than can be shown on one screen, you can use the arrow keys,
the PgUp/PgDn keys, or the ‘Hand’ tool to navigate through the echogram.
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Oscilloscope: Show Chart: Toggles the oscilloscope chart on or off. The Oscilloscope display
shows depth on the Y axis and signal amplitude on the X axis.
Oscilloscope: Show Grid: Toggles the oscilloscope grid overlay on or off. The grid makes it easier
to get rough measurements of echo level without having to use the cursor.
Use Region Tool: Allows you to draw a box on the echogram for either zooming in on or other
actions you can access by right-clicking your mouse in the box.
Use Pan Tool: Left-click on your mouse to drag your view of the echogram around.
Drop-Down Menu – Window
New Window (Ctrl+N): Opens a new window in Data View. This allows you to view the data
file’s echogram differently in each new window (different threshold, zooming factor, etc.). You
can have up to 10 windows open in Data View.
Close Window (Ctrl+F4): Closes the active window.
Close All but active window: If you have more than one window open in Data View, selecting
this will close all of them EXCEPT for the active window.
Close All Windows: Closes all of the open windows in Data View.
Cascade: Arranges the open Data View windows such that they overlap one another, with the
title bar remaining visible so that you can always see which windows are open.
Tile Horizontal: Arranges the open Data View windows (up to 3) as non-overlapping frames with
the long axis orientated horizontally.
Tile Vertical: Arranges the open Data View windows (up to 3) as non-overlapping frames with
the long axis orientated vertically.
Tile All: This option is available when more than three windows are open in Data View and
arranges the open windows such that they do not overlap each other.
Apply Chart Layout to All Windows: Applies the chart settings of the active window (threshold,
zoom, ping range, etc.) to all the other open windows.
Lock Scrolling: Applies the scrolling actions of the active window to all the other windows. This
helps ensure you are looking at the same region of each open window regardless of zoom
factor.
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Open Window List: The area at the bottom of the ‘Chart’ drop-down menu will list all of the
open windows in Data View.
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APPENDIX A: INTERMEDIATE FILE DESCRIPTIONS

When you run a Bottom Type analysis in Visual Habitat, and you have checked one or both of
the “Intermediate Results Files” checkboxes in the Bottom Type section of the Analysis
Parameters dialog, several files are created in the AnalysisResults folder of your dataset. Each
of these files contains one rectangular matrix of numbers. Depending on which of the
checkboxes you checked, a CSV and/or MAT file is created for each matrix. CSV is a text format
that can be loaded into spreadsheet programs such as Microsoft Excel, and also read into
analysis packages such as R, MATLAB, Octave, etc. MAT is a binary format that is more compact
than CSV and can be loaded more quickly into R, MATLAB and Octave. Each MAT file conforms
to the Level 4 MAT-file format and contains one matrix variable with the same name as the
MAT file. The details of each matrix are described below as they are in the CSV files. Each CSV
file contains the same matrix as the corresponding MAT file, but with column headers and
sometimes row headers, which are not present in the MAT file. In the MAT file the matrix is
transposed relative to the CSV file – that is, each column of the matrix in the MAT file
corresponds to a row of the CSV file.
Here are the details of the files produced. Let N be the number of clusters you specified for
your bottom type analysis. Let P1 be the total number of pings in all the files you are doing
your bottom type analysis on. Let P2 be the number of pings that are accepted for
classification, as reported in the bottom type results window.
Featraw.csv: This has P1 rows and 18 columns. The first column is the number of the file that
the ping belongs to (files analyzed are numbered in alphabetical order of filename starting at
1). The second column is the ping number within that file. The third column is 1 if the ping was
accepted for classification, 0 otherwise. The remaining 15 columns are the features computed
on the bottom echo: fractal dimension, E1, E1’, and 12 spectral moments. Note that the energy
filter is based on the sum E1+E1’.
Featnorm.csv: This has P2 rows and 17 columns. Same as Featraw.csv except only pings
accepted for classification are listed, there is no column indicating whether a ping has been
accepted, and the feature values have been normalized so that each feature value, over all
pings accepted for classification, has mean zero and standard deviation one.
Covar.csv: This has 15 rows and 15 columns. It is the covariance matrix of the normalized
features for all pings accepted for classification.
Featrot.csv: Same as Featnorm.csv except the features are expressed in the principal
component coordinate axes.
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Pctvar.csv: This has 1 row and 15 columns. It shows the percent of variance explained by each
principal component, similar to a scree plot.
Clscent.csv: This has N rows and 6 columns. Each row is the center of the cluster corresponding
to a particular bottom type, in the 6-dimensional space formed by the first 6 principal
component axes. This is the space in which clustering is performed.
Clsmemb.csv: This has P2 rows and N columns. Each row contains the membership weights for
each cluster for a particular ping that was accepted for classification. These are the weights
that come out of the fuzzy C-means clustering algorithm.
Clsstd.csv: This has N rows and 6 columns. Each element is the standard deviation of the
coordinates corresponding to a particular principal component axis over all the pings that were
assigned to a particular cluster.
If you click on “View/Change Bottom Type Clusters” in the “Run Analysis” dialog, then only the
cluster-related files (clscent.*,clsmemb.*, and clsstd.*) are updated.
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User Guide

BioSonics, Inc. | Seattle, WA USA | 206.782.2211

END-USER LICENSE AGREEMENT .................................................................................................... 3

END-USER LICENSE AGREEMENT

IMPORTANT – READ CAREFULLY BEFORE COPYING, INSTALLING, OR USING THE SOFTWARE.

6. Ownership and Intellectual Property Rights

End-User License Agreement

A ruggedized Toughbook class computer with anti-glare, anti-reflective sunlight viewable

WHAT'S NEW IN THIS RELEASE (2.0)

STEP 2 – SELECT FILES TO ANALYZE

Figure 1. Visual Habitat File View data file window

Figure 2. File View window in Visual Habitat

Figure 5. Map View window (overlaid on File View window)

Select Base Map Properties’

Figure 6. Base Map Properties window

Clicking on ‘Map Image: Select’ brings up mapping options.

Figure 7. Base Map Configuration and Map Type windows

Figure 8. Web Map Server Configuration Window

Clicking on ‘Set’ will import your background image.

Figure 9. Coordinate Reference System window

Once you’ve made your selection, click OK to close the window.

Figure 10. Map View Window showing imported image

Figure 11. Map View with stray transects (circled)

STEP 3 – PERFORM YOUR ANALYSIS

Visualize the Acoustic Data

Figure 12. File View (with second file highlighted)

Determining Bottom Depth

The Rising Edge Method

The Trailing Edge Method

The Trailing Edge Offset (pulse length)

Figure 15. Run Analysis window

Manual Editing Tools

Determining SAV Location and Coverage

Figure 18. Analysis Parameters window for plant detection.

Other parameters shown include:

Please note that the bottom depth must be established first.

Identifying Plants on the Echogram

Bottom Type Analysis

User definable analysis parameters for Bottom Feature Extraction:

User definable Bottom Type Parameters:

STEP 4: MAP CREATION AND DATA EXPORT

Map Properties Data

Figure 25. Report Interval setting (pings)

Figure 26. Plant Height Threshold setting

Figure 27. Map View Data Type selection

Figure 28. Color scale and palette options window

Color scale minimum value: 2

Map View Custom Palette Window

Finally, enter a name for your survey.

REMEMBER – IF YOU REDO OR CHANGE STEPS 1, 2, 3, OR 4 ABOVE, YOU MUST

Gridding Data Using Each of the Three Methods.

Method 1 – Triangulated Linear

Method 2 – Inverse Distance Weighting

Search Neighborhood Shape and Transect Analysis

Advanced Search Parameters

Figure 50. Gridding / Contouring window displays settings for Kriging

Search Neighborhood Shape and Transect Analysis

Nugget: Value at which the variogram model intercepts the Y-axis.

Automatically Optimize Nugget and Sill Option: This feature is

Figure 51. Kriging parameters window

Figure 52. 'File' drop-down menu in File View

Add Files: Select which files to add to your dataset.

Remove Files: Remove highlighted files from your dataset.