BIOQUANT Topographer Handbook

BIOQUANT Topographer
Help Procedures
This documents contains the help files for BIOQUANT Life Science or BIOQUANT OSTEO version 11.2.6 for Microsoft Windows 7. Use the Contents for quick direction to particular topics. Use the Index to find specific topics. Use the Search functionality for refined direction to specific topics. For directed help on individual items:
For Boxes: click the Help button or ? button to get help on that box. For Menu Items: Highlight a menu item with you mouse and click F1 on the keyboard for help on menu items that dont have boxes.
This document is also available in PDF format on the BIOQUANT installation disk.
Copyright 2010, 2011
BIOQUANT Image Analysis Corporation 5611 Ohio Avenue, Nashville, TN 37209 phone: 800-221-0549 or 615-350-7866 fax: 615-350-7282 email: bioquant.support@bioquant.com web: www.bioquant.com Revision 11.2, 2-28-2011
Table of Contents
Topographer Introduction- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1-1
The Topographer Three Work Areas ...................................................................... General Steps Required to Create a 2D Map ......................................................... General Steps Required to Create a 3D Model ...................................................... Additional Topographer Features ........................................................................... Viewing BIOQUANT Sample 2D Maps and 3D Models .......................................... 1-2 1-4 1-4 1-5 1-5
2D Mapping - Review & Optimize - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 2-1

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

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

Introduction to the Atlas Modeler ............................................................................ 4-2 Changing the Characteristics of the Model ............................................................. 4-7 Activating Continuous Rotation............................................................................. 4-11 Record or Play an AVI Movie................................................................................ 4-14 Saving and Loading a Surface Rendering Parameters File.................................. 4-17 Special Formatting Options................................................................................... 4-19 Printing, Saving, and Copying the Model .............................................................. 4-21 Exiting Atlas Modeler ............................................................................................ 4-25
The Atlas Viewer in Detail - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 5-1

Working With 3D Wire Frame Atlases .................................................................... 5-2 Printing, Copying, or Exporting an Atlas ............................................................... 5-34 Manipulating Data Arrays and Data Sets in the Atlas Viewer ............................... 5-38
The Atlas Shop in Detail - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 6-1

The File Menu ......................................................................................................... 6-2 The Select Menu..................................................................................................... 6-7 The View Menu ..................................................................................................... 6-16 The Edit Menu....................................................................................................... 6-27 Tools on the System Tool Bar............................................................................... 6-45
Table of Contents
Tools on the Vertical Tool Bar............................................................................... 6-47 Special Edits To Enhance Surface Rendering...................................................... 6-66 Taking Measurements from an Atlas .................................................................... 6-69
Planar & Contour Conversion - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 7-1

Understanding the Basics of Planar and Contour Conversion................................ 7-2 Planar Conversion .................................................................................................. 7-4 Displaying and Modifying the Planar Histogram ................................................... 7-17 Contour Conversion .............................................................................................. 7-25 Displaying and Modifying the Contour Converted Atlas........................................ 7-37
Index - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - index--i
Table of Contents
BIOQUANT Topographer Handbook
Topographer Introduction
This section explains important concepts and gives step by step instructions for viewing sample 2D maps and 3D surface-rendered models that can be installed from the BIOQUANT installation CD.
The Topographer Three Work Areas (page 1-2) General Steps Required to Create a 2D Map (page 1-4) General Steps Required to Create a 3D Model (page 1-4) Additional Topographer Features (page 1-5) Viewing BIOQUANT Sample 2D Maps and 3D Models (page 1-5)
Topographer Introduction
Page 1-2
THE TOPOGRAPHER THREE WORK AREAS

When the Save to Topo Array feature is active in the main BIOQUANT program, every mark and tracing generated during measurement is also recorded as a series of topographic data points. BIOQUANTs Topographer Plug-in uses this topographic data to reconstruct first a wire frame atlas, then a three dimensional, surface rendered model of the measured structures. The Topographer program has three separate parts: Atlas Viewer This is the Topographers front room. It is the where Topo arrays that contain the topographic data for the reconstruction are selected and displayed as a wire frame structure called an atlas. Once an atlas is displayed, door ways into the Atlas Shop and the Atlas Modeler become available. While in the Atlas Viewer, the user may experiment with color or rotational changes without fear of altering the original topo data. The atlas may also be printed or saved to a file while in the Atlas Viewer. (If you did not purchase the full Topographer plug-in, you have a subset of the Atlas Viewer called, Topo Reader.) The Atlas Viewer (Initial Display Environment)
Atlas Modeler This is the Topographers surface rendering environment, where a 3D atlas is rendered with a virtual skin to produce a solid or semi-solid model. Rotating models may be recorded as AVI movies.
BIOQUANT Topographer Handbook: Topographer Introduction
Page 1-3
The Atlas Modeler (Surface Rendering Environment)
Atlas Shop This is the Topographers editing and measuring environment. There are tools to correct topographic errors that were introduced during measurement, to apply special formatting to an atlas that is to be surface rendered, to convert an atlas to a planar histogram, and to take additional measurements directly from the reconstructed atlas. Possible measurements include: volume, area, counts, and distances between structures. The Atlas Shop (Editing and Measurement Environment)
Page 1-4 RELATED TOPICS

General Steps Required to Create a 2D Map (page 1-4) General Steps Required to Create a 3D Model (page 1-4) Additional Topographer Features (page 1-5) Viewing BIOQUANT Sample 2D Maps and 3D Models (page 1-5)
GENERAL STEPS REQUIRED TO CREATE A 2D MAP

Following is a quick outline of the general steps required to create a 2-D Map. For a detailed procedure, see the chapter entitled, 2-D Mapping: Data Collection, in the Life Science or OSTEO help or PDF manual.
STEPS
1. In the BIOQUANT Life Science or BIOQUANT OSTEO measurement program, collect Topo data while measuring a specimen. During data collection the 2D map can be displayed in Life Sciences or OSTEOs Overview window. In BIOQUANT Topographers Atlas Viewer select and display the map in an atlas window. If desired, adjust the display parameters (change line colors, turn cell markers into symbols, fill some areas with solid color, etc.), then print or export the 2D map. If the map contains errors, its tracings can be moved or modified in the Topographers Atlas Shop. It is important to back up original data before edits are made in the Atlas Shop.
2.
2D MAPPING INSTRUCTIONS
2D Mapping - Review & Optimize (page 2-1)
RELATED TOPICS
The Topographer Three Work Areas (page 1-2) General Steps Required to Create a 3D Model (page 1-4) Additional Topographer Features (page 1-5) Viewing BIOQUANT Sample 2D Maps and 3D Models (page 1-5)
GENERAL STEPS REQUIRED TO CREATE A 3D MODEL

Following is a quick outline of the general steps required to create a 3-D Model. For a detailed procedure, see the chapter entitled, 3-D Modeling: Data Collection, in the Life Science or OSTEO help or PDF manual.
STEPS
1. In the BIOQUANT Life Science or BIOQUANT OSTEO measurement program, collect Topo data while measuring the serial sections. For each section in the series, you will set a reference Landmark for all tracings on that section, and a Z Offset value to identify the sections position relative to other sections. In BIOQUANT Data Manager, back up the original data and, if necessary, use the Topo Array Exporter to gather all of the Topo data for the reconstruction from multiple data sets into a single master 3D data set. In BIOQUANT Topographers Atlas Viewer, select and display the initial wire frame reconstruction in an atlas window. If desired, adjust the colors that are used in the atlas display. (Color adjustments made in the Atlas Viewer do not change the default colors that are recorded in the Topo arrays.) Once displayed in the Atlas Viewer, the reconstruction is moved back and forth between the Atlas Modeler (where it is automatically surface rendered in the colors that were chosen in the Atlas Viewer) and the Atlas Shop (for editing), until the surface rendered model is both accurate and visually pleasing.
2. 3.
4.
Page 1-5 3D MODELING INSTRUCTIONS

3D Modeling - Review & Optimize the 3D Data (page 3-1) 3D Modeling: Surface Rending in the Atlas Modeler (page 4-1)
RELATED TOPICS
The Topographer Three Work Areas (page 1-2) General Steps Required to Create a 2D Map (page 1-4) Additional Topographer Features (page 1-5) Viewing BIOQUANT Sample 2D Maps and 3D Models (page 1-5)
ADDITIONAL TOPOGRAPHER FEATURES

In addition procedures for 2D mapping and 3D modeling, BIOQUANT Topographer has detailed instructions for using the Atlas Viewer and Atlas Shop outside of a procedural context. There is a also a chapter dedicated to Planar and Contour Conversion, a special Topographer tool. The Atlas Viewer in Detail (page 5-1) The Atlas Shop in Detail (page 6-1) Planar & Contour Conversion (page 7-1)) Both Planar Conversion and Contour Conversion quantitatively map deferentially labeled cell populations across serial brain sections, using the topographic tracings that were recorded in BIOQUANT during measurement. In both types of conversion, for each section, the process pulls cell markers within the section to the nearest point on the sections contour tracing. The number of cells at each point are represented by proportionally sized symbols. With Contour Conversion, section contour tracings retain their original configuration. With Planar Conversion, each sections contour tracing is broken at a defined point and stretched into a vertical line. The result is a Planar Histogram.
RELATED TOPICS
The Topographer Three Work Areas (page 1-2) General Steps Required to Create a 2D Map (page 1-4) General Steps Required to Create a 3D Model (page 1-4) Viewing BIOQUANT Sample 2D Maps and 3D Models (page 1-5)
VIEWING BIOQUANT SAMPLE 2D MAPS AND 3D MODELS

Looking at sample 2D maps and 3D Models will acquaint you with the Topographer and will show different types of finished reconstructions. Sample Data Sets are installed from the BIOQUANT Life Science or BIOQUANT OSTEO installation CD. One of the sample data sets is called General Atlas Set and contains finished 2D Maps and 3D models that can be displayed in the Topographer. The General Atlas Set has 18 Topo arrays, each of which is a separate specimen reconstruction. While working in the Topographer, keep in mind that the data and/or tracings of a particular reconstruction are called an atlas.
SAMPLE 2D MAPS LIST

The General Atlas Set contains the following two-dimensional atlases: D4 Cerebellum (cerebellum section) D5 Colon (colon cross-section) D6 Glia (map that distinguishes single labeled and dual labeled cells) D7 LC Cells (map of cells labeled with lipocortin) D8 Cortex (brain cortex section) D9 Hippo (hippocampus section) D11 Symbols (shows cell markers replaced with symbols) BIOQUANT Topographer Handbook: Topographer Introduction
Page 1-6
D18 Axon Counting (nerve cross-section for axon counting)
SAMPLE 3D MODELS LIST

The General Atlas Set contains the following three-dimensional atlases: D1 Rat Brain Normal (whole brain) D2 Rat Brain Caps (whole brain, formatted for surface-rendering that reveals internal structures) D3 Horizontals (brain sections showing sinuses and cells of interest) D10 Sections (sections that include two different cell populations) D12 Embryonic Rat Head (head sections showing major structure) D13 Milkweed (whole flower with petals and stamen) D14 Embryo Sagittal (sagittal sections of a rat embryo with internal structures) D15 Spinal Cord Small (spinal cord cross-sections) D16 Spinal Cord Large (more sections, high resolution, surface-renders very slowly) D17 Spinal Cord Decrease Resolution (same as D16 but formatted with fewer data points to speed surface rendering)
TO OPEN THE SAMPLES, CONTINUE TO

Procedures for Viewing Sample Reconstructions (page 1-6)
RELATED TOPICS
Procedures for Viewing Sample Reconstructions (page 1-6) The Topographer Three Work Areas (page 1-2) General Steps Required to Create a 2D Map (page 1-4) General Steps Required to Create a 3D Model (page 1-4) Additional Topographer Features (page 1-5)
PROCEDURES FOR VIEWING SAMPLE RECONSTRUCTIONS

Both 2D and 3D atlases are displayed first in the Atlas Viewer window. A finished, ideal view of each sample wireframe atlas will be accomplished by loading the display Parameters (.set) file that was saved for that atlas. Viewing the samples will begin with the selection of one of the Topo arrays in the General Atlas Set data set. If the selected array contains a 3D atlas, after it is displayed in the Atlas Viewer, it may be moved into the Atlas Modeler for surface rendering.
PROCEDURE 1 - OPEN THE GENERAL ATLAS SET

1. 2. On BIOQUANT Life Sciences or BIOQUANT OSTEOs system menu bar click Topographer. The Topographers Atlas Viewer will open. From the Atlas Viewers File menu, choose Open Data Set, or on the system tool bar click the Open Data Set button. The Open Data Set dialog box opens. 3. On the Open Data Set dialog box, click the Browse button. The Change BQ Volume Search Directory dialog box opens.
Page 1-7
Change BQ Volume Search Dialog Box
4.
Navigate to and open the Atlas Volume folder. Example Path: D:\BQLIFESCIENCE\Sample Data Sets\Atlas_Volume or D:\BQOSTEO\Sample Data Sets\Atlas_Volume. Click the Select button to close the Change BQ Volume Search Directory dialog box. There is only one data volume in this folder: Atlas Volume. Open Data Set Dialog Box
5.
6. 7. 8.
On the Open Data Set dialog box, click to highlight Atlas Volume. Data sets within the volume will be displayed in the lower box. In the Data Sets list, click to highlight General Atlas Set. Click the Open button. The 18 atlases (Topo arrays) in this data set will be listed in the Select Arrays dialog box.
PROCEDURE 2 - CHOOSE AND DISPLAY THE DESIRED ATLAS

To display a 2D map, on the Select Arrays dialog box, scroll through the Available Arrays list of atlases and double-click one of the following arrays for viewing. The index number of that atlas will be moved to the Selected column. The following arrays contain two-dimensional atlases: D4 Cerebellum (cerebellum section) D5 Colon (colon cross-section) D6 Glia (map that distinguishes single labeled and dual labeled cells) D7 LC Cells (map of cells labeled with lipocortin) D8 Cortex (brain cortex section) D9 Hippo (hippocampus section) BIOQUANT Topographer Handbook: Topographer Introduction
Page 1-8
D11 Symbols (shows cell markers replaced with symbols) D18 Axon Counting (nerve cross-section for axon counting)
To display a 3D reconstruction, on the Select Arrays dialog box, scroll thought the Available Arrays list of atlases and double-click one of the following arrays for viewing: The index number of that atlas will be moved to the Selected column. Three dimensional atlases must be displayed in the Atlas Viewer before they can be moved into the Atlas Modeler for surface rendering. The following arrays are three-dimensional atlases: D1 Rat Brain Normal (whole brain) D2 Rat Brain Caps (whole brain, formatted for surface-rendering that reveals internal structures) D3 Horizontals (brain sections showing sinuses and cells of interest) D10 Sections (sections that include two different cell populations) D12 Embryonic Rat Head (head sections showing major structure) D13 Milkweed (whole flower with petals and stamen) D14 Embryo Sagittal (sagittal sections of a rat embryo with internal structures) D15 Spinal Cord Small (spinal cord cross-sections) D16 Spinal Cord Large (more sections, high resolution, surface-renders very slowly) D17 Spinal Cord Decrease Resolution (same as D16 but formatted with fewer data points to speed surface rendering) button on the system tool bar, or choose Open from the Atlas menu.
1.
Verify that the desired Topo array is in the Selected column of the Select Arrays dialog box, then click the New Atlas Window
2. 3.
On the system tool bar click the Resize To Fit button. The atlas will be resized and centered in the window. Load the parameters (.set) file for this atlas by doing the following: a. From the File menu, choose Load Parameters. Load Parameters File Dialog Box
b.
In the large center box, double click the Parameter Files Atlas Set folder. This folder contains one or more parameter (.set) files for each atlas in the General Atlas Set.
Page 1-9
Open Parameters File Dialog Box
c.
Click to highlight the .set file that matches the name of the currently displayed atlas (the currently selected Topo array) and click the Open button. If more than one Parameters (.set) file is available for an atlas, it means that more than one view of the atlas was saved. Choose any .set file that reflects the name of the currently displayed atlas.
4.
To display a different sample reconstruction, do the following: a. b. c. d. In the Selected list of the Select Arrays dialog box, double-click the index number of the currently selected Topo array to remove it from the Selected list. In the Available Arrays list, double-click to select the desired Topo array. On the system tool bar click the Redraw button.
Repeat from step 2 to resize and display the new atlas.
PROCEDURE 3 - SURFACE RENDER A 3D ATLAS

After being displayed as a wire-frame in the Atlas Viewer, 3D atlases may be moved into the Atlas Modeler for surface rendering. A finished, ideal view of each surface rendered atlas may be accomplished by loading the Bioquant rendering (.bqr) file for that model. 1. 2. 3. In the Atlas Viewer, perform Procedure 2 - Choose and Display the Desired Atlas on page 1-7 to display the desired 3D atlas array and load its parameter file. On the Atlas Viewers tool bar, click the Atlas Modeler button. The Atlas Modeler opens and displays a default version of the surface rendered model. Load this models Bioquant rendering (.bqr) file by doing the following: a. From the Atlas Modelers File menu, choose Load Parameters. Open Parameters File Dialog Box
b.
Open (Look in) the Parameter Files Atlas Set folder. This folder contains one or more Bioquant rendering (.bqr) files for each 3D atlas in the General Atlas Set.
Page 1-10
Open Surface Rendering Parameters File Dialog Box
c.
Click to highlight the .bqr file that matches the name of the current model (the Topo array that was selected in the Atlas Viewer) and click the Open button. If more than one rendering parameters (.bqr) file is available for a model, it means that more than one view of the model was saved. Choose any .bqr file that reflects the name of the currently displayed model.
4.
On the system tool bar, click the Auto Movie Rotate button to see the model automatically rotate 360 degrees. To stop the rotation before the 360 degree cycle is complete, click the Auto Movie Rotate button again. (Optional) To hand-rotate the model, do the following: a. b. On the system tool bar, click the Rotate button. Anywhere in the model window, click and slowly drag the cursor a short distance in the direction you wish the model to rotate. Example: To rotate the model counter-clockwise (around its Z axis), click and hold the right mouse button, then slowly move the cursor in a straight, short line to the right.
HAND ROTATING TIPS

5. 6. Slow, short-distance drags of the cursor are best. Pause between each cursor-drag. Larger atlases will take a moment to respond.
If more than one Bioquant rendering file is available for this model, to see a different version of this same model, repeat from step 3 and choose an alternate .bqr file for this model. To open and view a completely different model, do the following: a. b. c. d. e. From the Atlas Modelers File menu, choose Exit Atlas Modeler. The Atlas Modeler closes and the Atlas Viewer re-opens. On the Atlas Viewers Select Arrays dialog box, in the Selected list, double-click the current Topo array index number to remove it from the Selected list. On the Atlas Viewers Select Arrays dialog box, in the Available Arrays list, double-click to select the desired Topo array. On the Atlas Viewers tool bar click the Redraw tracings from the new array. button to update the Atlas Window with the
From the Atlas Viewers File menu, choose Load Parameters and open the .set file that belongs to this atlas. See Procedure 2, step 3 (1-8) Repeat from step 2 to view the new surface rendered model.
f.
RELATED TOPICS
The Topographer Three Work Areas (page 1-2) General Steps Required to Create a 2D Map (page 1-4) General Steps Required to Create a 3D Model (page 1-4) Additional Topographer Features (page 1-5) Viewing BIOQUANT Sample 2D Maps and 3D Models (page 1-5)
2D Mapping - Review & Optimize

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

Clicking the word Topographer on BIOQUANT Life Sciences or BIOQUANT OSTEOs menu bar opens the Topographers Atlas Viewer. If the optional Topographer plug-in has not been purchased, then the Topo Reader, a reduced functionality free version of the Atlas Viewer opens. The Select Arrays dialog box is visible and initially shows the arrays that are available in the data set that was open in Life Science or OSTEO when the Topographer was launched. (Opening an alternate data set will be discussed shortly.) In the Topographer, only Topo arrays are selected on the Select Arrays dialog box. The topographic data that makes up a 2D map, as well as the display of the map, is called an atlas. The Atlas Viewer Desktop Before an Atlas is Selected and Displayed
THE ATLAS VIEWER

The Atlas Viewer is the Topographers front room. It is the where Topo arrays that contain the topographic data for the 2D map are selected and displayed. Once an atlas is displayed, a door way into the Atlas Shop becomes available. (The Atlas Modeler also becomes available, but is not used with 2D mapping.) While in the Atlas Viewer, the user may experiment with color or positional changes without fear of altering the original topo data. The atlas (map) may also be printed, saved to a file, or copied to the clipboard while in the Atlas Viewer.
TOPIC CONTENTS
Part 1-Open the Desired Data Set (page 2-3) Part 2-Select and Display the 2D Map (page 2-4) Part 3-Optimize the Map Display (page 2-10) Part 4-Prepare to Edit the 2D Map (page 2-19) Part 5-Correct Errors In Topo Data (page 2-22)
BIOQUANT Topographer Handbook: 2D Mapping - Review & Optimize

Print the Map (page 2-6) Export the Map to a File (page 2-7) Copy and Paste the Map into a Different Program (page 2-9) Manipulating the Map (page 2-10) Change Background and Increase Thickness of Tracings (page 2-11) Change Color/Symbols Parameters (page 2-12) Saving and Loading Display Parameters (page 2-15) Save Data Set (page 2-18) Exit Atlas Viewer (page 2-19)
PART 1-OPEN THE DESIRED DATA SET

By default, the data set that was open in BIOQUANT Life Science or BIOQUANT OSTEO when the Topographer program was accessed, is open in the Topographer and its arrays are visible in the Select Arrays dialog box. If this is the data set that contains the desired 2D map, skip to Part 2, otherwise, perform the following procedure to open the desired data set.
PROCEDURE
1. On the system tool bar click the Open Data Set display the Open a Data Set dialog box. The Open a Data Set Dialog Box button, or from the File menu choose Open Data Set, to
When a data volume is selected, the data sets contained in that volume will be displayed in the Data Sets list.
2.
In the Data Volumes list, click to highlight the data volume that contains the data for the desired 2D map. If the desired data volume is not in the list do the following: a. Click the Browse button to open the Choose BQ Volume Search Directory dialog box.
Page 2-4
The Choose BQ Volume Search DIrectory Dialog Box
b. c. d. 3. 4. 5.
In the Folders list, double-clicking to open or close folders, open the folder that contains the desired data volume. Click the OK button. Again on the Open Data Set dialog box, in the Data Volumes list, click to the desired data volume.
In the Data Sets list, click to highlight the desired data set. Click the Open button. The arrays of the data set appear in the Select Arrays box. Continue with Part 2-Select and Display the 2D Map on page 2-4.
MORE 2-D MAP REVIEW & OPTIMIZING TOPICS

Part 2-Select and Display the 2D Map (page 2-4) Part 3-Optimize the Map Display (page 2-10) Part 4-Prepare to Edit the 2D Map (page 2-19) Part 5-Correct Errors In Topo Data (page 2-22)
RELATED TOPICS
PART 2-SELECT AND DISPLAY THE 2D MAP

When the correct data set is open, the data for the 2D map is contained in one or more Topo arrays that are visible in the Available Arrays list of the Select Arrays dialog box.
PROCEDURE
1. In the Atlas Viewer, on the Select Arrays dialog box, in the Available Arrays box, double click any and all Topo arrays in the data set that contain data for the desired 2D map to move them to the Selected box. The index number of the selected array(s) will appear in the Selected list. Only Topo arrays should be selected. On the Atlas Viewers tool bar, click the New Atlas Window Open. button, or from the Atlas menu, choose
2.
Page 2-5
3. On the Atlas Viewers tool bar, click the Resize To Fit button. The atlas (2D map) is visible in the Atlas Window and the Atlas Parameters dialog box opens. 2D Map Displayed in the Atlas Viewer
4.
Examine the map for errors introduced during data collection. Consider the following questions: a. Are the default colors (those chosen during measurement) correct for all tracings and cell markers? During measurement, the user occasionally forgets to designate the intended Color in the Parameters region. Depending on circumstances, this can result in structures of the same type (which were intended to be the same color) being different colors. Small positional problems may arise if two parts of the specimen were measured at different magnifications through microscope objectives that were not parfocaled. For example, cell markers that were generated at 40X, on cells that lay close to a structures edge, might now appear to be outside the structures contour tracing that was created at 4X. During automatic measurement an inaccurate tracing might be generated, for example, if the user failed to notice, before clicking the Measure button, that the automatic preview outline included something that was not intended to be measured. During manual measurement the user may have mis-traced a segment of a structures contour, or, if Spacebar to End was active, may have clicked points that were too far apart to accurately define segments of the structures edge.
b.
Are all of the tracings and/or cell markers positioned correctly, relative to one another?
c.
Do tracings accurately represent the shape of the objects that were measured?
DATA CORRECTIONS ARE DONE IN THE ATLAS SHOP

If data corrections are needed, go to Part 4-Prepare to Edit the 2D Map (page 2-19), then proceed to Part 5Correct Errors In Topo Data (page 2-22). 5. Examine the atlas for aesthetic qualities. Consider these questions: a. b. c. d. e. Do the default colors (those chosen during measurement) look good? Would the map be more visible against a black background? Would small objects such as cells look better represented by symbols? Would filling some areas with solid color enhance the map? Are there any duel-labeled structures? BIOQUANT Topographer Handbook: 2D Mapping - Review & Optimize
Page 2-6
The Fill and Overlap options can display overlapping areas in a distinctive third color.
DISPLAY ENHANCEMENTS ARE DONE IN THE ATLAS VIEWER

To enhance the appearance of the map, see Part 3-Optimize the Map Display (page 2-10). 6. When the map needs no further correction or enhancements, it is ready to be printed, exported to a file, or copied to the clipboard. Print the Map (page 2-6) Export the Map to a File (page 2-7) Copy and Paste the Map into a Different Program (page 2-9)

Part 3-Optimize the Map Display (page 2-10) Part 4-Prepare to Edit the 2D Map (page 2-19) Part 5-Correct Errors In Topo Data (page 2-22)
RELATED TOPICS
PRINT THE MAP

Print Atlas is available when the Atlas Window is open. Topographer prints an atlas out at five inches by five inches. It titles the atlas with the names of the data volume and data set and the date. To print the atlas at a different size, export the atlas as a bitmap or metafile and print it from a graphics application (e.g. Adobe Photoshop).
PROCEDURE
1. From the File menu, choose Print Atlas to open the Print box. The Print Box
2. 3.
Adjust any printing options. Click the OK button.
ADDITIONAL NOTE
Control-P opens the Print box. BIOQUANT Topographer Handbook: 2D Mapping - Review & Optimize
Page 2-7 2-D MAP REVIEW & OPTIMIZING TOPICS

RELATED TOPICS
Export the Map to a File (page 2-7) Copy and Paste the Map into a Different Program (page 2-9) Manipulating the Map (page 2-10) Change Background and Increase Thickness of Tracings (page 2-11) Change Color/Symbols Parameters (page 2-12) Saving and Loading Display Parameters (page 2-15) Save Data Set (page 2-18) Exit Atlas Viewer (page 2-19)
EXPORT THE MAP TO A FILE

An atlas can be exported as a BMP or a SVG. The bitmap is a two dimensional format, in essence a snapshot of the atlas. A bitmap of the atlas can also be copied to the clipboard and then pasted into another application. SVG is a two-dimensional vector format. This format is useful because it can be resized to a larger size without loss of data in another program. SVG files can be opened and viewed directly in most web browsers. They can be edited in graphics programs such as Inkscape or Adobe Illustrator. Inkscape is an open source graphics program that can be downloaded for free from www.inkscape.org. Export options are available on the File menu when an atlas window is open.
TOPIC CONTENTS
Export to BMP Procedure (page 2-7) Export to SVG Procedure (page 2-8)
2-D MAP REVIEW & OPTIMIZING TOPICS

RELATED TOPICS
Print the Map (page 2-6) Copy and Paste the Map into a Different Program (page 2-9) Manipulating the Map (page 2-10) Change Background and Increase Thickness of Tracings (page 2-11) Change Color/Symbols Parameters (page 2-12) Saving and Loading Display Parameters (page 2-15) Save Data Set (page 2-18) Exit Atlas Viewer (page 2-19)
EXPORT TO BMP PROCEDURE

Export Current View to BMP will save the view in the Atlas window to the BMP format. This format is a two dimension static format. If a BMP is resized to a larger size in another program details of the map could be lost. To save to a vector based format, where the resolution of the map is maintained, see Export to SVG Procedure on page 2-8.
PROCEDURE
1. From the File menu, choose Export Current View to BMP. BIOQUANT Topographer Handbook: 2D Mapping - Review & Optimize
Page 2-8
Save to BMP File Box
2.
Navigate to the folder in which the file should be saved. The default folder for Topographer files is the C:\BQLifeScience\Topographer or C:\BQOSTEO\Topographer folder. In the File name box, type a name for the BMP file. Click the Save button to create the file.
3. 4.

RELATED TOPICS
EXPORT TO SVG PROCEDURE

Export Current Topo to SVG will save the current Topo array (highlighted Topo array in the Selected list) to the SVG format. SVG is a two-dimensional vector format. This format is useful because it can be resized to a larger size without loss of data in another program. SVG files can be opened and viewed directly in most web browsers. They can be edited in graphics programs such as Inkscape or Adobe Illustrator. Inkscape is an open source graphics program that can be downloaded for free from www.inkscape.org. To export to a static format that can not be as easily increased in size, but is accepted by more third party programs, see Export to BMP Procedure on page 2-7.
PROCEDURE
1. On the Select Arrays box, in the Selected list, click to highlight the Topo array to be exported. As Export to SVG only works with one Topo array, if you have data from more than one Topo array that needs to be exported, simply select all Topo array and then go to the Atlas Shop and use Save As to save them to a new single Topo array. When you return to the Atlas Viewer, select only the single, combined Topo array for export. See File > Save as on page 6-3. From the File menu, choose Export Current Topo to SVG.
2.
Page 2-9
Save to SVG File Box
3.
Navigate to the folder in which the file should be saved. The default folder for Topographer files is the C:\BQLifeScience\Topographer or C:\BQOSTEO\Topographer folder. In the File name box, type a name for the SVG file. Click the Save button to create the file.
4. 5.

RELATED TOPICS
COPY AND PASTE THE MAP INTO A DIFFERENT PROGRAM

A quick way to transfer a bitmap of the 2D map to a different program, such as Microsoft PowerPoint or Adobe Photoshop, is to copy it to the clipboard. The Copy To Clipboard option is available on the Atlas menu when an Atlas window is open.
PROCEDURE
1. 2. 3. From the Atlas menu, choose Copy to Clipboard. Switch to the other application. From the Edit menu of the other application, choose Paste to insert the picture of the atlas.
ADDITIONAL NOTE
Choosing paste from the edit menu is the most common method of pasting in a bitmap, but applications vary. Check the documentation of the other application for details.
Page 2-10 2-D MAP REVIEW & OPTIMIZING TOPICS

RELATED TOPICS
Print the Map (page 2-6) Export the Map to a File (page 2-7) Manipulating the Map (page 2-10) Change Background and Increase Thickness of Tracings (page 2-11) Change Color/Symbols Parameters (page 2-12) Saving and Loading Display Parameters (page 2-15) Save Data Set (page 2-18) Exit Atlas Viewer (page 2-19)
PART 3-OPTIMIZE THE MAP DISPLAY

The Atlas Viewer has tools for altering the appearance of the 2D map. Changing display parameters in the Atlas Viewer does not change the data in the Topo array. When a pleasing view of the atlas is established, the parameters for that view may be saved to a Parameters (.set) file that can be re-loaded any time in the future, to instantly configure the atlas according to the saved parameters.
TOPIC CONTENTS
Manipulating the Map (page 2-10) Change Background and Increase Thickness of Tracings (page 2-11) Change Color/Symbols Parameters (page 2-12) Saving and Loading Display Parameters (page 2-15) Save Data Set (page 2-18) Exit Atlas Viewer (page 2-19)

Part 1-Open the Desired Data Set (page 2-3) Part 2-Select and Display the 2D Map (page 2-4) Part 4-Prepare to Edit the 2D Map (page 2-19) Part 5-Correct Errors In Topo Data (page 2-22)
RELATED TOPICS
MANIPULATING THE MAP

The following tools are used to manipulate the map in the atlas window.
REDRAW
Redraw is used to refresh obscured tracings in the atlas window or to update the atlas window with a new set of tracings after a different Topo array has been selected. BIOQUANT Topographer Handbook: 2D Mapping - Review & Optimize
Page 2-11
On the system tool bar, click the Redraw button, or from the Atlas menu choose Redraw.
ZOOM
Activates the Zoom cursor so the atlas may be magnified or reduced in size. 1. 2. On the system tool bar, click the to a magnifying glass. To magnify or reduce the atlas: 3. To zoom, click and release the left mouse button over the atlas. Magnification centers on the point clicked. To shrink, click and release the right mouse button over the atlas. To simultaneously zoom and pan to a particular location, click and drag the cursor using the left mouse button. Zoom button, or choose Zoom from the Atlas menu. The cursor changes
Click to release the Zoom button to deactivate the Zoom cursor.
RESIZE TO FIT
Centers and resizes the atlas so it fills the Atlas Window. From the Atlas menu, choose Resize to Fit. Click the Resize to Fit button on the system tool bar.
PAN
Readies the cursor to move the atlas to a new location in the Atlas Window. 1. 2. 3. On the system tool bar, click the Pan button; the cursor changes to a cross hair over the atlas.
Click and drag the panning cursor to move the atlas. Click to release the Pan button to deactivate the panning cursor.
CENTER
Moves the topographic center of the atlas to the center of the Atlas Window. On the system tool bar, click the window. Center button. The center of the atlas moves to the center of the atlas

RELATED TOPICS
Print the Map (page 2-6) Export the Map to a File (page 2-7) Copy and Paste the Map into a Different Program (page 2-9) Change Background and Increase Thickness of Tracings (page 2-11) Change Color/Symbols Parameters (page 2-12) Saving and Loading Display Parameters (page 2-15) Save Data Set (page 2-18) Exit Atlas Viewer (page 2-19)
CHANGE BACKGROUND AND INCREASE THICKNESS OF TRACINGS

BLACK BACKGROUND
Changes the background color in the Atlas window from white to black. BIOQUANT Topographer Handbook: 2D Mapping - Review & Optimize
Page 2-12 PROCEDURE

To display a black background, on the Atlas menu click to check Black Background. To re-display a white background, on the Atlas menu click to uncheck Black Background.
THICK TRACINGS
Increases the thickness of atlas lines prior to printing. The default thickness is 1 pixel, which is ideal and recommended while making adjustments to the atlas display. When printing an atlas it is sometimes better to thicken the tracings.
PROCEDURE
To redraw the atlas with thick tracings, on the Atlas menu click to check Thick Tracings. To redraw the atlas with normal tracings, on the Atlas menu click to uncheck Thick Tracings.
Before and After Thick Tracings
Thick tracings are recommended only when printing the atlas.

RELATED TOPICS
Print the Map (page 2-6) Export the Map to a File (page 2-7) Copy and Paste the Map into a Different Program (page 2-9) Manipulating the Map (page 2-10) Change Color/Symbols Parameters (page 2-12) Saving and Loading Display Parameters (page 2-15) Save Data Set (page 2-18) Exit Atlas Viewer (page 2-19)
CHANGE COLOR/SYMBOLS PARAMETERS

The Color/Symbols tab of the Atlas Parameters dialog box is used to change colors displayed in the map.
Page 2-13
Color/Symbol Tab of the Atlas Parameters Dialog Box
LINE/SYM LIST: CHANGE LINE COLORS

When Line/Symbol color changes are applied, tracings of all items in the atlas window of the targeted color will change to the new color. If symbols are currently being displayed, symbol outlines of the targeted color will change. 1. 2. 3. In the Atlas window, notice the current default color that you would like to change. Choose a new color by clicking the cursor on one of the 16 color squares in the Colors area. Do not choose the N (No Draw) square or the D (Default) square. Entries in the Line/Sym list are number 1 through 16 and each is a different color. Find and click the entry that matches the current tracing color that is to be changed. The entry in the Line/Sym list changes to the new color. Repeat for each color in the map you wish to change. Click the Apply button to update the atlas display to the new color(s).
4. 5.
FILL CHECK BOX: FILL POLYGONAL TRACINGS WITH COLOR

To display the default fill color, click to check the Fill check box at the bottom of the Colors area. To remove the Fill display, click to uncheck the Fill check box.
OVERLAP CHECK BOX: DISTINGUISH DUAL LABELED STRUCTURES

To show areas of overlapping fill colors in a distinctive third color, click to check both the Fill and Overlap check boxes at the bottom of the Colors area. To turn remove the overlap color, click to uncheck the Overlap check box.
FILL LIST: CHANGE FILL COLOR

1. 2. 3. 4. Turn Fill on by clicking to check the Fill check box at the bottom of the Colors area. In the Atlas window, notice the current fill color of the group of objects for which the fill color is to be changed. Choose a new color be clicking one of the 16 colored squares in the Colors area. (The N square is for No Draw and the D square is for Default.) Entries in the Fill list are number 1 through 16 and each is a different color. Find and click the entry that matches the current Fill color of the objects for which color is to be changed. The entry in the Fill list changes to the new color. BIOQUANT Topographer Handbook: 2D Mapping - Review & Optimize
Page 2-14
5. 6. Repeat for each fill color you wish to change. Click the Apply button to update the atlas display with the new fill color(s).
SYMBOLS CHECK BOX: TURN ON/OFF SYMBOLS

Small objects can be made more visible by marking them with symbols. When the Symbols feature is activated, objects that have data points equal to or less than the Maximum Object Size value, will be displayed with the currently assigned symbol. To display the currently assigned symbol for small objects, click to check the Symbols check box at the bottom of the Symbols area. Alternatively, from the Atlas menu, click to check Symbols. To remove the symbolic display, click to uncheck the Symbols check box. Alternatively, from the Atlas menu, click to uncheck Symbols.
AVAILABLE LIST: ASSIGN A DIFFERENT SYMBOL

The default symbol assigned by the system to a particular color group may be changed to any of the alternate symbols on the Available symbol drop list. Symbols are most often used to replace dots in the atlas. But, there are two cases in which it is advantageous to assign the dot symbol to tracings, or replace a larger symbol with a dot symbol: During measurement, an Area array is sometimes used for cell counting in order to take advantage of BIOQUANTs Auto Exclude feature. This generates a tracing with multiple data points rather than a single dot. In this case, if desirable, the area tracings can be replaced by the dot symbol. When there is a very large number of object count markers in the atlas (e.g. cells), the default symbol assigned to the markers color may be too big and the symbolized display appears crowded. In this case the larger default symbol may be changed to the smaller dot symbol.
1. 2. 3. 4. 5.
Display the current symbol(s) in the atlas by clicking to check the Symbols check box. In the Atlas window, identify the color of the group of objects for which the symbol should be changed. In the Symbols area, in the Available field, click the down arrowhead to display a small scroll list. Using the two small scroll buttons, scroll through the available symbols and click to choose the desired symbol. In the Symbol list, find and click the entry that matches the color of objects of interest (identified in step 2). The symbol associated with that entry will change to the new symbol. Click the Apply button to update the atlas display. If all of the objects in the designated color group do not symbolize, it means that the group includes objects that are larger than the Maximum Object Size. Increase the value in the Maximum Object Size field and click the Apply button again. Continue to increase the Maximum Object Size until all the objects in the color group are replaced by the chosen symbol.
SYMBOL SIZE: SYMBOLIZE LARGER OBJECTS

The Maximum Object Size value may be increased so slightly larger objects may be displayed as symbols. By default, the system sets the Maximum Object Size value to 2, which allows only single point objects to be symbolized. Objects that appear in the atlas as single points or dots (such as those counted with an Object Count array), actually have two data points with zero distance between them. So the Maximum Object Size value must be at least 2. 1. 2. 3. In the Maximum Object Size field, scroll to or type in a higher number. Click the Apply button to display the changes. Repeat steps 1 and 2 as needed until all of the desired tracings are symbolized.
MAXIMUM OBJECT SIZE: CHANGE THE SIZE OF THE SYMBOLS

The default size of symbols is eight pixels by eight pixels. This can be increased or decreased as needed. Changes in symbol size are applied to all symbols (not just the symbol of one selected color group). To adjust the height of the symbols, increase or decrease the value in the Symbol Size Height field by scrolling to or typing in a larger value. To adjust the width of the symbols, increase or decrease the value in the Symbol Size Width field.
Page 2-15 SHOW EVERY NTH SYMBOL: REDUCE THE NUMBER OF DENSELY PACKED SYMBOLS
When Show Every (nth) Symbol is set to 1, a symbol is displayed for every single object that meets the Maximum Object Size criterion. The symbols representing a group of objects may be thinned out by increasing the nth value to a number greater than 1. A value of 2 will display every second symbol. A value of 3 will display every third symbol, and so on. 1. 2. 3. In the Show Every (nth) Symbol field, increase the current value by 1. Click the Apply button. If symbols are still too numerous, repeat steps 1 and 2.
RESTORE COLOR AND SYMBOL DEFAULTS

To restore the default assignment of one color entry in either the Line/Sym list or the Fill list, click the Default (D) square in the Colors area, then click that entry in the list. To restore all the entries in the Line/Sym list or the Fill list to their default assignments, click the Default (D) square in the Colors area, then click and drag the cursor across all the entries in the list. To restore all the default Line/Sym, Fill, and Symbol assignments on the Colors/Symbols tab, click the Restore button.

RELATED TOPICS
Print the Map (page 2-6) Export the Map to a File (page 2-7) Copy and Paste the Map into a Different Program (page 2-9) Manipulating the Map (page 2-10) Change Background and Increase Thickness of Tracings (page 2-11) Saving and Loading Display Parameters (page 2-15) Save Data Set (page 2-18) Exit Atlas Viewer (page 2-19)
SAVING AND LOADING DISPLAY PARAMETERS

This section covers saving and loading Display Parameter files. A Parameter file records which arrays were used to generate the reconstruction and saves the Perspective and Color/Symbols settings for a particular view of the atlas. Anytime in the future that the same data set is opened, its Parameter file may be loaded to instantly recall the preferred settings.
TOPIC CONTENTS
Save Parameters (page 2-16) Load Parameters (page 2-17)


Print the Map (page 2-6) Export the Map to a File (page 2-7) Copy and Paste the Map into a Different Program (page 2-9) Manipulating the Map (page 2-10) Change Background and Increase Thickness of Tracings (page 2-11) Change Color/Symbols Parameters (page 2-12) Save Data Set (page 2-18) Exit Atlas Viewer (page 2-19)
SAVE PARAMETERS
Save Parameters is available when the Atlas Window is open. A Parameter file records which arrays were used to generate the reconstruction and saves the Perspective and Color/Symbols settings for a particular view of the atlas. Anytime in the future that the same data set is opened, its Parameter file may be loaded to instantly recall the preferred settings.
PROCEDURE
1. Open the Save Parameters dialog box using any of the following methods: 2. On the system tool bar click the Save Parameters From the File menu choose Save Parameters. Click the Save button on either the Perspective or Color/Symbols tab of the Atlas Parameters dialog box. button.
The default Save in location is BQOSTEO\Topographer. For ease of finding the parameters file again, it is recommended that you create a subdirectory in the Topographer folder that is named the same as your Data Volume and Data Set. Then when you later need to find and open the parameter files for a particular Data Set you can easily navigate to them. To do this: a. Click the Create New Folder button. The Save Parameter File Dialog Box
b.
Rename the New Folder to your Data Volume and Data Set Name. The Save Parameter File Dialog Box
c.
Double click the new folder to open it.
Page 2-17
You will save in this location. 3. Type a file name into the File name text box. The Save Parameter File Dialog Box
4.
Click the Save button to save the file.
ADDITIONAL NOTES
Control-S opens the Save Parameters box. Parameter files have .set extensions.

RELATED TOPICS
LOAD PARAMETERS
Load Parameters is available both when the Atlas Window is closed and open. Loading a Parameters file instantly selects the arrays that were originally used to generate the atlas and resets the Perspective and Color/Symbol parameters that were active when the parameters file was saved.
PROCEDURE
1. 2. On the system tool bar click the Load Parameters to open the Open Parameter File dialog box. button, or from the File menu choose Load Parameters,
The default location for saving parameter files is BQOSTEO\Topographer. If you created a subdirectory associated with your Data Volume and Data Set as recommended in the Save Parameters procedure, it will be listed here. Navigate to the folder that contains the Parameter file for the current data set.
Page 2-18
The Open Parameter File Dialog Box
3.
Click on the parameter file to be opened. The Open Parameter File Dialog Box
4.
Click the Open button. The appearance of the atlas will change to reflect the loaded parameters.
ADDITIONAL NOTES
If the error message, Parameter File Error: Sequence list not for this data set! File ignored. appears, the parameter file is for a different data set. Choose a different Parameter file or open the data set for which the file was saved. Control-L opens the Load Parameters box. Parameter files have .set extensions.

RELATED TOPICS
SAVE DATA SET

The Save Data Set feature on the file menu will save changes to the current data set. BIOQUANT Topographer Handbook: 2D Mapping - Review & Optimize
Page 2-19 PROCEDURE

From the File menu, choose Save Data Set. NOTE: The Save Data Set option is only available when the Atlas Window is closed.

RELATED TOPICS
Print the Map (page 2-6) Export the Map to a File (page 2-7) Copy and Paste the Map into a Different Program (page 2-9) Manipulating the Map (page 2-10) Change Background and Increase Thickness of Tracings (page 2-11) Change Color/Symbols Parameters (page 2-12) Saving and Loading Display Parameters (page 2-15) Exit Atlas Viewer (page 2-19)
EXIT ATLAS VIEWER

The Exit menu is used to exit the Topographer and return to BIOQUANT Life Science or BIOQUANT OSTEO.
PROCEDURE
From the File menu, choose Exit. The Topographer will close and BIOQUANT Life Science or BIOQUANT OSTEO will open.

RELATED TOPICS
Print the Map (page 2-6) Export the Map to a File (page 2-7) Copy and Paste the Map into a Different Program (page 2-9) Manipulating the Map (page 2-10) Change Background and Increase Thickness of Tracings (page 2-11) Change Color/Symbols Parameters (page 2-12) Saving and Loading Display Parameters (page 2-15) Save Data Set (page 2-18)
PART 4-PREPARE TO EDIT THE 2D MAP

BACKUP ORIGINAL TOPO DATA
Before any editing is done in the Atlas Shop, the data for the 2D map is saved to a new Topo array. Corrections are applied to the data in the new array. This insures that original data does not become corrupted during editing. If the original data for the map is distributed in several different Topo arrays, the backup process will consolidate the atlas into a single, new array. 1. In the Atlas Viewer, verify that the desired 2D map is displayed in the atlas window. BIOQUANT Topographer Handbook: 2D Mapping - Review & Optimize
Page 2-20
2. Open the Atlas Shop by clicking the Atlas Shop button on the Atlas Viewers tool bar, or by choosing Atlas Shop from the Tools menu. NOTE: The Atlas Shop button is not available if you have the free Topo Reader. Consider upgrading to the full BIOQUANT Topographer plug-in for editing capabilities. If necessary, click the Resize To Fit Atlas Shop Desktop button.
3.
THE ATLAS SHOP

Atlas Shop is the part of the Topographer that is used to backup original data and correct any color, positional, or tracing errors introduced during measurement. The Atlas Shop is also where several additional measurements may be taken from the 2D map (e.g. determine distance between structures, count all objects of a certain type, etc.) Different versions of the atlas data may be created using the Atlas Shops Save As option. 4. 5. In the Atlas Shop, to insure that all parts of the atlas are selected, from the Select menu, choose Select All Sections. From the Atlas Shops File menu, choose Save As, to open the Save Array As dialog box. Save Array As Dialog Box
If there were any Topo arrays in the data set that were not selected as part of the current atlas, their names would be visible in the lower pane of the Save Array As dialog box.
6.
On the Save Array As dialog box, click the New Array button to add a new, empty Topo array to the data set.
Page 2-21
Save Array As Dialog Box With New Topo Array Added and Renamed
7. 8. 9. 10.
Edit the name of the new Topo array to reflect the fact that it will contain an edited or enhanced version of the atlas. Click the Save button, then the Close button on the Save Array As dialog box. Return to the Atlas Viewer by choosing Exit Atlas Shop from the File menu. In the Atlas Viewer, on the Select Arrays dialog box, remove the currently selected array(s) from the Selected list by doing one of the following: From the Select menu on the Select Arrays dialog box, choose Unselect All Arrays. In the Selected list, double-click the index number(s) of the currently selected array(s).
11. 12.
In the Available Arrays list, double-click the new Topo array that was added in the Atlas Shop, to move its index number to the Selected list. On the system tool bar click the Open Atlas button, then the Resize To Fit button. The data in the new Topo array is now ready for editing in the Atlas Shop (and the original data is safely preserved in its original array). Re-open the Atlas Shop by clicking the Atlas Shop Atlas Shop from the Tools menu. button on the Atlas Viewers tool bar, or by choosing
13.

Part 1-Open the Desired Data Set (page 2-3) Part 2-Select and Display the 2D Map (page 2-4) Part 3-Optimize the Map Display (page 2-10) Part 5-Correct Errors In Topo Data (page 2-22)
RELATED TOPICS
Page 2-22
PART 5-CORRECT ERRORS IN TOPO DATA

TOPIC CONTENTS
Atlas Shop Tool Bars (page 2-22) The Three Selection Modes (page 2-23) Verify How Data are Grouped in the Atlas Topo Array (page 2-23) Selection Methods (page 2-24) About Saving Edits (page 2-26) Color Correction Procedures (page 2-26) The Line Editing Tools (page 2-30) Reposition or Resize Parts of the Map (page 2-35)

Part 1-Open the Desired Data Set (page 2-3) Part 2-Select and Display the 2D Map (page 2-4) Part 3-Optimize the Map Display (page 2-10) Part 4-Prepare to Edit the 2D Map (page 2-19)
RELATED TOPICS
ATLAS SHOP TOOL BARS

The Atlas Shop has two tool bars: the horizontal system tool bar and the Vertical Tool Bar. Atlas Shop System Tool Bar
In addition to buttons, the system tool bar contains a Color Palette that is used with the Select By Color and Change Color tools on the Vertical Tool Bar.
When the cursor is held still over a tool bar button, a tool tip appears briefly to reveal the buttons name. Tool tips appear for the system tool bar only when the system title bar is active (colored, instead of gray). Tool Tips for the Vertical Tool Bar appear only when the title bar of the Vertical Tool Bar is active. To activate either title bar, click the cursor on it. Most, but not all, buttons on the system tool bar and on the Vertical Tool Bar are shortcuts to frequently used options on the system menus.


The Three Selection Modes (page 2-23) Verify How Data are Grouped in the Atlas Topo Array (page 2-23) Selection Methods (page 2-24) About Saving Edits (page 2-26) Color Correction Procedures (page 2-26) The Line Editing Tools (page 2-30) Reposition or Resize Parts of the Map (page 2-35)
THE THREE SELECTION MODES

In order to work with individual parts of the map, the particular tracing(s) or markers of interest must first be selected. A selected part of the atlas will be displayed in color in the Atlas Shop work space. When not selected, tracings or point markers appear white. There are three selection modes in the Atlas Shop: Section Mode, Object Mode, and Point Mode. By default, the Atlas Shop opens in Section Mode, meaning that the Section Mode depressed. button on the system tool bar is
In Section Mode , all operations (e.g. Translate, Rotate, etc.) are applied to all tracings and markers in the selected topographic section(s). Usually there is only one topographic section in a 2D map (because usually there is only one Landmark set for a single-plane specimen). When the Object Mode button is depressed, all operations are applied only to the selected object(s). Every tracing or marker in the map is a separate object. In Point Mode , all operations apply only to the currently selected data point(s). Point Mode is rarely used when correcting errors in a 2D map.

RELATED TOPICS
Atlas Shop Tool Bars (page 2-22) Verify How Data are Grouped in the Atlas Topo Array (page 2-23) Selection Methods (page 2-24) About Saving Edits (page 2-26) Color Correction Procedures (page 2-26) The Line Editing Tools (page 2-30) Reposition or Resize Parts of the Map (page 2-35)
VERIFY HOW DATA ARE GROUPED IN THE ATLAS TOPO ARRAY

For a 2D map, there is usually only one topographic section in the atlas Topo array, because usually there was only one Landmark placed on the specimen during measurement. However, if this is not the case, it is important to be aware of the existence of multiple sections before data selection begins in the Atlas Shop.
PROCEDURE
1. 2. 3. Click to activate the Section Mode button.
From the Select menu, choose Select All Sections. The number of topographic sections in the atlas Topo array can be determined by looking at the Section notation in the Atlas Shops title bar. BIOQUANT Topographer Handbook: 2D Mapping - Review & Optimize
Page 2-24
Section #0, means there is only one topographic section. Section #0-n, (where n = a number) means there is more than one topographic section. Section numbering in the Atlas Shop always begins with 0. Examples: Section #0-1, means there are two topographic sections. Section #0-2 means there are three topographic sections.
IMPORTANT
If multiple topographic sections exist, the section that contains objects of interest must always be selected in Section Mode before switching to Object Mode or Point Mode.

RELATED TOPICS
Atlas Shop Tool Bars (page 2-22) The Three Selection Modes (page 2-23) Selection Methods (page 2-24) About Saving Edits (page 2-26) Color Correction Procedures (page 2-26) The Line Editing Tools (page 2-30) Reposition or Resize Parts of the Map (page 2-35)
SELECTION METHODS
There are several different ways to select sections, objects, or single data points of interest. With experience you may come to favor one selection method over another, but if that method proves to be awkward when working with a particular specimen, you will need to be familiar with the alternate methods. In the unusual case that the 2D map is contained in multiple topographic sections, (see Verify How Data are Grouped in the Atlas Topo Array (page 2-23)), remember that the section of interest must be selected in Section Mode before switching to Object Mode to work with individual tracings or markers.
SELECT BY COLOR
Select By Color operates across the entire atlas, regardless of which Selection Mode is currently active. 1. 2. On the Vertical Tool Bar, click the Select By Color button
On the system tool bars color palette, click the color that matches the color of the objects that need to be selected. The system instantly selects all tracings and markers of that color.
SELECT NEXT / SELECT PREVIOUS

The Select Next and Select Previous tools on the Vertical Tool Bar can be used to sequence through sections (in Section Mode), objects (in Object Mode), or data points (in Point Mode). When working with 2D maps these tools are most often used in Object Mode to select individual tracings in a map that contains few or no cell markers. 1. 2. Click to activate Object Mode . buttons on the system tool bar to sequence through
Click the Select Next or Select Previous individual tracings (or markers) in the map.
SELECT USING RECTANGLE OR POLYGON

The Select Using Rectangle and Select Using Polygon tools on the Vertical Tool Bar can be used to select one or more sections (in Section Mode), one or more objects (in Object Mode), or one or more data points (in Point Mode). If even one data point of a tracing falls within the selection box or polygon, the whole tracing will be selected. When working with 2D maps, these tools are most often used in Object Mode to select individual or multiple objects (tracings or cell markers). BIOQUANT Topographer Handbook: 2D Mapping - Review & Optimize
Page 2-25 PROCEDURE: SELECT USING RECTANGLE

a. b. c. Click to activate Object Mode . button.
On the Vertical Tool Bar, click the Select Using Rectangle
Position the cursor close to the objects that need to be selected, then click and hold the left mouse button while dragging the cursor diagonally to from a selection box around (or across tracings of) the objects of interest. Tracings with one or more data points inside the box will be selected.
PROCEDURE: SELECT USING POLYGON

a. b. c. Click to activate Object Mode . button.
On the Vertical Tool Bar, click the Select Using Polygon
Position the cursor close to the objects that need to be selected, then click a series of points to create a selection polygon around (or across tracings of) the objects of interest. Tracings with one or more data points inside the polygon will be selected.
SELECT FROM A LIST

Sections (in Section Mode) and objects (in Object Mode) may be selected from a Go To list. When working with 2D maps, the Go To Object list is best used with maps that do not have lots of cell markers. Every cell marker is listed as a separate object, so maps that have hundreds or thousands of cells will result in a very long list. 1. 2. Click to activate Object Mode .
From the Select menu, choose GoTo, to open the Go To Object list. Go To Object List With Four Objects Selected
The Ctrl key was used to help select non-contiguous objects in the list.
To select a single object, click to highlight its entry in the list. To select multiple, contiguous objects, click the first object, press and hold the Shift key, then click the last object in the series. All objects between and including the first and the last will be selected. To select multiple, non-contiguous objects, click one object, press and hold the Ctrl key, then click each additional object that is to be selected.
SELECT BY ADDING INTERIOR OBJECTS

Add Interior Objects to Selection is an option on the Select menu than can be used when a currently selected tracing encircles other tracings that need to be added to the selection. Add Interior Object to Selection is used only in Object Mode. 1. Click to activate Object Mode .
Page 2-26
2. 3. Use any convenient method to select the tracing (object) that encircles other objects. From the Select menu, choose Add Interior Object to Selection.

RELATED TOPICS
Atlas Shop Tool Bars (page 2-22) The Three Selection Modes (page 2-23) Verify How Data are Grouped in the Atlas Topo Array (page 2-23) About Saving Edits (page 2-26) Color Correction Procedures (page 2-26) The Line Editing Tools (page 2-30) Reposition or Resize Parts of the Map (page 2-35)
ABOUT SAVING EDITS

Most edits made to a map can be saved directly to the current atlas Topo array, by simply choosing Save on the Atlas Shop File menu. Save As is also an option on the Atlas Shop File menu, and is used any time a new version of the atlas needs to be saved. Three special editing routines actually rearrange the topographic data, and the only way to save the new arrangement is to write the data to a new Topo array (using Save As). These routines are: Change Resolution, and anytime Internal Cut, Internal Copy, or Internal Paste are used. These edits are done only under special circumstances that will be explained later. Save As may also be used to save selected parts of the map in a new Topo array, to produce a whole new map.
ADDITIONAL INFORMATION
The Atlas Shop has many features that are not used when working with a 2D map. These other features are explained in the 3D Modeling chapters.

RELATED TOPICS
Atlas Shop Tool Bars (page 2-22) The Three Selection Modes (page 2-23) Verify How Data are Grouped in the Atlas Topo Array (page 2-23) Selection Methods (page 2-24) Color Correction Procedures (page 2-26) The Line Editing Tools (page 2-30) Reposition or Resize Parts of the Map (page 2-35)
COLOR CORRECTION PROCEDURES

This section covers color correction procedures used in the Atlas Shop.
Page 2-27 TOPIC CONTENTS

Assign a New Color to a Group of Objects (page 2-27) Change A Single Tracing Color (page 2-28) Change the Color of One or More Cell Markers (page 2-29)

RELATED TOPICS
Atlas Shop Tool Bars (page 2-22) The Three Selection Modes (page 2-23) Verify How Data are Grouped in the Atlas Topo Array (page 2-23) Selection Methods (page 2-24) About Saving Edits (page 2-26) The Line Editing Tools (page 2-30) Reposition or Resize Parts of the Map (page 2-35)
ASSIGN A NEW COLOR TO A GROUP OF OBJECTS

A group of like-colored objects (tracings or cell markers) may be quickly selected using the Select By Color tool.
PROCEDURE
1. Click to depress the Section Mode button on the system tool bar. Since this procedure selects objects of the same color across all sections of the atlas, it does not matter which topographic section is currently selected. On the Vertical Tool Bar, click the Select by Color tool.
2. 3. 4. 5. 6.
On the color palette (on the system tool bar), click to designate the current color of the objects of interest. All objects (tracings and/or cell markers) in the atlas of the designated color will be selected. On the Vertical Tool Bar, click the Change Color tool.
On the color palette, click to designate the desired new color. The selected objects in the atlas will change to the new color. From the File menu, choose Save.


Change A Single Tracing Color (page 2-28) Change the Color of One or More Cell Markers (page 2-29) Atlas Shop Tool Bars (page 2-22) The Three Selection Modes (page 2-23) Verify How Data are Grouped in the Atlas Topo Array (page 2-23) Selection Methods (page 2-24) About Saving Edits (page 2-26) The Line Editing Tools (page 2-30) Reposition or Resize Parts of the Map (page 2-35)
CHANGE A SINGLE TRACING COLOR

PROCEDURE
1. If necessary, click the Resize to Fit button on the Atlas Shop system tool bar. This positions and sizes the atlas to fit the work space. If multiple topographic sections exist (see Verify How Data are Grouped in the Atlas Topo Array (page 223)), do the following: a. b. Verify that the Section Mode button is activated (depressed).
Using the Select Next and Select Previous buttons as needed, sequence through the individual sections in the map, until a section that contains a tracing that needs to be changed to a new color is selected.
2.
Click the Object Mode button on the system tool bar. Only the first object in the section should remain colored. All other objects will be displayed in white. TIP: If it appears that nothing in the map has been selected, it is likely that the first object in the section is a tiny Object Count marker. This is of no concern.
3.
Using the most convenient selection method, select the desired tracing. Example: If there are very few, or no, object markers, it may be convenient to use the Select Next and Select Previous buttons to sequence through individual objects, until the object that needs to be changed to a new color is selected. For alternate selection methods, see Selection Methods (page 2-24).
4.
On the Vertical Tool Bar, click the Change Color a.
button.
On the system tool bar, click to choose the desired new color on the color palette. The selected tracing will change to the chosen color.
5. 6.
Repeat from step 3 for any other tracings in this section that need a color change. From the File menu, choose Save. Choosing Save on the File menu permanently alters the data in the current atlas Topo array.


Assign a New Color to a Group of Objects (page 2-27) Change the Color of One or More Cell Markers (page 2-29) Atlas Shop Tool Bars (page 2-22) The Three Selection Modes (page 2-23) Verify How Data are Grouped in the Atlas Topo Array (page 2-23) Selection Methods (page 2-24) About Saving Edits (page 2-26) The Line Editing Tools (page 2-30) Reposition or Resize Parts of the Map (page 2-35)
CHANGE THE COLOR OF ONE OR MORE CELL MARKERS

One or more individual cell markers may be quickly selected with the Select Using Rectangle or Select Using Polygon tools.
PROCEDURE
1. If necessary, click the Resize to Fit button on the Atlas Shop system tool bar. This positions and sizes the atlas to fit the work space. If multiple topographic sections exist (see Verify How Data are Grouped in the Atlas Topo Array (page 223)), do the following: a. b. Verify that the Section Mode button is activated (depressed).
Using the Select Next and Select Previous buttons as needed, sequence through the individual sections in the map, until a section that contains a tracing that needs to be changed to a new color is selected.
2.
Click the Object Mode button on the system tool bar. Only the first object in the section should remain colored. All other objects will be displayed in white. TIP: If it appears that nothing in the map has been selected, it is likely that the first object in the section is a tiny Object Count marker. This is of no concern.
3.
(Optional) When selecting small objects like cell markers, it is often useful to magnify the area of interest before using the selection tools. To zoom the area of interest, do the following: a. b. c. On the Vertical Tool Bar, click the Zoom tool. Using the left mouse button, click the area of interest to zoom up one level. Continue to click the area until the area is sufficiently magnified. If necessary, use the Pan tool to reposition the zoomed tracings in the work space, as follows: i. ii. iii. On the Vertical Tool Bar, click the Pan tool. Place the hand-cursor over a point that you would like to move to the center of the work space. Click and drag the hand-cursor to reposition the tracings.
4. Clicking the right mouse button will zoom out, making the section tracings smaller. Clicking the Resize To Fit button on the system tool bar will resize and center the atlas to fit the work space.
On the Vertical Tool Bar, click the Select Using Rectangle button or the Select Using Polygon button, then do the following to select the cell markers of interest: With the Select Using Rectangle tool, click and drag the cursor diagonally to form a rectangular selection box around the objects of interest.
Page 2-30
With the Select Using Polygon tool, click a series of points to form a selection polygon around the objects of interest.
All objects fully or partially contained within the box or polygon will be selected. 5. 6. 7. On the Vertical Tool Bar, click the Change Color tool.
On the color palette (system tool bar), click to designate the desired new color. The selected objects will change to the new color. From the File menu, choose Save. Choosing Save on the File menu permanently alters the data in the current atlas Topo array.

RELATED TOPICS
Assign a New Color to a Group of Objects (page 2-27) Change A Single Tracing Color (page 2-28) Atlas Shop Tool Bars (page 2-22) The Three Selection Modes (page 2-23) Verify How Data are Grouped in the Atlas Topo Array (page 2-23) Selection Methods (page 2-24) About Saving Edits (page 2-26) The Line Editing Tools (page 2-30) Reposition or Resize Parts of the Map (page 2-35)
THE LINE EDITING TOOLS

The line editing tools on the vertical tool bar correct tracing errors made during data collection. The Line Editing Tools on the Vertical Toolbar
From top to bottom the tools are Straighten Edge, Combine Two Objects, Separate Two Objects, Redefine Edge, Delete.
TOPIC CONTENTS
Straighten Edge (page 2-31) Combine Two Objects (page 2-32) Separate Two Objects separate (page 2-33) Redefining an Objects Edge (page 2-34) Deleting Objects (page 2-34)
Page 2-31 MORE 2-D MAP REVIEW & OPTIMIZING TOPICS

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


Combine Two Objects (page 2-32) Separate Two Objects separate (page 2-33) Redefining an Objects Edge (page 2-34) Deleting Objects (page 2-34) Assign a New Color to a Group of Objects (page 2-27) Change A Single Tracing Color (page 2-28) Change the Color of One or More Cell Markers (page 2-29) Atlas Shop Tool Bars (page 2-22) The Three Selection Modes (page 2-23) Verify How Data are Grouped in the Atlas Topo Array (page 2-23) Selection Methods (page 2-24) About Saving Edits (page 2-26) Reposition or Resize Parts of the Map (page 2-35)
COMBINE TWO OBJECTS

Sometimes a single object will be thresholded and traced as two separate halves. This procedure corrects this. The Combine Two Objects tool on the vertical tool bar connects two objects with straight lines which are defined by a series of 4 mouse clicks. Combine Objects Example
Clicking in the order shown will connect these two objects
1. 2. 3. 4. 5. 6.
Select the objects that are to be combined. Click the Combine Objects button.
Click where one end of the connecting line should be on object A. Click where the other end of the connecting line should be on object B. Click where one end of the second connecting line should be on object B. Click where the other end of the connecting line should be on object A.
ADDITIONAL NOTES
Click the right mouse button to cancel before the series of 4 clicks is finished. Click the Undo button to undo the last edit.


Straighten Edge (page 2-31) Separate Two Objects separate (page 2-33) Redefining an Objects Edge (page 2-34) Deleting Objects (page 2-34) Assign a New Color to a Group of Objects (page 2-27) Change A Single Tracing Color (page 2-28) Change the Color of One or More Cell Markers (page 2-29) Atlas Shop Tool Bars (page 2-22) The Three Selection Modes (page 2-23) Verify How Data are Grouped in the Atlas Topo Array (page 2-23) Selection Methods (page 2-24) About Saving Edits (page 2-26) Reposition or Resize Parts of the Map (page 2-35)
SEPARATE TWO OBJECTS SEPARATE

Sometimes, two objects that lie close together are traced as one. This procedure corrects this. Clicking two points defines the location for a gap that will separate the single tracing into two separate objects.
PROCEDURE
1. 2. 3. Select the tracing that needs to be separated into two objects. Click the Separate Two Objects button on the vertical toolbar.
Click one side of the single tracing, then click the opposite side. A dividing gap will appear, creating two separate tracings.
ADDITIONAL NOTES
Click the right mouse button after the first click to cancel the separation. Click the undo button to undo the separation.

RELATED TOPICS
Straighten Edge (page 2-31) Combine Two Objects (page 2-32) Redefining an Objects Edge (page 2-34) Deleting Objects (page 2-34) Assign a New Color to a Group of Objects (page 2-27) Change A Single Tracing Color (page 2-28) Change the Color of One or More Cell Markers (page 2-29) Atlas Shop Tool Bars (page 2-22) The Three Selection Modes (page 2-23) Verify How Data are Grouped in the Atlas Topo Array (page 2-23) Selection Methods (page 2-24) About Saving Edits (page 2-26) Reposition or Resize Parts of the Map (page 2-35)
Page 2-34
REDEFINING AN OBJECTS EDGE

A segment of a section or objects contour tracing can be redrawn with the Redefine Edge tool. This tool is recommended (instead of the Straighten Edge tool) any time a significant portion of an objects tracing needs to be altered. Line segments are re-defined by first identifying the beginning and end points of the segment, then clicking a series of points in a counterclockwise direction from the beginning point. The end point must always lie counterclockwise from the beginning point.
PROCEDURE:
1. 2. Click the Redefine Edge tool on the vertical tool bar.
Define the end points of the segment that is to be redefined, by doing the following: a. b. Click to mark the beginning point of the segment that is to be redefined. Keep in mind that the end of the segment must lie counterclockwise from the segments beginning point. Click to mark the end of the segment.
3. 4.
Starting from the segments beginning point and moving in a counterclockwise direction, click a series of data points to define the new contour. Click the right mouse button to end the construction of the new edge.
SAVING THE EDIT

After Redefine Edge is used, if the atlas is saved using Save on the File menu, or by responding YES to the Save Data message when exiting the Atlas Shop, the data in the original atlas Topo array are permanently changed. If desirable, Save As on the File menu may be used instead, to save the edited version of the atlas to a new Topo array.
ADDITIONAL NOTES:
Click the Undo button on the vertical tool bar to undo the redefinition of the contour.

RELATED TOPICS
Straighten Edge (page 2-31) Combine Two Objects (page 2-32) Separate Two Objects separate (page 2-33) Deleting Objects (page 2-34) Assign a New Color to a Group of Objects (page 2-27) Change A Single Tracing Color (page 2-28) Change the Color of One or More Cell Markers (page 2-29) Atlas Shop Tool Bars (page 2-22) The Three Selection Modes (page 2-23) Verify How Data are Grouped in the Atlas Topo Array (page 2-23) Selection Methods (page 2-24) About Saving Edits (page 2-26) Reposition or Resize Parts of the Map (page 2-35)
DELETING OBJECTS
The Delete tool on the vertical toolbar is used to permanently remove the data of a chosen object from the original Topo array. The object immediately disappears from the atlas window. BIOQUANT Topographer Handbook: 2D Mapping - Review & Optimize
Page 2-35 PROCEDURE:

1. 2. Click the Delete Object tool on the vertical tool bar.
Click on the tracing of the object to be deleted. Note: The removed data is temporarily stored in the Topographers backup buffer and the delete does not become permanent until the edits are saved using Save on the File menu or by responding YES to the Save Data message on exiting the Atlas Shop.
ADDITIONAL NOTES:
The most recent unsaved deletion may be canceled by clicking the Undo button on the vertical tool bar. All unsaved edits may be canceled by choosing Restore Original from the File menu.

RELATED TOPICS
Straighten Edge (page 2-31) Combine Two Objects (page 2-32) Separate Two Objects separate (page 2-33) Redefining an Objects Edge (page 2-34) Assign a New Color to a Group of Objects (page 2-27) Change A Single Tracing Color (page 2-28) Change the Color of One or More Cell Markers (page 2-29) Atlas Shop Tool Bars (page 2-22) The Three Selection Modes (page 2-23) Verify How Data are Grouped in the Atlas Topo Array (page 2-23) Selection Methods (page 2-24) About Saving Edits (page 2-26) Reposition or Resize Parts of the Map (page 2-35)
REPOSITION OR RESIZE PARTS OF THE MAP

This section covers tools used to reposition or resize parts of the map.
TOPIC CONTENTS
Rotate (page 2-36) Translate (page 2-37) Resize (page 2-38)


Straighten Edge (page 2-31) Combine Two Objects (page 2-32) Separate Two Objects separate (page 2-33) Redefining an Objects Edge (page 2-34) Deleting Objects (page 2-34) Assign a New Color to a Group of Objects (page 2-27) Change A Single Tracing Color (page 2-28) Change the Color of One or More Cell Markers (page 2-29) Atlas Shop Tool Bars (page 2-22) The Three Selection Modes (page 2-23) Verify How Data are Grouped in the Atlas Topo Array (page 2-23) Selection Methods (page 2-24) About Saving Edits (page 2-26) Reposition or Resize Parts of the Map (page 2-35)
ROTATE
PROCEDURE
1. If multiple sections exist, in Section mode rotated. Selection Methods (page 2-24) Click to activate Object Mode Selection Methods (page 2-24) , select the section that contains the object(s) that need to be
2.
, the select the object(s) that need to be rotated.
3.
Click the Rotate button on the vertical tool bar. A red marker will appear on the selected object. The object will rotate around this marker. If desirable, click and drag the red marker to a different location on the object. To rotate the object clockwise, place the cursor any where in the atlas window, then click and drag the cursor straight down. To rotate the object counter-clockwise, place the cursor anywhere in the atlas window, then click and drag the cursor straight up.
4. 5.
SAVING THE EDIT

After Rotate is used, if the atlas is saved using Save on the File menu, or by responding YES to the Save Data message when exiting the Atlas Shop, the data in the original atlas Topo array(s) are permanently changed. If desirable, Save As on the File menu may be used instead, to save the edited version of the atlas to a new Topo array.
The Undo button on the vertical tool bar will undo the last rotation. Choosing Restore Original from the File menu will undo all unsaved changes to the atlas.


Translate (page 2-37) Resize (page 2-38) Straighten Edge (page 2-31) Combine Two Objects (page 2-32) Separate Two Objects separate (page 2-33) Redefining an Objects Edge (page 2-34) Deleting Objects (page 2-34) Assign a New Color to a Group of Objects (page 2-27) Change A Single Tracing Color (page 2-28) Change the Color of One or More Cell Markers (page 2-29) Atlas Shop Tool Bars (page 2-22) The Three Selection Modes (page 2-23) Verify How Data are Grouped in the Atlas Topo Array (page 2-23) Selection Methods (page 2-24) About Saving Edits (page 2-26) Reposition or Resize Parts of the Map (page 2-35)
TRANSLATE
Choosing Translate from the Edit menu or clicking the Translate button on the vertical tool bar readies the cursor to reposition the selected part of the atlas in the XY plane.
PROCEDURE:
1. If multiple sections exist, in Section mode rotated. Selection Methods (page 2-24) Click to activate Object Mode Selection Methods (page 2-24) Click the Translate , select the section that contains the object(s) that need to be
2. 3. 4.
, the select the object(s) that need to be rotated.
button on the vertical tool bar, or choose Translate from the Edit menu.
Move the selected item using one of the following methods: a. b. Using the left mouse button, click and drag the selected item(s) to the new position. Press and hold the Control key, then use the arrow keys on the keyboard to move the selected item up, down, right, or left.
5.
If necessary, click the Undo button on the vertical tool bar to undo the last translation, or choose Restore Original from the File menu to undo all unsaved changes to the atlas.
SAVING THE EDIT

After Translate is used, if the atlas is saved using Save on the File menu, or by responding YES to the Save Data message when exiting the Atlas Shop, the data in the original atlas Topo array(s) are permanently changed. If desirable, Save As on the File menu may be used instead, to save the edited version of the atlas to a new Topo array.


Rotate (page 2-36) Resize (page 2-38) Straighten Edge (page 2-31) Combine Two Objects (page 2-32) Separate Two Objects separate (page 2-33) Redefining an Objects Edge (page 2-34) Deleting Objects (page 2-34) Assign a New Color to a Group of Objects (page 2-27) Change A Single Tracing Color (page 2-28) Change the Color of One or More Cell Markers (page 2-29) Atlas Shop Tool Bars (page 2-22) The Three Selection Modes (page 2-23) Verify How Data are Grouped in the Atlas Topo Array (page 2-23) Selection Methods (page 2-24) About Saving Edits (page 2-26) Reposition or Resize Parts of the Map (page 2-35)
RESIZE
PROCEDURE
1. If multiple sections exist, in Section mode rotated. Selection Methods (page 2-24) Click to activate Object Mode Selection Methods (page 2-24) Click the Resize , select the section that contains the object(s) that need to be
2. 3.
, the select the object(s) that need to be resized.
button on the vertical tool bar. A resizing box will appear around the selected object(s).
To expand or shrink the object while maintaining its current height and width ratio, click and drag the resize control point in the lower left corner of the resize box. To narrow or widen the object while maintaining its current height, click and drag the resize control point on the right side of the resize box. To increase or decrease the height of the object while maintaining its current width, click and drag the resize control point on the top of the resize box.
SAVING THE EDIT

After Resize is used, if the atlas is saved using Save on the File menu, or by responding YES to the Save Data message when exiting the Atlas Shop, the data in the original atlas Topo array(s) are permanently changed. If desirable, Save As on the File menu may be used instead, to save the edited version of the atlas to a new Topo array.
Clicking the Undo button on the vertical tool bar will undo the last resizing. Choosing Restore Original from the File menu will undo all unsaved edits. When resizing is finished for the currently selected item, sequencing to the Next item will cause the resize box to automatically adjust to fit the size of the new selection. To remove the resize box from the atlas, click an alternate tool on the vertical tool bar. The selection may be resized without maintaining the height to width ratio using Numeric Transform.
Page 2-39 MORE 2-D MAP REVIEW & OPTIMIZING TOPICS

RELATED TOPICS
Rotate (page 2-36) Translate (page 2-37) Straighten Edge (page 2-31) Combine Two Objects (page 2-32) Separate Two Objects separate (page 2-33) Redefining an Objects Edge (page 2-34) Deleting Objects (page 2-34) Assign a New Color to a Group of Objects (page 2-27) Change A Single Tracing Color (page 2-28) Change the Color of One or More Cell Markers (page 2-29) Atlas Shop Tool Bars (page 2-22) The Three Selection Modes (page 2-23) Verify How Data are Grouped in the Atlas Topo Array (page 2-23) Selection Methods (page 2-24) About Saving Edits (page 2-26) Reposition or Resize Parts of the Map (page 2-35)
Page 2-40
3D Modeling 3D Modeling - Review & Review & Optimize the 3D Data Optimize the This section gives instructions for finding and 3D Data
BIOQUANT Topographer Handbook correcting errors introduced during measurement and for applying special formatting to enhance the quality of a surface rendered model. Procedures below that begin with the word Part should be performed in the given order.
Entering the Topographer (page 3-2) Part 1-Display The Atlas (page 3-2) Part 2-A Quick Look at the Surface Rendered Model (page 3-5) Part 3-Save the Atlas to a New Array (page 3-6) Part 4-General Section Review (page 3-7) Introduction To The Atlas Shop (page 3-11) Color Editing Procedures (page 3-27) Section Alignment Procedures (page 3-32) Z-Axis Re-Distribution Procedures (page 3-37) Special Formatting Features (page 3-48) Other Atlas Shop Features (page 3-53)
Page 3-2
ENTERING THE TOPOGRAPHER

When the word Topographer is clicked on the Life Science or OSTEO menu bar, the Topographers Atlas Viewer opens. Following is a brief review of the Topographers three parts. Atlas Viewer - This is the Topographers front room. It is the where Topo arrays that contain the topographic data for the reconstruction are selected and displayed as a wire frame structure called an atlas. Once an atlas is displayed, door ways into the Atlas Shop and the Atlas Modeler become available. While in the Atlas Viewer, the user may experiment with color or rotational changes without fear of altering the original topo data. The atlas may also be printed or saved to a file while in the Atlas Viewer. Atlas Shop - This is the part of the Topographer that is used to check for and correct any errors introduced during measurement, make adjustments that increase the speed of rendering, or add formatting that will produce special effects in the surface rendered model. The Atlas Shop is also were measurements (e.g. volume, distance between structures, etc.) may be taken directly from the 3D atlas. Different versions of the atlas may be saved using the Atlas Shops Save As option. Atlas Modeler - The final surface rendered model is generated in the Atlas Modeler. In the Atlas Modeler, the reconstruction may be moved, resized, rotated, and lighted in various ways. To reveal internal structures, surfaces may be made more transparent or hidden completely. The model can be saved in various file formats, printed, or recorded in a movie while it rotates. Different versions of the surface rendered model may be saved in the Atlas Modeler.
TOPIC CONTENTS
Part 1-Display The Atlas (page 3-2) Part 2-A Quick Look at the Surface Rendered Model (page 3-5) Part 3-Save the Atlas to a New Array (page 3-6) Part 4-General Section Review (page 3-7)
RELATED TOPICS
Color Editing Procedures (page 3-27) Section Alignment Procedures (page 3-32) Z-Axis Re-Distribution Procedures (page 3-37) Special Formatting Features (page 3-48) Other Atlas Shop Features (page 3-53)
PART 1-DISPLAY THE ATLAS

1. Look at the Data Volume and Data Set listed on the Topographers title bar. If this is not the data set you would like opened, do the following to open the desired data set: By default, the data set that was open in BIOQUANT Life Science or BIOQUANT OSTEO when the Topographer program was accessed is open in the Topographer and its arrays are visible in the Select Arrays dialog box. a. b. If the Atlas Window is open, then from the Atlas menu, choose Close to close the Atlas Window. From the File menu, choose Open Data Set to display the Open a Data Set dialog box.
BIOQUANT Topographer Handbook: 3D Modeling - Review & Optimize the 3D Data
Page 3-3
The Open a Data Set Dialog Box
c. d.
Click on a data volume in the Data Volumes list to display its data sets in the Data Sets list. If the desired data volume is not shown: i. Click the Browse button to open the Choose BQ Volume Search Directory box. The Choose BQ Volume Search DIrectory Box
ii. iii. e. f. 2.
Select the directory that contains the desired data volume. Click the Select button.
Click on the desired data set in the Data Sets list. Click the Open button. The arrays of the data set appear in the Select Arrays box.
In the Atlas Viewer, on the Select Arrays dialog box, double click each of the Topo arrays that contain data for the desired reconstruction, to move its index number into the Selected list. Alternately: All of the arrays in the set may be selected at once by choosing Select All Arrays from the Select menu on the Select Arrays dialog box. Then, any measurement arrays or Topo arrays, that do not contain relevant data, may be removed from the Selected list by double clicking the arrays index number in the Selected list. On the Atlas Viewers tool bar, click the New Atlas Window button, or from the Atlas menu choose New.
3. 4.
On the Atlas Viewers tool bar, click the Resize To Fit button. The wire frame atlas will be visible in the Atlas Window and the Atlas Parameters dialog box will open.
Page 3-4 ADDITIONAL INFORMATION

In the Atlas Viewer, the wire frame atlas may also be manipulated in various ways and/or printed. For instance, in addition to creating a fully surface rendered model, it is sometimes useful to create a version of the wire frame atlas in the Atlas Viewer that shows internal structure tracings filled with color. Atlas Viewer features, Fill, Print, and many others. Working With 3D Wire Frame Atlases (page 5-2) The Atlas Viewer Desktop With an Open Atlas Window
When the Topographer first opens, only the Select Arrays dialog box is visible in the Atlas Viewers work space. An Atlas Window is opened after Topo arrays, containing data for the desired reconstruction, are selected.
5.
Continue with Part 2-A Quick Look at the Surface Rendered Model on page 3-5. Taking a quick look at the atlas in its surface rendered form is both fun and informative. Afterward, even if the rendering appears adequate at first glance, it is important to move the atlas into the Atlas Shop for closer examination. Do not be concerned if the model does not look good at this point. Small changes made in the Atlas Shop can make a dramatic difference in how the model is rendered. If a surface rendered model does not show up at all, it usually indicates that all section maps currently have the same Z Value. This is easily corrected in the Atlas Shop.
MORE 3-D MODELING REVIEWING & OPTIMIZATION TOPICS

RELATED TOPICS
Page 3-5
PART 2-A QUICK LOOK AT THE SURFACE RENDERED MODEL

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


PART 3-SAVE THE ATLAS TO A NEW ARRAY

Before work in the Atlas Shop begins, it is prudent to save the original atlas data to a new Topo array. Doing this serves two purposes: First, it insures that an original copy of the data is readily accessible if needed. Second, if the data for the atlas exists in multiple Topo arrays, it combines all of the data into a single array, which is easier to manipulate.
PROCEDURE
1. 2. If still in the Atlas Viewer, click the Atlas Shop Shop) to open the Atlas Shop. button on the system tool bar (or choose Tools menu> Atlas
In the Atlas Shop, from the File menu, choose Save As to open the Save Array As dialog box. Save Array As Dialog Box (before and after atlas data is saved to a new Topo array)
The atlas data (whether it is currently in a single Topo array or distributed in many Topo arrays) is saved to a new Topo array to preserve the original data in its unedited form.
3.
On the Save Array As dialog box, click the New Array button to add a new Topo array to the data set. If there are Topo arrays in the data set that were NOT selected as part of the current atlas, their names will be listed on the Save Array As dialog box. If one of the listed arrays is empty (has no data), you may select it instead of adding another Topo array. Click to highlight the empty array in the Topo array list. Its name will appear in the Array Name edit field. In the Array Name edit field, rename the empty or newly added Topo array. Use a name that distinguishes it from the original. Example: If the original atlas data are distributed in multiple Topo arrays, you might name this copy of the atlas Atlas 1, since the new Topo array will contain all the data for the atlas. Later, if it becomes necessary to save another new version of the atlas, the next version might be named Atlas 2, and so on. Click the Save button. All of the data for the atlas will be copied into the one new array. The original atlas arrays must now be unselected and the new atlas array selected for use. From the File menu, choose Exit Atlas Shop to return to the Atlas Viewer. In the Atlas Viewer, on the Select Arrays dialog box, click the Arrays menu, then choose Unselect All Arrays. All of the arrays in the Selected list will be removed. In the Available Arrays list of the Select Arrays dialog box, scroll to and double click the new Atlas Topo array, to move its index number into the Selected list. On the system tool bar, click the Redraw On the system tool bar, click the Atlas Shop button to update the Atlas Window with the new atlas. button to reopen the Atlas Shop.
4.
5. 6. 7. 8. 9. 10.
Page 3-7
11. Continue with Part 4-General Section Review on page 3-7. Scrolling through the atlas, section by section, will reveal the sources of any problems that were apparent in the surfaced rendered model, and/or will provided an opportunity to make desirable color changes or add special formatting to improve the appearance of the rendered model.

RELATED TOPICS
PART 4-GENERAL SECTION REVIEW

Scrolling through the atlas, section by section, will reveal the sources of any problems that were apparent in the surfaced rendered model, and/or will provided an opportunity to make desirable color changes or add special formatting to improve the appearance of the rendered model. During the process of finding and correcting problems, keep in mind the following points: Anytime an edited version of the atlas is saved to a new array, before any further edits are made, you must momentarily exit the Atlas Shop and in the Atlas Viewer select the new array. See steps 6-10 of the procedure: Part 3-Save the Atlas to a New Array (page 3-6). During the review and editing process, it is useful to exit the Atlas Shop occasionally, and take another quick look at the atlas in the Atlas Modeler, to see the effects of editing. Part 2-A Quick Look at the Surface Rendered Model (page 3-5) The system numbers topographic sections according to their positions in the Topo array. If physical sections were measured out of order, during the section by section review, the out-of-order section numbers may be confusing. The Z Sort option rearranges topographic sections according to their assigned Z Values. IF SECTIONS WERE MEASURED OUT OF ORDER, before beginning the General Section Review, perform the procedure: Z-Sort Topographic Sections (page 3-40)
PROCEDURE
1. 2. 3. Click the Resize to Fit button on the Atlas Shop system tool bar. button is depressed on the system tool bar. This positions and sizes the atlas to fit the work space. Verify that the Section Mode
Select Section 0. See The Selection Methods on 3-15. Glance at the system title bar to verify that Section 0 is selected. (Optional) If you want to hide all tracings that are not part of the selected section map, on the View menu, click to place a check mark next to Selection Only. Use this option when there is a clear reason to do so. Hiding all but the tracings of the currently selected section is sometimes helpful, sometimes not. Using the Select Next and Select Previous buttons on the system tool bar, you will sequence through all of the sections in the atlas several times, looking for and correcting any of the problems that are listed below. Possible Color Problems (page 3-8) BIOQUANT Topographer Handbook: 3D Modeling - Review & Optimize the 3D Data
4.
Page 3-8
5. Possible Alignment Problems (page 3-9) Possible Z-Axis Spacing Problems (page 3-9) Possibility of a Branched Structure (page 3-11)
Continue with 3D Modeling: Surface Rending in the Atlas Modeler on page 4-1. The default surface rendering of an atlas may be modified to enhance the final three dimensional model. The rotating model can be recorded in an AVI movie.

RELATED TOPICS
POSSIBLE COLOR PROBLEMS

An atlas that has been correctly colored for surface rendering will have certain characteristics. If your atlas does not have these characteristics, use the suggested corrective procedure. The surface-defining outlines of sections in all section maps will be the same color. If this is not the case, change the color of each incorrectly colored outline using the procedure: Change A Single Tracing Color (page 3-27). Within any individual section map: Every tracing will be a unique color. The exception to this rule is small tracings or markers that represent clusters of the same type cell. If this is not the case, to assign a new, unique color to a tracing use the procedure: Change A Single Tracing Color (page 3-27). (If a change is necessary, also see the next bullet point.) For any un-branched structure that spans multiple sections, tracings will be the same color in every section map in which the structure appears. If this is not the case, change the color of each incorrectly colored tracing using the procedure: Change A Single Tracing Color (page 3-27). For any branched (Y or V-shaped) structure that spans multiple sections, tracings will initially be the same color on all sections. Tracings that comprise one branch, usually the shortest, must be assigned a different color in the Atlas Shop to insure proper rendering. If a 3D branched structure exists in the atlas, use the procedure: Change the Color Of One Branch of a Y or VShaped Structure (page 3-30) Cell markers or cell area tracings for any one type of cell will be the same color in all section maps. If this is not the case, use the procedure: Change the Color of One or More Cell Markers (page 3-28) If a color that was used during measurement is not satisfactory, you may simultaneously change all tracings or markers of that color, anywhere in the atlas, to a new color using the procedure: Assign a New Color to a Group of Objects (page 3-28).
RETURN TO
Part 4-General Section Review (page 3-7)

POSSIBLE ALIGNMENT PROBLEMS

The system initially stacks topographic sections (the individual section maps) by aligning their landmarks. This is a good start, but the initial alignment almost always needs to be refined. Misalignment of section maps can be caused by forgetting to place a Landmark on one or more sections during measurement, placing the Landmark indiscriminately on sections that do not contain the landmark structure that was used on other sections, or may be due simply to differences in size or orientation of the original physical sections. If there is any evidence of misalignment, perform the section alignment procedures that seem relevant and save the edits.
If the edited version of the atlas is saved to a new Topo array (using Save As), be sure to return to the Atlas Viewer, deselect the currently selected atlas array, and select the new array, before continuing with the section by section review in the Atlas Shop. As often as necessary or desirable, move the atlas into the Atlas Modeler to see the effects of editing.
EVIDENCE OF MISALIGNMENT
In the Atlas Modeler, there were unexpected nicks, shelves, or open spaces in the rendered surface. Section Alignment Procedures (page 3-32) In the Atlas Modeler, non-adjacent section outlines appeared to have been connected during surface rendering. (The surface should connect a section outline with the ones that are immediately adjacent to it.) Section Alignment Procedures (page 3-32) In the Atlas Shop, it is obvious that some sections need to be moved or rotated to line up properly with adjacent sections. Section Alignment Procedures (page 3-32) In the Atlas Shop, it is obvious that some object tracings are incorrect and need to be deleted or redefined using the Line Edit tools. The Line Editing Tools (page 3-24)
RETURN TO
RELATED TOPICS
POSSIBLE Z-AXIS SPACING PROBLEMS

In Z Perspective, the black panel to the right of the atlas work space, reveals the spacing of section maps along the Z axis.
Page 3-10 PROCEDURE

1. On the system tool bar, verify that both the Section Mode and the Z Perspective buttons are depressed. In Z Perspective mode, the vertical line in the black Perspective panel represents the Z axis. Horizontal lines represent individual section maps as they are currently defined in the Topo array. From the Select menu, choose Select All Sections. In the Atlas Shops title bar, note the total number of section maps in the atlas. Example: If there are 20 section maps in the atlas, the title bar will show: Section #0-19 Decide if there is evidence of Z-axis spacing problems by scrolling through the atlas and comparing what you see to the points below. If it is necessary to turn to a corrective procedure, afterwards return to this page and check for other Z-axis spacing problems.
2. 3. 4.
EVIDENCE OF Z-AXIS SPACING PROBLEMS

The atlas has multiple section maps, but there is only one horizontal line in the black Perspective panel. This indicates that all sections currently have the same Z Offset Value. Use the corrective procedure: Distribute Section Maps Evenly Along the Z-Axis (page 3-37) The total number of section maps reported in the Atlas Shops title bar is less than the number of physical sections you measured. There are conjoint section maps due to the lack of a landmark on one or more sections. Use the procedure: Dealing With Conjoint Sections (page 3-42), to evaluate the situation further and make corrections if necessary. Occasionally, when you click Next Section, two or more section maps are selected, instead of only one. This also indicates conjoint section maps due to the lack of a landmark on one or more sections. Use the procedure: Dealing With Conjoint Sections (page 3-42), to evaluate the situation further and make corrections if necessary. The number of section lines in the black Perspective panel is less than the number of total sections indicted in the Atlas Shops title bar. One or more section maps currently have the same Z Offset value. Use the corrective procedure: Change the Z Value of a Section Map (page 3-38) The physical sections you measured were equal distances apart, but section lines in the black Perspective panel are not. The Z Offset value currently assigned to one or more sections is incorrect. Use the corrective procedure: Distribute Section Maps Evenly Along the Z-Axis (page 3-37) The section lines in the Perspective panel are positioned as expected, but there are unwanted gaps in their spacing, due the fact that one or more physical sections were missing and could not be measured. An existing section map may be duplicated and reassigned an appropriate Z Value, to fill-in for missing sections. Use the procedure: Duplicate A Section (page 3-45) In the Perspective panel, there is a stray vertical line (other than the Z axis line) between two of the horizontal section lines. If data point in one of the sections is corrupted or misplaced. Use the corrective procedure: Reposition Misplaced Points (page 3-47)
REMINDER
Anytime an edited version of the atlas is saved to a new Topo array (using Save As or using any of the special Save Array As dialog boxes that open during editing), be sure to return to the Atlas Viewer, deselect the currently selected atlas array, and select the new array, before continuing with the section by section review in the Atlas Shop.
RETURN TO

POSSIBILITY OF A BRANCHED STRUCTURE

The system creates surfaces by looking for corresponding points of the same color on adjacent section maps. For branched (Y or V shaped) structures, the defining surface outline breaks into two sets of outlines and the system must deal with the sudden appearance of too many points that do not correspond. Making the shorter branch of the Y or V shaped structure a different color, eliminates the confusion. The shorter branch will have fewer total tracings (will appear on fewer section maps), than the longer branch.
PROCEDURE
1. 2. As you scroll through the 2D section maps in the atlas, THINK 3D. Look for tracings on adjacent section maps that define a three dimensional branched structure. If there are any branched structures in the atlas that span multiple section maps, go to the procedure: Change the Color Of One Branch of a Y or V-Shaped Structure (page 3-30)
RETURN TO
RELATED TOPICS
INTRODUCTION TO THE ATLAS SHOP

IMPORTANT
Selection Modes and Selection Methods, included in this Introduction, are important to understand, because you will be using them repeatedly during the section review. The atlas is displayed for review, editing, or measurement on the Atlas Shops work space. A two-axis sketch of the atlas is also shown in the black Perspective panel along the right hand side of the work space. When the Z Perspective is chosen, the Perspective panel shows the section maps as horizontal lines distributed along the vertical Z axis.
Page 3-12
The Atlas Shop Interface
The system tool bar (horizontal) and the Vertical Tool Bar hold action buttons. The system tool bar also holds a color palette.
TOPIC CONTENTS
Title Bar and Tool Bars (page 3-13) Save Versus Save As (page 3-13) The Three Selection Modes (page 3-14) The Selection Methods (page 3-15) The Line Editing Tools (page 3-24)
RELATED TOPICS
Possible Color Problems (page 3-8) Possible Alignment Problems (page 3-9) Possible Z-Axis Spacing Problems (page 3-9) Distribute Section Maps Evenly Along the Z-Axis (page 3-37) Change the Z Value of a Section Map (page 3-38) Z-Sort Topographic Sections (page 3-40) Dealing With Conjoint Sections (page 3-42) Duplicate A Section (page 3-45) Reposition Misplaced Points (page 3-47) Color Editing Procedures (page 3-27) Section Alignment Procedures (page 3-32) Z-Axis Re-Distribution Procedures (page 3-37) Other Atlas Shop Features (page 3-53) Numeric Transform (page 3-54) Special Atlas Shop FEatures (page 3-58)
3-D MODELING REVIEWING & OPTIMIZATION TOPICS

Page 3-13
TITLE BAR AND TOOL BARS

The Atlas Shop title bar not only displays the name of the program, but also the section number of the currently selected section (or the range of multiple sections that are currently selected). This display will be used for reference many times during the editing process. Section numbers always begin at 0. In the title bar below, it is apparent that seven sections are selected (Section # 0 - 6) Atlas Shop Title, Menu, and System Tool Bars
Tool Tips (button labels that appear briefly to reveal a buttons name) appear for the system tool bar only when the system title bar is active (colored, instead of gray). Tool Tips for the Vertical Tool Bar appear only when the title bar of the Vertical Tool Bar is active. To activate either title bar, click the cursor on it. Most, but not all, buttons on the system tool bar and on the Vertical Tool Bar are shortcuts to frequently used options on the system menus.
RELATED TOPICS
Save Versus Save As (page 3-13) The Three Selection Modes (page 3-14) The Selection Methods (page 3-15) The Line Editing Tools (page 3-24) Possible Color Problems (page 3-8) Possible Alignment Problems (page 3-9) Possible Z-Axis Spacing Problems (page 3-9) Distribute Section Maps Evenly Along the Z-Axis (page 3-37) Change the Z Value of a Section Map (page 3-38) Z-Sort Topographic Sections (page 3-40) Dealing With Conjoint Sections (page 3-42) Duplicate A Section (page 3-45) Reposition Misplaced Points (page 3-47) Color Editing Procedures (page 3-27) Section Alignment Procedures (page 3-32) Z-Axis Re-Distribution Procedures (page 3-37) Other Atlas Shop Features (page 3-53) Numeric Transform (page 3-54) Special Atlas Shop FEatures (page 3-58)

SAVE VERSUS SAVE AS

Most edits can be saved directly to the current atlas Topo array, by simply choosing Save on the Atlas Shop File menu. Save As is also an option on the Atlas Shop File menu, and is used any time a new version of the atlas needs to be saved. Three special editing routines actually rearrange the topographic data, and the only way to save the new arrangement is to write the data to a new Topo array (using Save As). These routines are: Z-Sort, and anytime Internal Cut, Internal Copy, or Internal Paste are used. These edits are done only under special circumstances that will be explained later. Save As may also be used in order to make multiple versions of the atlas, with different colors or special formatting.

Title Bar and Tool Bars (page 3-13) The Three Selection Modes (page 3-14) The Selection Methods (page 3-15) The Line Editing Tools (page 3-24) Possible Color Problems (page 3-8) Possible Alignment Problems (page 3-9) Possible Z-Axis Spacing Problems (page 3-9) Distribute Section Maps Evenly Along the Z-Axis (page 3-37) Change the Z Value of a Section Map (page 3-38) Z-Sort Topographic Sections (page 3-40) Dealing With Conjoint Sections (page 3-42) Duplicate A Section (page 3-45) Reposition Misplaced Points (page 3-47) Color Editing Procedures (page 3-27) Section Alignment Procedures (page 3-32) Z-Axis Re-Distribution Procedures (page 3-37) Other Atlas Shop Features (page 3-53) Numeric Transform (page 3-54) Special Atlas Shop FEatures (page 3-58)

THE THREE SELECTION MODES

In order to work with parts of the atlas, the particular section, object, or points of interest must first be selected. Selected sections, objects, or points are displayed in color both in the Atlas Shop work space and in the black Axis Perspective panel. When not selected, section, object, or point tracings appear gray. By default, the Atlas Shop opens in Section Mode, meaning that the Section Mode button on the system tool bar is depressed. In Section Mode all operations (e.g. Translate, Rotate, etc.) are applied to the selected section(s). When the Object Mode button is depressed, all operations are applied only to the selected object(s). In Point Mode , all operations apply only to the currently selected data point(s). As you go through the procedures below you will become aware that there are several different ways to select sections, objects, or single points of interest. With experience you may come to favor one selection method over another. If you are an experienced user, in the following procedures, feel free to substitute your preferred selection method any time you are asked to select a section, object, or point marker.

Title Bar and Tool Bars (page 3-13) Save Versus Save As (page 3-13) The Selection Methods (page 3-15) The Line Editing Tools (page 3-24) Possible Color Problems (page 3-8) Possible Alignment Problems (page 3-9) Possible Z-Axis Spacing Problems (page 3-9) Distribute Section Maps Evenly Along the Z-Axis (page 3-37) Change the Z Value of a Section Map (page 3-38) Z-Sort Topographic Sections (page 3-40) Dealing With Conjoint Sections (page 3-42) Duplicate A Section (page 3-45) Reposition Misplaced Points (page 3-47) Color Editing Procedures (page 3-27) Section Alignment Procedures (page 3-32) Z-Axis Re-Distribution Procedures (page 3-37) Other Atlas Shop Features (page 3-53) Numeric Transform (page 3-54) Special Atlas Shop FEatures (page 3-58)

THE SELECTION METHODS

There are several different ways to select sections, objects, or single data points of interest. With experience you may come to favor one selection method over another, but if that method proves to be awkward when working with a particular specimen, you will need to be familiar with the alternate methods.
TOPIC CONTENTS
Select By Color (page 3-16) Select Next / Select Previous (page 3-17) Select Using Rectangle or Polygon (page 3-18) Select From a List (page 3-21) Select by Adding Interior Objects (page 3-23)

Title Bar and Tool Bars (page 3-13) Save Versus Save As (page 3-13) The Three Selection Modes (page 3-14) The Selection Methods (page 3-15) The Line Editing Tools (page 3-24) Possible Color Problems (page 3-8) Possible Alignment Problems (page 3-9) Possible Z-Axis Spacing Problems (page 3-9) Distribute Section Maps Evenly Along the Z-Axis (page 3-37) Change the Z Value of a Section Map (page 3-38) Z-Sort Topographic Sections (page 3-40) Dealing With Conjoint Sections (page 3-42) Duplicate A Section (page 3-45) Reposition Misplaced Points (page 3-47) Color Editing Procedures (page 3-27) Section Alignment Procedures (page 3-32) Z-Axis Re-Distribution Procedures (page 3-37) Other Atlas Shop Features (page 3-53) Numeric Transform (page 3-54) Special Atlas Shop FEatures (page 3-58)

SELECT BY COLOR
Select By Color operates across the entire atlas, regardless of which Selection Mode is currently active. It simply selects all tracings and/or markers of the same color, throughout the entire atlas.
PROCEDURE
1. 2. On the Vertical Tool Bar, click the Select By Color button
On the system tool bars color palette, click the color that matches the color of the objects that need to be selected. System Tool Bar With Color Palette
When the Select By Color tool on the Vertical Tool Bar is active, clicking a colored square on the system tool bars Color Palette selects all objects in the atlas of that color.

Select Next / Select Previous (page 3-17) Select Using Rectangle or Polygon (page 3-18) Select From a List (page 3-21) Select by Adding Interior Objects (page 3-23) Title Bar and Tool Bars (page 3-13) Save Versus Save As (page 3-13) The Three Selection Modes (page 3-14) The Selection Methods (page 3-15) The Line Editing Tools (page 3-24) Possible Color Problems (page 3-8) Possible Alignment Problems (page 3-9) Possible Z-Axis Spacing Problems (page 3-9) Distribute Section Maps Evenly Along the Z-Axis (page 3-37) Change the Z Value of a Section Map (page 3-38) Z-Sort Topographic Sections (page 3-40) Dealing With Conjoint Sections (page 3-42) Duplicate A Section (page 3-45) Reposition Misplaced Points (page 3-47) Color Editing Procedures (page 3-27) Section Alignment Procedures (page 3-32) Z-Axis Re-Distribution Procedures (page 3-37) Other Atlas Shop Features (page 3-53) Numeric Transform (page 3-54) Special Atlas Shop FEatures (page 3-58)

SELECT NEXT / SELECT PREVIOUS

The Select Next and Select Previous tools on the Vertical Tool Bar can be used to sequence through sections (in Section Mode), objects (in Object Mode), or data points (in Point Mode).
PROCEDURE
1. 2. Click to activate Section Mode Click the Select Next individual sections. . buttons on the system tool bar to sequence through
or Select Previous
Within any currently selected section, you may sequence through individual objects (tracings and cell markers) within that section by doing the following: a. b. Click to activate Object Mode .
Click the Select Next or Select Previous buttons on the system tool bar to sequence through individual tracings (or markers) within the current section.
Within any currently selected object you may sequence through individual data points, although there is rarely a reason to do so. a. b. Click to activate Point Mode .
Click the Select Next or Select Previous buttons on the system tool bar to sequence through individual data points within the current object.

A objects tracing may have hundreds or thousands of data points. A cell marker, which appears to the eye to be a single point, actually contains two data points with zero distance between them.
RELATED TOPICS
Select By Color (page 3-16) Select Using Rectangle or Polygon (page 3-18) Select From a List (page 3-21) Select by Adding Interior Objects (page 3-23) Title Bar and Tool Bars (page 3-13) Save Versus Save As (page 3-13) The Three Selection Modes (page 3-14) The Selection Methods (page 3-15) The Line Editing Tools (page 3-24) Possible Color Problems (page 3-8) Possible Alignment Problems (page 3-9) Possible Z-Axis Spacing Problems (page 3-9) Distribute Section Maps Evenly Along the Z-Axis (page 3-37) Change the Z Value of a Section Map (page 3-38) Z-Sort Topographic Sections (page 3-40) Dealing With Conjoint Sections (page 3-42) Duplicate A Section (page 3-45) Reposition Misplaced Points (page 3-47) Color Editing Procedures (page 3-27) Section Alignment Procedures (page 3-32) Z-Axis Re-Distribution Procedures (page 3-37) Other Atlas Shop Features (page 3-53) Numeric Transform (page 3-54) Special Atlas Shop FEatures (page 3-58)


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

1. 2. Click to activate Section Mode . tool or the Select Using Polygon tool,
On the Vertical Tool Bar, click either the Select Using Rectangle then do the following:
If Select Using Rectangle is active, click and hold the left mouse button while dragging the cursor diagonally to form a small selection box that crosses the outline of the section(s) that you want to select. If Select Using Polygon is active, click a series of points to create a selection polygon of any shape that crosses the outline of the section(s) you want to select.
Page 3-19
Selecting Sections Using the Select With Rectangle or Polygon Tool
On the left is a selection rectangle across the outlines of three sections. In the middle is a selection polygon across the same outlines. The result is shown on the right: All tracings and markers within those three sections are selected. A selection polygon can be any shape.
If even one data point of a section falls within the rectangle or polygon, all tracings and markers within that section are selected.
PROCEDURE: SELECT OBJECTS

An object is any individual tracing or cell marker. To work with objects, a section must first be selected in Section mode, then Object mode is activated. In Object mode, the Select Using Rectangle and Select Using Polygon tools operate only on the current section, unless a special feature called Select Across Sections is turned on. The Select Across Sections feature works only in Object mode and tells the system to select objects on all sections in an area that corresponds to the selection box or polygon that is being created on the current section. 1. 2. 3. In Section mode , using the most convenient method, select the section of interest. .
Click to activate Object Mode
If you want the system to select objects on all sections that correspond to the objects you intend to select on this section, on the Select menu, click to check Select Across Sections. If the objects of interest are small and need to be magnified to make selection easier, you may simultaneously zoom and pan them to the middle of the work space by doing the following: a. b. On the vertical tool bar, click the Zoom tool. With the cursor positioned over the objects of interest, using the left mouse button, click and drag the objects of interest toward the center of the work space. Release the cursor button. Repeat as needed.
To Zoom without panning, verify that the Zoom tool is active, position the cursor anywhere in the work space, and click the left mouse button once. Repeat as needed to increase the zoom level. To return to an un-zoomed state, verify that the Zoom tool is active, position the cursor anywhere in the work space, and click the right mouse button once. Repeat if needed to return the atlas to fully un-zoomed state. To pan with out zooming, on the Vertical Tool bar, click to activate the Pan tool, then using the left mouse button, click and drag the atlas to the desired location. On the Vertical Tool Bar, click either the Select Using Rectangle then do the following: tool or the Select Using Polygon tool,
4.
If Select Using Rectangle is active, click and hold the left mouse button while dragging the cursor diagonally to form a small selection box that encloses or touches all the objects you want to select. If Select Using Polygon is active, click a series of points to create a selection polygon of any shape that encloses or touches all the objects you want to select. BIOQUANT Topographer Handbook: 3D Modeling - Review & Optimize the 3D Data
Page 3-20
Selecting Objects Using the Select With Rectangle or Polygon Tool During Zoom
The illustrated section has small cell markers in the middle that need to be selected. After the atlas is zoomed, cells of interest are selected with the Select Using Rectangle tool (upper right) or the Select Using Polygon tool (lower right).
PROCEDURE: SELECT DATA POINTS

1. 2. Using the most convenient method, select first the section map, then the object within that section that contains the data points of interest. If the data points of interest need to be magnified to make selection easier, while still in Object mode, you may simultaneously zoom and pan them to the middle of the work space by doing the following: a. b. On the vertical tool bar, click the Zoom tool. With the cursor positioned over the selected objects, using the left mouse button, click and drag the object(s) toward the center of the work space. Release the cursor button. Repeat as needed. button. tool or the Select Using Polygon tool,
3. 4.
On the system tool bar, click the Points Mode
If Select Using Rectangle is active, click and hold the left mouse button while dragging the cursor diagonally to form a small selection box that encloses all the data points you want to select. If Select Using Polygon is active, click a series of points to create a selection polygon of any shape that encloses all of the data points you want to select.

Select By Color (page 3-16) Select Next / Select Previous (page 3-17) Select From a List (page 3-21) Select by Adding Interior Objects (page 3-23) Title Bar and Tool Bars (page 3-13) Save Versus Save As (page 3-13) The Three Selection Modes (page 3-14) The Selection Methods (page 3-15) The Line Editing Tools (page 3-24) Possible Color Problems (page 3-8) Possible Alignment Problems (page 3-9) Possible Z-Axis Spacing Problems (page 3-9) Distribute Section Maps Evenly Along the Z-Axis (page 3-37) Change the Z Value of a Section Map (page 3-38) Z-Sort Topographic Sections (page 3-40) Dealing With Conjoint Sections (page 3-42) Duplicate A Section (page 3-45) Reposition Misplaced Points (page 3-47) Color Editing Procedures (page 3-27) Section Alignment Procedures (page 3-32) Z-Axis Re-Distribution Procedures (page 3-37) Other Atlas Shop Features (page 3-53) Numeric Transform (page 3-54) Special Atlas Shop FEatures (page 3-58)

SELECT FROM A LIST

Sections (in Section Mode) and objects (in Object Mode) may be selected from a GoTo list. The GoTo Section list is almost always the fastest way to select the desired section(s). The GoTo Object list is a quick way to select objects, unless the current section has dozens or hundreds of cell markers. In this case the object list would be very long and possibly tedious to use.

1. 2. Click to activate the Section mode button.
From the Select menu, choose GoTo, to open the GoTo Section list box.
Page 3-22
GoTo Section List With the First Section Selected
To select a single section, click to highlight its entry in the list. To select multiple, contiguous sections, click the first section, press and hold the Shift key, then click the last section in the series that is to be selected. All sections between and including the first and the last will be selected. To select multiple, non-contiguous sections, click one section, press and hold the Ctrl key, then click each additional section that is to be selected.

1. 2. 3. In Section mode interest. , using the most convenient method, select the section that contains the objects of .
From the Select menu, choose GoTo, to open the Go To Object list. Example GoTo Object Lists
The Ctrl key was used to help select non-contiguous objects.
To select a single object, click to highlight its entry in the list. To select multiple, contiguous objects, click the first object, press and hold the Shift key, then click the last object in the series. All objects between and including the first and the last will be selected.
Page 3-23
To select multiple, non-contiguous objects, click one object, press and hold the Ctrl key, then click each additional object that is to be selected.
RELATED TOPICS
Select By Color (page 3-16) Select Next / Select Previous (page 3-17) Select Using Rectangle or Polygon (page 3-18) Select by Adding Interior Objects (page 3-23) Title Bar and Tool Bars (page 3-13) Save Versus Save As (page 3-13) The Three Selection Modes (page 3-14) The Selection Methods (page 3-15) The Line Editing Tools (page 3-24) Possible Color Problems (page 3-8) Possible Alignment Problems (page 3-9) Possible Z-Axis Spacing Problems (page 3-9) Distribute Section Maps Evenly Along the Z-Axis (page 3-37) Change the Z Value of a Section Map (page 3-38) Z-Sort Topographic Sections (page 3-40) Dealing With Conjoint Sections (page 3-42) Duplicate A Section (page 3-45) Reposition Misplaced Points (page 3-47) Color Editing Procedures (page 3-27) Section Alignment Procedures (page 3-32) Z-Axis Re-Distribution Procedures (page 3-37) Other Atlas Shop Features (page 3-53) Numeric Transform (page 3-54) Special Atlas Shop FEatures (page 3-58)

SELECT BY ADDING INTERIOR OBJECTS

Add Interior Objects to Selection is an option on the Select menu than can be used when a currently selected tracing (object) encircles other tracings that need to be added to the selection. Add Interior Object to Selection is used only in Object Mode.
PROCEDURE
1. 2. 3. 4. In Section mode interest. , using the most convenient method, select the section that contains the objects of .
Using the most convenient method, select the tracing (object) that surrounds another set of objects that need to be selected. From the Select menu, choose Add Interior Objects to Selection.

Select By Color (page 3-16) Select Next / Select Previous (page 3-17) Select Using Rectangle or Polygon (page 3-18) Select From a List (page 3-21) Title Bar and Tool Bars (page 3-13) Save Versus Save As (page 3-13) The Three Selection Modes (page 3-14) The Selection Methods (page 3-15) The Line Editing Tools (page 3-24) Possible Color Problems (page 3-8) Possible Alignment Problems (page 3-9) Possible Z-Axis Spacing Problems (page 3-9) Distribute Section Maps Evenly Along the Z-Axis (page 3-37) Change the Z Value of a Section Map (page 3-38) Z-Sort Topographic Sections (page 3-40) Dealing With Conjoint Sections (page 3-42) Duplicate A Section (page 3-45) Reposition Misplaced Points (page 3-47) Color Editing Procedures (page 3-27) Section Alignment Procedures (page 3-32) Z-Axis Re-Distribution Procedures (page 3-37) Other Atlas Shop Features (page 3-53) Numeric Transform (page 3-54) Special Atlas Shop FEatures (page 3-58)

THE LINE EDITING TOOLS

The line editing tools on the vertical tool bar correct tracing errors made when the topographic data were collected in the measurement software. The Line Editing Tools on the Vertical Toolbar
STRAIGHTEN EDGE
In this procedure, the second of two clicked points must lie counterclockwise from the first. A new straight line segment will be constructed (counterclockwise) from the first point to the second point. 1. 2. Select the tracing that needs to be Line edited. On the vertical tool bar, click the Straighten Edge button.
Page 3-25
3. 4. Click one end of the segment to be straightened. Click the other end of the segment.
ADDITIONAL NOTES
Click the right mouse button to cancel after the first click. Click the Undo button to undo the last edit.
COMBINE TWO OBJECTS

Sometimes a single object will be thresholded and traced as two separate halves. This procedure corrects this. The Combine Two Objects tool on the vertical toolbar connects two objects with straight lines which are defined by mouse clicks. Combine Objects Example
1. 2. 3. 4. 5. 6.
Click where one end of the connecting line should be on object A. Click where the other end of the connecting line should be on object B. Click where one end of the second connecting line should be on object B. Click where the other end of the connecting line should be on object A.
ADDITIONAL NOTES
Click the right mouse button to cancel before the series of 4 clicks is finished. Click the button to undo the last edit.
SEPARATE TWO OBJECTS

Sometimes, two objects are traced as one. This procedure corrects this. Clicking two points defines the location for a gap that will separate the object into two. 1. 2. 3. Select the objects that need to be separated. Click the Separate Two Objects button on the vertical toolbar.
ADDITIONAL NOTES
Click the right mouse button after the first click to cancel the separation. Click the Undo button to undo the separation.

A segment of an objects contour tracing can be redrawn with the Redefine Edge tool. This tool is recommended (instead of the Straighten Edge tool) when editing atlases that are to be surface rendered or any other time that a significant portion of an objects tracing needs to be altered. 1. Click the Redefine Edge tool on the vertical tool bar. BIOQUANT Topographer Handbook: 3D Modeling - Review & Optimize the 3D Data
Page 3-26
2. 3. 4. 5. Click to mark one end of the segment that is to be redefined. Click to mark the other end of the segment. Starting from the first point, click a series of data points to define the new contour. If the atlas is to be surface rendered, click the series of data points fairly close together. Click the right mouse button to end the construction of the new edge.
SAVING THE EDIT

After Redefine Edge is used, if the atlas is saved using Save on the File menu, or by responding YES to the Save Data message when exiting the Atlas Shop, the data in the original atlas Topo array(s) are permanently changed. If desirable, Save As on the File menu may be used instead, to save the edited version of the atlas to a new Topo array.
ADDITIONAL NOTES:
The most recent unsaved deletion may be canceled by clicking the Undo tool bar. button on the vertical
All unsaved edits may be canceled by choosing Restore Original from the File menu.
DELETING OBJECTS
The Delete tool on the vertical toolbar is used to permanently remove the data of a chosen object from the original Topo array. The object immediately disappears from the atlas window. 1. 2. Click the Delete Object tool on the vertical tool bar.
Click on the tracing of the object to be deleted. Note: The removed data is temporarily stored in the Topographers backup buffer and the delete does not become permanent until the data is saved using Save on the File menu or by responding YES to the Save Data message on exiting the Atlas Shop.
ADDITIONAL NOTES:
RELATED TOPICS
Numeric Transform (page 3-54) Special Atlas Shop FEatures (page 3-58) Possible Color Problems (page 3-8) Possible Alignment Problems (page 3-9) Possible Z-Axis Spacing Problems (page 3-9) Distribute Section Maps Evenly Along the Z-Axis (page 3-37) Change the Z Value of a Section Map (page 3-38) Z-Sort Topographic Sections (page 3-40) Dealing With Conjoint Sections (page 3-42) Duplicate A Section (page 3-45) Reposition Misplaced Points (page 3-47) Color Editing Procedures (page 3-27) Section Alignment Procedures (page 3-32) Z-Axis Re-Distribution Procedures (page 3-37) Other Atlas Shop Features (page 3-53)

Page 3-27
COLOR EDITING PROCEDURES

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

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

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

PROCEDURE
1. 2. 3. 4. If necessary, in Section Mode , select the section of interest. The Selection Methods (page 3-15) Click Object Mode button, to activate Object mode.
Select the object (tracing or marker) for which the color needs to be changed. The Selection Methods (page 3-15) On the Vertical Tool Bar, click the Change Color a. button.
On the system tool bar, click to choose the desired new color on the color palette. The selected tracing will change to the chosen color.
5. 6. 7.
Repeat from step 3 for any tracing in this section that needs a color change. From the File menu, choose Save. Choosing Save on the File menu permanently alters the data in the current atlas Topo array. If appropriate, return to: Part 4-General Section Review (page 3-7).
RELATED TOPICS
Assign a New Color to a Group of Objects (page 3-28) Change the Color of One or More Cell Markers (page 3-28) Change the Color Of One Branch of a Y or V-Shaped Structure (page 3-30) Close Gap in a Branched Structure (page 3-31) Color Editing Procedures (page 3-27) Section Alignment Procedures (page 3-32) Z-Axis Re-Distribution Procedures (page 3-37) The Line Editing Tools (page 3-24) Special Formatting Features (page 3-48) Other Atlas Shop Features (page 3-53) BIOQUANT Topographer Handbook: 3D Modeling - Review & Optimize the 3D Data
Page 3-28 3-D MODELING REVIEWING & OPTIMIZATION TOPICS

ASSIGN A NEW COLOR TO A GROUP OF OBJECTS

A group of like-colored objects (tracings or cell markers) may be quickly selected using the Select By Color tool.
PROCEDURE
1. Click to depress the Section Mode button on the system tool bar. Since this procedure selects objects of the same color across all sections of the atlas, it does not matter which section map is currently selected. On the Vertical Tool Bar, click the Select by Color tool.
2. 3. 4. 5. 6. 7.
On the color palette (on the system tool bar), click to designate the current color of the objects of interest. All objects (tracings and/or cell markers) in the atlas of the designated color will be selected. On the Vertical Tool Bar, click the Change Color tool.
On the color palette, click to designate the desired new color. The selected objects in the atlas will change to the new color. From the File menu, choose Save. If appropriate, return to: Part 4-General Section Review (page 3-7).
RELATED TOPICS
Change A Single Tracing Color (page 3-27) Change the Color of One or More Cell Markers (page 3-28) Change the Color Of One Branch of a Y or V-Shaped Structure (page 3-30) Close Gap in a Branched Structure (page 3-31) Color Editing Procedures (page 3-27) Section Alignment Procedures (page 3-32) Z-Axis Re-Distribution Procedures (page 3-37) Special Formatting Features (page 3-48) The Line Editing Tools (page 3-24) Other Atlas Shop Features (page 3-53)

CHANGE THE COLOR OF ONE OR MORE CELL MARKERS

One or more individual cell markers (single point objects) may be quickly selected with the Select Using Rectangle or Select Using Polygon tools.
PROCEDURE
1. 2. Verify that the Section Mode button is depressed on the system tool bar.
Select a section that contains mis-colored cell markers (single point objects) using one of the following methods:
Page 3-29
Use the Select Next or Select Previous buttons to sequence through sections. Use the GoTo Section dialog box (Select menu> GoTo). Click to highlight the desired section in the GoTo Section list. The dialog box may be closed by clicking the Close button. If it remains open, it will change to the GoTo Objects list when Object Mode is activated (in step 3), but the object list will not be needed for this procedure. button.
3. 4.
On the system tool bar, click to depress the Object Mode
(Optional) When selecting single point objects, it is often useful to magnify the area of interest before using the selection tools. To zoom the area of interest, do the following: a. b. c. On the Vertical Tool Bar, click the Zoom tool. Using the left mouse button, click the area of interest to zoom up one level. Continue to click the area until the area is sufficiently magnified. If necessary, use the Pan tool to reposition the zoomed tracings in the work space, as follows: i. ii. On the Vertical Tool Bar, click the Pan tool. Place the hand-cursor over a point that you would like to move to the center of the work space.
iii. Click and drag the hand-cursor to reposition the tracings. NOTE: Clicking the right mouse button will zoom out, making the section tracings smaller. Clicking the Resize To Fit 5. button on the system tool bar will resize and center the atlas to fit the work space. button or the Select Using Polygon button,
On the Vertical Tool Bar, click the Select Using Rectangle then do the following to select the cell markers of interest:
With the Select Using Rectangle tool, click and drag the cursor diagonally to form a rectangular selection box around the objects of interest.
With the Select Using Polygon tool, click a series of points to form a selection polygon around the objects of interest. All objects fully or partially contained within the box or polygon will be selected. 6. 7. 8. 9. On the Vertical Tool Bar, click the Change Color tool.
On the color palette (system tool bar), click to designate the desired new color. The selected single point objects will change to the new color. From the File menu, choose Save. Choosing Save on the File menu permanently alters the data in the current atlas Topo array. If appropriate, return to: Part 4-General Section Review (page 3-7).
If the Zoom tool was used, clicking the Resize to Fit button on the system tool bar will redraw and center the atlas to fit the work space. When the Select Across Sections option is checked on the Select menu, the Select Using Rectangle and Select Using Polygon tools may also be used to select objects in corresponding regions on all sections at once. See Select Using Rectangle or Polygon on 3-18.
RELATED TOPICS
Change A Single Tracing Color (page 3-27) Assign a New Color to a Group of Objects (page 3-28) Change the Color Of One Branch of a Y or V-Shaped Structure (page 3-30) Close Gap in a Branched Structure (page 3-31) Color Editing Procedures (page 3-27) Section Alignment Procedures (page 3-32) The Line Editing Tools (page 3-24) Z-Axis Re-Distribution Procedures (page 3-37) Special Formatting Features (page 3-48) Other Atlas Shop Features (page 3-53)

CHANGE THE COLOR OF ONE BRANCH OF A Y OR V-SHAPED STRUCTURE

When a structure branches, the Atlas Modeler has difficulty distinguishing which data points belong to which branch if all of the data points for the structure are the same color. For this reason, tracings that define the smaller branch are assigned a different color. A Y or V-shaped structure will always have 3 parts: two branches and an un-divided base to which each branch is connected. The connecting base may be very thin and may be defined by a single tracing in only one section map. When working with a branched structure it is usually best to focus entirely on that structure, locating its tracings on each section and making color changes as needed. This means switching back and forth between Object Mode and Section Mode several times, and ignoring other types of color-related issues until all of the tracings for the structures smallest branch have been changed to a new color.
PROCEDURE
1. Decide which color to use for the tracings of the structures smaller branch. When possible, choose a color that has a similar hue or brightness as the original color (e.g. red and pink, blue and dark blue, purple and brown). It may not be possible to use a similar color, since the new color must also be one that has NOT already been used for another type of structure in the atlas. In Section Mode , select the first section map that has a tracing that belongs to the structures shortest branch. The Selection Methods (page 3-15) Click to depress the Object Mode button, to activate Object mode.
2.
3. 4. 5. 6.
Select the tracing that belongs to the shortest branch of the structure. The Selection Methods (page 3-15) On the Vertical Tool Bar, click the Change Color tool.
On the color palette (system tool bar), click to designate the desired new color. The selected tracing will change to the new color. On the system tool bar, click the Section Mode section), then click the Object Mode button, click the Select Next button (to select the next
7.
button (to re-activate Object mode).
8. 9.
Repeat from step 4 until all of the tracings that define the smaller branch have been changed to the desired color. From the File menu, choose Save. Choosing Save on the File menu permanently alters the data in the current atlas Topo array.
Now, when the atlas is moved into the Atlas Modeler, the uniquely colored branch will render correctly as an object that is separate from the other branch. However, treating it as separate object, may introduce a visible gap between the uniquely colored branch and the rest of the structure. If this proves to be the case, the gap may be closed by changing the Z-Value of the tracing in the color-altered branch that is closest to the base, to match the Z-Value of the closest base tracing. This procedure is given below.

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

CLOSE GAP IN A BRANCHED STRUCTURE

PROCEDURE
1. 2. Verify that the Section Mode button is depressed on the system tool bar.
Using any convenient method, select the section map that contains the desired base-tracing (the one that is closest to the section map that contains the first tracing of the shortest branch), and determine its Z-Value doing the following: a. b. c. On the Vertical Tool Bar, click the Change Z open the Change Z dialog box. button (or from the Edit menu, choose Change Z) to
Note the sections Z-Value in the Change All Sections To field. You will change nothing at this point. Simply view the Z Value of the currently selected section map. Click the Close button.
3. 4.
Use the Select Next or Select Previous button to select the adjacent section map that contains the first tracing for the uniquely colored branch. Click the Object Mode button on the system tool bar and select the tracing of the uniquely colored branch. The Selection Methods (page 3-15) On the Vertical Tool Bar, click the Change Z the Change Z dialog box. button (or from the Edit menu, choose Change Z) to open
5.
The Change Z Dialog Box in Change Selected Sections Mode
6. 7.
On the Change Z dialog box, change the value in the Change All Z-Values To field to match the Z-Value observed in step 2. Click the Apply button, then click the Close button. BIOQUANT Topographer Handbook: 3D Modeling - Review & Optimize the 3D Data
Page 3-32
8. 9. From the File menu, choose Save. If appropriate, return to: Part 4-General Section Review (page 3-7).
RELATED TOPICS
Change A Single Tracing Color (page 3-27) Assign a New Color to a Group of Objects (page 3-28) Change the Color of One or More Cell Markers (page 3-28) Change the Color Of One Branch of a Y or V-Shaped Structure (page 3-30) Color Editing Procedures (page 3-27) Section Alignment Procedures (page 3-32) Z-Axis Re-Distribution Procedures (page 3-37) Special Formatting Features (page 3-48) The Line Editing Tools (page 3-24) Other Atlas Shop Features (page 3-53)

SECTION ALIGNMENT PROCEDURES

For a variety of reasons, the sections maps in the atlas may not line up optimally to produce a smooth and beautiful 3D model. The Atlas Shop provides tools for section realignment. The first tool is the automatic Align Sections feature that simultaneously rotates section map Start Points into alignment. However, this option is only useful if, during measurement, the user controlled the starting point of each sections outline and placed that point at corresponding locations on each section. Individual section maps, or objects within individual section maps, may be manually translated, rotated, or resized to better line up with tracings in adjacent sections. Tracings from other section maps may be overlaid for visual reference while moving, rotating, or resizing a selected section map.
TOPIC CONTENTS
Simultaneously Align All Sections That have Corresponding Start Points (page 3-32) Manually Align Section Maps (page 3-33) Translate (Move) a Section Map (page 3-34) Rotate A Section Map (page 3-35) Resize A Section Map (page 3-36)
RELATED TOPICS
Color Editing Procedures (page 3-27) Section Alignment Procedures (page 3-32) Z-Axis Re-Distribution Procedures (page 3-37) Special Formatting Features (page 3-48) The Line Editing Tools (page 3-24) Other Atlas Shop Features (page 3-53)

SIMULTANEOUSLY ALIGN ALL SECTIONS THAT HAVE CORRESPONDING START

Page 3-33
POINTS
The automatic Align Sections feature should only be used if during data collection, measurement Start Points of section outlines were deliberately placed in corresponding positions on all sections. The automatic Align Sections feature acts on all section maps in the atlas, regardless of which selection mode is currently active.
PROCEDURE
1. From the Edit menu, choose Align Sections. All section maps in the atlas will automatically rotate so that the measurement Start Points on the outermost section outlines line up. If appropriate, return to the section by section review (3-9).
2.
RELATED TOPICS
Manually Align Section Maps (page 3-33) Translate (Move) a Section Map (page 3-34) Rotate A Section Map (page 3-35) Resize A Section Map (page 3-36) Color Editing Procedures (page 3-27) Section Alignment Procedures (page 3-32) Z-Axis Re-Distribution Procedures (page 3-37) Special Formatting Features (page 3-48) The Line Editing Tools (page 3-24) Other Atlas Shop Features (page 3-53)

MANUALLY ALIGN SECTION MAPS

Before translating, rotating, or resizing an individual section map, it is best to overlay one or more adjacent maps to use for visual reference. The overlaid tracings will be gray. The Overlay Section dialog box must remain open as long as the reference tracings are needed. The procedure for overlaying reference sections is given immediately below and referred to in the Translate, Rotate, and Resize procedures that follow.
PROCEDURE: OVERLAY REFERENCE SECTIONS

1. In Section Mode , select a section map that needs to be translated (moved in the XY plane), rotated, or resized. The Selection Methods (page 3-15) Overlay at least one unselected section map for visual reference by doing the following: a. From the View menu, choose Overlay Sections to open the Overlay Section dialog box. With the cursor on its title bar, click and drag the Overlay Section dialog box to the back Perspective Panel. This will keep the dialog box from obscuring the atlas during the edit procedure.
2.
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Overlay Section Dialog Box
b.
Although various combinations of reference maps may be used, the simplest is to superimpose only the previous section. To use the simplest approach, do the following: i. ii. On the Overlay Section dialog box, type 1 in the previous section edit field and verify that there is a check mark next to it. Click the Apply button.
The tracings in overlaid section maps will remain gray, indicating that they are not currently selected. To learn more about Overly Section options see: View> Overlay Sections (page 6-20)
RELATED TOPICS
Simultaneously Align All Sections That have Corresponding Start Points (page 3-32) Translate (Move) a Section Map (page 3-34) Rotate A Section Map (page 3-35) Resize A Section Map (page 3-36) Color Editing Procedures (page 3-27) Section Alignment Procedures (page 3-32) Z-Axis Re-Distribution Procedures (page 3-37) The Line Editing Tools (page 3-24) Special Formatting Features (page 3-48) Other Atlas Shop Features (page 3-53)

TRANSLATE (MOVE) A SECTION MAP

1. 2. In Section mode , select a section map that needs to be moved in the same XY plane to a new location. The Selection Methods (page 3-15) Overlay at least one adjacent section map for visual reference by doing the following: a. From the View menu, choose Overlay Sections to open the Overlay Section dialog box. With the cursor on its title bar, click and drag the Overlay Section dialog box to the back Perspective Panel. This will keep the dialog box from obscuring the atlas during the edit procedure.
Page 3-35
Overlay Section Dialog Box
b.
Although various combinations of reference maps may be used, the simplest is to superimpose only the previous section. To use the simplest approach, do the following: i. ii. On the Overlay Section dialog box, type 1 in the previous section edit field and verify that there is a check mark next to it. Click the Apply button. tool.
3. 4.
On the Vertical Tool Bar, click the Translate The cursor takes the shape of crossed arrows.
Place the cursor over the selected section, then using the left mouse button, click and drag the section map so that its tracings are better aligned with the reference (gray) section. When the cursor button is released, the moved tracing will settle into its new position. If needed, repeat step 4 to refine the placement.
5.
ALTERNATE PROCEDURE
Sections may also be moved a known micron distance using Numeric Transform. See Numeric Transform on 354.
To remove the overlaid tracings, close the Overlay Section dialog box. To learn more about Overly Section options see: View> Overlay Sections (page 6-20) Choosing Save on the File menu permanently saves the edit in the current atlas Topo array.
RELATED TOPICS
Simultaneously Align All Sections That have Corresponding Start Points (page 3-32) Manually Align Section Maps (page 3-33) Rotate A Section Map (page 3-35) Resize A Section Map (page 3-36) Color Editing Procedures (page 3-27) Section Alignment Procedures (page 3-32) Z-Axis Re-Distribution Procedures (page 3-37) Special Formatting Features (page 3-48) The Line Editing Tools (page 3-24) Other Atlas Shop Features (page 3-53)

ROTATE A SECTION MAP

1. In Section mode , select a section map that needs to be rotated. The Selection Methods (page 3-15)
Page 3-36
2. 3. 4. Overlay at least one adjacent section map for visual reference. View> Overlay Sections (page 6-20) On the Vertical Tool Bar, click the Rotate The special rotate cursor will appear. tool.
Place the cursor anywhere on the Atlas Shop work space, then click and hold the left mouse button while moving the cursor in either a clockwise or counter-clockwise circle. When the cursor button is released, the rotated section will settle into its new orientation. If needed, repeat step 4 to refine the rotation.
5.
ALTERNATE PROCEDURE
Sections may also be rotated by a degree using Numeric Transform. See Numeric Transform on 3-54.)
To remove the overlaid tracings, close the Overlay Section dialog box. Choosing Save on the File menu permanently saves the edit in the current atlas Topo array.
RELATED TOPICS
Simultaneously Align All Sections That have Corresponding Start Points (page 3-32) Manually Align Section Maps (page 3-33) Translate (Move) a Section Map (page 3-34) Resize A Section Map (page 3-36) Color Editing Procedures (page 3-27) Section Alignment Procedures (page 3-32) Z-Axis Re-Distribution Procedures (page 3-37) The Line Editing Tools (page 3-24) Special Formatting Features (page 3-48) Other Atlas Shop Features (page 3-53)

RESIZE A SECTION MAP

1. 2. 3. 4. 5. In Section mode , select a section map that needs to be resized. The Selection Methods (page 3-15) Overlay at least one adjacent section map for visual reference. View> Overlay Sections (page 6-20) On the Vertical Tool Bar, click the Resize tool. A box with a pull-point at each corner will appear around the section. Click and drag one of the pull-points outward to increase the size or inward to decrease the size. When the cursor button is released, the resized tracing will settle into its new position. If needed, repeat step 4 to refine the size.
ALTERNATE PROCEDURE
Sections may also be resized by a known percentage using Numeric Transform. See Numeric Transform on 354.)
To remove the overlaid tracings, close the Overlay Section dialog box. Choosing Save on the File menu permanently saves the edit in the current atlas Topo array.

Simultaneously Align All Sections That have Corresponding Start Points (page 3-32) Manually Align Section Maps (page 3-33) Translate (Move) a Section Map (page 3-34) Rotate A Section Map (page 3-35) Color Editing Procedures (page 3-27) Section Alignment Procedures (page 3-32) The Line Editing Tools (page 3-24) Z-Axis Re-Distribution Procedures (page 3-37) Special Formatting Features (page 3-48) Other Atlas Shop Features (page 3-53)

Z-AXIS RE-DISTRIBUTION PROCEDURES

Problems with section distribution along the Z axis show up in the black Perspective panel. There are several different sources of Z-axis problems: Individual section maps may have the wrong Z Offset value. Some of the section maps may be conjoint (meaning that there is more than one section map in a topographic section). There may be unnatural gaps along the Z axis, because one of more physical tissue sections in the series was lost or damaged and could not be measured. There are one or more short vertical lines connecting the horizontal section lines in the black Perspective panel. (This sometime happens when a data point becomes misplaced during editing.) The following procedures address these problems.
TOPIC CONTENTS
Distribute Section Maps Evenly Along the Z-Axis (page 3-37) Change the Z Value of a Section Map (page 3-38) Z-Sort Topographic Sections (page 3-40) Dealing With Conjoint Sections (page 3-42) Duplicate A Section (page 3-45) Reposition Misplaced Points (page 3-47)
RELATED TOPICS
Color Editing Procedures (page 3-27) Section Alignment Procedures (page 3-32) Z-Axis Re-Distribution Procedures (page 3-37) Special Formatting Features (page 3-48) The Line Editing Tools (page 3-24) Other Atlas Shop Features (page 3-53)

DISTRIBUTE SECTION MAPS EVENLY ALONG THE Z-AXIS

If there is only one horizontal section line displayed in the Perspective panel, it means all topographic sections have the same Z-Value. If sections were originally taken at regular intervals from the physical tissue, but the section lines are unevenly spaced along the Z-axis, it means that incorrect Z-Values were assigned to one or more sections. If either of these is the case, do the following: BIOQUANT Topographer Handbook: 3D Modeling - Review & Optimize the 3D Data
Page 3-38
1. 2. On the Vertical Tool Bar, click the Change Z the Change Z dialog box. button (or from the Edit menu, choose Change Z) to open
On the Change Z dialog box, click to activate the Change All Sections radio button. The Change Z Dialog Box in Change All Sections Mode
3. 4. 5.
In the Z Offset Between Sections edit field, type in the micron distance that should separate one section from the next. The Z-Offset of First Section is usually kept at zero. Click the Apply button. Click the Close button. From the system File menu, choose Save.
RELATED TOPICS
Change the Z Value of a Section Map (page 3-38) Z-Sort Topographic Sections (page 3-40) Dealing With Conjoint Sections (page 3-42) Duplicate A Section (page 3-45) Reposition Misplaced Points (page 3-47) Color Editing Procedures (page 3-27) Section Alignment Procedures (page 3-32) Z-Axis Re-Distribution Procedures (page 3-37) Special Formatting Features (page 3-48) Other Atlas Shop Features (page 3-53)

CHANGE THE Z VALUE OF A SECTION MAP

Use this procedure to change the Z Offset Value of any one section. 1. Verify that Section Mode is active, then select the section for which the Z-Value is incorrect. If the desired section map cannot be selected independently because it is conjoined to the tracings of another section: See Dealing With Conjoint Sections on 3-42. Click the Change Z button (or from the Edit menu, choose Change Z) to open the Change Z dialog box. By default the Change Selected Section(s) radio button is active and the current Z-Value of the selected section is displayed in the Change All Z Values to edit field.
2.
Page 3-39
3.
Type the correct Z-Offset Value for this section into the Change All Z Values to edit field. With the Change Selected Sections radio button is active, Change All Z Values refers only to the selected sections. The value in the Raise/Lower All Z Values By field should remain 0. Click the Apply button, then the Close button. From the system File menu, choose Save. ATLAS: Tracings belonging to two (or more) physical sections are selected. PERSPECTIVE PANEL: Only one line is selected. (See illustration below, then perform the indicated corrective procedure.) Atlas With Tracings From 2 Physical Sections
4. 5. 6.
The GoTo Section dialog box shows that a conjoint set of section tracings exist in a single topographic section.
This indicates that the selected topographic section contains sets of tracings from two (or more) physical tissue sections and all of the tracings share a common Z-Value. CORRECTION: Perform the Separate Conjoint Sections procedure on (3-42). 7. Click the Select Next button (or click the next section in the GoTo Section list) to select the next topographic section in the series. Repeat from step 3 until all topographic sections in the atlas have been reviewed and Z-Values corrected if necessary.
IMPORTANT ADDITIONAL INFORMATION

8. Corrective procedures that include Internal Cut and Internal Paste alter the number of topographic sections in the atlas. Keep this fact in mind when reviewing sections after these types of edits are made. Use Z Sort to rearrange topographic sections in the Topo array in a logical, sequential order. Z-Sort Topographic Sections (page 3-40)

Distribute Section Maps Evenly Along the Z-Axis (page 3-37) Z-Sort Topographic Sections (page 3-40) Dealing With Conjoint Sections (page 3-42) Duplicate A Section (page 3-45) Reposition Misplaced Points (page 3-47) Color Editing Procedures (page 3-27) Section Alignment Procedures (page 3-32) Z-Axis Re-Distribution Procedures (page 3-37) Special Formatting Features (page 3-48) Other Atlas Shop Features (page 3-53)

Z-SORT TOPOGRAPHIC SECTIONS

The system numbers topographic sections according to their order in the Topo array. If physical sections were measured out or order, or if section maps have been copied and pasted during the editing process, topographic sections will not be arranged in a logical, sequential order and this can cause considerable confusion during the section by section review. The confusion can be eliminated by using Z Sort, which rearranges all topographic sections in the Topo array according to their assigned Z Values. If sections were measured out of order, Z Sort should be used before the section by section review begins. It should also be used any time Z Values are changed.
PROCEDURE
1. From the Edit menu, choose Z Sort. A message box will open to inform you that the Z sorted atlas must be saved to a new array, and asks if you want to add a new array. Do one of the following: On the message box, click YES if you want the system to automatically add a Topo array named Z Sorted Topo. This default name cannot be changed. When YES is clicked, the message box will disappear and the Sort Sections by Z Value dialog box will open with the automatically added Z Sorted Topo selected in the Destination Array field. On the message box, click NO if you prefer to add a new Topo array with a different name or you would like to use an empty Topo array that already exists in the data set. When NO is clicked, the message box will disappear and the Sort Sections by Z Value dialog box will open with the last Topo array in the data set selected in the Destination Array field. NOTE 1: The Destination Array must be empty (must have no values). NOTE 2: If the last Topo array in the data set is empty and you do not object to its current name, it may be retained as the Destination Array. NOTE 3: If a different, empty Topo array exists in the data set, it may be selected from the Destination Array fields drop list (by clicking the down-arrow drop list). Sort Sections by Z Value dialog box button in that field to open the
If the Topo array that is currently designated in the Destination Array field is not suitable (if it already contains data or if you do not like its name), do the following:
Page 3-41
i. On the Sort Sections by Z Values dialog box, click the New Array button to open the New Array dialog box. In the Array Name field, type in the desired name for the new Topo array. Click the OK button to close the New Array box. In the Z Sort Options area of the Sort Sections by Z Value dialog box, click to choose either the Ascending or Descending radio button. Ascending places Section 0 at the bottom of the atlas. Descending places Section 0 at the top of the atlas. Click the Apply button to record the edited version of the atlas into the array that is specified in the Destination Array field.
ii.
iii.
iv. Click Close. In order to continue the atlas review (using the atlas in its new, Z-sorted state), you must take the following steps. 2. From the File menu, choose Exit Atlas Shop. If a Save Data message appears, it means that edits other than Z-Sort (which has already been saved) were made to the atlas and those changes have not yet been saved. Do one of the following. On the Save Data message, click YES if all of the unsaved changes to the atlas were meant to be saved. When the YES button is clicked, any unsaved changes that were made either before or after Z-Sort was performed, will be saved to both the currently open atlas array (which is not sorted by Z-Values) and to the newly added Z-Sorted atlas array. The Atlas Shop closes and the Atlas Viewer opens. On the Save Data message, click NO if the unsaved changes to the atlas were not meant to be saved. When the NO button is clicked, the Atlas Shop closes and the Atlas Viewer opens.
3.
In the Atlas Viewer, do the following: a. From the Select Arrays dialog boxs Select menu, choose Unselect All Arrays (to deselect the original atlas array). Alternately, in the Selected column, double-click the array index to remove it from the Selected list. In the Available Arrays list, scroll to and double-click to select the array that holds the Z Sorted version of the atlas. Click the Redraw Click the Atlas Shop button (to update the Atlas Window with the new version in the atlas). button to re-open the Atlas Shop.
b. c. d. 4.
In the Atlas Shop, click the Resize to Fit button. If appropriate, return to the Section By Section Review (3-7).
RELATED TOPICS
Distribute Section Maps Evenly Along the Z-Axis (page 3-37) Change the Z Value of a Section Map (page 3-38) Dealing With Conjoint Sections (page 3-42) Duplicate A Section (page 3-45) Reposition Misplaced Points (page 3-47) Color Editing Procedures (page 3-27) Section Alignment Procedures (page 3-32) Z-Axis Re-Distribution Procedures (page 3-37) Special Formatting Features (page 3-48) Other Atlas Shop Features (page 3-53)

Page 3-42
DEALING WITH CONJOINT SECTIONS

The maps of two (or more) physical tissue sections will show up as one topographic section in the atlas, when the user forgot to put a landmark on one (or more) of the sections during measurement. This is a problem only if the conjoined section maps have the same Z Offset Value and/or if one of the maps needs to be rotated or moved independently to improve its alignment with other maps. There are two ways to deal with conjoint sections that need editing: Select and cut the tracings that belong to one physical section, and paste them to create new topographic sections that can be independently selected in Section Mode. Create New Topographic Sections (page 3-42) Perform any needed edits for the conjoint sections by selecting their individual tracings in Object Mode. Use the following procedures as needed: Possible Color Problems (page 3-8) Possible Alignment Problems (page 3-9) Possible Z-Axis Spacing Problems (page 3-9)
REMINDER
If each conjoint section has the correct Z Offset value (appears in its proper place on the Z axis) and none need to be independently moved or rotated, the conjoint sections do not need to be separated.
RELATED TOPICS
Distribute Section Maps Evenly Along the Z-Axis (page 3-37) Change the Z Value of a Section Map (page 3-38) Z-Sort Topographic Sections (page 3-40) Duplicate A Section (page 3-45) Reposition Misplaced Points (page 3-47) Color Editing Procedures (page 3-27) Section Alignment Procedures (page 3-32) Z-Axis Re-Distribution Procedures (page 3-37) Special Formatting Features (page 3-48) Other Atlas Shop Features (page 3-53)

CREATE NEW TOPOGRAPHIC SECTIONS

PROCEDURE
1. 1. 2. In Section Mode , select the conjoint section maps.
From the View menu, choose Selection Only. This will remove all but the conjoint section tracings from the work space. If the GoTo Section dialog box is not already open, from the Select menu, choose GoTo. If necessary, reposition the GoTo Section dialog box over the Perspective panel to keep from obscuring the tracings in the atlas.
Page 3-43
GoTo Section Dialog Box
Tracings from two different physical tissue sections residing in the one topographic section that is selected in the GoTo Section dialog box
3.
Click the Object Mode button on the system tool bar. The GoTo Section dialog box changes to GoTo Object. The very first object, belonging to the first set of physical tissue section tracings, will be automatically selected. GoTo Object Dialog Box With One Object Selected
Here, the first tracing (object) that was recorded in the topographic section, was the contour outline of the physical tissue section that received the Landmark.
4.
In the GoTo Object list, beginning with the object just below the initially selected one, click to momentarily select each successive object in the list until the first tracing from the second physical section is located (and selected). With the first tracing from the second physical section highlighted, press and hold the Control (Ctrl) key on the keyboard, then in the GoTo Object list, continue to click successive objects until all of the tracings (objects) that belong to the second physical section are selected.
5.
Page 3-44
GoTo Object Dialog Box With Three Objects Selected
6.
Choose Internal Cut from the Edit menu. A Warning box will open to remind you that the altered atlas must be saved to a new array. Click OK to acknowledge the warning and cut the selected tracings(s) from the displayed atlas. (Clicking Cancel will cancel the Internal Cut command.) Choose Internal Paste from the Edit menu. A message box appears to let you know that each cut element (tracing) will ultimately be pasted as a new topographic section in the last array in the data set. Click OK to acknowledge the notice. At this point the pasted tracings are actually being held in a system buffer. A new Topo array will be added to the data set in step 9. From the Edit menu, choose Z Sort. A Warning box will open to inform you that the Z sorted atlas must be saved to a new array, and asks if you want to add a new array. Click the YES button to open the Sort Sections By Z Value dialog box. On the Sort Sections By Z Value dialog box, do the following: a. b. a. b. Click the New Array button to add a new Topo array to the end of the data set array list. In the Z Sort Options area, click to choose the Ascending or Descending radio button. (Usually ascending) Click the Apply button to record the edited version of the atlas to the new array, in the Destination Array field. Click Close on the Z-Sort dialog box.
7.
8.
9.
10.
In order to display or continue editing the changed version of the atlas, you must do the following: a. b. c. d. From the File menu, choose Exit Atlas Shop. A Save Data message will appear. On the Save Data message, click NO (since the changed version of the atlas has already been saved). The Atlas Shop closes and the Atlas Viewer reopens. In the Atlas Viewer, on the Select Arrays dialog box, deselect the original atlas array(s) and select the Topo array that holds the revised version of the atlas. To display the revised version of the atlas, click Redraw section by section review, click the Atlas Shop on the system tool bar, and to continue the
button to reopen the Atlas Shop.
11.
In the Atlas Shop, click the Resize to Fit button. At this point, the new topographic sections created by Internal Paste will still exist at the original Z-Offset position. In Section Mode , select one of the new topographic sections that was created when Internal Paste was used. One new topographic section was created for each tracing that was cut from the conjoint section.
12.
Page 3-45
13. 14. 15. On the Vertical Tool Bar, click the Change Z the Change Z dialog box. button (or from the Edit menu, choose Change Z) to open
The current Z-Value of the selected section will be displayed in the Change All Z-Values To field. On the Change Z dialog box, verify that the Change Selected Sections radio button is active.
16.
In the Change All Z Values to field, type in the Z-Value (Z-Offset Value) that should have been assigned to the physical section from which the displayed tracing was taken. The value in the Raise/Lower All Z Values By field should remain 0. Click the Apply button. Repeat from step 12 for any additional new topographic sections that were created when Internal Paste was used. Use Z Sort to rearrange topographic sections in the Topo array in a logical, sequential order. Z-Sort Topographic Sections (page 3-40) From the File menu, choose Save.
17. 18. 19. 20.
RELATED TOPICS
Possible Color Problems (page 3-8) Possible Alignment Problems (page 3-9) Possible Z-Axis Spacing Problems (page 3-9) Distribute Section Maps Evenly Along the Z-Axis (page 3-37) Change the Z Value of a Section Map (page 3-38) Z-Sort Topographic Sections (page 3-40) Dealing With Conjoint Sections (page 3-42) Duplicate A Section (page 3-45) Reposition Misplaced Points (page 3-47) Color Editing Procedures (page 3-27) Section Alignment Procedures (page 3-32) Z-Axis Re-Distribution Procedures (page 3-37) Special Formatting Features (page 3-48) Other Atlas Shop Features (page 3-53)

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

REPOSITION MISPLACED POINTS

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

Page 3-48
SPECIAL FORMATTING FEATURES

Particular editing and formatting tools in the Topographers Atlas Shop help improve the quality of a surface rendered model. The following procedures are all done in the Atlas Shop. After editing is finished, the edited atlas is opened again in the Atlas Modeler. If corrective edits, such as aligning sections and correcting errors in Z positioning, are needed, it is best that these be done prior to adding special surface rendering formats.
COMMON ADJUSTMENTS THAT ENHANCE SURFACE RENDERING

Change Resolution - The resolution (number of data points) in large atlases may be decreased to increase the speed at which a model is rendered or to produce a smoother surface. (3-48) Cap Object - The first and last contour tracings in an atlas can be marked as caps that will cover the open ends of a surface rendered model. (3-51) End of Object/Leave Open - A number of tracings in the atlas may be marked as open to create a transparent window in a surface rendered model, through which interior objects may be viewed, without reducing the opacity of the entire model. (3-51) Middle of Object - The cap or open markers on a tracing may be removed to return the tracing to its original Middle of Object default status. (3-52)
RELATED TOPICS
Possible Color Problems (page 3-8) Possible Alignment Problems (page 3-9) Possible Z-Axis Spacing Problems (page 3-9) Distribute Section Maps Evenly Along the Z-Axis (page 3-37) Change the Z Value of a Section Map (page 3-38) Z-Sort Topographic Sections (page 3-40) Dealing With Conjoint Sections (page 3-42) Duplicate A Section (page 3-45) Reposition Misplaced Points (page 3-47) Color Editing Procedures (page 3-27) Section Alignment Procedures (page 3-32) Z-Axis Re-Distribution Procedures (page 3-37) Other Atlas Shop Features (page 3-53)

REDUCE ATLAS RESOLUTION

When the atlas is displayed in the Atlas Modeler, if it takes a long time to render the surface or redraw the model after it has been moved in the Model Window, the resolution of the entire atlas or at least the resolution of the surface tracings should be reduced. CAUTION: Do not attempt to change the resolution of an entire atlas at one time. To do so will most likely corrupt the data, especially in larger atlases. When resolution is changed, the edited version of the atlas must be saved to a new Topo array. The original resolution was set by the smoothing limit in BIOQUANT Life Science or BIOQUANT OSTEO (the lower the Smoothing Limit the higher the resolution).
PROCEDURE:
1. Select a limited number of objects(s) (e.g. all section outlines) for which the resolution needs to be changed. Hint: If all section outlines (or other objects of interest) are of the same unique color, these may be selected quickly using Select by Color. See Assign a New Color to a Group of Objects on 3-28.
Page 3-49
2. Choose Resolution from the Edit menu to open the Set Image Resolution dialog box. When asked if you want to add a new Topo array, click Yes, unless you think the data set already contains an empty Topo array that can be used. Set Image Resolution
3.
On the Set Image Resolution dialog box, if a new Topo array was added in step 2, it will already be selected in the Destination Array field. Otherwise, click the down arrow in the Destination Array field and click to choose the desired empty Topo array from the drop list. If there is not an empty Topo array, do the following: a. b. c. Click the Add Topo button. The New Array dialog box opens. In the Array Name field, edit the name of the Topo array to indicate that this is a lower resolution version of the atlas. Click the OK button to close the New Array dialog box.
4. 5.
In the Resolution Distance field, increase the micron value between data points (to decrease the resolution), by doubling or tripling the initial default value in the Resolution Distance field. Click the Apply button to generate the lower resolution atlas in the selected Topo array. A warning will appear to remind you that any data in the selected array will be overwritten. Verify that the intended Destination Array is selected, then click OK. IMPORTANT: If a single Smoothing Limit was not maintained during data collection for the selected outlines, read the following carefully, then, if it seems necessary, repeat steps 4 and 5. a. b. The initial default value in the Resolution Distance field is the minimum distance the system found between any two data points in the selected portion of the atlas. The change in resolution, (the new micron distance) is only applied between pairs of data points in the selected outlines, for which the original distance matched the minimum (initial) value in the Resolution Distance field. If a single smoothing limit was maintained during measurement, the distance between all data points will match the minimum value, and all will be increased simultaneously to the new value. (Excess data points are discarded to maintain the original size of the tracings). In this case, simply doubling or tripling the default Resolution Distance and clicking the Apply button once, is usually enough to produce the desired effect. However, if the smoothing limit was changed during data collection, the number of data set pairs that are separated by the minimum distance may be small. In this case, it may be necessary to repeat steps 4 and 5 several times before the desired effect would be apparent in a surface rendered model.
c.
d.
6. 7.
Click the Close button to close the Set Image Resolution dialog box. To display or edit the new resolution atlas, exit the Atlas Shop. In the Atlas Viewer, on the Select Arrays dialog box, remove the original Topo arrays from the Selected list, and select the Topo array that contains the lower resolution version of the atlas. The lower resolution atlas is now ready to be displayed in the Atlas Viewer, Atlas Modeler, or Atlas Shop.

Reduce Atlas Resolution (page 3-48) Format Contour Lines (page 3-50) Possible Color Problems (page 3-8) Possible Alignment Problems (page 3-9) Possible Z-Axis Spacing Problems (page 3-9) Distribute Section Maps Evenly Along the Z-Axis (page 3-37) Change the Z Value of a Section Map (page 3-38) Z-Sort Topographic Sections (page 3-40) Dealing With Conjoint Sections (page 3-42) Duplicate A Section (page 3-45) Reposition Misplaced Points (page 3-47) Color Editing Procedures (page 3-27) Section Alignment Procedures (page 3-32) Z-Axis Re-Distribution Procedures (page 3-37) Other Atlas Shop Features (page 3-53)

FORMAT CONTOUR LINES

The Cap Object , End of Object/Leave Open , and Middle of Object special formatting to an atlas that is to be surface rendered. Surface Render Formatting Tools buttons on the system tool bar add
TOPIC CONTENTS
Cap Open Ends of A Model (page 3-51) Define a Transparent Window in a Model (page 3-51) Restore Middle of Object Status (page 3-52)
RELATED TOPICS
Reduce Atlas Resolution (page 3-48) Possible Color Problems (page 3-8) Possible Alignment Problems (page 3-9) Possible Z-Axis Spacing Problems (page 3-9) Distribute Section Maps Evenly Along the Z-Axis (page 3-37) Change the Z Value of a Section Map (page 3-38) Z-Sort Topographic Sections (page 3-40) Dealing With Conjoint Sections (page 3-42) Duplicate A Section (page 3-45) Reposition Misplaced Points (page 3-47) Color Editing Procedures (page 3-27) Section Alignment Procedures (page 3-32) Z-Axis Re-Distribution Procedures (page 3-37) Other Atlas Shop Features (page 3-53)

Page 3-51
CAP OPEN ENDS OF A MODEL

The Cap Object tool is used to tag the first and last outlines in the model as surface rendering caps. An outline that is tagged as a cap will automatically fill with the surface color when the atlas is opened in the Atlas Modeler. Because surface rendering connects points of the same color on adjacent surface defining outlines (usually section outlines), and there is no outline before the first tracing or after the last, the rendered surface stops abruptly, leaving open holes at the top and bottom of the rendered model. These holes may be closed using the Cap Object tool in the Atlas Shop.
PROCEDURE
1. 2. 3. 4. 5. 6. Click the Section Mode button on the system tool bar to activate Section Mode.
Select the topographic section that contains the first or last surface defining outline for the model. NOTE: For the bottom cap this is usually, but not always, Section 0. Click the Object Mode button to activate Object Mode.
If necessary, use the Select Next button on the system toolbar to cycle through the objects in the selected section, until the correct contour outline is selected. Click the Cap Object button on the system toolbar to mark the selected tracing as a "cap".
Repeat steps 1 through 5 to mark (as a cap) the tracing at the opposite end of the model.
RELATED PROCEDURE
Middle of Object - The cap or open markers on a tracing may be removed to return the tracing to its original Middle of Object default status. (3-52)
RELATED TOPICS
Define a Transparent Window in a Model (page 3-51) Restore Middle of Object Status (page 3-52) Reduce Atlas Resolution (page 3-48) Format Contour Lines (page 3-50) Reduce Atlas Resolution (page 3-48) Possible Color Problems (page 3-8) Possible Alignment Problems (page 3-9) Possible Z-Axis Spacing Problems (page 3-9) Distribute Section Maps Evenly Along the Z-Axis (page 3-37) Change the Z Value of a Section Map (page 3-38) Z-Sort Topographic Sections (page 3-40) Dealing With Conjoint Sections (page 3-42) Duplicate A Section (page 3-45) Reposition Misplaced Points (page 3-47) Color Editing Procedures (page 3-27) Section Alignment Procedures (page 3-32) Z-Axis Re-Distribution Procedures (page 3-37) Other Atlas Shop Features (page 3-53)

DEFINE A TRANSPARENT WINDOW IN A MODEL

The End of Object/Leave Open tool in the Atlas Shop makes it possible to create a limited transparent window in a surface rendered model, through which interior objects may be viewed, without reducing the opacity of the entire BIOQUANT Topographer Handbook: 3D Modeling - Review & Optimize the 3D Data
Page 3-52
model. The End of Object/Leave Open tool is used to mark a series of surface defining outlines that are to be left open. When the atlas is opened in the Atlas Modeler, all but the first and last outlines marked Leave Open will automatically be constructed as a transparent window. The very first and last outlines in a marked series, serve as End of Object markers that allow the system to recognize the intervening outlines as a separate object, even though the color of the open lines is identical to the rest of the surface.
PROCEDURE
1. 2. 3. 4. 5. 6. Click the Section Mode button on the system tool bar to activate Section Mode.
Select the topographic section that contains the first (or next) outline that is to be marked with Leave Open. Click the Object Mode button to activate Object Mode.
If necessary, use the Select Next button on the system tool bar to cycle through the objects in the selected section, until only the correct contour outline is selected. Click the End of Object/Leave Open "Leave Open". tool button on the system tool bar to mark the selected tracing as
Repeat steps 1 through 5 to mark (as Leave Open) all the tracings that are to be part of the transparent window.
RELATED TOPICS
Cap Open Ends of A Model (page 3-51) Restore Middle of Object Status (page 3-52) Reduce Atlas Resolution (page 3-48) Format Contour Lines (page 3-50) Reduce Atlas Resolution (page 3-48) Possible Color Problems (page 3-8) Possible Alignment Problems (page 3-9) Possible Z-Axis Spacing Problems (page 3-9) Distribute Section Maps Evenly Along the Z-Axis (page 3-37) Change the Z Value of a Section Map (page 3-38) Z-Sort Topographic Sections (page 3-40) Dealing With Conjoint Sections (page 3-42) Duplicate A Section (page 3-45) Reposition Misplaced Points (page 3-47) Color Editing Procedures (page 3-27) Section Alignment Procedures (page 3-32) Z-Axis Re-Distribution Procedures (page 3-37) Other Atlas Shop Features (page 3-53)

RESTORE MIDDLE OF OBJECT STATUS

The "cap" or "open" markers on a tracing may be removed to return a tracing to its original "Middle of Object" default status. Before special formatting is added, all tracings in an atlas are termed Middle of Object. The Middle of Object tool on the system tool bar removes the special formatting that was applied to a tracing using the Cap Object or End of Object/Leave Open tools
Page 3-53 PROCEDURE

1. 2. 3. 4. 5. Click the Section Mode button on the system tool bar to activate Section Mode.
Select the topographic section that contains the outline for which the Cap or End of Object/Leave Open formatting is to be removed. Click the Object Mode button to activate Object Mode.
If necessary, use the Select Next button on the system tool bar to cycle through the objects in the selected section, until only the specially formatted outline is selected. Click the Middle of Object button on the system toolbar to remove the special formatting and restore the tracings default Middle of Object status.
RELATED TOPICS
Cap Open Ends of A Model (page 3-51) Define a Transparent Window in a Model (page 3-51) Reduce Atlas Resolution (page 3-48) Format Contour Lines (page 3-50) Reduce Atlas Resolution (page 3-48) Possible Color Problems (page 3-8) Possible Alignment Problems (page 3-9) Possible Z-Axis Spacing Problems (page 3-9) Distribute Section Maps Evenly Along the Z-Axis (page 3-37) Change the Z Value of a Section Map (page 3-38) Z-Sort Topographic Sections (page 3-40) Dealing With Conjoint Sections (page 3-42) Duplicate A Section (page 3-45) Reposition Misplaced Points (page 3-47) Color Editing Procedures (page 3-27) Section Alignment Procedures (page 3-32) Z-Axis Re-Distribution Procedures (page 3-37) Other Atlas Shop Features (page 3-53)

OTHER ATLAS SHOP FEATURES

Following are Atlas Shop procedures that were not covered above.
TOPIC CONTENTS
Numeric Transform (page 3-54) The Line Editing Tools (page 3-24) Special Atlas Shop FEatures (page 3-58)

Possible Color Problems (page 3-8) Possible Alignment Problems (page 3-9) Possible Z-Axis Spacing Problems (page 3-9) Distribute Section Maps Evenly Along the Z-Axis (page 3-37) Change the Z Value of a Section Map (page 3-38) Z-Sort Topographic Sections (page 3-40) Dealing With Conjoint Sections (page 3-42) Duplicate A Section (page 3-45) Reposition Misplaced Points (page 3-47) Color Editing Procedures (page 3-27) Section Alignment Procedures (page 3-32) Z-Axis Re-Distribution Procedures (page 3-37) Other Atlas Shop Features (page 3-53)

NUMERIC TRANSFORM
Numeric Transform translates, rotates, or resizes the selected parts of the atlas by a known amount. The Numeric Transform dialog box is opened by choosing Numeric Transform from the Edit menu.
PROCEDURE: SETUP
1. 2. Select the section(s) or objects(s) or point(s) of interest. From the Atlas Shop Edit menu, choose Numeric Transform to open the Numeric Transform dialog box. Numeric Transform Dialog Box
TOPIC CONTENTS
Translate by Numeric Transform (page 3-55) Resize by Numeric Transform (page 3-56) Rotate by Numeric Transform (page 3-57)

The Line Editing Tools (page 3-24) Special Atlas Shop FEatures (page 3-58) Possible Color Problems (page 3-8) Possible Alignment Problems (page 3-9) Possible Z-Axis Spacing Problems (page 3-9) Distribute Section Maps Evenly Along the Z-Axis (page 3-37) Change the Z Value of a Section Map (page 3-38) Z-Sort Topographic Sections (page 3-40) Dealing With Conjoint Sections (page 3-42) Duplicate A Section (page 3-45) Reposition Misplaced Points (page 3-47) Color Editing Procedures (page 3-27) Section Alignment Procedures (page 3-32) Z-Axis Re-Distribution Procedures (page 3-37) Other Atlas Shop Features (page 3-53)

TRANSLATE BY NUMERIC TRANSFORM

PROCEDURE
1. 2. On the Numeric Transform dialog box, click to check the Translate check box. Decide whether or not the Relative check box should be checked.: If Relative is checked, the values that are typed into the X and Y fields designate the micron distance that the selection is to be moved relative to its current position in the atlas. If Relative is not checked, the values that are typed into the X and Y fields designate actual X and Y coordinates to which the first point in the selection is to be moved. (All other points in the selection will be moved to maintain their positional relationship to the first point.)
If Relative is checked, to move the selected item(s) Right: In the X field, enter a positive micron distance (the selection will be moved this distance to the right). Left: In the X field, enter a negative micron distance (the selection will be moved this distance to the left). Down: In the Y field, enter a positive micron distance (the selection will be moved this distance downwards). Up: In the Y field, enter a negative micron distance (the selection will be moved this distance upwards.
If Relative is not checked, to move the first point of the first object in the selection to a specific XY location a. b. In the X field, type the positive or negative X coordinate to which the first point in the first object should be moved. In the Y field, type the positive or negative Y coordinate to which the first point in the first object should be moved. Helpful Hint: As expected, the atlas landmark always occupies the XYZ(0,0,0 Offset) position of the current coordinate system. However, it should be noted that the XY plane of the coordinate system used by the Windows operating system is unconventional. The X and Y signs (x,y) in the various quadrants are given below: Lower Right Quadrant (+ , +) BIOQUANT Topographer Handbook: 3D Modeling - Review & Optimize the 3D Data
Page 3-56
3. Upper Left Quadrant (- , -) Lower Left Quadrant (- , +) Upper Right Quadrant (+ , -)
Click the Apply button.
SAVING THE NUMERIC TRANSFORM EDIT

After Numeric Transform is used, if the atlas is saved using Save on the File menu, or by responding YES to the Save Data message when exiting the Atlas Shop, the data in the current atlas Topo array(s) are permanently changed. If desirable, Save As on the File menu may be used instead, to save the edited version of the atlas to a new Topo array.
RELATED TOPICS
Numeric Transform (page 3-54) Resize by Numeric Transform (page 3-56) Rotate by Numeric Transform (page 3-57) The Line Editing Tools (page 3-24) Special Atlas Shop FEatures (page 3-58) Possible Color Problems (page 3-8) Possible Alignment Problems (page 3-9) Possible Z-Axis Spacing Problems (page 3-9) Distribute Section Maps Evenly Along the Z-Axis (page 3-37) Change the Z Value of a Section Map (page 3-38) Z-Sort Topographic Sections (page 3-40) Dealing With Conjoint Sections (page 3-42) Duplicate A Section (page 3-45) Reposition Misplaced Points (page 3-47) Color Editing Procedures (page 3-27) Section Alignment Procedures (page 3-32) Z-Axis Re-Distribution Procedures (page 3-37) Other Atlas Shop Features (page 3-53)

RESIZE BY NUMERIC TRANSFORM

PROCEDURE
1. 2. On the Numeric Transform dialog box, click to check the Resize check box. The current size of the selection is designated 100%. If the Maintain Aspect Ratio check box is checked, when a value is entered in either the Height or Width field, the other field automatically updates to the same value. If it is unchecked, Height and Width resizing are independent of each other. If desirable, click to uncheck the Maintain Aspect Ratio check box. To increase the size of the selected item(s), in the Width or/and Height field(s) type a percentage value that is greater than 100. To decrease the size of the selected item(s), in the Width or/and Height field(s) enter a percentage value that is less than 100. Click the Apply button. The selected item(s) are shown at the new size in the Atlas Window. NOTE: If subsequent resizing is done, the new size just applied is now the current size and is considered the 100% value for the selected item(s).
3.
Page 3-57 SAVING THE NUMERIC TRANSFORM EDIT

RELATED TOPICS
Numeric Transform (page 3-54) Translate by Numeric Transform (page 3-55) Rotate by Numeric Transform (page 3-57) The Line Editing Tools (page 3-24) Special Atlas Shop FEatures (page 3-58) Possible Color Problems (page 3-8) Possible Alignment Problems (page 3-9) Possible Z-Axis Spacing Problems (page 3-9) Distribute Section Maps Evenly Along the Z-Axis (page 3-37) Change the Z Value of a Section Map (page 3-38) Z-Sort Topographic Sections (page 3-40) Dealing With Conjoint Sections (page 3-42) Duplicate A Section (page 3-45) Reposition Misplaced Points (page 3-47) Color Editing Procedures (page 3-27) Section Alignment Procedures (page 3-32) Z-Axis Re-Distribution Procedures (page 3-37) Other Atlas Shop Features (page 3-53)

ROTATE BY NUMERIC TRANSFORM

PROCEDURE
1. 2. On the Numeric Transform dialog box, click to check the Rotate check box. To rotate clockwise, in the Angle field type the number of degrees the selected item(s) should be rotated. To rotate counter-clockwise, in the Angle field type the negative number of degrees the selected item(s) should be rotated. Click the Apply button.
SAVING THE NUMERIC TRANSFORM EDIT


Numeric Transform (page 3-54) Resize by Numeric Transform (page 3-56) Translate by Numeric Transform (page 3-55) The Line Editing Tools (page 3-24) Special Atlas Shop FEatures (page 3-58) Possible Color Problems (page 3-8) Possible Alignment Problems (page 3-9) Possible Z-Axis Spacing Problems (page 3-9) Distribute Section Maps Evenly Along the Z-Axis (page 3-37) Change the Z Value of a Section Map (page 3-38) Z-Sort Topographic Sections (page 3-40) Dealing With Conjoint Sections (page 3-42) Duplicate A Section (page 3-45) Reposition Misplaced Points (page 3-47) Color Editing Procedures (page 3-27) Section Alignment Procedures (page 3-32) Z-Axis Re-Distribution Procedures (page 3-37) Other Atlas Shop Features (page 3-53)

SPECIAL ATLAS SHOP FEATURES

There are three special Atlas Shop features that are not covered in this section: Taking Measurements From the Atlas, Planar Conversion, and Contour Conversion. These are briefly described below, and discussed detail in Section 8: The Atlas Viewer in Detail (page 5-1)
RELATED TOPICS
Title Bar and Tool Bars (page 3-13) Save Versus Save As (page 3-13) The Three Selection Modes (page 3-14) The Selection Methods (page 3-15) Possible Color Problems (page 3-8) Possible Alignment Problems (page 3-9) Possible Z-Axis Spacing Problems (page 3-9) Distribute Section Maps Evenly Along the Z-Axis (page 3-37) Change the Z Value of a Section Map (page 3-38) Z-Sort Topographic Sections (page 3-40) Dealing With Conjoint Sections (page 3-42) Duplicate A Section (page 3-45) Reposition Misplaced Points (page 3-47) Color Editing Procedures (page 3-27) Section Alignment Procedures (page 3-32) Z-Axis Re-Distribution Procedures (page 3-37) Other Atlas Shop Features (page 3-53) Numeric Transform (page 3-54) Special Atlas Shop FEatures (page 3-58)

Page 3-60
3D Modeling: 3D Modeling: Surface RendSurface ing in the Atlas Modeler Rending in the The default surface rendering of an atlas may be Atlas Modeler
BIOQUANT Topographer Handbook modified to enhance the final three dimensional model. The rotating model can be recorded in an AVI movie.
Introduction to the Atlas Modeler (page 4-2) Changing the Characteristics of the Model (page 4-7) Activating Continuous Rotation (page 4-11) Record or Play an AVI Movie (page 4-14) Saving and Loading a Surface Rendering Parameters File (page 4-17) Special Formatting Options (page 4-19) Printing, Saving, and Copying the Model (page 4-21) Exiting Atlas Modeler (page 4-25)
Page 4-2
INTRODUCTION TO THE ATLAS MODELER

The Atlas Modelers Toolbar
This sections is an introduction to the Atlas Modeler, the surface rending environment of the Topographer plug-in. In the Atlas model, the view can be changed from modeled, to wire frame, to points. The model can be zoomed in or out, panned, or rotated. The lighting and opacity can be changed. The model can be set to auto rotate and recorded as an AVI movie. Once settings have been refined, they can be saved as a Parameters file that can be reloaded upon returning to the Atlas Modeler for this model for quick retrieval.
TOPIC CONTENTS
Available Surface Types (page 4-2) Smoothing (page 4-3) Render Option 2 (page 4-4) Manipulating the Model (page 4-4) Using Ideal Test Forms (page 4-6)
RELATED TOPICS
Introduction to the Atlas Modeler (page 4-2) Changing the Characteristics of the Model (page 4-7) Activating Continuous Rotation (page 4-11) Record or Play an AVI Movie (page 4-14) Saving and Loading a Surface Rendering Parameters File (page 4-17) Special Formatting Options (page 4-19) Printing, Saving, and Copying the Model (page 4-21) Exiting Atlas Modeler (page 4-25)
AVAILABLE SURFACE TYPES

VIEW> SOLID
To display the surfaces of the rendered model as solid, click the Show Surface as Filled bar or choose Solid from the View menu. Surfaces Shown As Filled button on the tool
VIEW> WIRE FRAME

To display the surface as a series of lines, click the Show Surface as Lines choose Wireframe from the View menu. button on the tool bar or
BIOQUANT Topographer Handbook: 3D Modeling: Surface Rending in the Atlas Modeler
Page 4-3
Surfaces Shown As Lines
VIEW> POINTS
To display the surface as a series of dots, click the Show Surface as Points choose Points from the View menu. Surfaces Show As Points button on the tool bar or
RELATED TOPICS
Smoothing (page 4-3) Render Option 2 (page 4-4) Manipulating the Model (page 4-4) Using Ideal Test Forms (page 4-6) Introduction to the Atlas Modeler (page 4-2) Changing the Characteristics of the Model (page 4-7) Activating Continuous Rotation (page 4-11) Record or Play an AVI Movie (page 4-14) Saving and Loading a Surface Rendering Parameters File (page 4-17) Special Formatting Options (page 4-19) Printing, Saving, and Copying the Model (page 4-21) Exiting Atlas Modeler (page 4-25)
SMOOTHING
The Atlas Modeler's rendering algorithm produces a matt finish on the model. The Smoothing option modifies the BIOQUANT Topographer Handbook: 3D Modeling: Surface Rending in the Atlas Modeler
Page 4-4
surface to appear glossy.
PROCEDURE
1. 2. To show a glossier surface, click to check Smoothing on the Options menu. To remove the smoothing format, click to un-check Smoothing on the Options menu.
RELATED TOPICS
Available Surface Types (page 4-2) Render Option 2 (page 4-4) Manipulating the Model (page 4-4) Using Ideal Test Forms (page 4-6) Introduction to the Atlas Modeler (page 4-2) Changing the Characteristics of the Model (page 4-7) Activating Continuous Rotation (page 4-11) Record or Play an AVI Movie (page 4-14) Saving and Loading a Surface Rendering Parameters File (page 4-17) Special Formatting Options (page 4-19) Printing, Saving, and Copying the Model (page 4-21) Exiting Atlas Modeler (page 4-25)
RENDER OPTION 2
The Atlas Modelers primary rendering algorithm usually produces the most pleasing display. Render Option 2 uses a different algorithm that can sometimes render more accurately a specimen that includes one or more folded or accordion type structures.
PROCEDURE
To apply Render Option 2, click to check this option on the Options menu. To re-apply the primary rendering algorithm, click to uncheck Rendering Option 2 on the Options menu.
RELATED TOPICS
Available Surface Types (page 4-2) Smoothing (page 4-3) Manipulating the Model (page 4-4) Using Ideal Test Forms (page 4-6) Introduction to the Atlas Modeler (page 4-2) Changing the Characteristics of the Model (page 4-7) Activating Continuous Rotation (page 4-11) Record or Play an AVI Movie (page 4-14) Saving and Loading a Surface Rendering Parameters File (page 4-17) Special Formatting Options (page 4-19) Printing, Saving, and Copying the Model (page 4-21) Exiting Atlas Modeler (page 4-25)
MANIPULATING THE MODEL

VIEW> SCALE IMAGE
The size of the surface rendered model may be scaled up or down. 1. 2. 3. On the tool bar, click the Scale Image button.
To increase the size of the atlas, with the cursor anywhere in the image window, click and drag the cursor straight upwards on the screen. To decrease the size of the atlas, with the cursor anywhere in the image window, click and drag the cursor straight downwards on the screen.
Page 4-5 VIEW> PAN IMAGE

The surface rendered model may be moved around on the Atlas Modelers desktop. 1. 2. On the tool bar, click the Pan button.
With the cursor over the atlas, click and drag the cursor (and the atlas) to the desired location.
VIEW> ROTATE IMAGE

The perspective of the surface rendered model may be changed by rotating it in small increments using the arrow keys on the keyboard or by clicking and dragging the cursor in the model window. If Rotate and Auto Rotate are both active when the click and drag method is used, the model will continue to rotate in the indicated direction until the Auto Rotate button is released.
OPTION 1: ROTATE THE MODEL USING THE ARROW KEYS

1. 2. 3. Click the Rotate button on the tool bar, or choose Rotate from the View menu.
Use the right and left arrow keys to incrementally rotate the model clockwise and counter-clockwise respectively around the Z axis. Use the up and down arrow keys to incrementally rotate the model clockwise and counter-clockwise respectively around the X axis.
HELPFUL HINTS
Arrow key rotation is the easiest and most controlled method of changing the perspective of a model. It is the recommended method especially for large models. After a model has been rotated 180 degrees, clockwise and counter-clockwise directions will appear reversed on the screen.
OPTION 2: ROTATE THE MODEL USING THE CURSOR

1. 2. 3. Click the Rotate on the tool bar, or choose Rotate from the View menu.
With the cursor anywhere in the image window, click and slowly drag the cursor a short distance in the direction you want the atlas to rotate. Repeat step 2 until the desired perspective is reached.
HELPFUL HINTS
Slow, short moves of the cursor in a straight line in either the right or left direction, are recommended for starters. The speed at which the cursor moves on the screen dictates the speed at which the atlas model is rotated to its new perspective. The angle at which the cursor is dragged on the screen influences the axis around which the model rotates. To rotate the model at a precise angle use the controls on the Movie Parameters dialog box.
VIEW> BLACK BACKGROUND

A brightly colored surface rendered model on a black background makes a dramatic presentation. When printing a bitmap of the model, however, a black background is usually not ideal. To turn on Black Background, click to check this option on the View menu. To replace a black background with a white one, click to uncheck Black Background on the View menu.
HELPFUL HINT
When using a white background, light tracings can be made darker by returning to the Atlas Viewer and making a different Color assignment on the Color/Symbol tab of the Atlas Parameters dialog box.

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

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

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

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

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

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

Characteristics of the model may be changed in the Atlas Modeler. On the Color Parameters dialog box, the opacity of surface colors may by adjusted and objects of a particular color may be hidden. The Lighting Parameters dialog box allows the adjustment of the brightness of Global Ambient Light, parameters for a Spotlight Positioned on the Camera, and Surrounding Light.
TOPIC CONTENTS
Set Color Parameters (page 4-7) Set Lighting Parameters (page 4-9)
RELATED TOPICS
Available Surface Types (page 4-2) Smoothing (page 4-3) Render Option 2 (page 4-4) Manipulating the Model (page 4-4) Smoothing (page 4-3) Introduction to the Atlas Modeler (page 4-2) Changing the Characteristics of the Model (page 4-7) Activating Continuous Rotation (page 4-11) Record or Play an AVI Movie (page 4-14) Saving and Loading a Surface Rendering Parameters File (page 4-17) Special Formatting Options (page 4-19) Printing, Saving, and Copying the Model (page 4-21) Exiting Atlas Modeler (page 4-25)
SET COLOR PARAMETERS

On the Color Parameters dialog box, the opacity of surface colors may by adjusted and objects of a particular color may be hidden.
IMPORTANT
If the ultimate goal is to record a rotating atlas in an AVI movie, set the Movie Bounding Box and resize the model to fit the Bounding Box before setting the desired lighting parameters. See Options> Set Movie Parameters on page 4-11. The Color Parameters dialog box is opened by clicking the Set Color Parameters button on the system toolbar or choosing Set Color Parameters from the Options menu. It is closed by clicking the dialog box Close button.
Page 4-8
The Color Parameters Dialog Box
COLOR INDEX VERSES COLOR SHOWN

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

The opacity of an outer surface may be reduced so internal objects may be seen. 1. 2. 3. 4. On the color palette click the default color of the surface you wish to make less opaque. Click and drag the Opacity slider to a value less than 100%. Click the Apply button. Repeat steps 2 and 3 until the desired transparency is reached.
RELATED PROCEDURE
An alternate way to reveal internal structures, without reducing the opacity of the entire surface, is to apply a special Leave Open formatting to a selected number of surface tracings, thus creating a transparent window. Special formatting is applied in the Atlas Shop. See Format Contour Lines on page 3-50.
HIDE ALL OBJECTS OF A PARTICULAR COLOR

1. 2. On the color palette, click the default color of an object you wish to hide (remove from the display). Click to un-check the Show Objects of This Color check box. All objects of that color will be removed (hidden) from the surface rendered display.
Lighting, Color, and Movie parameters may be saved to a Surface Rendering Parameters file, then loaded for subsequent showings. See Saving and Loading a Surface Rendering Parameters File on page 4-17.

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

The Lighting Parameters dialog box allows the adjustment of the brightness of Global Ambient Light, parameters for a Spotlight Positioned on the Camera, and Surrounding Light.
If the ultimate goal is to record a rotating atlas in an AVI movie, set the Movie Bounding Box and resize the model to fit the Bounding Box before setting the desired lighting parameters. Options> Set Movie Parameters (page 4-11) It is usually beneficial to adjust lighting on the ideal Test shape that most closely resembles the shape of the atlas model, then display the atlas model using those settings. Using Ideal Test Forms (page 4-6)
Global Ambient Light and Spotlight Positioned On Camera are often used together. When Surrounding Light is used, it is usually better to turn off Global Ambient Light and Spotlight Positioned on Camera. The Lighting Parameters dialog box is opened by clicking the Set Lighting Parameters button on the system tool bar or choosing Set Lighting Parameters from the Options menu. It is closed by clicking the dialog box Close button.
Page 4-10
The Lighting Parameters Dialog Box
ADJUST GLOBAL AMBIENT LIGHT

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

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

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

Lighting, Color, and Movie parameters may be saved to a Surface Rendering Parameters file, then loaded for subsequent showings. Saving and Loading a Surface Rendering Parameters File (page 4-17)
RELATED TOPICS
Set Color Parameters (page 4-7) Available Surface Types (page 4-2) Smoothing (page 4-3) Render Option 2 (page 4-4) Manipulating the Model (page 4-4) Smoothing (page 4-3) Introduction to the Atlas Modeler (page 4-2) Changing the Characteristics of the Model (page 4-7) Activating Continuous Rotation (page 4-11) Record or Play an AVI Movie (page 4-14) Saving and Loading a Surface Rendering Parameters File (page 4-17) Special Formatting Options (page 4-19) Printing, Saving, and Copying the Model (page 4-21) Exiting Atlas Modeler (page 4-25)
ACTIVATING CONTINUOUS ROTATION

Controls on the Movie Parameters dialog box are used to precisely control the angle, speed, and number of times a surface rendered model is rotated. The rotating model may also be recorded and played as an AVI movie.
TOPIC CONTENTS
Options> Set Movie Parameters (page 4-11) Options> Auto Movie Rotate (page 4-13) Options> Auto Rotate (page 4-13)
RELATED TOPICS
Set Color Parameters (page 4-7) Available Surface Types (page 4-2) Smoothing (page 4-3) Render Option 2 (page 4-4) Manipulating the Model (page 4-4) Smoothing (page 4-3) Introduction to the Atlas Modeler (page 4-2) Changing the Characteristics of the Model (page 4-7) Activating Continuous Rotation (page 4-11) Record or Play an AVI Movie (page 4-14) Saving and Loading a Surface Rendering Parameters File (page 4-17) Special Formatting Options (page 4-19) Printing, Saving, and Copying the Model (page 4-21) Exiting Atlas Modeler (page 4-25)
OPTIONS> SET MOVIE PARAMETERS

The Movie Parameters dialog box is opened by clicking the Set Movie Parameters button on the system tool bar or choosing Set Movie Parameters from the Options menu. It is closed by clicking the dialog box Close button.
Page 4-12
The Movie Parameters Dialog Box
SET ROTATION PARAMETERS

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

Options> Auto Movie Rotate (page 4-13) Options> Auto Rotate (page 4-13) Set Color Parameters (page 4-7) Available Surface Types (page 4-2) Smoothing (page 4-3) Render Option 2 (page 4-4) Manipulating the Model (page 4-4) Smoothing (page 4-3) Introduction to the Atlas Modeler (page 4-2) Changing the Characteristics of the Model (page 4-7) Activating Continuous Rotation (page 4-11) Record or Play an AVI Movie (page 4-14) Saving and Loading a Surface Rendering Parameters File (page 4-17) Special Formatting Options (page 4-19) Printing, Saving, and Copying the Model (page 4-21) Exiting Atlas Modeler (page 4-25)
OPTIONS> AUTO MOVIE ROTATE

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

When Auto Rotate is active, the current speed and direction of the rotating surface rendered model continues until Auto Rotate is deactivated.
Page 4-14 PROCEDURE

1. 2. To activate Auto Rotate, click to depress the Auto Rotate Rotate on the Options menu. button on the tool bar, or click to check Auto
To deactivate Auto Rotate, click to release the Auto Rotate button, or click to uncheck Auto Rotate on the Options menu.
RELATED TOPICS
Options> Set Movie Parameters (page 4-11) Options> Auto Movie Rotate (page 4-13) Set Color Parameters (page 4-7) Available Surface Types (page 4-2) Smoothing (page 4-3) Render Option 2 (page 4-4) Manipulating the Model (page 4-4) Smoothing (page 4-3) Introduction to the Atlas Modeler (page 4-2) Changing the Characteristics of the Model (page 4-7) Activating Continuous Rotation (page 4-11) Record or Play an AVI Movie (page 4-14) Saving and Loading a Surface Rendering Parameters File (page 4-17) Special Formatting Options (page 4-19) Printing, Saving, and Copying the Model (page 4-21) Exiting Atlas Modeler (page 4-25)
RECORD OR PLAY AN AVI MOVIE

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

This procedure outlines recording and reviewing an AVI movie.
PROCEDURE
1. 2. 3. If the model is currently rotating, on the tool bar, click to release the Auto Movie Rotate rotations. If the Movie Parameters dialog box is not open, click the Set Movie Parameters Movie Parameters from the Options menu, to open it. button to stop the
button, or choose Set
On the Movie Parameters dialog box, in the Recording Parameters region, click the Set Bounding Box button. The Set Bounding Box dialog box opens. On the Set Bounding box dialog box, choose the desired Resolution (meaning the area of the Atlas Modelers display space that is to be included in the movie): For more information, see About the Bounding Box (page 4-16). High Resolution - Includes 1020 x 700 display space. Video Resolution - Includes a 640 x 480 area of the display space. Web Resolution - Includes a 320 x 240 area of the display space. Custom Resolution - Includes the space defined by the user. tool to resize the model to
4.
5. 6.
Close the Set Bounding Box dialog box and, if necessary, use the Scale Image fit within the Bounding Box.
If the opacity of the surface needs to be changed or particular colors hidden, open the Color Parameters button on the tool bar or choosing Set Color Parameters dialog box by clicking the Set Color Parameters from the Options menu. Make the desired changes, then close the Color Parameters dialog box. Set Color Parameters (page 4-7)
7.
If the lighting on the model needs to be adjusted, click the Set Lighting Parameters button, or choose Set Lighting Parameters from the Options menu to open the Lighting Parameters dialog box. Make the desired adjustments, then close the Lighting Parameters dialog box. Set Lighting Parameters (page 4-9) On the Movie Parameters dialog box, set the desired Rotation parameters. Set Rotation Parameters (page 4-12) On the Movie Parameters dialog box, click the Record button to open the Save Surface Modeler Movie dialog box. On the Save Surface Modeler Movie dialog box, navigate to the desired Save In folder. When the desired destination folder is open in the Save In field, in the Name field, type a name that is easily associated with the current model. A three letter extension (.avi) will be automatically appended to the name when the Save button is pressed. Click the Save button. The Video Compression dialog box will open. On the Video Compression dialog box, click the down arrow at the end of the Compressor field to open a drop list of compression routines. Click to choose Microsoft Video 1 (recommended compression type). Click the OK button on the Video Compression dialog box. The model will rotate through one complete rotational cycle as the movie is being recorded. To review the movie, click the Play button. The Windows Media Player opens. On the Media Player dialog box, click the Edit menu and choose Options from the drop list. The Options dialog box opens. On the Options dialog box click to check Auto Repeat, then click the OK button. The Options dialog box will close. BIOQUANT Topographer Handbook: 3D Modeling: Surface Rending in the Atlas Modeler
8. 9. 10. 11.
12. 13. 14. 15. 16. 17.
Page 4-16
18. 19. On the Media Players button bar, click the Play button to start the movie. To stop the movie click the left mouse button.
Using Microsoft Video 1 compression and Full Resolution, each movie frame will save as a 1024x768 image. This produces a movie file of about 16 MB. An alternate resolution may be selected on the Movie Bounding Box dialog box if a smaller movie file is desirable. The movie will appear choppy if it runs at anything more than 10 frames per second. The frames per second may be loosely determined by dividing 1,000 by the Delay value. (To produce 10 frames per second the default Delay of 100 should is used.) After the Movie Bounding Box dialog box is closed, the bounding box may be displayed or hidden by clicking the Movie Bounding Box button on the tool bar.
RELATED TOPICS
About the Bounding Box (page 4-16) Options> Set Movie Parameters (page 4-11) Options> Auto Movie Rotate (page 4-13) Options> Auto Rotate (page 4-13) Set Color Parameters (page 4-7) Available Surface Types (page 4-2) Smoothing (page 4-3) Render Option 2 (page 4-4) Manipulating the Model (page 4-4) Smoothing (page 4-3) Introduction to the Atlas Modeler (page 4-2) Changing the Characteristics of the Model (page 4-7) Activating Continuous Rotation (page 4-11) Record or Play an AVI Movie (page 4-14) Saving and Loading a Surface Rendering Parameters File (page 4-17) Special Formatting Options (page 4-19) Printing, Saving, and Copying the Model (page 4-21) Exiting Atlas Modeler (page 4-25)
ABOUT THE BOUNDING BOX

Controls on the Movie Parameters dialog box allow a rotating model to be recorded and played as an AVI movie file. A Bounding Box defines how much of the Atlas Modeler's background space is included in the movie. Adjusting the size of the Bounding Box controls the size or resolution of the movie file.
SHOW BOUNDING BOX NOTE

To show the bounding box at all times, from the View menu, check Show Bounding Box.
PROCEDURE
1. 2. 3. If Auto Movie Rotate is active, on the tool bar, click to release the Auto Movie Rotate button and stop the rotation. Open the Set Bounding Box dialog box by clicking the Bounding Box button on the Movie Parameters dialog box, or by choosing Set Movie Size from the Options menu. On the Set Bounding Box dialog box, choose the desired Resolution (meaning the area of the Atlas Modeler's display space that is to be included in the movie): High Resolution - Includes 1020 x 700 display space. Video Resolution - Includes a 640 x 480 area of the display space. Web Resolution - Includes a 320 x 240 area of the display space. Custom Resolution - Includes a space defined by the user.
Page 4-17
4. Close the Set Bounding Box dialog box. If necessary, use the within the Bounding Box. Scale Image tool to resize the model to fit
RELATED TOPICS
Record And Review an AVI Movie (page 4-15) Options> Set Movie Parameters (page 4-11) Options> Auto Movie Rotate (page 4-13) Options> Auto Rotate (page 4-13) Set Color Parameters (page 4-7) Available Surface Types (page 4-2) Smoothing (page 4-3) Render Option 2 (page 4-4) Manipulating the Model (page 4-4) Smoothing (page 4-3) Introduction to the Atlas Modeler (page 4-2) Changing the Characteristics of the Model (page 4-7) Activating Continuous Rotation (page 4-11) Record or Play an AVI Movie (page 4-14) Saving and Loading a Surface Rendering Parameters File (page 4-17) Special Formatting Options (page 4-19) Printing, Saving, and Copying the Model (page 4-21) Exiting Atlas Modeler (page 4-25)
SAVING AND LOADING A SURFACE RENDERING PARAMETERS FILE

The preferred Color, Lighting, and Movie parameters for a rendered model may be saved to a Surface Rendering Parameters file. Anytime in the future that the model is reopened in the Atlas Modeler, the Parameter file may be loaded to instantly restore the preferred settings.
TOPIC CONTENTS
File> Save Parameters (page 4-18) File> Load Parameters (page 4-18)
RELATED TOPICS
Record And Review an AVI Movie (page 4-15) About the Bounding Box (page 4-16) Options> Set Movie Parameters (page 4-11) Options> Auto Movie Rotate (page 4-13) Options> Auto Rotate (page 4-13) Set Color Parameters (page 4-7) Available Surface Types (page 4-2) Smoothing (page 4-3) Render Option 2 (page 4-4) Manipulating the Model (page 4-4) Smoothing (page 4-3) Introduction to the Atlas Modeler (page 4-2) Changing the Characteristics of the Model (page 4-7) Activating Continuous Rotation (page 4-11) Record or Play an AVI Movie (page 4-14) Saving and Loading a Surface Rendering Parameters File (page 4-17) Special Formatting Options (page 4-19) Printing, Saving, and Copying the Model (page 4-21) Exiting Atlas Modeler (page 4-25)
Page 4-18
FILE> SAVE PARAMETERS

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

If a Surface Rendering Parameters file was saved for the current model, the Parameters file may be reloaded to automatically restore previously set Color, Lighting, and Movie parameters.
PROCEDURE
1. 2. Click the Load Parameters button on the system tool bar or from the File menu, choose Load Parameters to open the Open Surface Rendering Parameters dialog box. The default location for saving parameter files is BQOSTEO\Topographer. If you created a subdirectory associated with your Data Volume and Data Set as recommended in the Save Parameters procedure, it will be listed here. Navigate to the folder that contains the Parameter file for the current data set. Click to highlight the desired Parameters field. This will place its name in the File Name field. Click the Open button.
3. 4.

File> Load Parameters (page 4-18) Record And Review an AVI Movie (page 4-15) About the Bounding Box (page 4-16) Options> Set Movie Parameters (page 4-11) Options> Auto Movie Rotate (page 4-13) Options> Auto Rotate (page 4-13) Set Color Parameters (page 4-7) Available Surface Types (page 4-2) Smoothing (page 4-3) Render Option 2 (page 4-4) Manipulating the Model (page 4-4) Smoothing (page 4-3) Introduction to the Atlas Modeler (page 4-2) Changing the Characteristics of the Model (page 4-7) Activating Continuous Rotation (page 4-11) Record or Play an AVI Movie (page 4-14) Saving and Loading a Surface Rendering Parameters File (page 4-17) Special Formatting Options (page 4-19) Printing, Saving, and Copying the Model (page 4-21) Exiting Atlas Modeler (page 4-25)
SPECIAL FORMATTING OPTIONS

Particular formatting tools in the Topographers Atlas Viewer and Atlas Shop help improve the quality of a surface rendered model.
TOPIC CONTENTS
Adjustment in the Atlas Viewer that Enhances Surface Rendering (page 4-20) Adjustments in the Atlas Shop that enhance surface rendering. (page 4-20)
RELATED TOPICS
File> Save Parameters (page 4-18) File> Load Parameters (page 4-18) Record And Review an AVI Movie (page 4-15) About the Bounding Box (page 4-16) Options> Set Movie Parameters (page 4-11) Options> Auto Movie Rotate (page 4-13) Options> Auto Rotate (page 4-13) Set Color Parameters (page 4-7) Available Surface Types (page 4-2) Smoothing (page 4-3) Render Option 2 (page 4-4) Manipulating the Model (page 4-4) Smoothing (page 4-3) Introduction to the Atlas Modeler (page 4-2) Changing the Characteristics of the Model (page 4-7) Activating Continuous Rotation (page 4-11) Record or Play an AVI Movie (page 4-14) Saving and Loading a Surface Rendering Parameters File (page 4-17) Special Formatting Options (page 4-19) Printing, Saving, and Copying the Model (page 4-21) Exiting Atlas Modeler (page 4-25)
Page 4-20
ADJUSTMENT IN THE ATLAS VIEWER THAT ENHANCES SURFACE RENDERING

When an atlas contains multiple small area tracings of the same color, for example when an Area array was used to trace cells within a structure, the Atlas Modeler has no way to recognize them as separate individual objects. Assigning the Dot symbol to such tracings and turning on Symbols in the Atlas Viewer, signals the Atlas Modeler to render the designated tracings as discrete objects.
PROCEDURE: ASSIGN THE DOT SYMBOL TO REPLACE SMALL AREA TRACINGS

1. 2. 3. 4. 5. 6. 7. Exit the Atlas Modeler. In the Atlas Viewer, on the Atlas Parameters dialog box click the Colors/Symbols tab. Display the current default symbol(s) in the atlas by clicking to check the Symbol check box. In the Symbols section, in the Available field, click the down arrow to display a small scroll list. Using the two small scroll buttons, scroll to and click to choose the Dot symbol. In the color coded Symbols list, click on the color (and current symbol) of the group for which the Dot symbol is to be applied. Click the Apply button. Click the Atlas Modeler discrete objects. button to reopen the Atlas Modeler. The small area tracings will now render as
RELATED TOPICS
Adjustments in the Atlas Shop that enhance surface rendering. (page 4-20) File> Save Parameters (page 4-18) File> Load Parameters (page 4-18) Record And Review an AVI Movie (page 4-15) About the Bounding Box (page 4-16) Options> Set Movie Parameters (page 4-11) Options> Auto Movie Rotate (page 4-13) Options> Auto Rotate (page 4-13) Set Color Parameters (page 4-7) Available Surface Types (page 4-2) Smoothing (page 4-3) Render Option 2 (page 4-4) Manipulating the Model (page 4-4) Smoothing (page 4-3) Introduction to the Atlas Modeler (page 4-2) Changing the Characteristics of the Model (page 4-7) Activating Continuous Rotation (page 4-11) Record or Play an AVI Movie (page 4-14) Saving and Loading a Surface Rendering Parameters File (page 4-17) Special Formatting Options (page 4-19) Printing, Saving, and Copying the Model (page 4-21) Exiting Atlas Modeler (page 4-25)
ADJUSTMENTS IN THE ATLAS SHOP THAT ENHANCE SURFACE RENDERING.

Change Resolution - The resolution (number of data points) in large atlases may be decreased to speed surface rendering. Reduce Atlas Resolution (page 3-48) Change Colors in a Branched Structure - Y or V shaped three dimensional structures will surface render more accurately if one of the legs of the Y or V is assigned a different color. Change the Color Of One Branch of a Y or V-Shaped Structure (page 3-30)
Page 4-21
Cap Object - The first and last contour tracings in an atlas can be marked as caps that will cover the open ends of a surface rendered model. Cap Open Ends of A Model (page 3-51) End of Object/Leave Open - A number of tracings in the atlas may be marked as open to create a transparent window in a surface rendered model, through which interior objects may be viewed, without reducing the opacity of the entire model. Define a Transparent Window in a Model (page 3-51) Middle of Object - The cap or open markers on a tracing may be removed to return the tracing to its original Middle of Object default status. Restore Middle of Object Status (page 3-52)
RELATED TOPICS
Adjustment in the Atlas Viewer that Enhances Surface Rendering (page 4-20) File> Save Parameters (page 4-18) File> Load Parameters (page 4-18) Record And Review an AVI Movie (page 4-15) About the Bounding Box (page 4-16) Options> Set Movie Parameters (page 4-11) Options> Auto Movie Rotate (page 4-13) Options> Auto Rotate (page 4-13) Set Color Parameters (page 4-7) Available Surface Types (page 4-2) Smoothing (page 4-3) Render Option 2 (page 4-4) Manipulating the Model (page 4-4) Smoothing (page 4-3) Introduction to the Atlas Modeler (page 4-2) Changing the Characteristics of the Model (page 4-7) Activating Continuous Rotation (page 4-11) Record or Play an AVI Movie (page 4-14) Saving and Loading a Surface Rendering Parameters File (page 4-17) Special Formatting Options (page 4-19) Printing, Saving, and Copying the Model (page 4-21) Exiting Atlas Modeler (page 4-25)
PRINTING, SAVING, AND COPYING THE MODEL

This section describes how to save the model as a bitmap or DXF file, print the model, and copy the model to the clipboard.
TOPIC CONTENTS
File>Save Image As (page 4-22) File> Print Image (page 4-23) File> Copy Image to Clipboard (page 4-24)

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

File> Print Image (page 4-23) File> Copy Image to Clipboard (page 4-24) Adjustment in the Atlas Viewer that Enhances Surface Rendering (page 4-20) File> Save Parameters (page 4-18) File> Load Parameters (page 4-18) Record And Review an AVI Movie (page 4-15) About the Bounding Box (page 4-16) Options> Set Movie Parameters (page 4-11) Options> Auto Movie Rotate (page 4-13) Options> Auto Rotate (page 4-13) Set Color Parameters (page 4-7) Available Surface Types (page 4-2) Smoothing (page 4-3) Render Option 2 (page 4-4) Manipulating the Model (page 4-4) Smoothing (page 4-3) Introduction to the Atlas Modeler (page 4-2) Changing the Characteristics of the Model (page 4-7) Activating Continuous Rotation (page 4-11) Record or Play an AVI Movie (page 4-14) Saving and Loading a Surface Rendering Parameters File (page 4-17) Special Formatting Options (page 4-19) Printing, Saving, and Copying the Model (page 4-21) Exiting Atlas Modeler (page 4-25)
FILE> PRINT IMAGE

The surface rendered model may be printed. For most printers, it is better to change the models background color to white. 1. 2. 3. From the View menu, click to uncheck Black Background. Click the Print Image dialog box opens. button on the system tool bar or from the File menu, choose Print Image. The Print
On the Print dialog box, if necessary adjust printing options as follows: Click the down-arrow in the Printer field to choose an alternate printer. Change the number of copies to be printed. Click the Properties button to select Portrait or Landscape, change paper size, etc.
4.
Click the Print button.

File>Save Image As (page 4-22) File> Copy Image to Clipboard (page 4-24) Adjustment in the Atlas Viewer that Enhances Surface Rendering (page 4-20) File> Save Parameters (page 4-18) File> Load Parameters (page 4-18) Record And Review an AVI Movie (page 4-15) About the Bounding Box (page 4-16) Options> Set Movie Parameters (page 4-11) Options> Auto Movie Rotate (page 4-13) Options> Auto Rotate (page 4-13) Set Color Parameters (page 4-7) Available Surface Types (page 4-2) Smoothing (page 4-3) Render Option 2 (page 4-4) Manipulating the Model (page 4-4) Smoothing (page 4-3) Introduction to the Atlas Modeler (page 4-2) Changing the Characteristics of the Model (page 4-7) Activating Continuous Rotation (page 4-11) Record or Play an AVI Movie (page 4-14) Saving and Loading a Surface Rendering Parameters File (page 4-17) Special Formatting Options (page 4-19) Printing, Saving, and Copying the Model (page 4-21) Exiting Atlas Modeler (page 4-25)
FILE> COPY IMAGE TO CLIPBOARD

A bitmap image of the surface rendered model may be copied to the clipboard.
PROCEDURE
1. From the File menu, choose Copy Image to Clipboard.

File> Print Image (page 4-23) File>Save Image As (page 4-22) Adjustment in the Atlas Viewer that Enhances Surface Rendering (page 4-20) File> Save Parameters (page 4-18) File> Load Parameters (page 4-18) Record And Review an AVI Movie (page 4-15) About the Bounding Box (page 4-16) Options> Set Movie Parameters (page 4-11) Options> Auto Movie Rotate (page 4-13) Options> Auto Rotate (page 4-13) Set Color Parameters (page 4-7) Available Surface Types (page 4-2) Smoothing (page 4-3) Render Option 2 (page 4-4) Manipulating the Model (page 4-4) Smoothing (page 4-3) Introduction to the Atlas Modeler (page 4-2) Changing the Characteristics of the Model (page 4-7) Activating Continuous Rotation (page 4-11) Record or Play an AVI Movie (page 4-14) Saving and Loading a Surface Rendering Parameters File (page 4-17) Special Formatting Options (page 4-19) Printing, Saving, and Copying the Model (page 4-21) Exiting Atlas Modeler (page 4-25)
EXITING ATLAS MODELER

To exit the Atlas Modeler and return to the Atlas Viewer, from the File menu, choose Exit Atlas Modeler.
RELATED TOPICS
File> Print Image (page 4-23) File> Copy Image to Clipboard (page 4-24) Adjustment in the Atlas Viewer that Enhances Surface Rendering (page 4-20) File> Save Parameters (page 4-18) File> Load Parameters (page 4-18) Record And Review an AVI Movie (page 4-15) About the Bounding Box (page 4-16) Options> Set Movie Parameters (page 4-11) Options> Auto Movie Rotate (page 4-13) Options> Auto Rotate (page 4-13) Set Color Parameters (page 4-7) Available Surface Types (page 4-2) Smoothing (page 4-3) Render Option 2 (page 4-4) Manipulating the Model (page 4-4) Smoothing (page 4-3) Introduction to the Atlas Modeler (page 4-2) Changing the Characteristics of the Model (page 4-7) Activating Continuous Rotation (page 4-11) Record or Play an AVI Movie (page 4-14) Saving and Loading a Surface Rendering Parameters File (page 4-17) Special Formatting Options (page 4-19) Printing, Saving, and Copying the Model (page 4-21) Exiting Atlas Modeler (page 4-25) BIOQUANT Topographer Handbook: 3D Modeling: Surface Rending in the Atlas Modeler
Page 4-26
The Atlas Viewer in Detail

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

The wire frame reconstruction in the Atlas Viewer can sometimes show off important aspects of a specimen, in ways that the surface rendered model does not.
TOPIC CONTENTS
Atlas Viewer Menu and Tool Bars (page 5-2) Manipulating the Atlas in the Atlas Window (page 5-2) Using the Atlas Parameters Dialog Box (page 5-7) Setting Atlas Parameters - Perspective Tab (page 5-7) Setting Atlas Parameters - Colors/Symbols Tab (page 5-10) Setting Atlas Parameters - Rotation Tab (page 5-25) Using Alternate Display Options (page 5-29) Saving and Loading an Atlas Parameter File (page 5-30)
RELATED TOPICS
Printing, Copying, or Exporting an Atlas (page 5-34) Manipulating Data Arrays and Data Sets in the Atlas Viewer (page 5-38)
ATLAS VIEWER MENU AND TOOL BARS

The Atlas Viewers menu bar and tool bar have two different configurations, depending on whether or not an Atlas Window is open. The tool bar is also called the control bar.
THE CONTROL BAR - BEFORE AN ATLAS WINDOW IS OPEN
THE MENU AND CONTROL BAR - AFTER AN ATLAS WINDOW IS OPEN
PROCEDURE
To hide the Control Bar, on the Atlas menu, click to check Show Control Bar. To hide the Control Bar, on the Atlas menu, click to uncheck Show Control Bar.
RELATED TOPICS
Manipulating the Atlas in the Atlas Window (page 5-2) Using the Atlas Parameters Dialog Box (page 5-7) Setting Atlas Parameters - Perspective Tab (page 5-7) Setting Atlas Parameters - Colors/Symbols Tab (page 5-10) Setting Atlas Parameters - Rotation Tab (page 5-25) Using Alternate Display Options (page 5-29) Saving and Loading an Atlas Parameter File (page 5-30) Working With 3D Wire Frame Atlases (page 5-2) Printing, Copying, or Exporting an Atlas (page 5-34) Manipulating Data Arrays and Data Sets in the Atlas Viewer (page 5-38)
MANIPULATING THE ATLAS IN THE ATLAS WINDOW

The following tools are used to open, re-position, and/or resize the wire frame atlas in the Atlas Window.
BIOQUANT Topographer Handbook: The Atlas Viewer in Detail

Atlas> Open or Close (page 5-3) Atlas> Resize to Fit (page 5-4) Atlas> Zoom (page 5-4) Atlas> Pan (page 5-5) Atlas> Center (page 5-6) Atlas> Redraw (page 5-6)
RELATED TOPICS
ATLAS> OPEN OR CLOSE

When Topographers Atlas Viewer first opens, only the Select Arrays dialog box is visible on the desk top. To see the topographic map or 3D reconstruction (known as the Atlas in the Topographer), an Atlas window needs to be opened. Close becomes available on the Atlas menu any time an Atlas window is open. The Atlas Window
A simple reconstruction
PROCEDURE
1. 2. On the Select Arrays dialog box, select the one or more Topo arrays that contain the topographic data that is to be viewed. Open the Atlas Window by doing one of the following: Click the New Atlas Window button on the tool bar.
From the Atlas menu choose Open.
To close the Atlas Window, do one of the following: From the Atlas menu, choose Close. Click the Close button in the upper right corner of the Atlas Window.

Atlas> Resize to Fit (page 5-4) Atlas> Zoom (page 5-4) Atlas> Pan (page 5-5) Atlas> Center (page 5-6) Atlas> Redraw (page 5-6) Manipulating the Atlas in the Atlas Window (page 5-2) Using the Atlas Parameters Dialog Box (page 5-7) Setting Atlas Parameters - Perspective Tab (page 5-7) Setting Atlas Parameters - Colors/Symbols Tab (page 5-10) Setting Atlas Parameters - Rotation Tab (page 5-25) Using Alternate Display Options (page 5-29) Saving and Loading an Atlas Parameter File (page 5-30) Working With 3D Wire Frame Atlases (page 5-2) Printing, Copying, or Exporting an Atlas (page 5-34) Manipulating Data Arrays and Data Sets in the Atlas Viewer (page 5-38)
ATLAS> RESIZE TO FIT

Simultaneously centers and resizes the atlas so it fills the Atlas Window.
PROCEDURES
From the Atlas menu, choose Resize to Fit. Click the Resize to Fit button on the system tool bar.
RELATED TOPICS
Atlas> Open or Close (page 5-3) Atlas> Zoom (page 5-4) Atlas> Pan (page 5-5) Atlas> Center (page 5-6) Atlas> Redraw (page 5-6) Manipulating the Atlas in the Atlas Window (page 5-2) Using the Atlas Parameters Dialog Box (page 5-7) Setting Atlas Parameters - Perspective Tab (page 5-7) Setting Atlas Parameters - Colors/Symbols Tab (page 5-10) Setting Atlas Parameters - Rotation Tab (page 5-25) Using Alternate Display Options (page 5-29) Saving and Loading an Atlas Parameter File (page 5-30) Working With 3D Wire Frame Atlases (page 5-2) Printing, Copying, or Exporting an Atlas (page 5-34) Manipulating Data Arrays and Data Sets in the Atlas Viewer (page 5-38)
ATLAS> ZOOM
Activates the Zoom cursor so the atlas may be magnified or reduced in size. Magnification centered on the point clicked, occurs when the left mouse button is pressed and released. Reduction occurs when the right mouse button is pressed and released. Clicking and dragging the Zoom cursor with the left mouse button, simultaneously Zooms and Pans.
PROCEDURE
1. 2. On the Control Bar, click the To magnify or reduce the atlas: Zoom button; the cursor changes to a magnifying glass.
Page 5-5
3. To zoom, click and release the left mouse button over the atlas. To shrink, click and release the right mouse button over the atlas. To zoom and pan to a particular location, click and drag with the left mouse button.
Click to release the Zoom button to deactivate the Zoom cursor.
A precise zoom can be set numerically on the Perspective tab of the Atlas Parameters box. Zoom Factor (page 5-8) To automatically resize the atlas to fill the Atlas Window, click the Resize to Fit bar. button on the system tool
RELATED TOPICS
Atlas> Open or Close (page 5-3) Atlas> Resize to Fit (page 5-4) Atlas> Pan (page 5-5) Atlas> Center (page 5-6) Atlas> Redraw (page 5-6) Manipulating the Atlas in the Atlas Window (page 5-2) Using the Atlas Parameters Dialog Box (page 5-7) Setting Atlas Parameters - Perspective Tab (page 5-7) Setting Atlas Parameters - Colors/Symbols Tab (page 5-10) Setting Atlas Parameters - Rotation Tab (page 5-25) Using Alternate Display Options (page 5-29) Saving and Loading an Atlas Parameter File (page 5-30) Working With 3D Wire Frame Atlases (page 5-2) Printing, Copying, or Exporting an Atlas (page 5-34) Manipulating Data Arrays and Data Sets in the Atlas Viewer (page 5-38)
ATLAS> PAN
Readies the cursor to move the atlas to a new location in the Atlas Window.
PROCEDURE
1. 2. 3. On the system tool bar, click the Pan button; the cursor changes to a cross hair over the atlas.
Click and drag the panning cursor to move the atlas. Click to release the Pan button to deactivate the panning cursor.
RELATED TOPICS
Atlas> Open or Close (page 5-3) Atlas> Resize to Fit (page 5-4) Atlas> Zoom (page 5-4) Atlas> Center (page 5-6) Atlas> Redraw (page 5-6) Manipulating the Atlas in the Atlas Window (page 5-2) Using the Atlas Parameters Dialog Box (page 5-7) Setting Atlas Parameters - Perspective Tab (page 5-7) Setting Atlas Parameters - Colors/Symbols Tab (page 5-10) Setting Atlas Parameters - Rotation Tab (page 5-25) Using Alternate Display Options (page 5-29) Saving and Loading an Atlas Parameter File (page 5-30) Working With 3D Wire Frame Atlases (page 5-2) Printing, Copying, or Exporting an Atlas (page 5-34) Manipulating Data Arrays and Data Sets in the Atlas Viewer (page 5-38) BIOQUANT Topographer Handbook: The Atlas Viewer in Detail
Page 5-6
ATLAS> CENTER
Moves the center of the atlas to the center of the Atlas Window.
PROCEDURE
On the Control Bar, click the window. Center button. The center of the atlas moves to the center of the atlas
RELATED TOPICS
Atlas> Open or Close (page 5-3) Atlas> Resize to Fit (page 5-4) Atlas> Zoom (page 5-4) Atlas> Center (page 5-6) Atlas> Redraw (page 5-6) Manipulating the Atlas in the Atlas Window (page 5-2) Using the Atlas Parameters Dialog Box (page 5-7) Setting Atlas Parameters - Perspective Tab (page 5-7) Setting Atlas Parameters - Colors/Symbols Tab (page 5-10) Setting Atlas Parameters - Rotation Tab (page 5-25) Using Alternate Display Options (page 5-29) Saving and Loading an Atlas Parameter File (page 5-30) Working With 3D Wire Frame Atlases (page 5-2) Printing, Copying, or Exporting an Atlas (page 5-34) Manipulating Data Arrays and Data Sets in the Atlas Viewer (page 5-38)
ATLAS> REDRAW
Redraw is used any time the Atlas Window is open and either of the following is the case: The current atlas needs to be refreshed. A alternate array or set of arrays has been selected on the Select Arrays dialog box and the Atlas Window needs to be updated with the new atlas.
PROCEDURE
On the Control Bar, click the Redraw button.
RELATED TOPICS
Atlas> Open or Close (page 5-3) Atlas> Resize to Fit (page 5-4) Atlas> Zoom (page 5-4) Atlas> Pan (page 5-5) Atlas> Center (page 5-6) Manipulating the Atlas in the Atlas Window (page 5-2) Using the Atlas Parameters Dialog Box (page 5-7) Setting Atlas Parameters - Perspective Tab (page 5-7) Setting Atlas Parameters - Colors/Symbols Tab (page 5-10) Setting Atlas Parameters - Rotation Tab (page 5-25) Using Alternate Display Options (page 5-29) Saving and Loading an Atlas Parameter File (page 5-30) Working With 3D Wire Frame Atlases (page 5-2) Printing, Copying, or Exporting an Atlas (page 5-34) Manipulating Data Arrays and Data Sets in the Atlas Viewer (page 5-38)
Page 5-7
USING THE ATLAS PARAMETERS DIALOG BOX

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

TOPIC CONTENTS
Zoom Factor (page 5-8) Z-Shift (page 5-9) Adjust X, Y, or Z Perspective (page 5-9)
Page 5-8
The Atlas Parameters: Perspective Tab
RELATED TOPICS
Manipulating the Atlas in the Atlas Window (page 5-2) Using the Atlas Parameters Dialog Box (page 5-7) Setting Atlas Parameters - Colors/Symbols Tab (page 5-10) Setting Atlas Parameters - Rotation Tab (page 5-25) Using Alternate Display Options (page 5-29) Saving and Loading an Atlas Parameter File (page 5-30) Working With 3D Wire Frame Atlases (page 5-2) Printing, Copying, or Exporting an Atlas (page 5-34) Manipulating Data Arrays and Data Sets in the Atlas Viewer (page 5-38)
ZOOM FACTOR
When the Atlas Parameters dialog box is first opened, the Zoom setting defaults to the current zoomed state of the atlas. The zoomed state of the atlas in the Atlas window may be increased or decreased using either the Zoom (5-4) or by changing the Zoom Factor. tool
PROCEDURE: CHANGE ZOOM FACTOR

To increase the zoom of the atlas, on the Perspective tab of Atlas Parameters, increase the value in the Zoom Factor field. To decrease the zoom, decrease the value in the Zoom Factor field.

Z-Shift (page 5-9) Adjust X, Y, or Z Perspective (page 5-9) Manipulating the Atlas in the Atlas Window (page 5-2) Using the Atlas Parameters Dialog Box (page 5-7) Setting Atlas Parameters - Perspective Tab (page 5-7) Setting Atlas Parameters - Colors/Symbols Tab (page 5-10) Setting Atlas Parameters - Rotation Tab (page 5-25) Using Alternate Display Options (page 5-29) Saving and Loading an Atlas Parameter File (page 5-30) Working With 3D Wire Frame Atlases (page 5-2) Printing, Copying, or Exporting an Atlas (page 5-34) Manipulating Data Arrays and Data Sets in the Atlas Viewer (page 5-38)
Z-SHIFT
Initially the atlas is displayed with sections stacked one on top of the other. Z Shift allows each successive section to be displaced a bit to the right or left for better viewing. The Effect of Z Shift
PROCEDURE
To shift sections to the right, type a positive micron distance in the Z Shift field. The first section in the series remains in its initial position. Each successive section is shifted to the right relative to the previous section, by the micron distance in the Z Shift field. To shift sections to the left, type a negative micron distance in the Z Shift field.
RELATED TOPICS
Zoom Factor (page 5-8) Adjust X, Y, or Z Perspective (page 5-9) Manipulating the Atlas in the Atlas Window (page 5-2) Using the Atlas Parameters Dialog Box (page 5-7) Setting Atlas Parameters - Perspective Tab (page 5-7) Setting Atlas Parameters - Colors/Symbols Tab (page 5-10) Setting Atlas Parameters - Rotation Tab (page 5-25) Using Alternate Display Options (page 5-29) Saving and Loading an Atlas Parameter File (page 5-30) Working With 3D Wire Frame Atlases (page 5-2) Printing, Copying, or Exporting an Atlas (page 5-34) Manipulating Data Arrays and Data Sets in the Atlas Viewer (page 5-38)
ADJUST X, Y, OR Z PERSPECTIVE
The X, Y, and Z Perspective fields specify the degree the atlas is to be rotated on each axis to reach the desired perspective. Positive values rotate the atlas clockwise as seen from the positive end of the axis. BIOQUANT Topographer Handbook: The Atlas Viewer in Detail
Page 5-10
Windows uses a left-handed system for its axes: The positive Y axis points down. The positive X axis points right. The positive Z axis points out of the monitor.
The Rotate Around radio buttons control the point around which the atlas rotates. The Landmark button rotates around the landmark of the atlas, i.e. the origin (0, 0, 0,). The Center button rotates around the center of the atlas. The Start Point button rotates around the first point in the atlas. Center is the most commonly used point.
PROCEDURE
1. 2. 3. In the X, Y, or Z perspective text boxes, enter the desired degree of rotation. Choose one of the Rotate Around radio buttons to determine the point around which the atlas will rotate. In most cases, rotation around the center of the atlas (Object) is used. Click the Apply button to display the new orientation.
ADDITIONAL NOTE
When an ideal or pleasing display is accomplished, its settings may be saved in a Parameters file that can be reloaded at a later time to instantly restore the preferred display. See Saving and Loading an Atlas Parameter File on 5-30.
RELATED TOPICS
Zoom Factor (page 5-8) Z-Shift (page 5-9) Manipulating the Atlas in the Atlas Window (page 5-2) Using the Atlas Parameters Dialog Box (page 5-7) Setting Atlas Parameters - Perspective Tab (page 5-7) Setting Atlas Parameters - Colors/Symbols Tab (page 5-10) Setting Atlas Parameters - Rotation Tab (page 5-25) Using Alternate Display Options (page 5-29) Saving and Loading an Atlas Parameter File (page 5-30) Working With 3D Wire Frame Atlases (page 5-2) Printing, Copying, or Exporting an Atlas (page 5-34) Manipulating Data Arrays and Data Sets in the Atlas Viewer (page 5-38)
SETTING ATLAS PARAMETERS - COLORS/SYMBOLS TAB

A topographic objects default color is the color that was used to trace or count the object in BIOQUANT. Changing the color properties of the atlas on the Color/Symbols tab does not change the default colors recorded in the Topo array. (If there is a reason to permanently change the default colors in the Topo array, this may be done in the Topographers Atlas Shop.) All objects of the same color comprise a group. Changes made on the Colors/Symbols tab are applied to all objects in the atlas that are the specified color. The color used to draw an object can be changed to any of 16 colors or can be set not to draw at all. Closed polygon objects (e.g. those created with area measurements) can be filled in any of 16 colors or can be set not to fill while other objects do. Small objects can be marked with any of 16 symbol shapes of customizable sizes.

How To Use the Selection Lists (page 5-11) About The Apply, Save, and Restore Buttons (page 5-12) Change Tracing (Line or Symbol) Color (page 5-13) Fill Polygonal Tracings With Color (page 5-14) Distinguish Dual Labeled Structures (page 5-15) Change Fill Color (page 5-16) Restore Color and Symbol Defaults (page 5-17) Exclude Certain Objects or Symbols (page 5-18) Fill Some Objects But Not Others (page 5-19) Display Small Objects As Symbols (page 5-20) Symbolize Larger Objects (page 5-21) Assign a Different Symbol (page 5-22) Change the Size of the Symbols (page 5-23) Reduce The Number of Densely Packed Symbols (page 5-24) The Colors/Symbols Dialog Box
RELATED TOPICS
HOW TO USE THE SELECTION LISTS

Each of the three long selection lists (Line/Sym, Fill, and Symbols) has 16 entries and, before any changes are made by the user, each entry is a different color. Since everything in the displayed atlas must be one of these 16 colors, these lists are used to identify for the system which parts of the atlas you want to change. In other words, selecting items to be changed is a color matching process. Whether changing the color of tracings, or the fill color for particular objects, or assigning a different symbol to represent particular objects, the basic steps are the same: BIOQUANT Topographer Handbook: The Atlas Viewer in Detail
Page 5-12
a. b. c. d. The user notes the current color of the item in the Atlas window. The user chooses a new color on the color palette, or a new symbol from the Available symbols drop list. The user clicks the entry in the relevant list that matches the current color of the item in the Atlas window. When the entry in the list is clicked, its default color or default symbol changes to the new one. The user clicks the Apply button, and all items in the Atlas window that matched the original, default color of the clicked entry, changes to the new color or to the new symbol.
RELATED TOPICS
About The Apply, Save, and Restore Buttons (page 5-12) Change Tracing (Line or Symbol) Color (page 5-13) Fill Polygonal Tracings With Color (page 5-14) Distinguish Dual Labeled Structures (page 5-15) Change Fill Color (page 5-16) Restore Color and Symbol Defaults (page 5-17) Exclude Certain Objects or Symbols (page 5-18) Fill Some Objects But Not Others (page 5-19) Display Small Objects As Symbols (page 5-20) Symbolize Larger Objects (page 5-21) Assign a Different Symbol (page 5-22) Change the Size of the Symbols (page 5-23) Reduce The Number of Densely Packed Symbols (page 5-24) Manipulating the Atlas in the Atlas Window (page 5-2) Using the Atlas Parameters Dialog Box (page 5-7) Setting Atlas Parameters - Perspective Tab (page 5-7) Setting Atlas Parameters - Colors/Symbols Tab (page 5-10) Setting Atlas Parameters - Rotation Tab (page 5-25) Using Alternate Display Options (page 5-29) Saving and Loading an Atlas Parameter File (page 5-30) Working With 3D Wire Frame Atlases (page 5-2) Printing, Copying, or Exporting an Atlas (page 5-34) Manipulating Data Arrays and Data Sets in the Atlas Viewer (page 5-38)
ABOUT THE APPLY, SAVE, AND RESTORE BUTTONS

The Apply button causes the atlas to be redrawn to include any changes that were made on the Color/ Symbols tab. The Save buttons on all three Atlas Parameters tabs, open the Save Parameters dialog box. When an ideal atlas display is created, the settings that generate that particular view of the atlas may be saved to a Parameter (.set) file. Anytime in the future when the atlas is displayed, its parameter file can be loaded to instantly recreate the ideal view. The Restore button erases all changes from the Color/Symbols tab and restores all original default color and symbol settings.

How To Use the Selection Lists (page 5-11) Change Tracing (Line or Symbol) Color (page 5-13) Fill Polygonal Tracings With Color (page 5-14) Distinguish Dual Labeled Structures (page 5-15) Change Fill Color (page 5-16) Restore Color and Symbol Defaults (page 5-17) Exclude Certain Objects or Symbols (page 5-18) Fill Some Objects But Not Others (page 5-19) Display Small Objects As Symbols (page 5-20) Symbolize Larger Objects (page 5-21) Assign a Different Symbol (page 5-22) Change the Size of the Symbols (page 5-23) Reduce The Number of Densely Packed Symbols (page 5-24) Manipulating the Atlas in the Atlas Window (page 5-2) Using the Atlas Parameters Dialog Box (page 5-7) Setting Atlas Parameters - Perspective Tab (page 5-7) Setting Atlas Parameters - Colors/Symbols Tab (page 5-10) Setting Atlas Parameters - Rotation Tab (page 5-25) Using Alternate Display Options (page 5-29) Saving and Loading an Atlas Parameter File (page 5-30) Working With 3D Wire Frame Atlases (page 5-2) Printing, Copying, or Exporting an Atlas (page 5-34) Manipulating Data Arrays and Data Sets in the Atlas Viewer (page 5-38)
CHANGE TRACING (LINE OR SYMBOL) COLOR

The Line/Sym list and the Fill list in the Colors area of the Colors/Symbols tab are used to change the display color for a particular group of objects. Since item selection is based entirely on color, any change that is made to Color/Symbol parameters is applied to all items in the Atlas window that match the selected color.
PROCEDURE
1. 2. 3. In the Atlas window, notice the current default color of the group of objects for which the color is to be changed. Choose a new color by clicking one of the 16 color squares in the Colors area. (The N square is for No Draw and the D square is for Default. Do not use these for this procedure.) Find and click the entry in the Line/Sym list that matches the current color of the objects for which color is to be changed. When clicked, the entry in the list changes to the new color. Repeat steps 1 through 3 for each color group you wish to change. Click the Apply button to update the atlas display to the new color(s).
4. 5.

How To Use the Selection Lists (page 5-11) About The Apply, Save, and Restore Buttons (page 5-12) Fill Polygonal Tracings With Color (page 5-14) Distinguish Dual Labeled Structures (page 5-15) Change Fill Color (page 5-16) Restore Color and Symbol Defaults (page 5-17) Exclude Certain Objects or Symbols (page 5-18) Fill Some Objects But Not Others (page 5-19) Display Small Objects As Symbols (page 5-20) Symbolize Larger Objects (page 5-21) Assign a Different Symbol (page 5-22) Change the Size of the Symbols (page 5-23) Reduce The Number of Densely Packed Symbols (page 5-24) Manipulating the Atlas in the Atlas Window (page 5-2) Using the Atlas Parameters Dialog Box (page 5-7) Setting Atlas Parameters - Perspective Tab (page 5-7) Setting Atlas Parameters - Colors/Symbols Tab (page 5-10) Setting Atlas Parameters - Rotation Tab (page 5-25) Using Alternate Display Options (page 5-29) Saving and Loading an Atlas Parameter File (page 5-30) Working With 3D Wire Frame Atlases (page 5-2) Printing, Copying, or Exporting an Atlas (page 5-34) Manipulating Data Arrays and Data Sets in the Atlas Viewer (page 5-38)
FILL POLYGONAL TRACINGS WITH COLOR

PROCEDURE
To display the default fill color, click to check the Fill check box at the bottom of the Colors area, or choose Fill from the Atlas menu. To remove the Fill display, click to uncheck the Fill check box, or uncheck Fill on the Atlas menu.
The Atlas Shops Close Polygon feature allows open-tracings made with Length arrays to be closed, so they will fill with color when the Fill option is active in the Atlas Viewer. The Atlas Shops Open Polygon feature allows the closed-tracings made with area arrays to be opened, so they will NOT fill with color when the Fill option is active in the Atlas Viewer.

How To Use the Selection Lists (page 5-11) About The Apply, Save, and Restore Buttons (page 5-12) Change Tracing (Line or Symbol) Color (page 5-13) Distinguish Dual Labeled Structures (page 5-15) Change Fill Color (page 5-16) Restore Color and Symbol Defaults (page 5-17) Exclude Certain Objects or Symbols (page 5-18) Fill Some Objects But Not Others (page 5-19) Display Small Objects As Symbols (page 5-20) Symbolize Larger Objects (page 5-21) Assign a Different Symbol (page 5-22) Change the Size of the Symbols (page 5-23) Reduce The Number of Densely Packed Symbols (page 5-24) Manipulating the Atlas in the Atlas Window (page 5-2) Using the Atlas Parameters Dialog Box (page 5-7) Setting Atlas Parameters - Perspective Tab (page 5-7) Setting Atlas Parameters - Colors/Symbols Tab (page 5-10) Setting Atlas Parameters - Rotation Tab (page 5-25) Using Alternate Display Options (page 5-29) Saving and Loading an Atlas Parameter File (page 5-30) Working With 3D Wire Frame Atlases (page 5-2) Printing, Copying, or Exporting an Atlas (page 5-34) Manipulating Data Arrays and Data Sets in the Atlas Viewer (page 5-38)
DISTINGUISH DUAL LABELED STRUCTURES

PROCEDURE
To show areas of overlapping fill colors in a distinctive third color, click to check both the Fill and Overlap check boxes at the bottom of the Colors area. Alternately, check both these options on the Atlas menu. To remove the overlap color, click to uncheck the Overlap check box, or uncheck Overlap on the Atlas menu.

How To Use the Selection Lists (page 5-11) About The Apply, Save, and Restore Buttons (page 5-12) Change Tracing (Line or Symbol) Color (page 5-13) Fill Polygonal Tracings With Color (page 5-14) Change Fill Color (page 5-16) Restore Color and Symbol Defaults (page 5-17) Exclude Certain Objects or Symbols (page 5-18) Fill Some Objects But Not Others (page 5-19) Display Small Objects As Symbols (page 5-20) Symbolize Larger Objects (page 5-21) Assign a Different Symbol (page 5-22) Change the Size of the Symbols (page 5-23) Reduce The Number of Densely Packed Symbols (page 5-24) Manipulating the Atlas in the Atlas Window (page 5-2) Using the Atlas Parameters Dialog Box (page 5-7) Setting Atlas Parameters - Perspective Tab (page 5-7) Setting Atlas Parameters - Colors/Symbols Tab (page 5-10) Setting Atlas Parameters - Rotation Tab (page 5-25) Using Alternate Display Options (page 5-29) Saving and Loading an Atlas Parameter File (page 5-30) Working With 3D Wire Frame Atlases (page 5-2) Printing, Copying, or Exporting an Atlas (page 5-34) Manipulating Data Arrays and Data Sets in the Atlas Viewer (page 5-38)
CHANGE FILL COLOR

PROCEDURE
1. 2. 3. 4. Turn Fill on by clicking to check the Fill check box at the bottom of the Colors area. In the Atlas window, notice the current fill color of the group of objects for which the fill color is to be changed. Choose a new color be clicking one of the 16 colored squares in the Colors area. (The N square is for No Draw and the D square is for Default.) Entries in the Fill list are number 1 through 16 and each is a different color. Find and click the entry that matches the current Fill color of the objects for which color is to be changed. The entry in the Fill list changes to the new color. Repeat steps 2 through 4 for each fill color you wish to change. Click the Apply button to update the atlas display with the new fill color(s).
5. 6.
NOTE
The fill color assigned on the Atlas Parameters dialog box is the color used to surface render the atlas if the Atlas Modeler is opened.

How To Use the Selection Lists (page 5-11) About The Apply, Save, and Restore Buttons (page 5-12) Change Tracing (Line or Symbol) Color (page 5-13) Fill Polygonal Tracings With Color (page 5-14) Distinguish Dual Labeled Structures (page 5-15) Restore Color and Symbol Defaults (page 5-17) Exclude Certain Objects or Symbols (page 5-18) Fill Some Objects But Not Others (page 5-19) Display Small Objects As Symbols (page 5-20) Symbolize Larger Objects (page 5-21) Assign a Different Symbol (page 5-22) Change the Size of the Symbols (page 5-23) Reduce The Number of Densely Packed Symbols (page 5-24) Manipulating the Atlas in the Atlas Window (page 5-2) Using the Atlas Parameters Dialog Box (page 5-7) Setting Atlas Parameters - Perspective Tab (page 5-7) Setting Atlas Parameters - Colors/Symbols Tab (page 5-10) Setting Atlas Parameters - Rotation Tab (page 5-25) Using Alternate Display Options (page 5-29) Saving and Loading an Atlas Parameter File (page 5-30) Working With 3D Wire Frame Atlases (page 5-2) Printing, Copying, or Exporting an Atlas (page 5-34) Manipulating Data Arrays and Data Sets in the Atlas Viewer (page 5-38)
RESTORE COLOR AND SYMBOL DEFAULTS

PROCEDURE
To restore the default assignment of one color entry in either the Line/Sym list or the Fill list, click the Default (D) square in the Colors area, then click that entry in the list. To restore all the entries in the Line/Sym list or the Fill list to their default assignments, click the Default (D) square in the Colors area, then click and drag the cursor across all the entries in the list. To restore all the default Line/Sym, Fill, and Symbol assignments on the Colors/Symbols tab, click the Restore button.

How To Use the Selection Lists (page 5-11) About The Apply, Save, and Restore Buttons (page 5-12) Change Tracing (Line or Symbol) Color (page 5-13) Fill Polygonal Tracings With Color (page 5-14) Distinguish Dual Labeled Structures (page 5-15) Change Fill Color (page 5-16) Exclude Certain Objects or Symbols (page 5-18) Fill Some Objects But Not Others (page 5-19) Display Small Objects As Symbols (page 5-20) Symbolize Larger Objects (page 5-21) Assign a Different Symbol (page 5-22) Change the Size of the Symbols (page 5-23) Reduce The Number of Densely Packed Symbols (page 5-24) Manipulating the Atlas in the Atlas Window (page 5-2) Using the Atlas Parameters Dialog Box (page 5-7) Setting Atlas Parameters - Perspective Tab (page 5-7) Setting Atlas Parameters - Colors/Symbols Tab (page 5-10) Setting Atlas Parameters - Rotation Tab (page 5-25) Using Alternate Display Options (page 5-29) Saving and Loading an Atlas Parameter File (page 5-30) Working With 3D Wire Frame Atlases (page 5-2) Printing, Copying, or Exporting an Atlas (page 5-34) Manipulating Data Arrays and Data Sets in the Atlas Viewer (page 5-38)
EXCLUDE CERTAIN OBJECTS OR SYMBOLS

The No Draw (N) square on the color palette in the Colors area of the Colors/Symbol tab is used to hide the tracings, symbols, or fill color for a specified group of objects.
PROCEDURE
1. 2. 3. 4. 5. In the Atlas window, notice the current color of the group of objects that need to be hidden. On the color palette, click the No Draw (N) square. Find and click the entry in the Line/Sym list that matches the current color of the objects that are to be hidden. Repeat steps 1 through 3 for each color group you wish to hide. Click the Apply button to update the atlas display.

How To Use the Selection Lists (page 5-11) About The Apply, Save, and Restore Buttons (page 5-12) Change Tracing (Line or Symbol) Color (page 5-13) Fill Polygonal Tracings With Color (page 5-14) Distinguish Dual Labeled Structures (page 5-15) Change Fill Color (page 5-16) Restore Color and Symbol Defaults (page 5-17) Fill Some Objects But Not Others (page 5-19) Display Small Objects As Symbols (page 5-20) Symbolize Larger Objects (page 5-21) Assign a Different Symbol (page 5-22) Change the Size of the Symbols (page 5-23) Reduce The Number of Densely Packed Symbols (page 5-24) Manipulating the Atlas in the Atlas Window (page 5-2) Using the Atlas Parameters Dialog Box (page 5-7) Setting Atlas Parameters - Perspective Tab (page 5-7) Setting Atlas Parameters - Colors/Symbols Tab (page 5-10) Setting Atlas Parameters - Rotation Tab (page 5-25) Using Alternate Display Options (page 5-29) Saving and Loading an Atlas Parameter File (page 5-30) Working With 3D Wire Frame Atlases (page 5-2) Printing, Copying, or Exporting an Atlas (page 5-34) Manipulating Data Arrays and Data Sets in the Atlas Viewer (page 5-38)
FILL SOME OBJECTS BUT NOT OTHERS

No Draw is assigned to entries in the Fill list when there are multiple types of objects (each associated with a unique color) and you want some types to display as filled and not others.
PROCEDURE
1. 2. 3. 4. 5. Turn Fill on by clicking to check the Fill check box at the bottom of the Colors area. In the Atlas window, notice the current fill color of the group of objects for which the fill color is to be hidden. On the color palette, click the No Draw (N) square. In the Fill list find and click the entry that matches the current fill color of the objects for which the fill color is to be hidden. Click the Apply button to update the atlas display.

How To Use the Selection Lists (page 5-11) About The Apply, Save, and Restore Buttons (page 5-12) Change Tracing (Line or Symbol) Color (page 5-13) Fill Polygonal Tracings With Color (page 5-14) Distinguish Dual Labeled Structures (page 5-15) Change Fill Color (page 5-16) Restore Color and Symbol Defaults (page 5-17) Exclude Certain Objects or Symbols (page 5-18) Display Small Objects As Symbols (page 5-20) Symbolize Larger Objects (page 5-21) Assign a Different Symbol (page 5-22) Change the Size of the Symbols (page 5-23) Reduce The Number of Densely Packed Symbols (page 5-24) Manipulating the Atlas in the Atlas Window (page 5-2) Using the Atlas Parameters Dialog Box (page 5-7) Setting Atlas Parameters - Perspective Tab (page 5-7) Setting Atlas Parameters - Colors/Symbols Tab (page 5-10) Setting Atlas Parameters - Rotation Tab (page 5-25) Using Alternate Display Options (page 5-29) Saving and Loading an Atlas Parameter File (page 5-30) Working With 3D Wire Frame Atlases (page 5-2) Printing, Copying, or Exporting an Atlas (page 5-34) Manipulating Data Arrays and Data Sets in the Atlas Viewer (page 5-38)
DISPLAY SMALL OBJECTS AS SYMBOLS

Small objects can be made more visible by marking them with symbols. When the Symbols feature is activated, objects that have data points equal to or less than the Maximum Object Size value, will be displayed with the currently assigned symbol. By default, the system sets the Maximum Object Size value to 2, which allows only single point objects to be symbolized. Objects that appear in the atlas as single points or dots (such as those counted with an Object Count array), actually have two data points with zero distance between them. So the Maximum Object Size value must be at least 2.
PROCEDURE
To display the currently assigned symbol for small objects, click to check the Symbols check box at the bottom of the Symbols area. Alternatively, from the Atlas menu, click to check Symbols. To remove the symbolic display, click to uncheck the Symbols check box. Alternatively, from the Atlas menu, click to uncheck Symbols.

How To Use the Selection Lists (page 5-11) About The Apply, Save, and Restore Buttons (page 5-12) Change Tracing (Line or Symbol) Color (page 5-13) Fill Polygonal Tracings With Color (page 5-14) Distinguish Dual Labeled Structures (page 5-15) Change Fill Color (page 5-16) Restore Color and Symbol Defaults (page 5-17) Exclude Certain Objects or Symbols (page 5-18) Fill Some Objects But Not Others (page 5-19) Symbolize Larger Objects (page 5-21) Assign a Different Symbol (page 5-22) Change the Size of the Symbols (page 5-23) Reduce The Number of Densely Packed Symbols (page 5-24) Manipulating the Atlas in the Atlas Window (page 5-2) Using the Atlas Parameters Dialog Box (page 5-7) Setting Atlas Parameters - Perspective Tab (page 5-7) Setting Atlas Parameters - Colors/Symbols Tab (page 5-10) Setting Atlas Parameters - Rotation Tab (page 5-25) Using Alternate Display Options (page 5-29) Saving and Loading an Atlas Parameter File (page 5-30) Working With 3D Wire Frame Atlases (page 5-2) Printing, Copying, or Exporting an Atlas (page 5-34) Manipulating Data Arrays and Data Sets in the Atlas Viewer (page 5-38)
SYMBOLIZE LARGER OBJECTS

The Maximum Object Size value may be increased so slightly larger objects may be displayed as symbols. 1. 2. 3. In the Maximum Object Size field, scroll to or type in a higher number. Click the Apply button to display the changes. Repeat steps 1 and 2 as needed until all of the desired tracings are symbolized.

How To Use the Selection Lists (page 5-11) About The Apply, Save, and Restore Buttons (page 5-12) Change Tracing (Line or Symbol) Color (page 5-13) Fill Polygonal Tracings With Color (page 5-14) Distinguish Dual Labeled Structures (page 5-15) Change Fill Color (page 5-16) Restore Color and Symbol Defaults (page 5-17) Exclude Certain Objects or Symbols (page 5-18) Fill Some Objects But Not Others (page 5-19) Display Small Objects As Symbols (page 5-20) Assign a Different Symbol (page 5-22) Change the Size of the Symbols (page 5-23) Reduce The Number of Densely Packed Symbols (page 5-24) Manipulating the Atlas in the Atlas Window (page 5-2) Using the Atlas Parameters Dialog Box (page 5-7) Setting Atlas Parameters - Perspective Tab (page 5-7) Setting Atlas Parameters - Colors/Symbols Tab (page 5-10) Setting Atlas Parameters - Rotation Tab (page 5-25) Using Alternate Display Options (page 5-29) Saving and Loading an Atlas Parameter File (page 5-30) Working With 3D Wire Frame Atlases (page 5-2) Printing, Copying, or Exporting an Atlas (page 5-34) Manipulating Data Arrays and Data Sets in the Atlas Viewer (page 5-38)
ASSIGN A DIFFERENT SYMBOL

The default symbol assigned by the system to a particular color group may be changed to any of the alternate symbols on the Available symbol drop list. Symbols are most often used to replace dots in the atlas. But, there are two cases in which it is advantageous to assign the dot symbol to tracings, or replace a larger symbol with a dot symbol: a. During measurement, an Area array is sometimes used for cell counting in order to take advantage of BIOQUANTs Auto Exclude feature. This generates a tracing with multiple data points rather than a single dot. In this case, if desirable, the area tracings can be replaced by the dot symbol. When there is a very large number of object count markers in the atlas (e.g. cells), the default symbol assigned to the markers color may be too big and the symbolized display appears crowded. In this case the larger default symbol may be changed to the smaller dot symbol.
b.
PROCEDURE
1. 2. 3. 4. 5. Display the current symbol(s) in the atlas by clicking to check the Symbols check box. In the Atlas window, identify the color of the group of objects for which the symbol should be changed. In the Symbols area, in the Available field, click the down arrowhead to display a small scroll list. Using the two small scroll buttons, scroll through the available symbols and click to choose the desired symbol. In the Symbol list, find and click the entry that matches the color of objects of interest (identified in step 2). The symbol associated with that entry will change to the new symbol. Click the Apply button to update the atlas display. If all of the objects in the designated color group do not symbolize, it means that the group includes objects that are larger than the Maximum Object Size. Increase the value in the Maximum Object Size field and click the Apply button again. Continue to increase the Maximum Object Size until all the objects in the color group are replaced by the chosen symbol.

How To Use the Selection Lists (page 5-11) About The Apply, Save, and Restore Buttons (page 5-12) Change Tracing (Line or Symbol) Color (page 5-13) Fill Polygonal Tracings With Color (page 5-14) Distinguish Dual Labeled Structures (page 5-15) Change Fill Color (page 5-16) Restore Color and Symbol Defaults (page 5-17) Exclude Certain Objects or Symbols (page 5-18) Fill Some Objects But Not Others (page 5-19) Display Small Objects As Symbols (page 5-20) Symbolize Larger Objects (page 5-21) Change the Size of the Symbols (page 5-23) Reduce The Number of Densely Packed Symbols (page 5-24) Manipulating the Atlas in the Atlas Window (page 5-2) Using the Atlas Parameters Dialog Box (page 5-7) Setting Atlas Parameters - Perspective Tab (page 5-7) Setting Atlas Parameters - Colors/Symbols Tab (page 5-10) Setting Atlas Parameters - Rotation Tab (page 5-25) Using Alternate Display Options (page 5-29) Saving and Loading an Atlas Parameter File (page 5-30) Working With 3D Wire Frame Atlases (page 5-2) Printing, Copying, or Exporting an Atlas (page 5-34) Manipulating Data Arrays and Data Sets in the Atlas Viewer (page 5-38)
CHANGE THE SIZE OF THE SYMBOLS

The default size of symbols is eight pixels by eight pixels. This can be increased or decreased as needed. Changes in symbol size are applied to all symbols (not just the symbol of one selected color group).
PROCEDURE
To adjust the height of the symbols, increase or decrease the value in the Symbol Size Height field by scrolling to or typing in a larger value. To adjust the width of the symbols, increase or decrease the value in the Symbol Size Width field.

How To Use the Selection Lists (page 5-11) About The Apply, Save, and Restore Buttons (page 5-12) Change Tracing (Line or Symbol) Color (page 5-13) Fill Polygonal Tracings With Color (page 5-14) Distinguish Dual Labeled Structures (page 5-15) Change Fill Color (page 5-16) Restore Color and Symbol Defaults (page 5-17) Exclude Certain Objects or Symbols (page 5-18) Fill Some Objects But Not Others (page 5-19) Display Small Objects As Symbols (page 5-20) Symbolize Larger Objects (page 5-21) Assign a Different Symbol (page 5-22) Reduce The Number of Densely Packed Symbols (page 5-24) Manipulating the Atlas in the Atlas Window (page 5-2) Using the Atlas Parameters Dialog Box (page 5-7) Setting Atlas Parameters - Perspective Tab (page 5-7) Setting Atlas Parameters - Colors/Symbols Tab (page 5-10) Setting Atlas Parameters - Rotation Tab (page 5-25) Using Alternate Display Options (page 5-29) Saving and Loading an Atlas Parameter File (page 5-30) Working With 3D Wire Frame Atlases (page 5-2) Printing, Copying, or Exporting an Atlas (page 5-34) Manipulating Data Arrays and Data Sets in the Atlas Viewer (page 5-38)
REDUCE THE NUMBER OF DENSELY PACKED SYMBOLS

When Show Every (nth) Symbol is set to 1, a symbol is displayed for every single object that meets the Maximum Object Size criterion. The symbols representing a group of objects may be thinned out by increasing the nth value to a number greater than 1. A value of 2 will display every second symbol. A value of 3 will display every third symbol, and so on.
PROCEDURE
1. 2. 3. In the Show Every (nth) Symbol field, increase the current value by 1. Click the Apply button. If symbols are still too numerous, repeat steps 1 and 2.

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

TOPIC CONTENTS
Dynamically Rotate the Wire Frame Atlas (page 5-26) Record a Movie of a Rotating Wire Frame Atlas (page 5-27) Play a Movie of a Rotating Atlas (page 5-28)
Page 5-26
The Atlas Parameters: Rotation Tab
RELATED TOPICS
Manipulating the Atlas in the Atlas Window (page 5-2) Using the Atlas Parameters Dialog Box (page 5-7) Setting Atlas Parameters - Perspective Tab (page 5-7) Setting Atlas Parameters - Colors/Symbols Tab (page 5-10) Using Alternate Display Options (page 5-29) Saving and Loading an Atlas Parameter File (page 5-30) Working With 3D Wire Frame Atlases (page 5-2) Printing, Copying, or Exporting an Atlas (page 5-34) Manipulating Data Arrays and Data Sets in the Atlas Viewer (page 5-38)
DYNAMICALLY ROTATE THE WIRE FRAME ATLAS

A rotating wire frame atlas may be recorded as an AVI movie. In the Atlas Viewer, the Rotation tab of the Atlas Parameters dialog box is where AVI movie parameters are set. Dynamically rotating an atlas is done much like animation: a series of still images, each slightly changed from the one before, are played in rapid succession to create the illusion of motion. This motion will appear choppy until it is recorded and played back in an AVI movie. (The smaller the change between images, the smoother the motion.) Rotations on the Atlas Parameters dialog box are limited to a maximum of 360 frames. The Delay value specifies the millisecond pause before the next frame is loaded. If Loop is checked, the rotation repeats itself. The Step button advances through the rotation frame by frame. The Cancel button stops the rotation.
PROCEDURE
1. 2. Decide around which axis the atlas is to rotate (X, Y, or Z). Provide the number of frames required for one complete 360 degree rotation by doing the following: a. b. 3. 4. Divide 360 by the number of degrees the atlas is to rotate for each frame (e.g. 10), then subtract 1 from that number. Example:(360/10) - 1 = 35 Type this value in the Number of Frames field.
In the Degree Rotation per Frame field for the desired axis, type the number of degrees that the atlas should be rotated (e.g. 10). The atlas may be rotated by the following methods. To view one complete rotation, click the Rotate button.
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To change the speed of rotation, increase or decrease the millisecond value in the Delay field and click the Rotate button. To advance the rotation one frame at a time, click the Step button. To view a continuous rotation, click to check the Loop check box, then press the Rotate button. To stop a continuous rotation, click the Cancel button.
RELATED TOPICS
Record a Movie of a Rotating Wire Frame Atlas (page 5-27) Play a Movie of a Rotating Atlas (page 5-28) Manipulating the Atlas in the Atlas Window (page 5-2) Using the Atlas Parameters Dialog Box (page 5-7) Setting Atlas Parameters - Perspective Tab (page 5-7) Setting Atlas Parameters - Colors/Symbols Tab (page 5-10) Setting Atlas Parameters - Rotation Tab (page 5-25) Using Alternate Display Options (page 5-29) Saving and Loading an Atlas Parameter File (page 5-30) Working With 3D Wire Frame Atlases (page 5-2) Printing, Copying, or Exporting an Atlas (page 5-34) Manipulating Data Arrays and Data Sets in the Atlas Viewer (page 5-38)
RECORD A MOVIE OF A ROTATING WIRE FRAME ATLAS

Note: The freeware BIOQUANT Topo Reader cannot be used to record AVI movies. To record a movie, the full BIOQUANT Topographer Plug-In is required.
PROCEDURE
1. Set the desired rotation parameters, then in the Recording Parameters area click the Record button to open the Save Movie File navigation box. The Save Movie File Box
2.
On the Save Movie File box, navigate to the desired destination drive using the following guide lines: The movie file will be saved to the drive or folder that is in the Save In field. Clicking the down arrow folder may be chosen. Clicking the Up Folder in the Save In field will open a drop list, from which an alternate drive or button will close the folder in the Save In field and open its parent folder.
Clicking the New Folder button will add a new folder to the drive or folder that is currently displayed in the Save In field. Click the cursor in the New Folder edit field and type an appropriate name for the new folder. Double clicking a folder in the center list will place it in the Save In field.
3.
When the desired destination folder is in the Save In field, click the cursor in the File Name text box, and type a name for the movie file.
Page 5-28
4. 5. Click the Save button to create frames of the movie. Depending on the number of frames, this may take a while. When all the frames have been captured, the Video Compression dialog box opens. From the Compressor drop list, choose Microsoft Video 1. The Video Compression Box
6.
Click the OK button to create the AVI file.
RELATED TOPICS
Dynamically Rotate the Wire Frame Atlas (page 5-26) Play a Movie of a Rotating Atlas (page 5-28) Manipulating the Atlas in the Atlas Window (page 5-2) Using the Atlas Parameters Dialog Box (page 5-7) Setting Atlas Parameters - Perspective Tab (page 5-7) Setting Atlas Parameters - Colors/Symbols Tab (page 5-10) Setting Atlas Parameters - Rotation Tab (page 5-25) Using Alternate Display Options (page 5-29) Saving and Loading an Atlas Parameter File (page 5-30) Working With 3D Wire Frame Atlases (page 5-2) Printing, Copying, or Exporting an Atlas (page 5-34) Manipulating Data Arrays and Data Sets in the Atlas Viewer (page 5-38)
PLAY A MOVIE OF A ROTATING ATLAS

PROCEDURE
1. Open the Load Movie File dialog box in any of the following ways: On the Rotate tab of the Atlas Parameters dialog box, click the Load button. Choosing Play Movie from the File menu. Click the Play Movie button on the system tool bar.
The Load Movie Box
2. 3. 4.
Navigate to the folder that contains the movie file (.avi). Click to highlight the movie file to be opened. Click the Open button. The first frame of the movie will display in the atlas window.
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5. Click the Play button to play the movie.
ADDITIONAL NOTES
AVI video files can also be played using the Media Player (found in the multi-media accessories) or by simply double clicking on the AVI file in My Computer or the Explorer. AVI video files can be viewed on any computer with the Windows Media Player. The computer does not need to have BIOQUANTs Topographer installed. Control-M will also open the Load Movie File box.
RELATED TOPICS
Dynamically Rotate the Wire Frame Atlas (page 5-26) Record a Movie of a Rotating Wire Frame Atlas (page 5-27) Manipulating the Atlas in the Atlas Window (page 5-2) Using the Atlas Parameters Dialog Box (page 5-7) Setting Atlas Parameters - Perspective Tab (page 5-7) Setting Atlas Parameters - Colors/Symbols Tab (page 5-10) Setting Atlas Parameters - Rotation Tab (page 5-25) Using Alternate Display Options (page 5-29) Saving and Loading an Atlas Parameter File (page 5-30) Working With 3D Wire Frame Atlases (page 5-2) Printing, Copying, or Exporting an Atlas (page 5-34) Manipulating Data Arrays and Data Sets in the Atlas Viewer (page 5-38)
USING ALTERNATE DISPLAY OPTIONS

TOPIC CONTENTS
Atlas> Black Background (page 5-29) Atlas> Thick Tracings (page 5-30)
RELATED TOPICS
Using the Atlas Parameters Dialog Box (page 5-7) Setting Atlas Parameters - Perspective Tab (page 5-7) Setting Atlas Parameters - Colors/Symbols Tab (page 5-10) Setting Atlas Parameters - Rotation Tab (page 5-25) Using Alternate Display Options (page 5-29) Saving and Loading an Atlas Parameter File (page 5-30) Working With 3D Wire Frame Atlases (page 5-2) Printing, Copying, or Exporting an Atlas (page 5-34) Manipulating Data Arrays and Data Sets in the Atlas Viewer (page 5-38)
ATLAS> BLACK BACKGROUND

The colors in the atlas sometimes show better against a black background.
PROCEDURE
To display a black background, on the Atlas menu click to check Black Background. To re-display a white background, on the Atlas menu click to uncheck Black Background.
A black background is generally not recommended when printing an atlas.

Atlas> Thick Tracings (page 5-30) Using the Atlas Parameters Dialog Box (page 5-7) Setting Atlas Parameters - Perspective Tab (page 5-7) Setting Atlas Parameters - Colors/Symbols Tab (page 5-10) Setting Atlas Parameters - Rotation Tab (page 5-25) Using Alternate Display Options (page 5-29) Saving and Loading an Atlas Parameter File (page 5-30) Working With 3D Wire Frame Atlases (page 5-2) Printing, Copying, or Exporting an Atlas (page 5-34) Manipulating Data Arrays and Data Sets in the Atlas Viewer (page 5-38)
ATLAS> THICK TRACINGS

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

TOPIC CONTENTS
File> Save Parameters (page 5-31) File> Load Parameters (page 5-32) BIOQUANT Topographer Handbook: The Atlas Viewer in Detail

Using the Atlas Parameters Dialog Box (page 5-7) Setting Atlas Parameters - Perspective Tab (page 5-7) Setting Atlas Parameters - Colors/Symbols Tab (page 5-10) Setting Atlas Parameters - Rotation Tab (page 5-25) Using Alternate Display Options (page 5-29) Saving and Loading an Atlas Parameter File (page 5-30) Working With 3D Wire Frame Atlases (page 5-2) Printing, Copying, or Exporting an Atlas (page 5-34) Manipulating Data Arrays and Data Sets in the Atlas Viewer (page 5-38)
FILE> SAVE PARAMETERS

Save Parameters is available when the Atlas Window is open. A Parameter file records which arrays were used to generate the reconstruction and saves the Perspective and Color/Symbols settings for a particular view of the atlas. Anytime in the future that the same data set is opened, its Parameter file may be loaded to instantly recall the preferred settings.
PROCEDURE
1. Open the Save Parameters dialog box using any of the following methods: 2. On the system tool bar click the Save Parameters From the File menu choose Save Parameters. Click the Save button on either the Perspective or Color/Symbols tab of the Atlas Parameters dialog box. button.
The default Save in location is BQOSTEO\Topographer. For ease of finding the parameters file again, it is recommended that you create a subdirectory in the Topographer folder that is named the same as your Data Volume and Data Set. Then when you later need to find and open the parameter files for a particular Data Set you can easily navigate to them. To do this: a. Click the Create New Folder button. The Save Parameter File Dialog Box
b.
Rename the New Folder to your Data Volume and Data Set Name.
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The Save Parameter File Dialog Box
c. 3.
Double click the new folder to open it. You will save in this location.
Type a file name into the File name text box. The Save Parameter File Dialog Box
4.
Click the Save button to save the file.
ADDITIONAL NOTES
Control-S opens the Save Parameters box. Parameter files have .set extensions.
RELATED TOPICS
File> Load Parameters (page 5-32) Using the Atlas Parameters Dialog Box (page 5-7) Setting Atlas Parameters - Perspective Tab (page 5-7) Setting Atlas Parameters - Colors/Symbols Tab (page 5-10) Setting Atlas Parameters - Rotation Tab (page 5-25) Using Alternate Display Options (page 5-29) Saving and Loading an Atlas Parameter File (page 5-30) Working With 3D Wire Frame Atlases (page 5-2) Printing, Copying, or Exporting an Atlas (page 5-34) Manipulating Data Arrays and Data Sets in the Atlas Viewer (page 5-38)
FILE> LOAD PARAMETERS

Load Parameters is available both when the Atlas Window is closed and open. Loading a Parameters file instantly selects the arrays that were originally used to generate the atlas and resets the Perspective and Color/Symbol parameters that were active when the parameters file was saved.
PROCEDURE
1. On the system tool bar click the Load Parameters to open the Open Parameter File dialog box. button, or from the File menu choose Load Parameters,
Page 5-33
2. The default location for saving parameter files is BQOSTEO\Topographer. If you created a subdirectory associated with your Data Volume and Data Set as recommended in the Save Parameters procedure, it will be listed here. Navigate to the folder that contains the Parameter file for the current data set. The Open Parameter File Dialog Box
3.
Click on the parameter file to be opened. The Open Parameter File Dialog Box
4.
Click the Open button. The appearance of the atlas will change to reflect the loaded parameters.
ADDITIONAL NOTES
If the error message, Parameter File Error: Sequence list not for this data set! File ignored. appears, the parameter file is for a different data set. Choose a different Parameter file or open the data set for which the file was saved. Control-L opens the Load Parameters box. Parameter files have .set extensions.
RELATED TOPICS
File> Save Parameters (page 5-31) Using the Atlas Parameters Dialog Box (page 5-7) Setting Atlas Parameters - Perspective Tab (page 5-7) Setting Atlas Parameters - Colors/Symbols Tab (page 5-10) Setting Atlas Parameters - Rotation Tab (page 5-25) Using Alternate Display Options (page 5-29) Saving and Loading an Atlas Parameter File (page 5-30) Working With 3D Wire Frame Atlases (page 5-2) Printing, Copying, or Exporting an Atlas (page 5-34) Manipulating Data Arrays and Data Sets in the Atlas Viewer (page 5-38)
Page 5-34
PRINTING, COPYING, OR EXPORTING AN ATLAS

TOPIC CONTENTS
Printing a Wire Frame Atlas (page 5-34) Copying a Wire Frame Atlas (page 5-35) Exporting a 2D Atlas (page 5-35)
RELATED TOPICS
Atlas Viewer Menu and Tool Bars (page 5-2) Manipulating the Atlas in the Atlas Window (page 5-2) Using the Atlas Parameters Dialog Box (page 5-7) Setting Atlas Parameters - Perspective Tab (page 5-7) Setting Atlas Parameters - Colors/Symbols Tab (page 5-10) Setting Atlas Parameters - Rotation Tab (page 5-25) Using Alternate Display Options (page 5-29) Saving and Loading an Atlas Parameter File (page 5-30) Working With 3D Wire Frame Atlases (page 5-2) Manipulating Data Arrays and Data Sets in the Atlas Viewer (page 5-38)
PRINTING A WIRE FRAME ATLAS

Print Atlas is available on the Atlas Viewers File menu when the Atlas Window is open. Topographer prints an atlas out at five inches by five inches. It titles the atlas with the names of the data volume and data set and the date. To print the atlas at a different size, export the atlas as a bitmap or metafile and print it from a graphics application (e.g. Adobe Photoshop or JASC Paint Shop Pro).
PROCEDURE
1. From the Atlas Viewers File menu, choose Print Atlas, to open the Print dialog box. The Print Box
2. 3.
Adjust any printing options. Click the OK button.
ADDITIONAL NOTE
Control-P opens the Print dialog box.

Copying a Wire Frame Atlas (page 5-35) Exporting a 2D Atlas (page 5-35) Atlas Viewer Menu and Tool Bars (page 5-2) Manipulating the Atlas in the Atlas Window (page 5-2) Using the Atlas Parameters Dialog Box (page 5-7) Setting Atlas Parameters - Perspective Tab (page 5-7) Setting Atlas Parameters - Colors/Symbols Tab (page 5-10) Setting Atlas Parameters - Rotation Tab (page 5-25) Using Alternate Display Options (page 5-29) Saving and Loading an Atlas Parameter File (page 5-30) Working With 3D Wire Frame Atlases (page 5-2) Printing, Copying, or Exporting an Atlas (page 5-34) Manipulating Data Arrays and Data Sets in the Atlas Viewer (page 5-38)
COPYING A WIRE FRAME ATLAS

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

Printing a Wire Frame Atlas (page 5-34) Copying a Wire Frame Atlas (page 5-35) Atlas Viewer Menu and Tool Bars (page 5-2) Manipulating the Atlas in the Atlas Window (page 5-2) Using the Atlas Parameters Dialog Box (page 5-7) Setting Atlas Parameters - Perspective Tab (page 5-7) Setting Atlas Parameters - Colors/Symbols Tab (page 5-10) Setting Atlas Parameters - Rotation Tab (page 5-25) Using Alternate Display Options (page 5-29) Saving and Loading an Atlas Parameter File (page 5-30) Working With 3D Wire Frame Atlases (page 5-2) Printing, Copying, or Exporting an Atlas (page 5-34) Manipulating Data Arrays and Data Sets in the Atlas Viewer (page 5-38)
USING EXPORT CURRENT VIEW TO BMP

The bitmap is a two dimensional format, in essence a snapshot of the atlas. It can be opened by many programs, including Adobe Photoshop, Microsoft Word, and Microsoft PowerPoint. A bitmap loses integrity if the size is enlarged in another program. To save in a 2D vector format that can be resized in another program, see Using Export Current Topo to SVG (page 5-37).
PROCEDURE
1. From the Atlas Viewers File menu, choose Export Current View to BMP. Export to BMP Box
2. 3. 4.
Navigate to the folder where the file should be saved. Type a filename into the File Name text box. Click the OK button to create the file.

Using Export Current Topo to SVG (page 5-37) Printing a Wire Frame Atlas (page 5-34) Copying a Wire Frame Atlas (page 5-35) Exporting a 2D Atlas (page 5-35) Atlas Viewer Menu and Tool Bars (page 5-2) Manipulating the Atlas in the Atlas Window (page 5-2) Using the Atlas Parameters Dialog Box (page 5-7) Setting Atlas Parameters - Perspective Tab (page 5-7) Setting Atlas Parameters - Colors/Symbols Tab (page 5-10) Setting Atlas Parameters - Rotation Tab (page 5-25) Using Alternate Display Options (page 5-29) Saving and Loading an Atlas Parameter File (page 5-30) Working With 3D Wire Frame Atlases (page 5-2) Printing, Copying, or Exporting an Atlas (page 5-34) Manipulating Data Arrays and Data Sets in the Atlas Viewer (page 5-38)
USING EXPORT CURRENT TOPO TO SVG

Scalable Vector Graphic (SVG) is a two-dimensional vector format that can be opened with many programs, including Inkscape, Firefox, and Chrome. If you need a free SVG view, download Inkscape from http://www.inkscape.org.
PROCEDURE
1. 2. In the Atlas Viewer, in the Select Arrays Selected box, select the Topo array to export. In the Atlas Viewer, click the Resize to Fit button to center and size the Topo data. BIOQUANT currently exports the raw Topo data colors. Do not use the Parameters box to change colors. If you want to change colors, use the Atlas Shop to first save to a new Topo array, and then permanently change the colors. BIOQUANT currently exports only the current Topo array. If there are several Topo arrays you would like exported, use the Atlas Shop to combine the Topo arrays into a single, new Topo array. Then export it.
3.
From the Atlas Viewers File menu, choose Export Current Topo to SVG. The Save TOPO Array to SVG File Box
4.
Navigate to the folder where the file should be saved. The default folder for saving Topographer parameter files is BQOSTEO\Topographer or BQLifeScience\Topographer. Type a filename into the File Name text box. Click the OK button to create the file.
5. 6.

Using Export Current View to BMP (page 5-36) Printing a Wire Frame Atlas (page 5-34) Copying a Wire Frame Atlas (page 5-35) Exporting a 2D Atlas (page 5-35) Atlas Viewer Menu and Tool Bars (page 5-2) Manipulating the Atlas in the Atlas Window (page 5-2) Using the Atlas Parameters Dialog Box (page 5-7) Setting Atlas Parameters - Perspective Tab (page 5-7) Setting Atlas Parameters - Colors/Symbols Tab (page 5-10) Setting Atlas Parameters - Rotation Tab (page 5-25) Using Alternate Display Options (page 5-29) Saving and Loading an Atlas Parameter File (page 5-30) Working With 3D Wire Frame Atlases (page 5-2) Printing, Copying, or Exporting an Atlas (page 5-34) Manipulating Data Arrays and Data Sets in the Atlas Viewer (page 5-38)
MANIPULATING DATA ARRAYS AND DATA SETS IN THE ATLAS VIEWER

Following are Atlas Viewer features that were not covered in detail elsewhere in this manual.
TOPIC CONTENTS
Using Select Arrays in the Atlas Viewer (page 5-38) Using List Data in the Atlas Viewer (page 5-40) Using Save Data and Save Data Set (page 5-45) Converting BQ-OS/2 Data to Topo Data (page 5-46)
RELATED TOPICS
Atlas Viewer Menu and Tool Bars (page 5-2) Manipulating the Atlas in the Atlas Window (page 5-2) Using the Atlas Parameters Dialog Box (page 5-7) Setting Atlas Parameters - Perspective Tab (page 5-7) Setting Atlas Parameters - Colors/Symbols Tab (page 5-10) Setting Atlas Parameters - Rotation Tab (page 5-25) Using Alternate Display Options (page 5-29) Saving and Loading an Atlas Parameter File (page 5-30) Working With 3D Wire Frame Atlases (page 5-2) Printing, Copying, or Exporting an Atlas (page 5-34)
USING SELECT ARRAYS IN THE ATLAS VIEWER

SELECT ARRAYS
Select Arrays is available on the Atlas Viewers Arrays menu regardless of whether the Atlas Window is closed or open. The Select Arrays box determines which topo arrays are drawn in the Atlas Window. The Available Arrays list shows all the arrays in the data set. The arrays in the Selected list are the arrays used to construct the atlas. These are also the arrays that are available for editing in the Atlas Shop when the full Topographer Plug-in program is present. Only Topo arrays can be put in the Selected list. Each data set can memorize a group of arrays which is moved collectively into the Selected list. The arrays is the selected list are also saved in the Parameter file. The Select Arrays box can be used to rename arrays. To add and delete arrays, use the Add/Delete Topo Arrays box that is on the Arrays menu when there is no atlas open.
Page 5-39
The Select Arrays Dialog Box
GENERAL SELECT ARRAYS FUNCTIONS

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

Using List Data in the Atlas Viewer (page 5-40) Using Save Data and Save Data Set (page 5-45) Converting BQ-OS/2 Data to Topo Data (page 5-46) Atlas Viewer Menu and Tool Bars (page 5-2) Manipulating the Atlas in the Atlas Window (page 5-2) Using the Atlas Parameters Dialog Box (page 5-7) Setting Atlas Parameters - Perspective Tab (page 5-7) Setting Atlas Parameters - Colors/Symbols Tab (page 5-10) Setting Atlas Parameters - Rotation Tab (page 5-25) Using Alternate Display Options (page 5-29) Saving and Loading an Atlas Parameter File (page 5-30) Working With 3D Wire Frame Atlases (page 5-2) Printing, Copying, or Exporting an Atlas (page 5-34) Manipulating Data Arrays and Data Sets in the Atlas Viewer (page 5-38)
USING LIST DATA IN THE ATLAS VIEWER

The List Data window shows the data in array(s). On rare occasions, it may seem necessary or desirable to view, print, or delete the data in a Topo array. This can be done by selecting the Topo array on the Select Arrays dialog box and using the appropriate tools on the List window. Unlike measurement arrays, the data in Topo arrays cannot be edited in the List window. When a Topo array is selected, five of the six data editing buttons on the List toolbar become unavailable (grayed out). The only data editing tool that remains is Delete Listed Data . If the current data set is password protected (a password was assigned and Password Protection was enabled in Life Science or OSTEO), the correct password must be entered before Topo data can be deleted on the Atlas Viewers List window.
TOPIC CONTENTS
Viewing Topo Data (page 5-40) Printing Topo Data (page 5-41) Deleting Data From a Topo Array (page 5-42) Adding and Deleting Topo Arrays (page 5-43)
RELATED TOPICS
Using Select Arrays in the Atlas Viewer (page 5-38) Using List Data in the Atlas Viewer (page 5-40) Using Save Data and Save Data Set (page 5-45) Converting BQ-OS/2 Data to Topo Data (page 5-46) Atlas Viewer Menu and Tool Bars (page 5-2) Manipulating the Atlas in the Atlas Window (page 5-2) Using the Atlas Parameters Dialog Box (page 5-7) Setting Atlas Parameters - Perspective Tab (page 5-7) Setting Atlas Parameters - Colors/Symbols Tab (page 5-10) Setting Atlas Parameters - Rotation Tab (page 5-25) Using Alternate Display Options (page 5-29) Saving and Loading an Atlas Parameter File (page 5-30) Working With 3D Wire Frame Atlases (page 5-2) Printing, Copying, or Exporting an Atlas (page 5-34) Manipulating Data Arrays and Data Sets in the Atlas Viewer (page 5-38)
VIEWING TOPO DATA

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

There may be many thousands of data points in a single Topo array, so printing topographic data is a time and paper consuming job. Fortunately, printing Topo data is rarely necessary, but it is possible. BIOQUANT Topographer Handbook: The Atlas Viewer in Detail
Page 5-42 PROCEDURE

1. 2. 3. On the Select Arrays dialog box, select the desired Topo array. From the Array menu, choose List Data to open the List dialog box. Click the Print button on the List toolbar to open the Print Setup dialog box.
The List windows Print Setup dialog box
4.
On the Print Setup dialog box do one or more of the following: To include the array name on the printout, click to check the Print Array Names check box. To change the default header (title) information on the printout, click the cursor in the field that is to be edited, delete the existing text, and type the desired information. Click the OK button to print the data report.
RELATED TOPICS
Viewing Topo Data (page 5-40) Deleting Data From a Topo Array (page 5-42) Adding and Deleting Topo Arrays (page 5-43) Using Select Arrays in the Atlas Viewer (page 5-38) Using List Data in the Atlas Viewer (page 5-40) Using Save Data and Save Data Set (page 5-45) Converting BQ-OS/2 Data to Topo Data (page 5-46) Atlas Viewer Menu and Tool Bars (page 5-2) Manipulating the Atlas in the Atlas Window (page 5-2) Using the Atlas Parameters Dialog Box (page 5-7) Setting Atlas Parameters - Perspective Tab (page 5-7) Setting Atlas Parameters - Colors/Symbols Tab (page 5-10) Setting Atlas Parameters - Rotation Tab (page 5-25) Using Alternate Display Options (page 5-29) Saving and Loading an Atlas Parameter File (page 5-30) Working With 3D Wire Frame Atlases (page 5-2) Printing, Copying, or Exporting an Atlas (page 5-34) Manipulating Data Arrays and Data Sets in the Atlas Viewer (page 5-38)
DELETING DATA FROM A TOPO ARRAY

PROCEDURE
1. 2. 3. On the Select Arrays dialog box, select the desired Topo array. From the Array menu, choose List Data to open the List dialog box. Click the Delete Listed Data 4. button on the List toolbar.
If a Password box opens, enter the correct password, then click the OK button.
On the Warning message box... Click the Yes button to continue the delete procedure. Click the No button to cancel the delete command.
5.
On the Verify message box...
Page 5-43
Click the Yes button to delete the data in the listed Topo array. Click the No button to cancel the delete command.
RELATED TOPICS
Adding and Deleting Topo Arrays (page 5-43) Viewing Topo Data (page 5-40) Printing Topo Data (page 5-41) Using Select Arrays in the Atlas Viewer (page 5-38) Using List Data in the Atlas Viewer (page 5-40) Using Save Data and Save Data Set (page 5-45) Converting BQ-OS/2 Data to Topo Data (page 5-46) Atlas Viewer Menu and Tool Bars (page 5-2) Manipulating the Atlas in the Atlas Window (page 5-2) Using the Atlas Parameters Dialog Box (page 5-7) Setting Atlas Parameters - Perspective Tab (page 5-7) Setting Atlas Parameters - Colors/Symbols Tab (page 5-10) Setting Atlas Parameters - Rotation Tab (page 5-25) Using Alternate Display Options (page 5-29) Saving and Loading an Atlas Parameter File (page 5-30) Working With 3D Wire Frame Atlases (page 5-2) Printing, Copying, or Exporting an Atlas (page 5-34) Manipulating Data Arrays and Data Sets in the Atlas Viewer (page 5-38)
ADDING AND DELETING TOPO ARRAYS

Add/Delete Topo is available on the Atlas Viewers Array menu only when the Atlas Window is closed. The Add/ Delete Topo Array dialog box is used to add, rename, and remove Topo arrays from the currently open data set. As Topo arrays are added, they are given the next available index (e.g. D3). Arrays can only be deleted from the bottom of the index series up. For example, the D4 array must be deleted before the D3 array can be deleted.
ADDING A TOPO ARRAY

When topo arrays are added, they are given the next available D# index and given the default name Topo, which can be changed to a more descriptive name. 1. 2. If the Atlas Window is open, from the Atlas menu, choose Close to close it. From the Array menu, choose Add/Delete Topo... to open the Add/Delete Topo Array box. The Add/Delete Topo Array Dialog Box
3. 4. 5. 6. 7.
Click the Add Topo button to add a topo array. In the Arrays list, click on the new topo array to display its name in the Name field. Type in a new name for the array. Click the Update button to update the name of the array in the arrays list. Click the Close button to close the Add/Delete Topo Array dialog box.
Page 5-44 ADDITIONAL NOTES

Arrays can be renamed in the Select Arrays box too.
DELETING A TOPO ARRAY

Arrays can only be deleted from the bottom of the index series up. For example, the D4 array would have to be deleted before the D3 array could be deleted. 1. 2. If the Atlas Window is open, from the Atlas menu, choose Close to close it. From the Array menu, choose Add/Delete Topo... to open the Add/Delete Topo Array box. The Add/Delete Topo Dialog Box
The name of the highlighted array is displayed in the Name field.
3. 4.
In the Arrays list, click to highlight the name of the array that is to be deleted. Click the Delete button. A delete Warning message will appear. Click the Yes button to delete the array. Click the No button to cancel the delete command. If a Delete Failed message appears with the message Arrays with the same letter in the index must be deleted from the bottom up. (Example: D3 must be deleted before D2.) then the other arrays must be deleted before the currently chosen array can be deleted.
5. 6.
Repeat from step 3 for each Topo array that needs to be deleted. Click the Close button to close the Add/Delete dialog box.
RENAMING AN ADDED TOPO ARRAY

1. 2. 3. If the Atlas Window is open, from the Atlas menu, choose Close to close it. From the Array menu, choose Add/Delete Topo... to open the Add/Delete Topo Array box. In the Arrays list, click to highlight the array that is to be renamed. Its current name will appear in the Name edit field. The Add/Delete Topo Dialog Box
The name of the highlighted array is displayed in the Name field.
4. 5. 6.
Click the cursor in the Name edit field and type in a new name. Click the Update button to update the name in the array list. Click the Close button to close the Add/Delete Topo dialog box.

Viewing Topo Data (page 5-40) Printing Topo Data (page 5-41) Deleting Data From a Topo Array (page 5-42) Using Select Arrays in the Atlas Viewer (page 5-38) Using List Data in the Atlas Viewer (page 5-40) Using Save Data and Save Data Set (page 5-45) Converting BQ-OS/2 Data to Topo Data (page 5-46) Atlas Viewer Menu and Tool Bars (page 5-2) Manipulating the Atlas in the Atlas Window (page 5-2) Using the Atlas Parameters Dialog Box (page 5-7) Setting Atlas Parameters - Perspective Tab (page 5-7) Setting Atlas Parameters - Colors/Symbols Tab (page 5-10) Setting Atlas Parameters - Rotation Tab (page 5-25) Using Alternate Display Options (page 5-29) Saving and Loading an Atlas Parameter File (page 5-30) Working With 3D Wire Frame Atlases (page 5-2) Printing, Copying, or Exporting an Atlas (page 5-34) Manipulating Data Arrays and Data Sets in the Atlas Viewer (page 5-38)
USING SAVE DATA AND SAVE DATA SET

When an Atlas Window is open, the Save Data button is available on the system tool bar. Save Data is used to permanently record changes in data or array comments in the data sets existing arrays. When the Atlas Window is closed, Save Data Set is available on the File menu to permanently record structural changes in the data set (e.g. when new arrays are added while in the Topographer), as well as changes in the data or array comments. Although the system performs both of these functions automatically, any time the Topographer is deliberately closed, it is best to save changes immediately after making them. If the computer should malfunction while the Topographer is open, unsaved changes would be lost.
PROCEDURE: SAVE DATA

After making a change in an arrays data or the notation in an arrays Comment field, click the Save Data button on the system tool bar.
PROCEDURE: SAVE DATA SET

1. 2. If the Atlas Window is open, from the Atlas menu, choose Close. From the File menu, choose Save Data Set.
RELATED TOPICS
Using Select Arrays in the Atlas Viewer (page 5-38) Using List Data in the Atlas Viewer (page 5-40) Converting BQ-OS/2 Data to Topo Data (page 5-46) Atlas Viewer Menu and Tool Bars (page 5-2) Manipulating the Atlas in the Atlas Window (page 5-2) Using the Atlas Parameters Dialog Box (page 5-7) Setting Atlas Parameters - Perspective Tab (page 5-7) Setting Atlas Parameters - Colors/Symbols Tab (page 5-10) Setting Atlas Parameters - Rotation Tab (page 5-25) Using Alternate Display Options (page 5-29) Saving and Loading an Atlas Parameter File (page 5-30) Working With 3D Wire Frame Atlases (page 5-2) Printing, Copying, or Exporting an Atlas (page 5-34) Manipulating Data Arrays and Data Sets in the Atlas Viewer (page 5-38)
Page 5-46
CONVERTING BQ-OS/2 DATA TO TOPO DATA

Convert OS/2 Data is available on the Atlas Viewers Array menu when the Atlas Window is closed. Before topography collected with the OS/2 BIOQUANT system can be viewed, it must be converted from the Quickdraw format to the Topographer format.
PROCEDURE
1. 2. If the Atlas Window is open, then from the Atlas menu, choose Close to close the Atlas Window. From the File menu, choose Open Data Set to display the Open a Data Set box. The Open a Data Set Box
3.
If the desired data volume is not shown in the Data Volume list: a. click the Change Dir button to open the Choose BQ Volume Search Directory box. The Choose BQ Volume Search DIrectory Box
b. c. 4. 5. 6. 7.
Select the directory that contains the desired data volume. Click the OK button.
Click to highlight the desired data volume in the Data Volumes list. The data sets in the highlighted Volume will be displayed in the Data Sets list. Click to highlight the desired data set in the Data Sets list. Click the Open button. The arrays of the data set appear in the Select Arrays box. Choose Convert OS/2 Data... from the Array menu to open the Convert OS/2 Quickdraw Array to Topo Array box. The Convert OS/2 Quickdraw Data to Topo Data
8.
Click the Add Topo button to add an empty topo array.
Page 5-47
9. 10. 11. 12. 13. Click on the Quickdraw array to be converted in the Select Quickdraw list. Click the empty topo array in the Select Destination Topo list. Click the Convert button; the computer beeps when the conversion is done. Click the Close button. Choose Save from the File menu.
RELATED TOPICS
Using Select Arrays in the Atlas Viewer (page 5-38) Using List Data in the Atlas Viewer (page 5-40) Using Save Data and Save Data Set (page 5-45) Converting BQ-OS/2 Data to Topo Data (page 5-46) Atlas Viewer Menu and Tool Bars (page 5-2) Manipulating the Atlas in the Atlas Window (page 5-2) Using the Atlas Parameters Dialog Box (page 5-7) Setting Atlas Parameters - Perspective Tab (page 5-7) Setting Atlas Parameters - Colors/Symbols Tab (page 5-10) Setting Atlas Parameters - Rotation Tab (page 5-25) Using Alternate Display Options (page 5-29) Saving and Loading an Atlas Parameter File (page 5-30) Working With 3D Wire Frame Atlases (page 5-2) Printing, Copying, or Exporting an Atlas (page 5-34) Manipulating Data Arrays and Data Sets in the Atlas Viewer (page 5-38)
Page 5-48
The Atlas Shop in Detail

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

The atlas is displayed for editing or measurement on the Atlas Shops desktop. A two-axis sketch of the atlas is also shown in a black Perspective panel along the right hand side of the work space. The Atlas Shop Desktop
The black Perspective panel shows section distribution along the Z axis.
TOPIC CONTENTS
The File Menu (page 6-2) The Select Menu (page 6-7) The View Menu (page 6-16) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66)
THE FILE MENU

This section covers the File menu items in the Atlas Shop.
TOPIC CONTENTS
File > Save (page 6-3) File > Save as (page 6-3) File > Save Selection As (page 6-4) File> Restore Original (page 6-5) File> Exit Atlas Shop (page 6-6)
BIOQUANT Topographer Handbook: The Atlas Shop in Detail

The Select Menu (page 6-7) The View Menu (page 6-16) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66)
FILE > SAVE

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

Save As on the File menu opens the Save Array As dialog box where the entire atlas may be saved to a new Topo array before editing begins, to consolidate the atlas data into a single Topo array, or to save alternate versions of the atlas after editing.
WAYS TO OPEN THE SAVE ARRAY AS DIALOG BOX:

Choose Save As from the File menu. Use Ctrl-Shift-S on the keyboard. (Press and hold the Control and Shift keys, then tap the S key.)
Page 6-4
The Save Array As Box
Save Array As dialog box before (left) and after (right) a new Topo array has been added.
PROCEDURE:
1. 2. 3. 4. Open the Save As dialog box using one of the above methods. If there is not an empty topo array in the list of arrays, click the New Array button to add one. If there is an empty topo array, scroll through the Available Arrays list and click to choose the desired destination array. In the Array Name text box, delete the default name and type in a name that identifies the version of the atlas that is being saved. Click the Save button to save the atlas to that array. Click the Close button to close the Save Array As dialog box.
RELATED TOPICS
File > Save (page 6-3) File > Save Selection As (page 6-4) File> Restore Original (page 6-5) File> Exit Atlas Shop (page 6-6) The File Menu (page 6-2) The Select Menu (page 6-7) The View Menu (page 6-16) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66)
FILE > SAVE SELECTION AS

Save Selection As is used to save selected portions of the atlas to a new Topo array. The New Array button on the Save Selection As dialog box is used to add a new Topo array to the data set. Although it is possible to replace data or append data in an existing Topo array, this is not recommended, because it puts the data being used in the current atlas at risk of being corrupted. If you are sure that an existing Topo array (listed on the Save Selection As dialog box) does NOT contain data for the current atlas, its data may be replaced or appended with the selected portion of the current atlas.
CAUTION
Replace or append data in an existing Topo array ONLY IF the existing array does NOT contain data for the current atlas.
WAYS TO OPEN THE SAVE SELECTION AS DIALOG BOX:

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

Any unsaved edits made to the atlas can be cancelled by using the Restore Original option on the File menu.
PROCEDURE
1. From the File menu, choose Restore Original.

File > Save (page 6-3) File > Save as (page 6-3) File > Save Selection As (page 6-4) File> Exit Atlas Shop (page 6-6) The File Menu (page 6-2) The Select Menu (page 6-7) The View Menu (page 6-16) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66)
FILE> EXIT ATLAS SHOP

Choosing Exit Atlas Shop from the File menu, or pressing Alt-X on the keyboard, closes the Atlas Shop and returns the user to the Atlas Viewer. If unsaved edits exist, one of two Save Data message boxes will appear, depending on the type of edits made.
SAVE DATA MESSAGE 1

If there are unsaved edits that can be saved to the original Topo array(s), the following message box will open: The Save Data Box
Answer YES, if you want the edits to permanently change the original data in the atlas Topo array(s). Answer NO if edits are to be discarded. Click Cancel to stay in the Atlas Shop.
SAVE DATA MESSAGE 2

If Resolution, Z Sort, Internal Cut, Internal Copy, or Internal Paste were used, the following message will appear: The Save Data Box
Answer YES if you want to save the edited version of the atlas to a new array and you have not already done so. (The Save Array As dialog box will open.) Answer NO if you want to discard the changes. (The Atlas Shop will close.) Answer NO if you have already saved an edited version of the atlas using Save As from the File menu or the Save button on the special dialog boxes that appear during editing. (The Atlas Shop will close.) Click Cancel to stay in the Atlas Shop.

File > Save (page 6-3) File > Save as (page 6-3) File > Save Selection As (page 6-4) File> Restore Original (page 6-5) The File Menu (page 6-2) The Select Menu (page 6-7) The View Menu (page 6-16) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66)
THE SELECT MENU

This section covers the Select menu items in the Atlas Shop.
TOPIC CONTENTS
Select> Select Using Rectangle (page 6-7) Select> Select Using Polygon (page 6-8) Select> Select By Color (page 6-8) Select> Select All Sections (page 6-9) Select> Add Interior Objects to Selection (page 6-9) Select> Select None (page 6-10) Select> Section Mode (page 6-10) Select> Object Mode (page 6-11) Select> Point Mode (page 6-11) Select> Select Across Sections (page 6-12) Select> Next (page 6-13) Select> Back (page 6-13) Select> GoTo (page 6-14)
RELATED TOPICS
The File Menu (page 6-2) The View Menu (page 6-16) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66)
SELECT> SELECT USING RECTANGLE

Same as clicking the Select Using Rectangle tool on the Vertical Tool Bar.
See Select Using Rectangle or Polygon on 6-49.

Select> Select Using Polygon (page 6-8) Select> Select By Color (page 6-8) Select> Select All Sections (page 6-9) Select> Add Interior Objects to Selection (page 6-9) Select> Select None (page 6-10) Select> Section Mode (page 6-10) Select> Object Mode (page 6-11) Select> Point Mode (page 6-11) Select> Select Across Sections (page 6-12) Select> Next (page 6-13) Select> Back (page 6-13) Select> GoTo (page 6-14) The File Menu (page 6-2) The Select Menu (page 6-7) The View Menu (page 6-16) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66)
SELECT> SELECT USING POLYGON

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

Same as clicking the Select By Color See Select By Color on 6-52. tool on the Vertical Tool Bar.

Select> Select Using Rectangle (page 6-7) Select> Select Using Polygon (page 6-8) Select> Select All Sections (page 6-9) Select> Add Interior Objects to Selection (page 6-9) Select> Select None (page 6-10) Select> Section Mode (page 6-10) Select> Object Mode (page 6-11) Select> Point Mode (page 6-11) Select> Select Across Sections (page 6-12) Select> Next (page 6-13) Select> Back (page 6-13) Select> GoTo (page 6-14) The File Menu (page 6-2) The Select Menu (page 6-7) The View Menu (page 6-16) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66)
SELECT> SELECT ALL SECTIONS

To select every thing in the atlas, choose Select All Sections from the Select menu.
RELATED TOPICS
Select> Select Using Rectangle (page 6-7) Select> Select Using Polygon (page 6-8) Select> Select By Color (page 6-8) Select> Add Interior Objects to Selection (page 6-9) Select> Select None (page 6-10) Select> Section Mode (page 6-10) Select> Object Mode (page 6-11) Select> Point Mode (page 6-11) Select> Select Across Sections (page 6-12) Select> Next (page 6-13) Select> Back (page 6-13) Select> GoTo (page 6-14) The File Menu (page 6-2) The Select Menu (page 6-7) The View Menu (page 6-16) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66)
SELECT> ADD INTERIOR OBJECTS TO SELECTION

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

To un-select every thing in the atlas, choose Select None from the Select menu.
RELATED TOPICS
Select> Select Using Rectangle (page 6-7) Select> Select Using Polygon (page 6-8) Select> Select By Color (page 6-8) Select> Select All Sections (page 6-9) Select> Add Interior Objects to Selection (page 6-9) Select> Section Mode (page 6-10) Select> Object Mode (page 6-11) Select> Point Mode (page 6-11) Select> Select Across Sections (page 6-12) Select> Next (page 6-13) Select> Back (page 6-13) Select> GoTo (page 6-14) The File Menu (page 6-2) The Select Menu (page 6-7) The View Menu (page 6-16) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66)
SELECT> SECTION MODE

In Section mode, editing operations are applied to the selected section(s). To activate Section mode, choose Section Mode from the Select menu or click the Section Mode on the system tool bar. button

Select> Select Using Rectangle (page 6-7) Select> Select Using Polygon (page 6-8) Select> Select By Color (page 6-8) Select> Select All Sections (page 6-9) Select> Add Interior Objects to Selection (page 6-9) Select> Select None (page 6-10) Select> Object Mode (page 6-11) Select> Point Mode (page 6-11) Select> Select Across Sections (page 6-12) Select> Next (page 6-13) Select> Back (page 6-13) Select> GoTo (page 6-14) The File Menu (page 6-2) The Select Menu (page 6-7) The View Menu (page 6-16) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66)
SELECT> OBJECT MODE

In Object mode, editing operations are applied to the selected object(s). Objects are individual tracings or markers within a section map. To activate Object mode, choose Object Mode from the Select menu or click the Object Mode on the system tool bar. button
RELATED TOPICS
Select> Select Using Rectangle (page 6-7) Select> Select Using Polygon (page 6-8) Select> Select By Color (page 6-8) Select> Select All Sections (page 6-9) Select> Add Interior Objects to Selection (page 6-9) Select> Select None (page 6-10) Select> Section Mode (page 6-10) Select> Point Mode (page 6-11) Select> Select Across Sections (page 6-12) Select> Next (page 6-13) Select> Back (page 6-13) Select> GoTo (page 6-14) The File Menu (page 6-2) The Select Menu (page 6-7) The View Menu (page 6-16) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66)
SELECT> POINT MODE

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

In Object Mode, the Select Using Rectangle and Select Using Polygon tools can be made to work across the entire atlas. When active, the Select Across Sections feature tells the system to select objects on all sections in an area that corresponds to the selection box or polygon that is being created on the current section.
PROCEDURE
1. 2. 3. 4. In Section Mode select a section map that contains the area of interest. button.
Click the Object Mode
On the Select menu, click to check Select Across Sections. Use the Select Using Rectangle or Select Using Polygon the current section. Select Using Rectangle or Polygon (page 6-49) tool to define the desired selection area on

Select> Select Using Rectangle (page 6-7) Select> Select Using Polygon (page 6-8) Select> Select By Color (page 6-8) Select> Select All Sections (page 6-9) Select> Add Interior Objects to Selection (page 6-9) Select> Select None (page 6-10) Select> Section Mode (page 6-10) Select> Object Mode (page 6-11) Select> Point Mode (page 6-11) Select> Next (page 6-13) Select> Back (page 6-13) Select> GoTo (page 6-14) The File Menu (page 6-2) The Select Menu (page 6-7) The View Menu (page 6-16) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66)
SELECT> NEXT
Same as clicking the Select Next button on the system tool bar.
In Section mode, the next section map in the series is selected. In Object mode, the next tracing or marker in the current section is selected. In Point mode, the next point in the current object is selected.
RELATED TOPICS
Select> Select Using Rectangle (page 6-7) Select> Select Using Polygon (page 6-8) Select> Select By Color (page 6-8) Select> Select All Sections (page 6-9) Select> Add Interior Objects to Selection (page 6-9) Select> Select None (page 6-10) Select> Section Mode (page 6-10) Select> Object Mode (page 6-11) Select> Point Mode (page 6-11) Select> Select Across Sections (page 6-12) Select> Back (page 6-13) Select> GoTo (page 6-14) The File Menu (page 6-2) The Select Menu (page 6-7) The View Menu (page 6-16) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66)
SELECT> BACK
Same as clicking the Select Previous button on the system tool bar.
In Section mode, the previous section map in the series is selected. BIOQUANT Topographer Handbook: The Atlas Shop in Detail
Page 6-14
In Object mode, the previous tracing or marker in the current section is selected. In Point mode, the previous point in the current object is selected.
RELATED TOPICS
Select> Select Using Rectangle (page 6-7) Select> Select Using Polygon (page 6-8) Select> Select By Color (page 6-8) Select> Select All Sections (page 6-9) Select> Add Interior Objects to Selection (page 6-9) Select> Select None (page 6-10) Select> Section Mode (page 6-10) Select> Object Mode (page 6-11) Select> Point Mode (page 6-11) Select> Select Across Sections (page 6-12) Select> Next (page 6-13) Select> GoTo (page 6-14) The File Menu (page 6-2) The Select Menu (page 6-7) The View Menu (page 6-16) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66)
SELECT> GOTO
Sections (in Section Mode) and objects (in Object Mode) may be selected from a GoTo list. The GoTo Section list is almost always the fastest way to select multiple sections. The GoTo Object list is a quick way to select objects, unless the current section has dozens or hundreds of cell markers. In this case the object list would be very long and possibly tedious to use.
SELECT SECTIONS FROM GOTO SECTION LIST

1. 2. Click to activate the Section mode button.
From the Select menu, choose GoTo, to open the GoTo Section list box. GoTo Section List With the First Section Selected
To select a single section, click to highlight its entry in the list.
Page 6-15
To select multiple, contiguous sections, click the first section, press and hold the Shift key, then click the last section in the series that is to be selected. All sections between and including the first and the last will be selected. To select multiple, non-contiguous sections, click one section, press and hold the Ctrl key, then click each additional section that is to be selected.
SELECT OBJECTS FROM GOTO OBJECTS LIST

1. 2. 3. In Section mode interest. , using the most convenient method, select the section that contains the objects of .
From the Select menu, choose GoTo, to open the Go To Object list. Example GoTo Object Lists
The Ctrl key was used to help select non-contiguous objects in the short list on the left. The list of objects on the right is from a section with dozens of cell markers.
To select a single object, click to highlight its entry in the list. To select multiple, contiguous objects, click the first object, press and hold the Shift key, then click the last object in the series. All objects between and including the first and the last will be selected. To select multiple, non-contiguous objects, click one object, press and hold the Ctrl key, then click each additional object that is to be selected.

Select> Select Using Rectangle (page 6-7) Select> Select Using Polygon (page 6-8) Select> Select By Color (page 6-8) Select> Select All Sections (page 6-9) Select> Add Interior Objects to Selection (page 6-9) Select> Select None (page 6-10) Select> Section Mode (page 6-10) Select> Object Mode (page 6-11) Select> Point Mode (page 6-11) Select> Select Across Sections (page 6-12) Select> Next (page 6-13) Select> Back (page 6-13) The File Menu (page 6-2) The Select Menu (page 6-7) The View Menu (page 6-16) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66)
THE VIEW MENU

This section covers the View menu items in the Atlas Shop.
TOPIC CONTENTS
View> Resize to Fit (page 6-16) View> Zoom (page 6-17) View> Pan (page 6-17) View> Center (page 6-18) View> Flash Selection (page 6-18) View> Selection Only (page 6-19) View> Show All Sections (page 6-20) View> Overlay Sections (page 6-20) View>Show Start Point (page 6-21) View> Show Landmark (page 6-22) View> Show Data (page 6-22) View> Redraw (page 6-23) View> Auto Redraw (page 6-24) View> Z Perspective (page 6-25) View> Y Perspective (page 6-25) View> X Perspective (page 6-26)
RELATED TOPICS
The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66)
VIEW> RESIZE TO FIT

Centers and resizes the atlas to fit the Atlas Shop work space. Same as clicking the Resize to Fit system tool bar. BIOQUANT Topographer Handbook: The Atlas Shop in Detail button on the

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

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

Causes the currently selected section, object, or point to flash once. Same as clicking the Flash Selection the system tool bar. BIOQUANT Topographer Handbook: The Atlas Shop in Detail button on

View> Resize to Fit (page 6-16) View> Zoom (page 6-17) View> Pan (page 6-17) View> Center (page 6-18) View> Selection Only (page 6-19) View> Show All Sections (page 6-20) View> Overlay Sections (page 6-20) View>Show Start Point (page 6-21) View> Show Landmark (page 6-22) View> Show Data (page 6-22) View> Redraw (page 6-23) View> Auto Redraw (page 6-24) View> Z Perspective (page 6-25) View> Y Perspective (page 6-25) View> X Perspective (page 6-26) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66)
VIEW> SELECTION ONLY

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

Checking Show All Sections on the View menu displays all un-selected parts of the entire atlas, regardless of which selection mode is currently active. Un-checking Show All Sections on the View menu does the following: In Section Mode, removes all un-selected section maps from the work space. In Object Mode, removes all un-selected section maps except those in which objects are currently selected. In Points Mode, removes all un-selected section maps except the one in which points are currently selected.
RELATED TOPICS
View> Resize to Fit (page 6-16) View> Zoom (page 6-17) View> Pan (page 6-17) View> Center (page 6-18) View> Flash Selection (page 6-18) View> Selection Only (page 6-19) View> Overlay Sections (page 6-20) View>Show Start Point (page 6-21) View> Show Landmark (page 6-22) View> Show Data (page 6-22) View> Redraw (page 6-23) View> Auto Redraw (page 6-24) View> Z Perspective (page 6-25) View> Y Perspective (page 6-25) View> X Perspective (page 6-26) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66)
VIEW> OVERLAY SECTIONS

Choosing Overlay Section from the View menu opens the Overlay Section dialog box. Overlay Section provides a way to display a limited number of non-selected sections for visual reference during editing. This is particularly helpful when lining up sections with translate and rotate. The Overlay Section dialog box must remain open during editing, to retain the overlay of designated tracings. The Overlay Sections Dialog Box
PROCEDURE:
1. 2. Choose Overlay Section from the View menu to open the Overlay Section dialog box. To overlay a given number of previous sections, (those that precede the selected section in the Z plane) a. Click to check the Overlay previous sections check box.
Page 6-21
b. c. 3. Type or choose from the drop list the number of previous sections to overlay. Click the Apply button.
To overlay a given number of next sections (ones that follow the selected section in the Z plane): a. b. c. Click to check the Overlay next sections check box. Type or choose from the drop list the number of sections to overlay. Click the Apply button
4.
To overlay one or more particular sections: a. b. c. d. Click to uncheck the Overlay previous sections and Overlay next sections check boxes. Click to check the Overlay These Sections check box. In the list of sections, click to highlight the sections to be overlaid. Click the Apply button
5.
To overlay a given number of previous and/or next sections plus one or more particular sections: a. b. c. d. Click to check one or both of the Overlay previous and Overlay next check boxes, and check the Overlay These Sections check box. Designate the number of previous and/or next sections that are to be overlaid. In the list of sections, click to highlight the additional sections to be overlaid. Click the Apply button.
ADDITIONAL NOTES:
When the Overlay Section dialog box is closed, the limits imposed on the overlay are canceled and all non selected sections are redrawn on the atlas.
RELATED TOPICS
View> Resize to Fit (page 6-16) View> Zoom (page 6-17) View> Pan (page 6-17) View> Center (page 6-18) View> Flash Selection (page 6-18) View> Selection Only (page 6-19) View> Show All Sections (page 6-20) View>Show Start Point (page 6-21) View> Show Landmark (page 6-22) View> Show Data (page 6-22) View> Redraw (page 6-23) View> Auto Redraw (page 6-24) View> Z Perspective (page 6-25) View> Y Perspective (page 6-25) View> X Perspective (page 6-26) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66)
VIEW>SHOW START POINT

Show Start Point places a pink star at the location of the Start Point that was defined when tracing a contour.

View> Resize to Fit (page 6-16) View> Zoom (page 6-17) View> Pan (page 6-17) View> Center (page 6-18) View> Flash Selection (page 6-18) View> Selection Only (page 6-19) View> Show All Sections (page 6-20) View> Overlay Sections (page 6-20) View> Show Landmark (page 6-22) View> Show Data (page 6-22) View> Redraw (page 6-23) View> Auto Redraw (page 6-24) View> Z Perspective (page 6-25) View> Y Perspective (page 6-25) View> X Perspective (page 6-26) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66)
VIEW> SHOW LANDMARK

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

Choosing Show Data from the View menu opens the View BIOQUANT Data window and displays the content of the BIOQUANT Topographer Handbook: The Atlas Shop in Detail
Page 6-23
Topo arrays that make up the current atlas. IMPORTANT: The Z Position displayed in the View BIOQUANT Data window is always 10 times greater than the Z Offset value that was used during measurement, or the default Z Offset value shown in the Change All Z Values To field on the Change Z dialog box.
PROCEDURE: OPENING AND CLOSING THE VIEW BIOQUANT DATA WINDOW

1. 2. From the View menu, click to choose Show Data. The View BIOQUANT Data window will open. To close the View BIOQUANT Data window, click the X button in the windows upper right corner.
UNDERSTANDING THE TOPO DATA

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

When Auto Redraw is checked on the View menu, the system automatically refreshes the atlas display any time a dialog box is moved in the Atlas Shop. Usually the automatic refresh happens so quickly that is it hardly noticed. With extremely large atlases, however, the refresh is more apparent. To discontinue the auto refresh, click to uncheck Auto Redraw on the View menu. To reactivate auto refresh, click to check Auto Redraw on the View menu.
RELATED TOPICS
View> Resize to Fit (page 6-16) View> Zoom (page 6-17) View> Pan (page 6-17) View> Center (page 6-18) View> Flash Selection (page 6-18) View> Selection Only (page 6-19) View> Show All Sections (page 6-20) View> Overlay Sections (page 6-20) View>Show Start Point (page 6-21) View> Show Landmark (page 6-22) View> Show Data (page 6-22) View> Redraw (page 6-23) View> Z Perspective (page 6-25) View> Y Perspective (page 6-25) View> X Perspective (page 6-26) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66)
Page 6-25
VIEW> Z PERSPECTIVE
Activates Z Perspective in the black Perspective panel. Same as clicking the Z Perspective button on the system tool bar. See Z Perspective on 6-46.
RELATED TOPICS
View> Resize to Fit (page 6-16) View> Zoom (page 6-17) View> Pan (page 6-17) View> Center (page 6-18) View> Flash Selection (page 6-18) View> Selection Only (page 6-19) View> Show All Sections (page 6-20) View> Overlay Sections (page 6-20) View>Show Start Point (page 6-21) View> Show Landmark (page 6-22) View> Show Data (page 6-22) View> Redraw (page 6-23) View> Auto Redraw (page 6-24) View> Y Perspective (page 6-25) View> X Perspective (page 6-26) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66)
VIEW> Y PERSPECTIVE
Activates Y Perspective in the black Perspective panel. Same as clicking the Y Perspective button on the system tool bar. See Y Perspective on 6-46.

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

This section covers the Edit menu items in the Atlas Shop.
TOPIC CONTENTS
Edit> Undo (page 6-27) Edit> Internal Cut, Internal Copy, & Internal Paste (page 6-28) Edit> Translate (page 6-32) Edit> Rotate (page 6-33) Edit> Resize (page 6-33) Edit> Change Color (page 6-34) Edit> Change Z (page 6-35) Edit> Align Sections (page 6-35) Edit> Resolution (page 6-36) Edit> Z Sort (page 6-37) Edit > Open Polygon (page 6-39) Edit> Close Polygon (page 6-40) Edit> Numeric Transform (page 6-41)
RELATED TOPICS
EDIT> UNDO
Undo on the Edit menu reverses the most recent editing change. There is only one level of undo. However, Restore Original on the File menu restores the atlas to the way it looked when it was last saved. Choosing Undo on the Edit menu is the same as clicking the Undo button on the Vertical Tool Bar.
PROCEDURES
From the Edit menu, choose Undo. On the keyboard, tap Ctrl-Z (press and hold the control key, then tap Z).

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

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

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

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

Eliminate a Problem Section (page 6-29) Duplicate A Section (page 6-31) File> Restore Original (page 6-5) Edit> Undo (page 6-27) Edit> Internal Cut, Internal Copy, & Internal Paste (page 6-28) Edit> Translate (page 6-32) Edit> Rotate (page 6-33) Edit> Resize (page 6-33) Edit> Change Color (page 6-34) Edit> Change Z (page 6-35) Edit> Align Sections (page 6-35) Edit> Resolution (page 6-36) Edit> Z Sort (page 6-37) Edit > Open Polygon (page 6-39) Edit> Close Polygon (page 6-40) Edit> Numeric Transform (page 6-41) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66)
DUPLICATE A SECTION
Occasionally one or more tissue sections in a series is lost or damaged during tissue processing and the absence of those sections is obvious in the reconstructed atlas. Missing sections may be filled with duplicates made from near by sections.
PROCEDURE
1. 2. In Section mode select a section that approximates the size and shape of the missing section.
From the Edit menu, choose Internal Copy. A Warning box will open to remind you that the altered atlas must be saved to a new array. Click OK to acknowledge the Warning and copy the selected section. (Clicking Cancel will cancel the Internal Copy command.) From the Edit menu, choose Internal Paste. A Notice box appears to let you know that Elements will be pasted as a new section in the last array. (In this case the last array will be the new array that will be added in step 6.) Click OK to acknowledge the notice. If more than one duplicate of the selected tracing is needed, choose Internal Paste again for each additional tracing that is needed. (Alternately, select a different section to duplicate and repeat steps 2 and 3.) From the Edit menu, choose Z Sort. A Warning box will open to inform you that the Z sorted atlas must be saved to a new array, and asks if you want to add a new array. Click the YES button to open the Sort Sections By Z Value dialog box. On the Sort Sections By Z Value dialog box, do the following: a. Click the New Array button to add a new Topo array, or click the down arrow in the Destination Array field and choose an existing Topo array from the drop list. (The chosen Topo array cannot be one of the current atlas arrays.) In the Z Sort Options area, click to choose the Ascending or Descending radio button. Click the Apply button to record the edited version of the atlas to the array in the Destination Array field. If the chosen array is not new, click the OK button on the Warning box that says existing data will be overwritten. (Or, click Cancel, then add a New Array.) BIOQUANT Topographer Handbook: The Atlas Shop in Detail
3.
4.
5.
6.
b. c.
Page 6-32
d. 7. Click Close.
In order to display or continue editing the changed version of the atlas, you must do the following: e. f. g. From the File menu, choose Exit Atlas Shop. A Save Data message will appear. On the Save Data message, click NO (since the changed version of the atlas has already been saved). The Atlas Shop closes and the Atlas Viewer reopens. In the Atlas Viewer, on the Select Arrays dialog box, deselect the original atlas array and select the Topo array that holds the revised version of the atlas. To display the revised version of the atlas, click Redraw on the system tool bar, or to continue editing, click the Atlas Shop button.
ADDITIONAL NOTE
Keyboard shortcut: Control-C is the same as choosing Internal Cut from the Edit menu. Keyboard shortcut: Control-V is the same as choosing Internal Paste from the Edit menu.
RELATED TOPICS
Eliminate a Problem Section (page 6-29) Create a new Topographic Section From an Object Within a Section (page 6-30) File> Restore Original (page 6-5) Edit> Undo (page 6-27) Edit> Internal Cut, Internal Copy, & Internal Paste (page 6-28) Edit> Translate (page 6-32) Edit> Rotate (page 6-33) Edit> Resize (page 6-33) Edit> Change Color (page 6-34) Edit> Change Z (page 6-35) Edit> Align Sections (page 6-35) Edit> Resolution (page 6-36) Edit> Z Sort (page 6-37) Edit > Open Polygon (page 6-39) Edit> Close Polygon (page 6-40) Edit> Numeric Transform (page 6-41) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66)
EDIT> TRANSLATE
Activates the Translate tool on the Vertical Tool Bar. Same as clicking the Translate tool.
See Translate Selected Parts of the Atlas on 6-54.

Eliminate a Problem Section (page 6-29) Create a new Topographic Section From an Object Within a Section (page 6-30) Duplicate A Section (page 6-31) File> Restore Original (page 6-5) Edit> Undo (page 6-27) Edit> Internal Cut, Internal Copy, & Internal Paste (page 6-28) Edit> Rotate (page 6-33) Edit> Resize (page 6-33) Edit> Change Color (page 6-34) Edit> Change Z (page 6-35) Edit> Align Sections (page 6-35) Edit> Resolution (page 6-36) Edit> Z Sort (page 6-37) Edit > Open Polygon (page 6-39) Edit> Close Polygon (page 6-40) Edit> Numeric Transform (page 6-41) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66)
EDIT> ROTATE
Activates the Rotate tool on the Vertical Tool Bar. Same as clicking the Rotate tool. See Rotate Selected Parts of the Atlas on 6-53.
RELATED TOPICS
Eliminate a Problem Section (page 6-29) Create a new Topographic Section From an Object Within a Section (page 6-30) Duplicate A Section (page 6-31) File> Restore Original (page 6-5) Edit> Undo (page 6-27) Edit> Internal Cut, Internal Copy, & Internal Paste (page 6-28) Edit> Translate (page 6-32) Edit> Resize (page 6-33) Edit> Change Color (page 6-34) Edit> Change Z (page 6-35) Edit> Align Sections (page 6-35) Edit> Resolution (page 6-36) Edit> Z Sort (page 6-37) Edit > Open Polygon (page 6-39) Edit> Close Polygon (page 6-40) Edit> Numeric Transform (page 6-41) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66)
EDIT> RESIZE
Activates the Resize tool on the Vertical Tool Bar. Same as clicking the Resize tool. BIOQUANT Topographer Handbook: The Atlas Shop in Detail
Page 6-34
See Resize the Selected Parts of the Atlas on 6-55.
RELATED TOPICS
Eliminate a Problem Section (page 6-29) Create a new Topographic Section From an Object Within a Section (page 6-30) Duplicate A Section (page 6-31) File> Restore Original (page 6-5) Edit> Undo (page 6-27) Edit> Internal Cut, Internal Copy, & Internal Paste (page 6-28) Edit> Translate (page 6-32) Edit> Rotate (page 6-33) Edit> Change Color (page 6-34) Edit> Change Z (page 6-35) Edit> Align Sections (page 6-35) Edit> Resolution (page 6-36) Edit> Z Sort (page 6-37) Edit > Open Polygon (page 6-39) Edit> Close Polygon (page 6-40) Edit> Numeric Transform (page 6-41) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66)
EDIT> CHANGE COLOR

Activates the Change Color button on the Vertical Tool Bar. Same as clicking the Change Color tool. See Change Color of the Selected Parts of the Atlas on 6-57.
RELATED TOPICS
Eliminate a Problem Section (page 6-29) Create a new Topographic Section From an Object Within a Section (page 6-30) Duplicate A Section (page 6-31) File> Restore Original (page 6-5) Edit> Undo (page 6-27) Edit> Internal Cut, Internal Copy, & Internal Paste (page 6-28) Edit> Translate (page 6-32) Edit> Rotate (page 6-33) Edit> Resize (page 6-33) Edit> Change Z (page 6-35) Edit> Align Sections (page 6-35) Edit> Resolution (page 6-36) Edit> Z Sort (page 6-37) Edit > Open Polygon (page 6-39) Edit> Close Polygon (page 6-40) Edit> Numeric Transform (page 6-41) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66)
Page 6-35
EDIT> CHANGE Z
Opens the Change Z dialog box. Same as clicking the Change Z See Change Z on 6-63. tool on the Vertical Tool Bar.
RELATED TOPICS
Eliminate a Problem Section (page 6-29) Create a new Topographic Section From an Object Within a Section (page 6-30) Duplicate A Section (page 6-31) File> Restore Original (page 6-5) Edit> Undo (page 6-27) Edit> Internal Cut, Internal Copy, & Internal Paste (page 6-28) Edit> Translate (page 6-32) Edit> Rotate (page 6-33) Edit> Resize (page 6-33) Edit> Change Z (page 6-35) Edit> Align Sections (page 6-35) Edit> Resolution (page 6-36) Edit> Z Sort (page 6-37) Edit > Open Polygon (page 6-39) Edit> Close Polygon (page 6-40) Edit> Numeric Transform (page 6-41) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66)
EDIT> ALIGN SECTIONS

Serial sections that were measured with consistent landmarks and tracing start points may be automatically rotated to correct for differences in orientation of sections on slides. Serial sections that do not have these dual alignment points can be manually rotated when needed. Align Sections on the Edit menu operates on all sections in the atlas, without regard for the selection mode (Section, Object, or Point) that is currently active.
TO AUTOMATICALLY ALIGN SERIAL SECTIONS THAT HAVE DUAL ALIGNMENT POINTS:

1. 2. Choose Align Sections from the Edit menu. If needed, refine the alignment of particular sections using the manual alignment tools listed below.
MANUAL ALIGNMENT TOOLS

Rotate Selected Parts of the Atlas (page 6-53) Translate Selected Parts of the Atlas (page 6-54) Resize the Selected Parts of the Atlas (page 6-55) Edit> Numeric Transform (page 6-41)

Eliminate a Problem Section (page 6-29) Create a new Topographic Section From an Object Within a Section (page 6-30) Duplicate A Section (page 6-31) File> Restore Original (page 6-5) Edit> Undo (page 6-27) Edit> Internal Cut, Internal Copy, & Internal Paste (page 6-28) Edit> Translate (page 6-32) Edit> Rotate (page 6-33) Edit> Resize (page 6-33) Edit> Change Color (page 6-34) Edit> Change Z (page 6-35) Edit> Resolution (page 6-36) Edit> Z Sort (page 6-37) Edit > Open Polygon (page 6-39) Edit> Close Polygon (page 6-40) Edit> Numeric Transform (page 6-41) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66)
EDIT> RESOLUTION
When the atlas is displayed in the Atlas Modeler, if it takes a long time to render the surface or redraw the model after it has been moved in the Model Window, the resolution of the surface tracings should be reduced. CAUTION: Do not attempt to change the resolution of an entire atlas. To do so may corrupt the data, especially in larger atlases. When resolution is changed, the edited version of the atlas must be saved to a new Topo array. The original resolution was set by the smoothing limit in BIOQUANT Life Science or BIOQUANT OSTEO (the lower the Smoothing Limit the higher the resolution).
PROCEDURE:
1. Select a limited number of objects) (e.g. all section outlines) for which the resolution needs to be changed. Hint: If all section outlines (or other objects of interest) are of the same unique color, these may be selected quickly using Select by Color. See Select By Color on 6-52. Choose Resolution from the Edit menu to open the Set Image Resolution dialog box. When asked if you want to add a new Topo array, click Yes, unless you think the data set already contains an empty Topo array that can be used. Set Image Resolution
2.
3.
On the Set Image Resolution dialog box, if a new Topo array was added in step 2, it will already be selected in the Destination Array field. Otherwise, click the down arrow in the Destination Array field and click to choose the desired empty Topo array from the drop list. If there is not an empty Topo array, do the following: a. b. Click the Add Topo button. The New Array dialog box opens. In the Array Name field, edit the name of the Topo array to indicate that this is a lower resolution version of the atlas.
Page 6-37
c. 4. 5. Click the OK button to close the New Array dialog box.
In the Resolution Distance field, increase the micron value between data points (to decrease the resolution), by doubling or tripling the initial default value in the Resolution Distance field. Click the Apply button to generate the lower resolution atlas in the selected Topo array. A warning will appear to remind you that any data in the selected array will be overwritten. Verify that the intended Destination Array is selected, then click OK. IMPORTANT: If a single Smoothing Limit was not maintained during data collection for the selected outlines, read the following carefully, then, if it seems necessary, repeat steps 4 and 5. a. b. The initial default value in the Resolution Distance field is the minimum distance the system found between any two data points in the selected portion of the atlas. The change in resolution, (the new micron distance) is only applied between pairs of data points in the selected outlines, for which the original distance matched the minimum (initial) value in the Resolution Distance field. If a single smoothing limit was maintained during measurement, the distance between all data points will match the minimum value, and all will be increased simultaneously to the new value. (Excess data points are discarded to maintain the original size of the tracings). In this case, simply doubling or tripling the default Resolution Distance and clicking the Apply button once, is usually enough to produce the desired effect. However, if the smoothing limit was changed during data collection, the number of data set pairs that are separated by the minimum distance may be small. In this case, it may be necessary to repeat steps 4 and 5 several times before the desired effect would be apparent in a surface rendered model.
c.
d.
6. 7.
Click the Close button to close the Set Image Resolution dialog box. To display or edit the new resolution atlas, exit the Atlas Shop. In the Atlas Viewer, on the Select Arrays dialog box, remove the original Topo arrays from the Selected list, and select the Topo array that contains the lower resolution version of the atlas. The lower resolution atlas is now ready to be displayed in the Atlas Viewer, Atlas Modeler, or Atlas Shop.
RELATED TOPICS
Eliminate a Problem Section (page 6-29) Create a new Topographic Section From an Object Within a Section (page 6-30) Duplicate A Section (page 6-31) File> Restore Original (page 6-5) Edit> Undo (page 6-27) Edit> Internal Cut, Internal Copy, & Internal Paste (page 6-28) Edit> Translate (page 6-32) Edit> Rotate (page 6-33) Edit> Resize (page 6-33) Edit> Change Color (page 6-34) Edit> Change Z (page 6-35) Edit> Align Sections (page 6-35) Edit> Z Sort (page 6-37) Edit > Open Polygon (page 6-39) Edit> Close Polygon (page 6-40) Edit> Numeric Transform (page 6-41) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66)
EDIT> Z SORT
Topographer draws topographic units (sections or objects) in the atlas window and the black Axis Perspective panel in the order their data appear in the atlas topo array. So an item with a Z Offset Value of 100 that has been appended BIOQUANT Topographer Handbook: The Atlas Shop in Detail
Page 6-38
(pasted) to the end of the Topo array, will draw below an item that has a Z Offset Value of zero (0). This can lead to some strange looking atlas displays and may cause confusion during editing procedures. Z Sort generates an atlas in which all the topographic units are sorted by Z position, in either ascending or descending order. The Z sorted atlas must be saved to a new Topo array.
PROCEDURE:
1. From the Edit menu, choose Z Sort. A message box will open to inform you that the Z sorted atlas must be saved to a new array, and asks if you want to add a new array. Do one of the following: Click the YES button if you want the system to automatically add a Topo array named Z Sorted Topo. This default name cannot be edited. Click the NO button if you prefer to give the new Topo array a different name, or if the data set already contains a suitable Topo array (one that is empty or one that you wish to overwrite).
Sort Sections by Z Value dialog box
2.
If you choose NO in step 1, do one of the following: Click the New Array button to add a new Topo array, rename the new array on the New Array dialog box, and click the OK button to close the New Array box. Click the down arrow in the Destination Array field and choose an existing Topo array from the drop list. (The chosen Topo array cannot be one of the current atlas arrays.)
3. 4.
In the Z Sort Options area, click to choose the Ascending or Descending radio button. Click the Apply button to record the edited version of the atlas to the array in the Destination Array field. If the chosen array is not new, click the OK button on the Warning box that says existing data will be overwritten. (Or, click Cancel, then add a New Array.) Click Close. In order to display or continue editing the changed version of the atlas, you must do the following: a. b. c. From the File menu, choose Exit Atlas Shop. A Save Data message will appear. On the Save Data message, click NO (since the changed version of the atlas has already been saved). The Atlas Shop closes and the Atlas Viewer reopens. In the Atlas Viewer, on the Select Arrays dialog box, deselect the original atlas array and select the Topo array that holds the Z Sorted version of the atlas. To display the revised version of the atlas, click Redraw on the system tool bar, or to continue editing, click the Atlas Shop button.
5. 6.

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

Choosing Open Polygon from the Edit menu inserts a small disconnecting gap in the selected polygonal tracing (closed object). Open Polygon is used to create an open object that will not fill with color when the Fill option is used in the Atlas Viewer program. Open Polygon is only available in Object Mode.
PROCEDURE
1. 2. 3. In Section Mode select the section that contains the object of interest. button on the system tool bar, then select the polygonal tracing that is to be
Click the Object Mode opened.
Choose Open Polygon from the Edit menu.

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

Choosing Close Polygon from the Edit menu connects the loose ends of the selected tracing (open object) to change it into a closed polygon. Close Polygon is used to create a closed object that will fill with color when the Fill option is used in the Atlas Viewer program. Close Polygon is only available in Object Mode.
PROCEDURE
1. 2. 3. In Section Mode select the section that contains the object of interest. button on the system tool bar, then select the open object that is to be closed.
Click the Object Mode
Choose Close Polygon from the Edit menu.

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

Numeric Transform translates, rotates, or resizes the selected parts of the atlas by a known amount.
PROCEDURE: SETUP
1. Select the section(s) or objects) or point(s) of interest. 2. From the Atlas Shop Edit menu, choose Numeric Transform to open the Numeric Transform dialog box. Numeric Transform Dialog Box
CHOOSE FROM THE FOLLOWING

Translate by Numeric Transform (page 6-42) Resize by Numeric Transform (page 6-43) Rotate by Numeric Transform (page 6-44)

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

PROCEDURE
1. 2. On the Numeric Transform dialog box, click to check the Translate check box. Decide whether or not the Relative check box should be checked.: If Relative is checked, the values that are typed into the X and Y fields designate the micron distance that the selection is to be moved relative to its current position in the atlas. If Relative is not checked, the values that are typed into the X and Y fields designate actual X and Y coordinates to which the first point in the selection is to be moved. (All other points in the selection will be moved to maintain their positional relationship to the first point.)
If Relative is checked, to move the selected item(s) Right: In the X field, enter a positive micron distance (the selection will be moved this distance to the right). Left: In the X field, enter a negative micron distance (the selection will be moved this distance to the left). Down: In the Y field, enter a positive micron distance (the selection will be moved this distance downwards). Up: In the Y field, enter a negative micron distance (the selection will be moved this distance upwards.
If Relative is not checked, to move the first point of the first object in the selection to a specific XY location a. b. In the X field, type the positive or negative X coordinate to which the first point in the first object should be moved. In the Y field, type the positive or negative Y coordinate to which the first point in the first object should be moved. Helpful Hint: As expected, the atlas landmark always occupies the XYZ(0,0,0 Offset) position of the current coordinate system. However, it should be noted that the XY plane of the coordinate system used by the Windows operating system is unconventional. The X and Y signs (x,y) in the various quadrants are given below:
Page 6-43
3. Lower Right Quadrant (+ , +) Upper Left Quadrant (- , -) Lower Left Quadrant (- , +) Upper Right Quadrant (+ , -)
Click the Apply button.
SAVING THE EDIT

After Numeric Transform is used, if the atlas is saved using Save on the File menu, or by responding YES to the Save Data message when exiting the Atlas Shop, the data in the original atlas Topo array(s) are permanently changed. If desirable, Save As on the File menu may be used instead, to save the edited version of the atlas to a new Topo array.
RELATED TOPICS
Resize by Numeric Transform (page 6-43) Rotate by Numeric Transform (page 6-44) File> Restore Original (page 6-5) Edit> Undo (page 6-27) Edit> Internal Cut, Internal Copy, & Internal Paste (page 6-28) Edit> Translate (page 6-32) Edit> Rotate (page 6-33) Edit> Resize (page 6-33) Edit> Change Color (page 6-34) Edit> Change Z (page 6-35) Edit> Align Sections (page 6-35) Edit> Resolution (page 6-36) Edit> Z Sort (page 6-37) Edit > Open Polygon (page 6-39) Edit> Close Polygon (page 6-40) Edit> Numeric Transform (page 6-41) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66)
RESIZE BY NUMERIC TRANSFORM

PROCEDURE
1. 2. On the Numeric Transform dialog box, click to check the Resize check box. The current size of the selection is designated 100%. If the Maintain Aspect Ratio check box is checked, when a value is entered in either the Height or Width field, the other field automatically updates to the same value. If it is unchecked, Height and Width resizing are independent of each other. If desirable, click to uncheck the Maintain Aspect Ratio check box. To increase the size of the selected item(s), in the Width or/and Height field(s) type a percentage value that is greater than 100. To decrease the size of the selected item(s), in the Width or/and Height field(s) enter a percentage value that is less than 100. Click the Apply button. The selected item(s) are shown at the new size in the Atlas Window. NOTE: If subsequent resizing is done, the new size just applied is now the current size and is considered the 100% value for the selected item(s).
3.
Page 6-44 SAVING THE EDIT

RELATED TOPICS
Translate by Numeric Transform (page 6-42) Rotate by Numeric Transform (page 6-44) File> Restore Original (page 6-5) Edit> Undo (page 6-27) Edit> Internal Cut, Internal Copy, & Internal Paste (page 6-28) Edit> Translate (page 6-32) Edit> Rotate (page 6-33) Edit> Resize (page 6-33) Edit> Change Color (page 6-34) Edit> Change Z (page 6-35) Edit> Align Sections (page 6-35) Edit> Resolution (page 6-36) Edit> Z Sort (page 6-37) Edit > Open Polygon (page 6-39) Edit> Close Polygon (page 6-40) Edit> Numeric Transform (page 6-41) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66)
ROTATE BY NUMERIC TRANSFORM

PROCEDURE
1. 2. On the Numeric Transform dialog box, click to check the Rotate check box. To rotate clockwise, in the Angle field type the number of degrees the selected item(s) should be rotated. To rotate counter-clockwise, in the Angle field type the negative number of degrees the selected item(s) should be rotated. Click the Apply button.
SAVING THE EDIT


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

SECTION MODE
Activates Section mode. Same as choosing Section Mode from the Select menu.
OBJECT MODE
Activates Object mode. Same as choosing Object Mode from the Select menu.
POINT MODE
Activates Point mode. Same as choosing Point Mode from the Select menu.
SELECT PREVIOUS
In Section mode, selects the previous section map in the series. In Object mode, selects the previous object (tracing or marker) in the current section. In Point mode, selects the previous data point in the current object.
SELECT NEXT
In Section mode, selects the next section map in the series. In Object mode, selects the next object (tracing or marker) in the current section. In Point mode, selects the next data point in the current object.
CENTER
Centers the atlas in the Atlas Shop work space. Same as choosing Center from the View menu.
FLASH SELECTION
Causes the currently selected section, object, or data point to flash. Same as choosing Flash Selection from the View menu.
VIEW > REDRAW

Refreshes the atlas drawing in the Atlas Shops work space. Same as choosing Redraw from the View menu. BIOQUANT Topographer Handbook: The Atlas Shop in Detail
Page 6-46 VIEW > RESIZE TO FIT

Resizes and centers the atlas to fit the Atlas Shops work space. Same as choosing Resize To Fit from the View Menu.
CAP OBJECT
Formats the selected end tracings of an atlas to fill with color when the atlas is surface rendered in the Atlas Modeler. See Cap Object on 6-68.
END OF OBJECT/LEAVE OPEN

Formats three or more selected tracings in the atlas to be excluded from surface rendering when the atlas is moved into the Atlas Modeler, thus creating an open window through which interior structures in the model may be visible. See End of Object/Leave Open on 6-68.
MIDDLE OF OBJECT
Removes special formatting (Cap Object or End of Object/Leave Open) from the selected tracing(s). See Middle of Object on 6-69.
Z PERSPECTIVE
Causes the vertical line in the black Perspective panel to represent the Z axis, while the X axis of the atlas becomes the panels central horizontal line. Section maps appear as horizontal lines distributed along the vertical Z axis. Same as choosing Z Perspective from the View menu. Z Perspective
Y PERSPECTIVE
Causes the vertical line in the black Perspective panel to represent the Y axis, while the Z axis of the atlas becomes the panels central horizontal line. Section maps appear as shorter vertical lines adjacent to the vertical Y axis. Same as choosing Y Perspective from the View menu. Y Perspective
X PERSPECTIVE
Causes the vertical line in the black Perspective panel to represent the X axis, while the Z axis of the atlas points toward the viewer. Section maps create a miniature sketch of the atlas as it appears in the Atlas Shops work space. Same as choosing X Perspective from the View menu.
Page 6-47
X Perspective
HELP> HOW DO I
Opens the Atlas Shops How Do I... help window. The How Do I... help window provides links to comprehensive system help files for the features and special procedures that are covered in this manual.
THE COLOR PALETTE

The Color Palette
When the Select By Color tool on the Vertical Tool bar is active, clicking a square on the Color Palette selects all objects in the atlas of that color. tool on the Vertical Tool Bar is active, clicking a square on the Color Palette When the Change Color changes the currently selected sections, objects, or points to that color. The colored button at the left end of the Color Palette shows the color that was last chosen on the palette.
RELATED TOPICS
The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66)
TOOLS ON THE VERTICAL TOOL BAR

This section covers tools of the vertical toolbar in the Atlas Shop.
TOPIC CONTENTS
Zoom & Pan Tools (page 6-48) Select Tools (page 6-49) Align & Change Color Tools (page 6-52) Line Edit Tools (page 6-58) Change Z (page 6-63) Undo Tool (page 6-66)

ZOOM & PAN TOOLS

The Zoom and Pan tools on the Vertical Tool Bar operate on the entire atlas, regardless of which Selection mode is currently active. An atlas can be independently zoomed or panned, or it may be simultaneously zoomed and panned. Zoom and Pan Tools
ZOOM
1. 2. 3. Click the Zoom tool on the Vertical Tool Bar.
Position the cursor anywhere in the work space, and click the left mouse button once. Repeat as needed to increase the zoom level. To return to a less-zoomed state, verify that the Zoom tool is active, position the cursor anywhere in the work space, and click the right mouse button once. Repeat if needed to return the atlas to fully un-zoomed state.
PAN
1. 2. 3. Click the Pan tool on the Vertical Tool bar
Using the left mouse button, click and drag the atlas to the desired location. Repeat step 2 as need until the atlas is in the desired position.
SIMULTANEOUSLY ZOOM AND PAN

1. 2. 3. On the vertical tool bar, click the Zoom tool.
With the cursor positioned over the objects of interest, using the left mouse button, click and drag the objects of interest toward the center of the work space. Release the cursor button. Repeat step 2 as needed until the objects of interest are sufficiently enlarged and are in the center of the work space.
RELATED TOPICS
Select Tools (page 6-49) Align & Change Color Tools (page 6-52) Line Edit Tools (page 6-58) Change Z (page 6-63) Undo Tool (page 6-66) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66)
Page 6-49
SELECT TOOLS
The Select By Rectangle, Select By Polygon, and Select By Color tools are used to select individual parts of the atlas for editing. The action of each select tool depends on the selection mode that is currently active. Vertical Tool Bar Select Tools
TOPIC CONTENTS
Select Using Rectangle or Polygon (page 6-49) Select By Color (page 6-52)
RELATED TOPICS

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

1. 2. Click to activate Section Mode . tool or the Select Using Polygon tool,
If Select Using Rectangle is active, click and hold the left mouse button while dragging the cursor diagonally to form a small selection box that crosses the outline of the section(s) that you want to select. If Select Using Polygon is active, click a series of points to create a selection polygon of any shape that crosses the outline of the section(s) you want to select.
Page 6-50
Selecting Sections Using the Select With Rectangle or Polygon Tool
On the left is a selection rectangle across the outlines of three sections. In the middle is a selection polygon across the same outlines. The result is shown on the right: All tracings and markers within those three sections are selected. A selection polygon can be any shape.
If even one data point of a section falls within the rectangle or polygon, all tracings and markers within that section are selected.

An object is any individual tracing or cell marker. To work with objects, a section must first be selected in Section mode, then Object mode is activated. In Object mode, the Select Using Rectangle and Select Using Polygon tools operate only on the current section, unless a special feature called Select Across Sections is turned on. The Select Across Sections feature works only in Object mode and tells the system to select objects on all sections in an area that corresponds to the selection box or polygon that is being created on the current section. 1. 2. 3. 4. In Section mode , using the most convenient method, select the section of interest. .
If you want the system to select objects on all sections that correspond to the objects you intend to select on this section, on the Select menu, click to check Select Across Sections. If the objects of interest are small and need to be magnified to make selection easier, you may simultaneously zoom and pan them to the middle of the work space by doing the following: a. b. On the vertical tool bar, click the Zoom tool. With the cursor positioned over the objects of interest, using the left mouse button, click and drag the objects of interest toward the center of the work space. Release the cursor button. Repeat as needed. tool or the Select Using Polygon tool,
5.
If Select Using Rectangle is active, click and hold the left mouse button while dragging the cursor diagonally to form a small selection box that encloses or touches all the objects you want to select. If Select Using Polygon is active, click a series of points to create a selection polygon of any shape that encloses or touches all the objects you want to select.
Page 6-51
Selecting Zoomed Objects with Select Using Rectangle or Select Using Polygon
The illustrated section has small cell markers in the middle that need to be selected. After the atlas is zoomed, cells of interest are selected with the Select Using Rectangle tool (upper right) or the Select Using Polygon tool (lower right).
PROCEDURE: SELECT DATA POINTS

1. 2. Using the most convenient method, select first the section map, then the object within that section that contains the data points of interest. If the data points of interest need to be magnified to make selection easier, while still in Object mode, you may simultaneously zoom and pan the selected object(s) to the middle of the work space by doing the following: a. b. On the vertical tool bar, click the Zoom tool. With the cursor positioned over the selected object(s), using the left mouse button, click and drag the object(s) toward the center of the work space. Release the cursor button. Repeat as needed. button. tool or the Select Using Polygon tool,
3. 4.
On the system tool bar, click the Points Mode
If Select Using Rectangle is active, click and hold the left mouse button while dragging the cursor diagonally to form a small selection box that encloses all the data points you want to select. If Select Using Polygon is active, click a series of points to create a selection polygon of any shape that encloses all of the data points you want to select.
RELATED TOPICS
Select By Color (page 6-52) Select Tools (page 6-49) Align & Change Color Tools (page 6-52) Line Edit Tools (page 6-58) Change Z (page 6-63) Undo Tool (page 6-66) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66)
Page 6-52
SELECT BY COLOR
Select By Color operates across the entire atlas, regardless of which Selection Mode is currently active. It simply selects all tracings and/or markers of the same color, throughout the entire atlas.
PROCEDURE
1. 2. On the Vertical Tool Bar, click the Select By Color button
On the system tool bars color palette, click the color that matches the color of the objects that need to be selected. System Tool Bar With Color Palette
When the Select By Color tool on the Vertical Tool Bar is active, clicking a colored square on the system tool bars Color Palette selects all objects in the atlas of that color.
RELATED TOPICS
Select Using Rectangle or Polygon (page 6-49) Select Tools (page 6-49) Align & Change Color Tools (page 6-52) Line Edit Tools (page 6-58) Change Z (page 6-63) Undo Tool (page 6-66) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66)
ALIGN & CHANGE COLOR TOOLS

The three manual alignment tools (Rotate, Translate, Resize) and the Change Color tool operate only on the currently selected parts of the atlas. Rotate, Translate, Resize, and Change Color Tools
TOPIC CONTENTS
Rotate Selected Parts of the Atlas (page 6-53) Translate Selected Parts of the Atlas (page 6-54) Resize the Selected Parts of the Atlas (page 6-55) Change Color of the Selected Parts of the Atlas (page 6-57)

ROTATE SELECTED PARTS OF THE ATLAS

Sections or objects can be manually rotated to improve alignment with other sections or objects.
PROCEDURE: ROTATE A SECTION

1. 2. In Section mode select the section to be rotated.
If other section tracings are needed for reference and are not currently being displayed, choose Show All Sections from the View menu, or choose Overlay Sections from the View menu and select the particular sections to be overlaid. Click the Rotate button on the vertical tool bar. A red marker will appear on the section. The section will rotate around this marker. If desirable, click and drag the red marker to a different location. To rotate the section clockwise, place the cursor any where in the atlas window, then click and drag the cursor straight down. To rotate the section counter-clockwise, place the cursor anywhere in the atlas window, then click and drag the cursor straight up.
3. 4. 5.
PROCEDURE: ROTATE AN OBJECT

1. 2. 3. In Section mode In Object mode select the section that contains the object of interest. select the object of interest.
If other section tracings are needed for reference and are not currently being displayed, choose Show All Sections from the View menu, or choose Overlay Sections from the View menu and select the particular sections to be overlaid. Click the Rotate button on the vertical tool bar. A red marker will appear on the selected object. The object will rotate around this marker. If desirable, click and drag the red marker to a different location on the object. To rotate the object clockwise, place the cursor any where in the atlas window, then click and drag the cursor straight down. To rotate the object counter-clockwise, place the cursor anywhere in the atlas window, then click and drag the cursor straight up.
4.
5. 6.

After Rotate is used, if the atlas is saved using Save on the File menu, or by responding YES to the Save Data message when exiting the Atlas Shop, the data in the original atlas Topo array(s) are permanently changed. If desirable, Save As on the File menu may be used instead, to save the edited version of the atlas to a new Topo array. The Undo button on the vertical tool bar will undo the last rotation. Choosing Restore Original from the File menu will undo all unsaved changes to the atlas.
RELATED TOPICS
Translate Selected Parts of the Atlas (page 6-54) Resize the Selected Parts of the Atlas (page 6-55) Change Color of the Selected Parts of the Atlas (page 6-57) Select Tools (page 6-49) Align & Change Color Tools (page 6-52) Line Edit Tools (page 6-58) Change Z (page 6-63) Undo Tool (page 6-66) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66)
TRANSLATE SELECTED PARTS OF THE ATLAS

PROCEDURE: TRANSLATE A SECTION MAP
1. 2. In Section mode , select a section map that needs to be moved in the same XY plane to a new location.
Overlay at least one adjacent section map for visual reference by doing the following: a. From the View menu, choose Overlay Sections to open the Overlay Section dialog box. With the cursor on its title bar, click and drag the Overlay Section dialog box to the back Perspective Panel. This will keep the dialog box from obscuring the atlas during the edit procedure. Overlay Section Dialog Box
b.
Although various combinations of reference maps may be used, the simplest is to superimpose only the previous section. To use the simplest approach, do the following: i. ii. On the Overlay Section dialog box, type 1 in the previous section edit field and verify that there is a check mark next to it. Click the Apply button. tool.
3.
On the Vertical Tool Bar, click the Translate The cursor takes the shape of crossed arrows.
Page 6-55
4. Place the cursor over the selected section, then using the left mouse button, click and drag the section map so that its tracings are better aligned with the reference (gray) section. When the cursor button is released, the moved tracing will settle into its new position. If needed, repeat step 4 to refine the placement. If satisfied with the translation, choose Save from the File menu to permanently change the objects location.
5. 6.
ALTERNATE PROCEDURE
Sections may also be moved a known micron distance using Numeric Transform. See Edit> Numeric Transform on 6-41.
To remove the overlaid tracings, close the Overlay Section dialog box. To learn more about Overly Section options see: View> Overlay Sections (page 6-20) Choosing Save on the File menu permanently saves the edit in the current atlas Topo array.
PROCEDURE: TRANSLATE AN OBJECT

1. 2. 3. 4. In Section Mode select a section that contains an object that needs to be moved. In Object Mode select the object or objects that needs to be moved. On the Vertical Tool Bar, click the Translate The cursor takes the shape of crossed arrows. tool.
Place the cursor over the selected object(s), then using the left mouse button, click and drag the selected object(s) to the desired location. When the cursor button is released, the moved tracing will settle into its new position. If needed, repeat step 4 to refine the placement. If satisfied with the translation, choose Save from the File menu to permanently change the objects location.
5. 6.
RELATED TOPICS
Rotate Selected Parts of the Atlas (page 6-53) Resize the Selected Parts of the Atlas (page 6-55) Change Color of the Selected Parts of the Atlas (page 6-57) Select Tools (page 6-49) Align & Change Color Tools (page 6-52) Line Edit Tools (page 6-58) Change Z (page 6-63) Undo Tool (page 6-66) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66)
RESIZE THE SELECTED PARTS OF THE ATLAS

PROCEDURE: RESIZE A SECTION MAP
1. In Section mode select the section that is to be resized.
Page 6-56
2. If other section tracings are needed for reference and are not currently being displayed, choose Show All Sections from the View menu, or choose Overlay Sections from the View menu and select the particular sections to be overlaid. Click the Resize button on the vertical tool bar. A resizing box will appear around the selected section.
3. 4.
Do one of the following to resize the selected section: To expand or shrink the section map while maintaining its current height and width ratio, click and drag the resize control point in any corner of the resize box. To narrow or widen the section map while maintaining its current height, click and drag the resize control point on either side of the resize box. To increase or decrease the height of the section while maintaining its current width, click and drag the resize control point on the top or bottom of the resize box.
Sections and objects may also be resized using Numeric Transform. See Edit> Numeric Transform on 6-41.
PROCEDURE: RESIZE AN OBJECT

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

Rotate Selected Parts of the Atlas (page 6-53) Translate Selected Parts of the Atlas (page 6-54) Change Color of the Selected Parts of the Atlas (page 6-57) Select Tools (page 6-49) Align & Change Color Tools (page 6-52) Line Edit Tools (page 6-58) Change Z (page 6-63) Undo Tool (page 6-66) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66)
CHANGE COLOR OF THE SELECTED PARTS OF THE ATLAS

Choosing Change Color from the Edit menu or clicking the Change Color tool on the vertical tool bar readies the cursor to choose a new color for the selected parts of the atlas. IMPORTANT: After using Change Color, if the atlas is saved using Save on the File menu or saved when exiting the Atlas Shop, the default color for the selected objects is permanently changed in the original Topo array.
PROCEDURE
1. 2. 3. Select the section(s), object(s), or point(s) for which the color is to be changed. Click the Change Color button on the vertical tool bar or choose Change Color from the Edit menu.
On the system tool bars color palette, click to choose a new color. All currently selected items will change to the new color.
After Change Color is used, if the atlas is saved using Save on the File menu, or by responding YES to the Save Data message when exiting the Atlas Shop, the data in the original atlas Topo array(s) are permanently changed. If desirable, Save As on the File menu may be used instead, to save the edited version of the atlas to a new Topo array. The Undo button on the vertical tool bar will undo the last color change. Choosing Restore Original from the File menu will undo all unsaved changes to the atlas. Colors may be changed simply to improve the appearance of the atlas, or to group items differently. When displaying or editing an atlas, all objects of the same color may be manipulated as a group.

Rotate Selected Parts of the Atlas (page 6-53) Translate Selected Parts of the Atlas (page 6-54) Resize the Selected Parts of the Atlas (page 6-55) Change Color of the Selected Parts of the Atlas (page 6-57) Select Tools (page 6-49) Align & Change Color Tools (page 6-52) Line Edit Tools (page 6-58) Change Z (page 6-63) Undo Tool (page 6-66) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66)
LINE EDIT TOOLS

The line editing tools on the Vertical Tool Bar correct tracing errors made when the topographic data was collected in the measurement software. Line Edit tools are only used after an object (tracing) of interest has been selected in Object mode. The Line Editing Tools on the Vertical Toolbar
TOPIC CONTENTS
Straighten Edge (page 6-59) Combine Two Objects (page 6-59) Separate Two Objects (page 6-60) Redefining an Objects Edge (page 6-61) Deleting Objects (page 6-62)
RELATED TOPICS
Page 6-59
STRAIGHTEN EDGE
PROCEDURE
The new straight line segment will be constructed counterclockwise from the first point to the second point. 1. 2. 3. 4. Select the tracing that needs to be Line edited. On the vertical, click the Straighten Edge button.
Click the one end of the segment to be straightened. Click the other end of the segment.
ADDITIONAL NOTES
Click the right mouse button to cancel after the first click. Click the undo button to undo the last edit.
RELATED TOPICS
Combine Two Objects (page 6-59) Separate Two Objects (page 6-60) Redefining an Objects Edge (page 6-61) Deleting Objects (page 6-62) Select Tools (page 6-49) Align & Change Color Tools (page 6-52) Line Edit Tools (page 6-58) Change Z (page 6-63) Undo Tool (page 6-66) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66)
COMBINE TWO OBJECTS

Sometimes a single object will be thresholded and traced as two separate halves. This procedure corrects this. The Combine Two Objects tool on the vertical tool bar connects two objects with straight lines which are defined by mouse clicks. Combine Objects Example
1. 2. 3.
Click where one end of the connecting line should be on object A.
Page 6-60
4. 5. 6. Click where the other end of the connecting line should be on object B. Click where one end of the second connecting line should be on object B. Click where the other end of the connecting line should be on object A.
ADDITIONAL NOTES
Click the right mouse button to cancel before the series of 4 clicks is finished. Click the button to undo the last edit.
RELATED TOPICS
Straighten Edge (page 6-59) Separate Two Objects (page 6-60) Redefining an Objects Edge (page 6-61) Deleting Objects (page 6-62) Select Tools (page 6-49) Align & Change Color Tools (page 6-52) Line Edit Tools (page 6-58) Change Z (page 6-63) Undo Tool (page 6-66) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66)
SEPARATE TWO OBJECTS

Sometimes, two objects are traced as one. This procedure corrects this. Clicking two points defines the location for a gap that will separate the object into two.
PROCEDURE
1. 2. 3. Select the objects that need to be separated. Click the Separate Two Objects button on the vertical tool bar.
ADDITIONAL NOTES
Click the right mouse button after the first click to cancel the separation. Click the undo button to undo the separation.

Straighten Edge (page 6-59) Combine Two Objects (page 6-59) Redefining an Objects Edge (page 6-61) Deleting Objects (page 6-62) Select Tools (page 6-49) Align & Change Color Tools (page 6-52) Line Edit Tools (page 6-58) Change Z (page 6-63) Undo Tool (page 6-66) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66)

A segment of an objects contour tracing can be redrawn with the Redefine Edge tool. This tool is recommended (instead of the Straighten Edge tool) when editing atlases that are to be surface rendered or any other time that a significant portion of an objects tracing needs to be altered.
PROCEDURE:
1. 2. 3. 4. 5. Click the Redefine Edge tool on the vertical tool bar.
Click to mark one end of the segment that is to be redefined. Click to mark the other end of the segment. Starting from the first point, click a series of data points to define the new contour. If the atlas is to be surface rendered, click the series of data points fairly close together. Click the right mouse button to end the construction of the new edge.
SAVING THE EDIT

After Redefine Edge is used, if the atlas is saved using Save on the File menu, or by responding YES to the Save Data message when exiting the Atlas Shop, the data in the original atlas Topo array(s) are permanently changed. If desirable, Save As on the File menu may be used instead, to save the edited version of the atlas to a new Topo array.
ADDITIONAL NOTES:
Click the Undo button on the vertical tool bar to undo the redefinition of the contour. Click the undo button to undo the redefinition of the contour.

Straighten Edge (page 6-59) Combine Two Objects (page 6-59) Separate Two Objects (page 6-60) Deleting Objects (page 6-62) Select Tools (page 6-49) Align & Change Color Tools (page 6-52) Line Edit Tools (page 6-58) Change Z (page 6-63) Undo Tool (page 6-66) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66)
DELETING OBJECTS
The Delete tool on the vertical tool bar is used to permanently remove the data of a chosen object from the original Topo array. The object immediately disappears from the atlas window.
PROCEDURE:
1. 2. Click the Delete Object tool on the vertical tool bar.
Click on the tracing of the object to be deleted. Note: The removed data is temporarily stored in the Topographers backup buffer and the delete does not become permanent until the data is saved using Save on the File menu or by responding YES to the Save Data message on exiting the Atlas Shop.
ADDITIONAL NOTES:
RELATED TOPICS
Straighten Edge (page 6-59) Combine Two Objects (page 6-59) Separate Two Objects (page 6-60) Redefining an Objects Edge (page 6-61) Select Tools (page 6-49) Align & Change Color Tools (page 6-52) Line Edit Tools (page 6-58) Change Z (page 6-63) Undo Tool (page 6-66) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66)
Page 6-63
CHANGE Z
Change Z is used to change the Z Offset value of section maps, objects within section maps, or points within objects. Change Z can operate on all sections at once or only on selected sections, objects, or points. Change Z Tool
Choosing Change Z from the Edit menu or clicking the Change Z tool on the vertical tool bar opens the Change Z dialog box, so that sections, objects, or points may be repositioned along the Z axis. The initial (default) Z position of everything in the atlas is based on the Z Offset value that was displayed during measurement on the Parameters dialog box in BIOQUANT Life Science or BIOQUANT OSTEO. Reasons the default Z value may need to be changed: Items were measured or counted using the wrong Z Offset on the Parameters dialog box. The Z Offset was changed by mistake, before all measurements for one physical tissue section were complete. So part of the tissue section displays at one Z level, the rest at another. A section has been duplicated using Internal Copy or Cut and Internal Paste. Now the Z-Offset in the new section needs to be changed to properly position it on the Z axis.
TOPIC CONTENTS
Evenly Distribute Topographic Sections Along the Z Axis. (page 6-63) Relocate Selected Items to a Specific Z Offset Position (page 6-64) Shift Selected Items a Specific Micron Distance from Current Position (page 6-65)
RELATED TOPICS
Line Edit Tools (page 6-58) Undo Tool (page 6-66) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66)
EVENLY DISTRIBUTE TOPOGRAPHIC SECTIONS ALONG THE Z AXIS.

Change All Sections on the Change Z dialog box may be used to distribute sections evenly along the Z axis.
PROCEDURE:
1. 2. Click the Section Mode button on the system tool bar to activate Section Mode.
Click the Change Z tool on the vertical tool bar or choose Change Z from the Edit menu to open the Change Z dialog box. Change Z With Change All Sections Mode Active
In this example the first sections Z Offset is 0. The other sections will be evenly distributed along the Z axis with 20 microns between each.
3.
On the Change Z dialog box, click the Change All Sections radio button. BIOQUANT Topographer Handbook: The Atlas Shop in Detail
Page 6-64
4. 5. 6. 7. In the Z Value of First Section field, enter the Z value for the very first section in the atlas. (Often this value will be zero.) In the Z Offset Between Sections field, type the micron distance that is to separate each section from the proceeding one. Click the Apply button. Click the Close button to dismiss the Change Z dialog box.
RELATED TOPICS
Relocate Selected Items to a Specific Z Offset Position (page 6-64) Shift Selected Items a Specific Micron Distance from Current Position (page 6-65) Line Edit Tools (page 6-58) Change Z (page 6-63) Undo Tool (page 6-66) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66)
RELOCATE SELECTED ITEMS TO A SPECIFIC Z OFFSET POSITION

One or more sections, objects, or points may be relocated to a specific, known Z Offset. If multiple items are selected, all will be relocated to the same point on the Z axis.
PROCEDURE
1. 2. Select the section(s), object(s), or point(s) for which the Z value is to be changed. Click the Change Z button on the vertical tool bar or choose Change Z from the Edit menu to open the Change Z dialog box. Change Z With Change Selected Sections Active
In this example all selected items will be reset to a Z Offset of 70.
3.
Verify that the Change Selected Section(s) radio button is active. If only one item is selected, the default value in the Change All Z Value To field is the current Z Offset value for that item. If multiple items are selected, the Change All Z Value To field holds the current Z value of the first selected item. If the default value in the Change All Z Value To field is the desired Z Offset for all of the selected items, click the Apply button. If the default value is not the desired Z Offset for all selected items, do the following: a. b. Delete the current value in the Change All Z Value To field and type in the desired new Z value. Click the Apply button. All selected items will be relocated to the Z Offset position specified by the new Z value.
Page 6-65
4. Click the Close button to close the Change Z dialog box.
RELATED TOPICS
Evenly Distribute Topographic Sections Along the Z Axis. (page 6-63) Shift Selected Items a Specific Micron Distance from Current Position (page 6-65) Line Edit Tools (page 6-58) Change Z (page 6-63) Undo Tool (page 6-66) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66)
SHIFT SELECTED ITEMS A SPECIFIC MICRON DISTANCE FROM CURRENT POSITION

If multiple items are selected, this procedure preserves the relative distances between. In the Raise/Lower Z Value To field, the value that is entered is the number of microns that the selected items should be moved up or down. Positive values raise the selected parts, and negative values lower the selected parts.
PROCEDURE
1. 2. Select the section(s), object(s), or point(s) that are to be shifted up or down the Z axis. Click the Change Z button on the vertical tool bar or choose Change Z from the Edit menu to open the Change Z dialog box. Change Z With Change Selected Sections Active
Each selected section will be moved upward 10 microns from its current position.
3.
Verify that the Change Selected Section(s) radio button is active If only one item is selected, the default value in the Change All Z Value To field is the current Z Offset value for that item. If multiple items are selected, the Change All Z Value To field holds the current Z value of the first selected item. In the Raise/Lower All Z Values by field, do one of the following: To raise the Z value, type a positive micron distance (e.g. 10). To lower the Z value, type a negative micron distance (e.g. -10).
4.
5.
Click the Apply button. The micron distance will be added to (or subtracted from) the default value in the Change All Z Value To field, and all selected items will be shifted up (or down) from their current positions on the Z axis by the specified micron distance. Click the Close button to close the Change Z dialog box.
6.

After Change Z is used, the change may be saved to permanently alter the original data in the atlas array using Save on the File menu, or by responding YES to the Save Data message when exiting the Atlas Shop. To preserve the original data, Save As on the File menu may be used instead, to save the edited version of the atlas to a new Topo array. The current Z Positions for data viewed in the View BIOQUANT Data window, are exactly ten times greater than the Z Offset value of that same data. (Example: If the default Z Value for a selected item is 150 on the Change Z dialog box, its Z Position value in the View BIOQUANT Data window will be 1500.)
RELATED TOPICS
Evenly Distribute Topographic Sections Along the Z Axis. (page 6-63) Relocate Selected Items to a Specific Z Offset Position (page 6-64) Line Edit Tools (page 6-58) Change Z (page 6-63) Undo Tool (page 6-66) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66)
UNDO TOOL
The Undo tool on the Vertical Tool Bar performs the same function as the Undo option on the Edit menu. Both undo the last unsaved edit made in the atlas. Undo Tool
PROCEDURE
On the Vertical Tool Bar, click the Undo button.
RELATED TOPICS
File> Restore Original (page 6-5) Undo Tool (page 6-66) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66)
SPECIAL EDITS TO ENHANCE SURFACE RENDERING

Particular editing and formatting tools in the Topographers Atlas Shop help improve the quality of a surface rendered model. The following procedures are all done in the Atlas Shop. After editing is finished, the edited atlas is opened again in the Atlas Modeler. If corrective edits, such as aligning sections and correcting errors in Z positioning, are needed, it is best that these be done prior to adding special surface rendering formats.
COMMON ADJUSTMENTS THAT ENHANCE SURFACE RENDERING

Change Resolution - The resolution (number of data points) in large atlases may be decreased to speed the process of surface rendering. Edit> Resolution (page 6-36)
Page 6-67
Change Colors in a Branched Structure - Y or V shaped structures in an atlas surface render more accurately if one of the branches of the Y or V is a different color. Change Color in Branched structures (page 6-67) Cap Object - The first and last contour tracings in an atlas can be marked as caps that will cover the open ends of a surface rendered model. Cap Object (page 6-68) End of Object/Leave Open - A number of tracings in the atlas may be marked as open to create a transparent window in a surface rendered model, through which interior objects may be viewed, without reducing the opacity of the entire model. End of Object/Leave Open (page 6-68) Middle of Object - The cap or open markers on a tracing may be removed to return the tracing to its original Middle of Object default status. Middle of Object (page 6-69)
RELATED TOPICS
File> Restore Original (page 6-5) Undo Tool (page 6-66) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47)
CHANGE COLOR IN BRANCHED STRUCTURES

The system creates surfaces by looking for corresponding points of the same color on adjacent sections. For branched (Y or V shaped) structures, the defining surface outline breaks into two sets of outlines and the system must deal with the sudden appearance of too many points that do not correspond. Making the shortest leg or branch of the Y or V shaped structure a different color, eliminates the confusion. The shortest branch of the structure is the branch that is defined by the fewest tracings.
PROCEDURE
1. 2. If needed, make initial corrective edits to the atlas, such as aligning sections and correcting errors in Z positioning that may have been made during data collection. Click to activate Section Mode then select the first (or next) topographic section that contains a surface defining outline for the shortest branch of the Y or V shaped structure. If the outline is one of several objects within the selected topographic section, click the Object Mode button, then use the Select Next 4. 5. 6. Click the Change Color button until only the correct outline is selected.
3.
button on the vertical tool bar or choose Change Color from the Edit menu.
On the system tool bars color palette, click to choose a new color. The selected outline will change to the new color. Repeat steps 2 through 5 to select and change the color of all outlines that define this branch of the structure, using the same new color for each outline.
SAVING THE EDIT:

After Change Color is used, if the atlas is saved using Save on the File menu, or by responding YES to the Save Data message when exiting the Atlas Shop, the data in the original atlas Topo array(s) are permanently changed. If desirable, Save As on the File menu may be used instead, to save the edited version of the atlas to a new Topo array.

Format Contour Lines (page 6-68) Edit> Resolution (page 6-36) File> Restore Original (page 6-5) Undo Tool (page 6-66) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66)
FORMAT CONTOUR LINES

The Cap Object, End of Object/Leave Open, and Middle of Object buttons on the system tool bar add special formatting to an atlas that is to be surface rendered. Surface Render Formatting Tools
CAP OBJECT
The Cap Object tool is used to tag the first and last outlines in the model as surface rendering caps. An outline that is tagged as a cap will automatically fill with the surface color when the atlas is opened in the Atlas Modeler. Because surface rendering connects points of the same color on adjacent surface defining outlines (usually section outlines), and there is no outline before the first tracing or after the last, the rendered surface stops abruptly, leaving open holes at the top and bottom of the rendered model. These holes may be closed using the Cap Object tool in the Atlas Shop. 1. 2. Click the Section Mode button on the system tool bar to activate Section Mode.
Select the topographic section that contains the first or last surface defining outline for the model. NOTE: For the bottom cap this is usually, but not always, Section 0. Click the Object Mode button to activate Object Mode.
3. 4. 5. 6.
If necessary, use the Select Next button on the system tool bar to cycle through the objects in the selected section, until the correct contour outline is selected. Click the Cap Object button on the system tool bar to mark the selected tracing as a cap.
Repeat steps 1 through 5 to mark (as a cap) the tracing at the opposite end of the model.
END OF OBJECT/LEAVE OPEN

A number of tracings in the atlas may be marked as open to create a transparent window in a surface rendered model, through which interior objects may be viewed, without reducing the opacity of the entire model. The inner structures of a surface rendered model may be revealed while in the Atlas Modeler program, by simply decreasing the opacity of the entire outer surface. But, the resultant loss of surface details across the entire model may not be desirable. The End of Object/Leave Open tool in the Atlas Shop makes it possible to create a limited transparent window without reducing the opacity of the rest of the models surface. The tool is used to mark a series of surface defining outlines that are to be left open. When the atlas is opened in the Atlas Modeler, all but the first and last outlines marked Leave Open will automatically be constructed as a diffused linear cloud, rather than a solid line. The very first and last outlines in a marked series, are actually End of Object markers that allow the system to recognize the intervening outlines as a separate object, even though the color of the open lines is identical to the rest of the surface. 1. 2. Click the Section Mode button on the system tool bar to activate Section Mode.
Select the topographic section that contains the first (or next) outline that is to be marked with Leave Open.
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3. 4. Click the Object Mode button to activate Object Mode.
If necessary, use the Select Next button on the system tool bar to cycle through the objects in the selected section, until only the correct contour outline is selected. Click the End of Object/Leave Open Leave Open. tool button on the system tool bar to mark the selected tracing as
5. 6.
Repeat steps 1 through 5 to mark (as Leave Open) all the tracings that are to be part of the transparent window.
MIDDLE OF OBJECT
The cap or open markers on a tracing may be removed to return a tracing to its original Middle of Object default status. Before special formatting is added, all tracings in an atlas are termed Middle of Object. The Middle of Object tool on the system tool bar removes the special formatting that was applied to a tracing using the Cap Object or End of Object/Leave Open tools 1. 2. Click the Section Mode button on the system tool bar to activate Section Mode.
Select the topographic section that contains the outline for which the Cap or End of Object/Leave Open formatting is to be removed. Click the Object Mode button to activate Object Mode.
3. 4.
If necessary, use the Select Next button on the system tool bar to cycle through the objects in the selected section, until only the specially formatted outline is selected. Click the Middle of Object button on the system tool bar to remove the special formatting and restore the tracings default Middle of Object status.
5.
RELATED TOPICS
Change Color in Branched structures (page 6-67) Edit> Resolution (page 6-36) File> Restore Original (page 6-5) Undo Tool (page 6-66) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66)
TAKING MEASUREMENTS FROM AN ATLAS

Options on the Measure menu in the Atlas Shop are used to determine volumes, areas, counts, and distances within an atlas.
TOPIC CONTENTS
Measure Volume (page 6-70) Measure Region Of Interest Area (page 6-71) Measure Area of An Object (page 6-72) Count Objects (page 6-74) Measure Distance (page 6-76)

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

Should it be needed, the number of tracings that were used to determine the volume are recorded on the Count tab of the Calculate/Measure dialog box. Simply click the Count tab to reveal the tracing count.
DETERMINE COUNTS PER VOLUME

Once the volume of a structure has been determined and saved to an array, determining the number of objects in that volume provides a count per volume. Frequently the structure of interest is the entire atlas and the objects of interest are cell markers or cell area tracings that are all the same unique color. When this is the case, the Select By Color simultaneously select all cells in the atlas. 1. 2. 3. 4. Determine and save the volume of the structure using the above procedure. Select the internal objects that are to be counted. If all of the objects are the same unique color, use the Select By Color tool. From the Measure menu choose Count. The Calculate/Measure dialog box opens and the Count result is displayed. To save the count to an array click the Save button on the Calculate/Measure dialog box. a. b. c. On the Save Value to Array dialog box, click the New Array button to add an Attribute array. (The system automatically renames the Attribute array to reflect the type of measurement being saved.) To edit the name of the new array, click the cursor in the Destination array field and type the desired name. To record the object count in the destination array, click the Append button. tool can be used to
RELATED TOPICS
Measure Region Of Interest Area (page 6-71) Measure Area of An Object (page 6-72) Count Objects (page 6-74) Measure Distance (page 6-76) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66)
MEASURE REGION OF INTEREST AREA

In Object mode, the rectangle or polygon selection tools are used to define a region of interest (ROI) that is to be measured. The number of objects in the measured region is simultaneously recorded and may be saved to an array to determine count per area.
PROCEDURE
1. 2. 3. 4. If multiple sections exist, click the Section Mode of interest. button and select the section that contains the region
On the View menu, verify that Selection Only is not checked. If it is, click to uncheck it. Click the Object mode button on the system tool bar.
Construct the Region of Interest (ROI) To measure a rectangular area, click the Select With Rectangle and drag diagonally to define the ROI area. button on the vertical tool bar. Click
To measure a polygonal area, click the Select With Polygon button on the vertical tool bar. Click successive points to define the ROI area. Click the right mouse button to close the area.
Page 6-72
5. Choose ROI Area from the Measure menu. The Calculate/Measure dialog box opens on the Selection Area ROI tab with the ROI area reported in square microns. Calculate/Measure: Selected Area ROI
6.
To save the ROI Area to an array, click the Save button on the Calculate/Measure dialog box. a. b. c. d. On the Save Value to Array dialog box, click the New Array button to add an Attribute array. (The system automatically renames the Attribute array to reflect the type of measurement being saved.) To edit the name of the new array, click the cursor in the Destination array field and type the desired name. To record the ROI Area in the destination array, click the Append button. Click the Close button on the Save Value to Array dialog box.
DETERMINE OBJECT COUNT FOR THIS ROI AREA

1. Click the Count tab on the Calculate/Measure dialog box. The number of objects in the measured area is displayed. In order for an object to be included in the count, at least one of its data points must lie within or under the defining borders of the ROI. To save the count to an array click the Save button on the Calculate/Measure dialog box. a. b. c. On the Save Value to Array dialog box, click the New Array button to add an Attribute array. (The system automatically renames the Attribute array to reflect the type of measurement being saved.) To edit the name of the new array, click the cursor in the Destination array field and type the desired name. To record the count in the destination array, click the Append button.
2.
To append the current area measurement or object count a new element in an existing array, click the name of the array in the list to make it the Destination Array before clicking the Append button. To over write the datum in an existing Area or Object Count array click the name of the array in the list to make it the Destination Array and click the Replace button instead of the Append button.
RELATED TOPICS
Measure Volume (page 6-70) Measure Area of An Object (page 6-72) Count Objects (page 6-74) Measure Distance (page 6-76) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66)
MEASURE AREA OF AN OBJECT

The area of a selected object tracing may be measured. If the object contains internal structures, the number of individual objects within the larger tracing may also be determined. BIOQUANT Topographer Handbook: The Atlas Shop in Detail
Page 6-73 PROCEDURE

1. 2. 3. If multiple sections exist, in Section Mode select the section that contains the object of interest.
button and select the Object that is to be measured. If the object has smaller Click the Object Mode objects within it, at this time select only the contour outline of the primary object. Choose Object Area from the Measure menu. The Calculate/Measure dialog box opens with the Object Area in square microns displayed. Calculate/Measure: Object Area
4.
To save the object area to an array, click the Save button on the Calculate/Measure dialog box. a. b. c. d. On the Save Value to Array dialog box, click the New Array button to add an Attribute array. (The system automatically renames the Attribute array to reflect the type of measurement being saved.) To edit the name of the new array, click the cursor in the Destination array field and type the desired name. To record the Object Area in the destination array, click the Append button. Click the Close button on the Save Value to Array dialog box.
DETERMINE NUMBER OF OBJECTS WITHIN AN OBJECT AREA

1. 2. 3. 4. Click the Count tab on the Calculate/Measure dialog box. The number of selected objects included in the area measured is displayed. At this point the Count will be 1. From the Select menu, choose Add Interior Objects to Selection. On the Calculate/Measure dialog box, click the Measure button to update the count. Count will now be the number of objects inside the larger objects tracing plus 1 for the tracing of the larger object. To save the count to an array click the Save button on the Calculate/Measure dialog box. a. b. c. On the Save Value to Array dialog box, click the New Array button to add an Attribute array. (The system automatically renames the Attribute array to reflect the type of measurement being saved.) To edit the name of the new array, click the cursor in the Destination array field and type the desired name. To record the count in the destination array, click the Append button.
To append the current measurement to the data in an existing array, click the name of the array in the list to make it the Destination Array before clicking the Append button. To over write the datum in an existing array click the name of the array in the list to make it the Destination Array and click the Replace button instead of the Append button.

Measure Region Of Interest Area (page 6-71) Measure Volume (page 6-70) Count Objects (page 6-74) Measure Distance (page 6-76) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66)
COUNT OBJECTS
The number of objects within an area or volume may be automatically determined using Count on the Measure menu. Count is most useful for determining the number of single point objects (e.g. cells) in a given area or volume. It is important to be aware that the number of objects reported by the system is influenced by both the selection mode and the selection method used. Because there are advantages and disadvantages to each approach, review the scenarios below before performing the procedures.
MODE & METHOD FOR COUNT PLUS AREA OR VOLUME

In Object mode using one of the ROI selection tools (Rectangle or Polygon), the count reported is exactly the number of objects that lie in the defined area or volume. (Area or volume is simultaneously recorded.) In order for an object to be included in the count, at least one of its data points must lie within or under the defining borders of the ROI. In Object mode, if the count is to be taken from a volume, Select Across Sections must be checked on the Select menu. All objects, on all sections, with at least one data point in or under the defined borders of the ROI will be counted.
MODE & METHODS FOR COUNT ONLY

In Section mode , using Select by Color , the count reported is exactly the number of objects of that color in the entire atlas. (Volume of the atlas is not simultaneously recorded.) In Section mode, if any other selection method is used, the reported value will be the number of selected sections, not the number of objects. If a count per volume is needed, the volume of the atlas may be determined in a separate volume measurement. , using Select by Color , the count reported is exactly the number of objects of In Object mode that color in the currently selected section. (Area of the section is not simultaneously recorded.) Exception: If Select Across Sections is checked on the Select menu, the value reported is the number of objects of that color in the entire atlas (just as if Section mode were active.) If a count per area is needed, the area of the section may be determined in a separate Object Area measurement by selecting only the sections contour outline. , using the GoTo Object list, the count reported is exactly the number of objects that In Object mode are selected on the GoTo Object list. (Neither area nor volume is simultaneously recorded.) , selecting smaller objects inside a larger one using Add Interior Objects on the In Object mode Select menu, the count reported is the number of interior objects plus 1. The larger object is the extra one. (Area is not simultaneously recorded.)
COUNT OBJECTS IN AN AREA PROCEDURE

1. 2. 3. 4. Click the Section mode Click the Object mode button, then select the section that contains the objects of interest. button, to activate Object mode.
Click the Select menu and, if checked, click to uncheck Select Across Sections. Use one of the following methods to select the objects that are to be counted:
Page 6-75
Click the Select Using Rectangle (Area is simultaneously recorded.) tool, then click and drag a rectangular ROI around the objects.
Click the Select Using Polygon tool, then click a series of points to define an ROI around the objects. Click the left mouse button to close the polygon. (Area is simultaneously recorded.) If the objects are a unique color, click the Select by Color tool on the vertical tool bar, then click the color on the color palette that matches the objects of interest. (Area is not simultaneously recorded.) If a larger object contains the objects that are to be counted, first select the larger object, then choose Add Interior Objects from the Select menu. The resultant count will include the larger object as 1. (Area is not simultaneously recorded.)
5.
Choose Count from the Measure menu. The Calculate/Measure dialog box opens with the count of objects displayed. Calculate/Measure: Count
6.
The count may be saved to an array by doing the following: a. b. Click the Save button on the Calculate/Measure dialog box. On the Save Value to Array dialog box, click the New Array button to add an Attribute array to the data set. (The system automatically renames the Attribute array to reflect the type of measurement being saved.) To edit the name of the new array, click the cursor in the Destination array field and type the desired name. To record the Count in the destination array, click the Append button. Click the Close button on the Save Value to Array dialog box.
c. d. e. 7.
If objects were selected using either the Rectangle or Polygon tool, the area from which the count was taken may also be saved to an array as follows: a. b. c. d. e. f. Click the Selection Area ROI tab to display the square micron area in which the objects were counted. Click the Save button on the Calculate/Measure dialog box. On the Save Value to Array dialog box, click the New Array button to add an Attribute array. (The system automatically renames the Attribute array to reflect the type of measurement being saved.) To edit the name of the new array, click the cursor in the Destination array field and type the desired name. Click the Append button to record the area. Click the Close button on the Save Value to Array dialog box.
COUNT OBJECTS IN A VOLUME PROCEDURE

1. Use one of the following methods to select the objects of interest: If the objects are a unique color, you may... i. ii. Click the Section mode button.
Click the Select by Color tool on the vertical tool bar, then click the color on the color palette that matches the objects. (With this selection method, a volume will not be simultaneously recorded.)
If the color of the objects is not unique, or if a simultaneous volume measurement is desired... BIOQUANT Topographer Handbook: The Atlas Shop in Detail
Page 6-76
i. ii. iii. 2. Click the Object mode button.
From the Select menu choose Select Across Sections (to place a check mark next to this option). Click either the Select Using Rectangle or Select Using Polygon then construct an ROI around the objects. tool on the vertical tool bar,
Choose Count from the Measure menu to open the Calculate/Measure dialog box with the number of objects displayed. Calculate/Measure: Count
3.
The count may be saved to an array by doing the following: a. b. Click the Save button on the Calculate/Measure dialog box. On the Save Value to Array dialog box, click the New Array button to add an Attribute array to the data set. (The system automatically renames the Attribute array to reflect the type of measurement being saved.) To edit the name of the new array, click the cursor in the Destination array field and type the desired name. To record the Count in the destination array, click the Append button. Click the Close button on the Save Value to Array dialog box.
c. d. e. 4.
If objects were selected using either the Rectangle or Polygon tool, the volume from which the count was taken may also be saved to an array as follows: a. b. c. d. e. f. Click the Volume tab to display the cubic micron volume in which the objects were counted. Click the Save button on the Calculate/Measure dialog box. On the Save Value to Array dialog box, click the New Array button to add an Attribute array. (The system automatically renames the Attribute array to reflect the type of measurement being saved.) To edit the name of the new array, click the cursor in the Destination array field and type the desired name. Click the Append button to record the area. Click the Close button on the Save Value to Array dialog box.
RELATED TOPICS
Measure Region Of Interest Area (page 6-71) Measure Volume (page 6-70) Measure Distance (page 6-76) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66)
MEASURE DISTANCE
In Section mode, distances can be measured between two points on the same section, between points on two different sections, or between two arbitrary points any where in the atlas window. The Snap to Point option must be checked BIOQUANT Topographer Handbook: The Atlas Shop in Detail
Page 6-77
for specimen related distances and unchecked for arbitrary distances. In Object mode, the only distance that can be measured is between two points on one selected object.
TOPIC CONTENTS
Measure a Distance on One Section (page 6-77) Measure a Distance Between Sections (page 6-78) Measure an Arbitrary Distance in the Atlas Window (page 6-79) Measure a Distance on One Object (page 6-79) Save the Distance to an Array (page 6-80)
RELATED TOPICS
Measure Region Of Interest Area (page 6-71) Measure Volume (page 6-70) Count Objects (page 6-74) Measure Distance (page 6-76) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66)
MEASURE A DISTANCE ON ONE SECTION

PROCEDURE
1. 2. Click the Section mode button on the tool bar, or choose Section from the Select menu.
Choose Distance from the Measure menu to open the Calculate/Measure dialog box. Calculate/Measure: Distance
3. 4. 5. 6.
On the Calculate/Measure dialog box, click to check the Snap to Point check box. On the Calculate/Measure dialog box, click the Measure button. Click two points on the Atlas. The distance between the points will be displayed in microns. To save the distance value to an array, see the Save the Distance to a Array procedure below.

Measure a Distance Between Sections (page 6-78) Measure an Arbitrary Distance in the Atlas Window (page 6-79) Measure a Distance on One Object (page 6-79) Save the Distance to an Array (page 6-80) Measure Region Of Interest Area (page 6-71) Measure Volume (page 6-70) Count Objects (page 6-74) Measure Distance (page 6-76) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66)
MEASURE A DISTANCE BETWEEN SECTIONS

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

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

PROCEDURE
1. Click the Section mode button on the tool bar, select the section that contains the object of interest, button and select the object.
then click the Object mode 2. 3. 4. 5. 6.
Choose Distance from the Measure menu to open the Calculate/Measure dialog box. On the Calculate/Measure dialog box, click to check the Snap to Point check box. On the Calculate/Measure dialog box, click the Measure button. Click two points on one selected object. The distance between the points will be displayed in microns. To save the distance value to an array, see the Save the Distance to a Array procedure below.

Measure a Distance on One Section (page 6-77) Measure a Distance Between Sections (page 6-78) Measure an Arbitrary Distance in the Atlas Window (page 6-79) Save the Distance to an Array (page 6-80) Measure Region Of Interest Area (page 6-71) Measure Volume (page 6-70) Count Objects (page 6-74) Measure Distance (page 6-76) The File Menu (page 6-2) The Select Menu (page 6-7) The Edit Menu (page 6-27) Tools on the System Tool Bar (page 6-45) Tools on the Vertical Tool Bar (page 6-47) Special Edits To Enhance Surface Rendering (page 6-66)
SAVE THE DISTANCE TO AN ARRAY

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

This section covers planar and contour conversion in the Topographer. To collect data for planar or contour conversion, see instructions in the Life Science help or manual in the Topographer Data Collection chapter.
Understanding the Basics of Planar and Contour Conversion (page 7-2) Planar Conversion (page 7-4) Displaying and Modifying the Planar Histogram (page 717) Contour Conversion (page 7-25) Displaying and Modifying the Contour Converted Atlas (page 7-37)
Planar & Contour Conversion
Page 7-2
UNDERSTANDING THE BASICS OF PLANAR AND CONTOUR CONVERSION

Both Planar Conversion and Contour Conversion quantitatively map deferentially labeled cell populations across serial brain sections, using the topographic tracings that were recorded in BIOQUANT during measurement. In both types of conversion, for each section, the process pulls cell markers within the section to the nearest point on the sections contour tracing. The number of cells at each point are represented by proportionally sized symbols. With Contour Conversion, section contour tracings retain their original configuration. With Planar Conversion, each sections contour tracing is broken at a defined point and stretched into a vertical line. The result is a Planar Histogram. A Contour Converted atlas or Planar Histogram is displayed and may be printed in the Topographers Atlas Viewer. Also in the Atlas Viewer, display parameters for Converted atlases or Planar Histograms may be modified. There are five different data collection strategies that may be used. Each is described below.
TOPIC CONTENTS
General Guidelines (page 7-2) Data Collecting Strategies (page 7-3)
DATA COLLECTION NOTE

This section just provides a general overview of the basics of planar and contour conversion. Actual data collection for Planar or Contour Conversion is done in BIOQUANT Life Science. See the Topographer Data Collection section of the BIOQUANT Life Science help or manual. Once the data has been collected, return to this section for instruction on how to use the Topographers planar and contour conversion tools.
RELATED TOPICS
Planar Conversion (page 7-4) Displaying and Modifying the Planar Histogram (page 7-17) Contour Conversion (page 7-25) Displaying and Modifying the Contour Converted Atlas (page 7-37)
GENERAL GUIDELINES
Topographic data for Contour or Planar Conversion consist only of contour tracings and cell markers. Contour tracings are of whole tissue sections, or structures within sections. Contour tracings are constructed using either a Length array or Area array. There should be one length or area measurement per contour. The system is not able to join multiple length measurements into a single length measurement. Cell location markers are generated using an Object Count array. Every physical tissue section in a series will have a single Landmark point, a unique Z Offset value, and a known Start Point for its contour tracing. In the Topographer program, section Landmarks are automatically aligned when the tracings are stacked along the Z axis, therefore the Landmark should be placed at a similar point on all sections. In the Topographer program, a sections Z Offset value assigned during data collection dictates its position on the Z axis. The Z Offset value for the first section is commonly designated as zero (0). The Z Offset value for every other section reflects its micron distance from the first section. For Planar or Contour Conversion, the Start Points of all contour tracings must be deliberately placed by the user, ideally at a similar point on all sections. When Start Points are deliberately placed at a similar point on all sections, the Topographers Align Sections feature may be used to automatically reorient (rotate) tracings from all sections so they match. Planar Conversion does not require that section tracings have rotational alignment, although similar orientation of tracings can be visually helpful to the user. Alternately, if rotational alignment is desirable, but consistent Start Points were not maintained during data collection, tracings may be manually rotated, one by one, using the Topographers Rotate tool.
BIOQUANT Topographer Handbook: Planar & Contour Conversion
Page 7-3
Data collection may be automatic or manual. Structures that can be thresholded are usually automatically traced or counted. Structures that cannot be thresholded, must be manually traced or counted.
RELATED TOPICS
Data Collecting Strategies (page 7-3) Planar Conversion (page 7-4) Displaying and Modifying the Planar Histogram (page 7-17) Contour Conversion (page 7-25) Displaying and Modifying the Contour Converted Atlas (page 7-37)
DATA COLLECTING STRATEGIES

The most important point to note about saving Topo data for Planar or Contour Conversion is that the contour and cells for a section should be in the same Topo array. This guarantees that the cells remain associated with the Contour.
TOPO ARRAY STRATEGY

The contour tracing and cells for a section should be in the same Topo array. Multiple sections can be stored in a single Topo array, as long as both the contour tracing and cells for all sections are included.
STRATEGY 1: RECOMMENDED FOR SMALL STUDIES

Number of Topo arrays required = 1 Use only one Topo array for all outlines and all cell counts. This strategy is most appropriate when the number of tissue sections is relatively small and the number of cells per section is expected to be no more than a few hundred. Automatic Align Sections may be used with this method.
STRATEGY 2 - RECOMMENDED FOR MOST STUDIES

Number of Topo arrays required = less than the number of sections, otherwise users choice, depending on how many sections are to be analyzed. Use one Topo array for all of the data for several sections. Record both contour tracings and cell counts for a limited number of tissue sections in one Topo array. For instance, if sections are large and have many cells, you may want to limit the number of sections per Topo array to five or less. On the other hand, if there are hundreds of sections, you may want to store the data for up to ten sections in each Topo array. Automatic Align Sections may be used with this method.
STRATEGY 3 - RECOMMENDED FOR STUDIES WITH A LARGE NUMBER OF CELLS TO BE COUNTED

Number of Topo arrays required = number of sections Use one Topo array for each serial section. Record both the contour tracing and the cell counts in the Topo array designated for each section. This strategy is employed when the number of sections in the study is relatively small. The number of cells per section may be numerous or few. Automatic Align Sections may be used with this method.
RELATED TOPICS
General Guidelines (page 7-2) Planar Conversion (page 7-4) Displaying and Modifying the Planar Histogram (page 7-17) Contour Conversion (page 7-25) Displaying and Modifying the Contour Converted Atlas (page 7-37)
Page 7-4
PLANAR CONVERSION
Planar Conversion in the Topographers Atlas Shop is used to convert Topo data to a Planar Histogram format. The Planar Histogram is displayed in the Topographers Atlas Viewer.

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

RELATED TOPICS
STEP 2: BACKING UP THE RAW TOPO ARRAY(S)

Before we go further we will copy the data from the selected Topo array(s) into a new Topo array. We will perform the Planar and Contour Conversion on the new Topo array to preserve the integrity of the raw Topo arrays. In this way we can always make a new copy of the raw Topo arrays in the future.
PROCEDURE
1. 2. 3. 4. 5. 6. 7. 8. In the Atlas Shop, from the File menu, choose Save As. On the Save Array As dialog box, click the New Array button to add a new Topo array to the data set. In the Array Name edit file, rename the new Topo array to Master Raw Topo Data. Click the Save button. In the Atlas Shop, from the File menu, choose Exit Atlas Shop. You are returned to the Atlas Viewer. In the Atlas Viewer, on Select Arrays, from the Select menu, choose Unselect All Arrays. At this point there should not be any arrays selected. On Select Arrays, in the Available Arrays list, double click Topo array we just added, Master Raw Topo Data to move it to the Selected list. Click the Resize To Fit button on the system tool bar. The map drawn should equal the map generated from the raw Topo data. Click the Atlas Shop button (or choose Atlas Shop from the Tools menu). The Atlas Shop will open with Section Mode active.
9.
Page 7-7
10. Continue with Step 3: Setting up for Conversion (page 7-7).

RELATED TOPICS
STEP 3: SETTING UP FOR CONVERSION

1. (Optional) Align the rotation of all the sections by doing the following: a. b. c. d. 2. If necessary, click the Resize to Fit work space. button on the system tool bar to scale the atlas to the size of the
From the Select menu, choose Select All Sections. From the Edit menu, choose Align Sections. The sections rotate so that the start points on all sections are aligned. From the File menu, choose Save.
From the Tools menu, choose Planar Conversion to open the Planar dialog box. Planar
One DTI array is automatically displayed for each cell type that was counted. In this illustration, the atlas contains two cell types.
Page 7-8
3. Continue with Step 4: Customizing the DTI Array Parameters (page 7-8).

RELATED TOPICS
STEP 4: CUSTOMIZING THE DTI ARRAY PARAMETERS

DTI ARRAY EXPLANATION
When the Planar dialog box opens, one DTI array is listed (and added to the current data set) for each cell type in the selected Topo arrays. Cell data in this case is point data collected with an Object Count array. Cell types are identified by color. A symbol is used to represent the cell population at each data point along the specimen contour line. The shape, color, height to width ratio, magnitude, placement, and color parameters of the symbol are customizable. Symbol parameters that are changed from the default are automatically saved to the corresponding DTI arrays comment.
PROCEDURE: CUSTOMIZING DTI PARAMETERS

1. 2. In the DTI Array(s) box, click to highlight the first DTI array. In the Symbol Shape region, choose one of the following shapes: Line: Represents the cell type using a line. The height of the Line is always 1. Rectangle: Represent the cell type using a rectangle. The rectangle defaults to a height and width of 1.
Ellipse: Represent the cell type using an ellipse. The Ellipse defaults to a height and width of 1. The shape in the preview box changes to match the symbol type chosen. The default shape is Line. Shape: DTI Array Comment: Line Default - No comment Rectangle S1; Ellipse S2;
Page 7-9
3. In the Symbol Shape region, move the Ratio slider to the desired position. The Ratio determines the symbols height to width ratio. Moving the slider to the left decreases the height to width ratio. Moving the slider to the right increases the ratio. The ratio range available with the slider is between 0.3 and 3. The default ratio is 1. Ratios less than 1 do not affect the Line shape because the Lines height is always 1. The height is the Y distance from the vertical line. The width is the X distance along the vertical line. Ratio: DTI Array Comment: (Height/Width) 3/10 R0.3; 2/5 R0.4; 1/2 R0.5; 3/5 R0.6; 1/1 Default - No Comment 2/1 R2.0; 3/1 R3.0; In the Symbol Shape region, in the Mag edit box, type the desired magnitude. The height and width of the symbol are multiplied by the Magnitude. It is important to have the same Mag for all DTI arrays in a study. If you have a small number of cells, it might be useful to increase the Mag. If you have an extremely large number of cell counts, it might be useful to type in a Mag that is less than 1. The Mag can also be changed at a later point. Mag: DTI Array Comment: 0.05 M0.050000; 0.5 M0.500000 1 Default - No comment 2 M2.000000; 3 M3.000000; In the Position region, choose either Left, Center, or Right to indicate the orientation of the symbol to the line. The position of the shape to the contour line in the preview box changes to match the position chosen. The default position is Center. Position: DTI Array Comment: Left P2; Center Default - No comment Right P1; In the Color region, the Outline color of the symbol defaults to the original cell type measurement color. To change the outline color of the symbol for this cell type, first click the Outline radio button, then click the desired color. Color: DTI Array Comment: Blue No comment Red C2; Pink C3; Light Green C4; Light Blue C5; The color numbers increment by one for each remaining color in the palette, reading left to right. In the Color region, the Fill color of the symbol defaults to the original cell type measurement color. To change the fill color of the symbol for this cell type, first click the Fill radio button, then click the desired color. Fill is not available for the Line symbol. Color: DTI Array Comment: Blue No comment Red F2; Pink F3; Light Green F4; Light Blue F5; The color numbers increment by one for each remaining color in the palette, reading left to right. Repeat from step 1 for each DTI array in the DTI array(s) box. BIOQUANT Topographer Handbook: Planar & Contour Conversion
4.
5.
6.
7.
8.
Page 7-10 ADDITIONAL NOTES

9. If the ratio parameters offered do not meet requirements, manually type the desired parameter into the comment of the DTI array. It is important to have the same Mag for all DTI arrays in a study. The DTI parameters can also be changed at a later point. Continue with Step 5: Defining Fiduciary Points (page 7-10).

RELATED TOPICS
STEP 5: DEFINING FIDUCIARY POINTS

LINE ARRAY EXPLANATION
A Line Array is created when Topo data are converted to Planar data. The Line Array holds the information needed to stretch the specimen contour line into a straight vertical line. The user adds fiduciary points on the specimen contour where each lobule begins. The system represents each lobule by a different colored segment on the straight vertical line.
TOPIC CONTENTS
Procedure ONE: Defining Fiduciary Points (page 7-11) Procedure TWO: Going to the Next Outline (page 7-13) Then continue with Step 6: Setting a Shift Value (page 7-14)
IMPORTANT NOTE
It is important to sequence through your sections before this procedure and become familiar with how the lobules are organized within the sections. If all sections have all lobules, then this procedure is straight-forward. If some lobules are missing, especially from the middle of a contour, this procedure is more complicated. The
Page 7-11
goal is to make it so that the color coded lobules are the same lobules in each section.

RELATED TOPICS
PROCEDURE ONE: DEFINING FIDUCIARY POINTS

1. On the Planar dialog box, click the Add Fiduciary Points button, or from the Edit menu, choose Add Fiduciaries. The pointer changes to the Add Fiduciary cursor. If the sections in the background decrease the visibility of the current section, from the View menu, check Selection Only to display only the current section. On the specimen contour for the first section click once at the beginning of the lobule that you want to be the starting point of the Planar Histogram. Then, in a counter-clockwise direction, click once at the beginning of each lobule, using the following pointers. Atlas Shop
2.
Add a fiduciary marker at the beginning of each lobule.
Page 7-12 POINTERS

A fiduciary marker is placed on the specimen contour at each location clicked. The markers sequence through the colors on the color palette. You need to add fiduciary points in the same order, starting at the same location, for each section to avoid confusion caused by different colored markers. If a lobule in the middle of a contour does not exist for a particular section, click two fiduciary points very close together to skip that color. You want the lobules that do exist to show up in the correct sequenced segment color for comparison to other sections. If you set a fiduciary point at the end of the last lobule, then if you turn on Connect Fiduciary Points later there will be a line connecting the bottom of the histogram. It this is not required. There are special rules for deleting fiduciary points. If the point to be deleted IS THE LAST on the contour, then it may be deleted by itself. If the point is NOT THE LAST on the contour, then all the fiduciary points must be deleted on the contour. In this case use Add Fiduciary Points to redefine the points. This prevents the lobule color assignment from messing up. To delete fiduciary points, do the following: i. ii. Click the right mouse button to exit the Add Fiduciary Point mode. On the Planar dialog box, click the Delete Fiduciary Point Delete Fiduciary. The pointer changes to the Delete Fiduciary cursor. button, or from the Edit menu, choose
iii.
On the specimen contour for the current section click once on the fiduciary to be deleted. If the fiduciary point is not the last on the contour, then repeat to delete all fiduciary points on the current section. The fiduciary marker disappears.
iv. After unwanted fiduciary points have been deleted, click the right mouse button to exit Delete Fiduciary mode. v. If more fiduciary points need to be added, click the Add Fiduciary Points button. To move a fiduciary point along the contour, do the following. Moving a fiduciary point will not mess up the color assignment of the lobule, as long as you do not move it before a preceding fiduciary point or after a following fiduciary points. If you need to re-arrange the order of the fiduciary points, take care that the lobule color assignment matches corresponding lobules on other sections. If the color coding gets messed up, delete all the fiduciary points for the section and start over. i. ii. Click the right mouse button to exit the Add Fiduciary Point mode. On the Planar dialog box, click the Move Fiduciary Point Move Fiduciary. The pointer changes to the Move Fiduciary cursor. button, or from the Edit menu, choose
iii.
On the specimen contour for the current section click once at on the fiduciary to be moved to make it disappear. Then click the specimen contour at the location the fiduciary point should be. Repeat for all fiduciary points to be moved.
iv. After misplaced fiduciary points have been moved, click the right mouse button to exit Move Fiduciary mode. v. 3. If more fiduciary points need to be added, click the Add Fiduciary Points button.
After all fiduciary points have been defined for this section, click the right mouse button to exit Add Fiduciary Point mode.
Page 7-13
4. Continue with Procedure TWO: Going to the Next Outline (page 7-13).

RELATED TOPICS
PROCEDURE TWO: GOING TO THE NEXT OUTLINE

After the Fiduciary Points are in the correct locations on the first contour outline, do the following: 1. 2. 3. On the Planar dialog box, click the Next Outline button, or from the Edit menu, choose Next Outline.
Follow the procedure to set fiduciary points as previously described in Procedure ONE: Defining Fiduciary Points on page 7-11. When all Fiduciary Points have been set, from the Planar dialog box File menu, choose Save Fiduciary(s). This saves the positions of the fiduciary points to the array. If you want to return to edit DTI array parameters at a later point, or if you want to do a Contour Conversion at a later point, you will not need to re-define the fiduciary points. Atlas Shop
When you sequence back to the a section that already has fiduciary markers defined, they show up as larger points.

4. When an outline is reached that already has fiduciary points, the markers are drawn larger to indicate that the section has already been marked. If the sections in the background decrease the visibility of the current section, from the View menu, check Selection Only to display only the active section. To refresh the display, click the RD button on the tool bar. To refresh existing fiduciary points, click the Add Fiduciary Points button. Continue with Step 6: Setting a Shift Value (page 7-14).

RELATED TOPICS
STEP 6: SETTING A SHIFT VALUE

SHIFT EXPLANATION
The Shift determines the distance between the vertical lines used to represent the specimen contour. Shift multiplies the Z value by the number entered. The default Shift value is 1. If the Shift value is changed from the default, it adds a S=#; comment to the Line array. The Shift can be modified later, by adding or modifying the Line Array Comment. Shift: Line Array Comment: 1 Default - No comment 2 S=2; 3 S=3;
PROCEDURE: ENTERING A SHIFT VALUE

1. On Planar dialog box, from the Tools menu, choose Define Shift to open the Planar Shift dialog box. Shift
In this example, a shift of 5 has been entered.
2.
On the Shift dialog box, in the Shift edit box, type the desired value.
Page 7-15
3. Continue with Step 7: Choosing the Aligning Fiduciary (page 7-15).

RELATED TOPICS
STEP 7: CHOOSING THE ALIGNING FIDUCIARY

ALIGNMENT EXPLANATION
After converting the specimen contours to a straight vertical line with each lobule represented by a different color on the line, the system aligns the straight line contours of all section based on the user designated aligning fiduciary.
PROCEDURE: CHOOSING THE ALIGNING FIDUCIARY

1. 2. On the Planar dialog box, click the Select Aligning Fiduciary Point Alignment to open the Set Alignment dialog box. button, or Tools menu, choose Define
In the Lobule list, click to highlight the lobule with which all other will be aligned. Be sure the chosen lobule is present on all sections. Set Alignment
In this example, Lobule 3 has been selected as the aligning lobule.
3.
Click the OK button.
Page 7-16
4. Continue with Step 8: Converting to Planar Data (page 7-16).

RELATED TOPICS
STEP 8: CONVERTING TO PLANAR DATA

CONVERTING EXPLANATION
Converting redefines the Topo data as Planar data. It creates the Line Array from the Contour topo data and fills the DTI Arrays with cell references to the Line Array from the Cell topo data. If the DTI Array symbol shape, position, or color parameters are changed at a later point, or if the Line Array shift parameter is changed at a later point, you do not need to re-convert the Line Array. The parameter changes made will be automatically updated.
PROCEDURE: CONVERTING TO PLANAR DATA

1. 2. Before converting make sure that the DTI Array parameters have been defined and that the fiduciary points have been set. On Planar dialog box, click the Perform Conversion Conversion to convert the data to the Line Array. Be patient. This step may take awhile. button, or from the Tools menu, choose Perform
3.
Continue with Step 9: Exiting the Atlas Shop (page 7-17).

RELATED TOPICS
Page 7-17
STEP 9: EXITING THE ATLAS SHOP

1. 2. 3. On the Planar dialog box, click the Close button. From the File menu, choose Exit Atlas Shop. Continue with Displaying and Modifying the Planar Histogram (page 7-17).

RELATED TOPICS
DISPLAYING AND MODIFYING THE PLANAR HISTOGRAM

At this point you should have already followed the Planar Conversion procedure. See Planar Conversion on 7-4. You should be in the Atlas Viewer.
TOPIC CONTENTS
Step 1: Displaying the Planar Histogram (page 7-17) Step 2: Changing the DTI Array or Line Array Parameters (page 7-20) Step 3: Saving the Planar Display to a Parameters File (page 7-24) Step 4: Retrieving the Planar Display from a Parameters File (page 7-24)
RELATED TOPICS
General Guidelines (page 7-2) Planar Conversion (page 7-4) Displaying and Modifying the Planar Histogram (page 7-17) Contour Conversion (page 7-25)
STEP 1: DISPLAYING THE PLANAR HISTOGRAM

1. 2. On the Select Arrays dialog box, from the Select menu, choose Unselect All Arrays. On the Select Arrays dialog box, in the Available Arrays box, double click the Line=D# Array(s) to move it (or them) to the Selected box. The # references the original Topo data arrays used to create the Line array. On the system tool bar, click the Resize to Fit window. button to center the histogram and resize it to fit the Atlas
3.
Page 7-18
Planar Histogram
In this illustration there are two cell types, represented by light yellow and light green lines.
4.
Examine the planar histogram in the Atlas window and decide if any of the following changes would be beneficial: Display the histogram on a black background. Choose Black Background from the Atlas menu. Choose Connect Fiduciaries from the Atlas menu. Connect corresponding fiduciary points with a line.
Page 7-19
Planar Histogram
In this illustration Connect Fiduciaries has been activated. Note that the aligning fiduciary is more visible (pink line).
Fill the space between lines with the colors assigned to the individual lobules. From the Atlas Menu, check Fill. To change vertical line spacing while in the Atlas Viewer - See Procedure: Modify Distance Between Vertical Lines on 7-22. To change vertical line spacing in the Atlas Shop - See Modify Parameters in the Atlas Shop on 723. Move the vertical lines closer or further apart.
Change any of the following cell symbol attributes: shape, height to width ratio, magnitude, position relative to the vertical line (right, left, center), outline color, or fill color. To change cell symbol attributes while in the Atlas Viewer - See Procedure: Modify a Symbol on 720. To change cell symbol attributes in the Atlas Shop - See Modify Parameters in the Atlas Shop on 723.
5.
Continue with Step 2: Changing the DTI Array or Line Array Parameters (page 7-20).
Page 7-20 DISPLAYING AND MODIFYING THE PLANAR HISTOGRAM CONTENTS

RELATED TOPICS
STEP 2: CHANGING THE DTI ARRAY OR LINE ARRAY PARAMETERS

The DTI and LINE array parameters can be changed in two ways. The original Topo arrays can be re-selected, the Atlas Shop opened, and different DTI Array Parameters assigned, or, while still in the Atlas Viewer, the DTI and LINE Array comments can be modified on the Select Arrays dialog box. Many people prefer to remain in the Atlas Viewer and manually edit DTI and LINE array comments.
TOPIC CONTENTS
Modify Parameters in the Atlas Viewer (page 7-20) Modify Parameters in the Atlas Shop (page 7-23) Then continue with Step 2: Changing the DTI Array or Line Array Parameters (page 7-20).
DISPLAYING AND MODIFYING THE PLANAR HISTOGRAM CONTENTS

RELATED TOPICS
MODIFY PARAMETERS IN THE ATLAS VIEWER

While in the Atlas Viewer, a symbols shape, height to width ratio, magnitude, position, outline color, or fill color may be changed, and the distance between vertical lines may be adjusted.
PROCEDURE: MODIFY A SYMBOL

1. Do the following to determine the DTI array to be edited:
Page 7-21
Select Arrays
The D6 Line=D1 array is highlighted with its Name and Comment displayed. Note that D4 and D5 are referenced as the DTI arrays.
a. b. 2.
On Select Arrays, with the Line =D# array highlighted, click the Expand menu. The D# part of the Line arrays name references the raw data array from which it was created. In the Comment note any DTI=D# entries. These entries reference the DTI arrays used in the Planar display.
On Select Arrays, click the Expand menu to display the Name and Comment fields. Select Arrays
The D4 DTI array is highlighted with its Name and Comment displayed.
3.
On Select Arrays, in the Comment Field for the DTI Array, modify the comment of the symbol parameter. Then from the Atlas menu, choose Redraw to update the display.
DTI Array Comment Table: Shape: DTI Array Comment: Line Default - No comment Rectangle S1; Ellipse S2 Ratio: (Height/Width) 3/10 2/5 1/2 3/5 1/1 2/1 3/1 DTI Array Comment: R0.3; R0.4; R0.5; R0.6; Default - No Comment R2.0; R3.0;
Page 7-22
Magnitude:
DTI Array Comment:
The height and width of the symbol are multiplied by the Magnitude. It is important to have the same Mag for all DTI arrays in a study. If you have a small number of cells, it might be useful to increase the Mag. If you have an extremely large number of cell counts, it might be useful to type in a Mag that is less than 1. The Mag can also be changed at a later point. Mag: DTI Array Comment: 0.05 M0.050000; 0.5 M0.500000 1 Default - No comment 2 M2.000000; 3 M3.000000;
Plus any user customized magnitude. Position: Left Center Right Color: Blue Red Pink Light Green Light Blue Light Yellow Dark Grey Dark Blue Brown Dark Purple Dark Green Teal Black Light Grey
DTI Array Comment: P2; Default - No comment P1; DTI Array Comment: Outline Color No comment C2; C3; C4; C5; C6; C7; C8; C9; C10; C11; C12; C13; C14; Fill Color No comment F2; F3; F4; F5; F6; F7; F8; F9; F10; F11; F12; F13; F14;
PROCEDURE: MODIFY DISTANCE BETWEEN VERTICAL LINES

1. 2. On Select Arrays, in the Available Arrays box, click to highlight the Line Array. On Select Arrays, click the Expand menu to display the Name and Comment fields. Select Arrays
The D6 Line array is highlighted and its Name and Comment.
3.
On Select Arrays, in the Comment Field for the Line=D# Array, modify the S=#; comment. Increase the number to increase the distance between the lines. Decrease the number to decrease the distance between the lines. If the S=#; comment does not exist, add it.
Shift:
Line Array Comment:
Page 7-23
1 Default - No comment 2 S=2; 3 S=3; Plus any user customized shift value.
4. 5. On the Atlas Viewers system tool bar, click the Redraw new parameters. button to update the histogram display with the
Continue with Step 3: Saving the Planar Display to a Parameters File (page 7-24).

RELATED TOPICS
MODIFY PARAMETERS IN THE ATLAS SHOP

DTI cell and LINE parameters may be modified by returning to the Atlas Shop and choosing different parameters on the DTI Array Parameters dialog box. 1. In the Atlas Viewer, on the Select Arrays dialog box, de-select the LINE array(s), then select the Master Raw Topo array we created earlier. On the Atlas Viewers system tool bar, click the Redraw original atlas. Click the Atlas Shop Section Mode active. button to update the Atlas window with the
2. 3. 4. 5.
button (or choose File> Atlas Shop on the menu bar). The Atlas Shop will open with
In the Atlas Shop, from the Tools menu, choose Planar Conversion to open the Planar dialog box. The original DTI arrays with previous parameters are listed. Change any of the following parameters for the DTI Arrays: DO NOT Add Fiduciary Points again or convert data. a. b. c. d. Parameters in the Symbol Shape region Parameters in the Position region Parameters in the Color region The Shift value from the Tools>Shift menu.
6. 7. 8.
Close the Planar dialog box when finished. From the File menu, choose Exit Atlas Shop. Continue with Step 3: Saving the Planar Display to a Parameters File (page 7-24).
Page 7-24 DISPLAYING AND MODIFYING THE PLANAR HISTOGRAM CONTENTS

RELATED TOPICS
STEP 3: SAVING THE PLANAR DISPLAY TO A PARAMETERS FILE

The Planar Display can be saved to a Parameters file. Parameter files save the zoom, pan, orientation, and rotation of an atlas, as well as the selected array list. These files allow one atlas to have many views quickly accessed by loading parameter files. Note: The parameters files can also be used to quickly load and center the original Section Topo data using the same procedure.
PROCEDURE
1. Make sure that the Line Array is selected and the Planar Display is that way you want it in the Atlas window. Note: If you were saving a parameters file for the original Section data, the Topo Section Z# arrays would be selected and displayed in the Atlas window at this step. From the File menu, choose Save Parameters open the Save Parameter file dialog box. The Parameters file is a *.set file type. The default Save in location is BQOSTEO\Topographer or BQLifescience\Topographer. For ease of finding the parameters file again, it is recommended that you create a subdirectory in the Topographer folder that is named the same as your Data Volume and Data Set. Then when you later need to find and open the parameter files for a particular Data Set you can easily navigate to them. Type a file name into the File Name: text box. Click the OK button to save the Parameters file. Continue with Step 4: Retrieving the Planar Display from a Parameters File (page 7-24).
2. 3.
4. 5. 6.

RELATED TOPICS
STEP 4: RETRIEVING THE PLANAR DISPLAY FROM A PARAMETERS FILE

Once a data set is opened, any Parameter file for it can be loaded. Parameters file automatically selects the arrays and sets the zoom, pan, and orientation settings for an Atlas. 1. From the File menu, choose Load Parameters to open the Open Parameter File box.
Page 7-25
2. The default location for saving parameter files is BQOSTEO\Topographer. If you created a subdirectory associated with your Data Volume and Data Set as recommended in the Save Parameters procedure, it will be listed here. Navigate to the folder that contains the Parameter file for the current data set. Click on the Parameter file to be opened. Click the OK button. The atlas will change to reflect the loaded parameters
3. 4.

ADDITIONAL OUTPUT NOTES

The Planar Display can also be printed and saved as a Bitmap or Metafile. See Printing, Copying, or Exporting an Atlas on page 5-34.
RELATED TOPICS
CONTOUR CONVERSION
Contour Conversion in the Topographers Atlas Shop converts Topo data so that cell populations are represented by symbols that appear along section outline tracings. The Contour Converted atlas is displayed in the Topographers Atlas Viewer.

This section just provides a protocol for using Contour Conversion after data has been correctly collected in BIOQUANT Life Science. Actual data collection for Planar or Contour Conversion is done in BIOQUANT Life Science. See the Topographer Data Collection section of the BIOQUANT Life Science help or manual. Once the data has been collected, return to this section for instruction on how to use the Topographers planar and contour conversion tools.
TOPIC CONTENTS
Step 1: Selecting the Topo Arrays and Opening the Atlas Shop (page 7-26) Step 2: Backing Up the Raw Topo Array(s) (page 7-27) Step 3: Setting up for Conversion (page 7-28) Step 4: Customizing the DTI Array Parameters (page 7-29) Step 5: Defining Fiduciary Points (page 7-31) Step 6: Setting a Shift Value (page 7-35) Step 7: Converting to Contour Data (page 7-36) Step 8: Exiting the Atlas Shop (page 7-36)
RELATED TOPICS
Page 7-26
STEP 1: SELECTING THE TOPO ARRAYS AND OPENING THE ATLAS SHOP
1. On BIOQUANT Life Sciences or BIOQUANT OSTEOs system menu bar, click Topographer to execute the BIOQUANT Topographer program. The Topographer opens into the Atlas Viewer. On the Select Arrays dialog box, select the one or more Topo arrays that contain data to be converted. At this point only Topo arrays should be selected. The Topo arrays selected will be used to create special DTI and Contour arrays to display converted data. Click the Open Atlas Click the Resize To Fit button on the system tool bar (or choose Open from the Atlas menu). button on the system tool bar.
2.
3. 4.
Atlas Window
Resize to Fit centers the topographic map.
5.
Click the Atlas Shop button (or choose Atlas Shop from the Tools menu). The Atlas Shop will open with Section Mode active.
Page 7-27
Atlas Shop
6.
Continue with Step 2: Backing Up the Raw Topo Array(s) (page 7-27).
TOPIC CONTENTS
RELATED TOPICS
STEP 2: BACKING UP THE RAW TOPO ARRAY(S)

Before we go further we will copy the data from the selected Topo array(s) into a new Topo array. We will perform the Contour Conversion on the new Topo array to preserve the integrity of the raw Topo arrays. In this way we can always make a new copy of the raw Topo arrays in the future.
PROCEDURE
1. 2. 3. 4. In the Atlas Shop, from the File menu, choose Save As. On the Save Array As dialog box, click the New Array button to add a new Topo array to the data set. In the Array Name edit file, rename the new Topo array to Master Raw Topo Data. Click the Save button. BIOQUANT Topographer Handbook: Planar & Contour Conversion
Page 7-28
5. 6. 7. 8. In the Atlas Shop, from the File menu, choose Exit Atlas Shop. You are returned to the Atlas Viewer. In the Atlas Viewer, on Select Arrays, from the Select menu, choose Unselect All Arrays. At this point there should not be any arrays selected. On Select Arrays, in the Available Arrays list, double click Topo array we just added, Master Raw Topo Data to move it to the Selected list. Click the Resize To Fit button on the system tool bar. The map drawn should equal the map generated from the raw Topo data. Click the Atlas Shop button (or choose Atlas Shop from the Tools menu). The Atlas Shop will open with Section Mode active. Continue with Step 3: Setting up for Conversion (page 7-28).
9. 10.
TOPIC CONTENTS
RELATED TOPICS
STEP 3: SETTING UP FOR CONVERSION

1. (Optional) Align the rotation of all the sections by doing the following: a. b. c. d. 2. If necessary, click the Resize to Fit work space. button on the system tool bar to scale the atlas to the size of the
From the Select menu, choose Select All Sections. From the Edit menu, choose Align Sections. The sections rotate so that the start points on all sections are aligned. From the File menu, choose Save.
From the Tools menu, choose Contour Conversion to open the Contour dialog box.
Page 7-29
Contour
One DTI array is automatically displayed for each cell type that was counted. In this illustration, the atlas contains two cell types.
3.
Continue with Step 4: Customizing the DTI Array Parameters (page 7-29).
TOPIC CONTENTS
RELATED TOPICS
STEP 4: CUSTOMIZING THE DTI ARRAY PARAMETERS

DTI ARRAY EXPLANATION
When the Planar dialog box opens, one DTI array is listed (and added to the current data set) for each cell type in the selected Topo arrays. Cell data in this case is point data collected with an Object Count array. Cell types are identified by color. A symbol is used to represent the cell population at each data point along the specimen contour line. The shape, color, height to width ratio, magnitude, placement, and color parameters of the symbol are customizable. Symbol parameters that are changed from the default are automatically saved to the corresponding DTI arrays comment.
PROCEDURE: CUSTOMIZING DTI PARAMETERS

1. 2. In the DTI Array(s) box, click to highlight the first DTI array. In the Symbol Shape region, choose one of the following shapes: Line: Represents the cell type using a line. The height of the Line is always 1.
Page 7-30
Rectangle: Represent the cell type using a rectangle. The rectangle defaults to a height and width of 1.
Ellipse: Represent the cell type using an ellipse. The Ellipse defaults to a height and width of 1. The shape in the preview box changes to match the symbol type chosen. The default shape is Line. Shape: DTI Array Comment: Line Default - No comment Rectangle S1; Ellipse S2; 3. In the Symbol Shape region, move the Ratio slider to the desired position. The Ratio determines the symbols height to width ratio. Moving the slider to the left decreases the height to width ratio. Moving the slider to the right increases the ratio. The ratio range available with the slider is between 0.3 and 3. The default ratio is 1. Ratios less than 1 do not affect the Line shape because the Lines height is always 1. The height is the Y distance from the vertical line. The width is the X distance along the vertical line. Ratio: DTI Array Comment: (Height/Width) 3/10 R0.3; 2/5 R0.4; 1/2 R0.5; 3/5 R0.6; 1/1 Default - No Comment 2/1 R2.0; 3/1 R3.0; In the Symbol Shape region, in the Mag edit box, type the desired magnitude. The height and width of the symbol are multiplied by the Magnitude. It is important to have the same Mag for all DTI arrays in a study. If you have a small number of cells, it might be useful to increase the Mag. If you have an extremely large number of cell counts, it might be useful to type in a Mag that is less than 1. The Mag can also be changed at a later point. Mag: DTI Array Comment: 0.05 M0.050000; 0.5 M0.500000 1 Default - No comment 2 M2.000000; 3 M3.000000; In the Position region, choose either Left, Center, or Right to indicate the orientation of the symbol to the line. The position of the shape to the contour line in the preview box changes to match the position chosen. The default position is Center. Position: DTI Array Comment: Left P2; Center Default - No comment Right P1; In the Color region, the Outline color of the symbol defaults to the original cell type measurement color. To change the outline color of the symbol for this cell type, first click the Outline radio button, then click the desired color. Color: DTI Array Comment: Blue No comment Red C2; Pink C3; Light Green C4; Light Blue C5; The color numbers increment by one for each remaining color in the palette, reading left to right.
4.
5.
6.
Page 7-31
7. In the Color region, the Fill color of the symbol defaults to the original cell type measurement color. To change the fill color of the symbol for this cell type, first click the Fill radio button, then click the desired color. Fill is not available for the Line symbol. Color: DTI Array Comment: Blue No comment Red F2; Pink F3; Light Green F4; Light Blue F5; The color numbers increment by one for each remaining color in the palette, reading left to right. Repeat from step 1 for each DTI array in the DTI array(s) box.
8.
ADDITIONAL NOTES
9. If the ratio parameters offered do not meet requirements, manually type the desired parameter into the comment of the DTI array. It is important to have the same Mag for all DTI arrays in a study. The DTI parameters can also be changed at a later point.
Continue with Step 5: Defining Fiduciary Points (page 7-31).
TOPIC CONTENTS
RELATED TOPICS
STEP 5: DEFINING FIDUCIARY POINTS

CONTOUR ARRAY EXPLANATION
A Contour Array is created when Topo data are converted to Contour data. The Contour Array holds the information needed to display the specimen contours lobules in different colors. The user adds fiduciary points on the specimen contour where each lobule begins. The system represents each lobule by a different colored segment.
TOPIC CONTENTS
Procedure ONE: Defining Fiduciary Points (page 7-32) Procedure TWO: Going to the Next Outline (page 7-34) Then continue with Step 6: Setting a Shift Value (page 7-35)
IMPORTANT NOTE
It is important to sequence through your sections before this procedure and become familiar with how the lobules are organized within the sections. If all sections have all lobules, then this procedure is straight-forward. If some lobules are missing, especially from the middle of a contour, this procedure is more complicated. The
Page 7-32
goal is to make it so that the color coded lobules are the same lobules in each section.
TOPIC CONTENTS
RELATED TOPICS
PROCEDURE ONE: DEFINING FIDUCIARY POINTS

1. On the Contour dialog box, click the Add Fiduciary Points button, or from the Edit menu, choose Add Fiduciaries. The pointer changes to the Add Fiduciary cursor. If the sections in the background decrease the visibility of the current section, from the View menu, check Selection Only to display only the current section. On the specimen contour for the first section click once at the beginning of the lobule that you want to be the starting point. Then, in a counter-clockwise direction, click once at the beginning of each lobule, using the following pointers. Atlas Shop
2.
Add a fiduciary marker at the beginning of each lobule.
Page 7-33 POINTERS

A fiduciary marker is placed on the specimen contour at each location clicked. The markers sequence through the colors on the color palette. You need to add fiduciary points in the same order, starting at the same location, for each section to avoid confusion caused by different colored markers. If a lobule in the middle of a contour does not exist for a particular section, click two fiduciary points very close together to skip that color. You want the lobules that do exist to show up in the correct sequenced segment color for comparison to other sections. There are special rules for deleting fiduciary points. If the point to be deleted IS THE LAST on the contour, then it may be deleted by itself. If the point is NOT THE LAST on the contour, then all the fiduciary points must be deleted on the contour. In this case use Add Fiduciary Points to redefine the points. This prevents the lobule color assignment from messing up. To delete fiduciary points, do the following: i. ii. Click the right mouse button to exit the Add Fiduciary Point mode. On the Planar dialog box, click the Delete Fiduciary Point Delete Fiduciary. The pointer changes to the Delete Fiduciary cursor. button, or from the Edit menu, choose
iii.
On the specimen contour for the current section click once on the fiduciary to be deleted. If the fiduciary point is not the last on the contour, then repeat to delete all fiduciary points on the current section. The fiduciary marker disappears.
iv. After unwanted fiduciary points have been deleted, click the right mouse button to exit Delete Fiduciary mode. v. If more fiduciary points need to be added, click the Add Fiduciary Points button. To move a fiduciary point along the contour, do the following Moving a fiduciary point will not mess up the color assignment of the lobule, as long as you do not move it before a preceding fiduciary point or after a following fiduciary points. If you need to re-arrange the order of the fiduciary points, take care that the lobule color assignment matches corresponding lobules on other sections. If the color coding gets messed up, delete all the fiduciary points for the section and start over. i. ii. Click the right mouse button to exit the Add Fiduciary Point mode. On the Planar dialog box, click the Move Fiduciary Point Move Fiduciary. The pointer changes to the Move Fiduciary cursor. button, or from the Edit menu, choose
iii.
On the specimen contour for the current section click once at on the fiduciary to be moved to make it disappear. Then click the specimen contour at the location the fiduciary point should be. Repeat for all fiduciary points to be moved.
iv. After misplaced fiduciary points have been moved, click the right mouse button to exit Move Fiduciary mode. v. 3. If more fiduciary points need to be added, click the Add Fiduciary Points button.
After all fiduciary points have been defined for this section, click the right mouse button to exit Add Fiduciary Point mode.
Page 7-34
4. Continue with Step 6: Setting a Shift Value (page 7-35).
TOPIC CONTENTS
RELATED TOPICS
PROCEDURE TWO: GOING TO THE NEXT OUTLINE

After the Fiduciary Points are in the correct locations on the first contour outline, do the following: 1. 2. 3. On the Contour dialog box, click the Next Outline button, or from the Edit menu, choose Next Outline.
Follow the procedure to set fiduciary points as previously described in Procedure ONE: Defining Fiduciary Points on page 7-11. When all Fiduciary Points have been set, from the Contour dialog box File menu, choose Save Fiduciary(s). This saves the positions of the fiduciary points to the array. If you want to return to edit DTI array parameters at a later point, or if you want to do a Planar Conversion at a later point, you will not need to re-define the fiduciary points. Atlas Shop
When you sequence back to the a section that already has fiduciary markers defined, they show up as larger points.

4. When an outline is reached that already has fiduciary points, the markers are drawn larger to indicate that the section has already been marked. If the sections in the background decrease the visibility of the current section, from the View menu, check Selection Only to display only the active section. To refresh the display, click the RD button on the tool bar. To refresh existing fiduciary points, click the Add Fiduciary Points button.
Continue with Step 6: Setting a Shift Value (page 7-35).
TOPIC CONTENTS
RELATED TOPICS
STEP 6: SETTING A SHIFT VALUE

SHIFT EXPLANATION
The Shift determines the distance between the vertical lines used to represent the specimen contour. Shift multiplies the Z value by the number entered. The default Shift value is 1. If the Shift value is changed from the default, it adds a S=#; comment to the Line array. The Shift can be modified later, by adding or modifying the Line Array Comment. Shift: Line Array Comment: 1 Default - No comment 2 S=2; 3 S=3;
PROCEDURE: ENTERING A SHIFT VALUE

1. On Planar dialog box, from the Tools menu, choose Define Shift to open the Planar Shift dialog box. Shift
In this example, a shift of 5 has been entered.
2.
On the Shift dialog box, in the Shift edit box, type the desired value.
Page 7-36
3. Continue with Step 7: Converting to Contour Data (page 7-36).
TOPIC CONTENTS
RELATED TOPICS
STEP 7: CONVERTING TO CONTOUR DATA

CONVERTING EXPLANATION
Converting redefines the Topo data as Contour data. It creates the Contour Array from the raw topo data and fills the DTI Arrays with cell references to the Contour Array from the Cell topo data. If the DTI Array symbol shape, position, or color parameters are changed at a later point, or if the Contour Array shift parameter is changed at a later point, you do not need to re-convert the Contour Array. The parameter changes made will be automatically updated.
PROCEDURE: CONVERTING TO PLANAR DATA

1. 2. Before converting make sure that the DTI Array parameters have been defined and that the fiduciary points have been set. On Contour dialog box, click the Perform Conversion Conversion to convert the data to the Contour Array. Be patient. This step may take awhile. Continue with Step 8: Exiting the Atlas Shop (page 7-36). button, or from the Tools menu, choose Perform
3.
TOPIC CONTENTS
RELATED TOPICS
STEP 8: EXITING THE ATLAS SHOP

1. On the Contour dialog box, click the Close button.
Page 7-37
2. 3. From the File menu, choose Exit Atlas Shop. Continue with Displaying and Modifying the Contour Converted Atlas (page 7-37).
TOPIC CONTENTS
RELATED TOPICS
DISPLAYING AND MODIFYING THE CONTOUR CONVERTED ATLAS

TOPIC CONTENTS
Step 1: Displaying the Converted Atlas (page 7-37) Step 2: Changing the DTI or Contour Array Parameters (page 7-39) Step 3: Saving a Parameters File (page 7-42) Step 4: Loading a Parameters File (page 7-43)
RELATED TOPICS
STEP 1: DISPLAYING THE CONVERTED ATLAS

1. 2. On the Select Arrays dialog box, from the Select menu, choose Unselect All Arrays. On the Select Arrays dialog box, in the Available Arrays list, double click the Contour=D# array to move it to the Selected list. NOTE: The names of DTI arrays also include the word Contour, but DTI array names do NOT include an equal (=) sign. On the system tool bar, click the Redraw converted atlas in the Atlas window. button, then the Resize to Fit button, to center and resize the
3. 4.
(Optional) From the Atlas menu, choose Black Background.
Page 7-38
Contour Converted Atlas
In this illustration there are two different types of cells, one represented by red squares and the other represented by blue circles.
5.
Examine the Contour Converted atlas and decide if any of the following changes would be beneficial: Display the atlas on an alternate colored background. Check or uncheck Black Background on the Atlas menu. Change any of the following cell symbol attributes: shape, height to width ratio, magnitude, position relative to the contour outline (right, left, center), or fill color. To change cell symbol attributes while in the Atlas Viewer - See Modify Converted Atlas Parameters in the Atlas Viewer on 7-39. To change cell symbol attributes in the Atlas Shop - See Modify Converted Atlas Parameters in the Atlas Shop on 7-41.
Increase the Shift value so contour tracings are not stacked so closely on top of each other.
6.
Continue with Step 2: Changing the DTI or Contour Array Parameters (page 7-39).
DISPLAYING AND MODIFYING THE CONTOUR CONVERSION PROTOCOL:

RELATED TOPICS
Page 7-39
STEP 2: CHANGING THE DTI OR CONTOUR ARRAY PARAMETERS

The DTI and Contour array parameters can be changed in two ways. The original Master Raw Topo array can be reselected, the Atlas Shop opened, and different DTI Array Parameters assigned, or, while still in the Atlas Viewer, the DTI and Contour array comments can be modified on the Select Arrays dialog box. Many people prefer to remain in the Atlas Viewer and manually edit DTI and Contour array comments.
TOPIC CONTENTS
Modify Converted Atlas Parameters in the Atlas Viewer (page 7-39) Modify Converted Atlas Parameters in the Atlas Shop (page 7-41) Then continue with Step 3: Saving a Parameters File (page 7-42).

RELATED TOPICS
MODIFY CONVERTED ATLAS PARAMETERS IN THE ATLAS VIEWER

While in the Atlas Viewer, a symbols shape, height to width ratio, magnitude, position, outline color, or fill color may be changed, and the distance between vertical lines may be adjusted.
PROCEDURE: MODIFY A SYMBOL

1. To determine the DTI arrays associated with the Contour array, do the following: Select Arrays
The D16 Contour=D1 array is highlighted with its Name and Comment displayed. Note that D8 and D9 are referenced as the DTI arrays.
a. b. 2.
On Select Arrays, with the Contour =D# array highlighted, click the Expand menu. The D# part of the Contour arrays name references the raw data array from which it was created. In the Comment note any DTI=D# entries. These entries reference the DTI arrays used in the Contour display.
On Select Arrays, in the Available Arrays box, click to highlight one of the DTI=D#:Contour D# array that was referenced in the Contour array to edit it. The Contour D# portion of this arrays name references the raw data array from which it was created. On Select Arrays, click the Expand menu to display the Name and Comment fields.
3.
Page 7-40
Select Arrays
The D8 DTI:Contour array is highlighted with its Name and Comment displayed.
4.
On Select Arrays, in the Comment Field for the DTI Array, modify the comment of the symbol parameter. Then from the Atlas menu, choose Redraw to update the display.
DTI Array Comment Table: Shape: DTI Array Comment: Line Default - No comment Rectangle S1; Ellipse S2 Ratio: (Height/Width) 3/10 2/5 1/2 3/5 1/1 2/1 3/1 Magnitude: DTI Array Comment: R0.3; R0.4; R0.5; R0.6; Default - No Comment R2.0; R3.0; DTI Array Comment:
The height and width of the symbol are multiplied by the Magnitude. It is important to have the same Mag for all DTI arrays in a study. If you have a small number of cells, it might be useful to increase the Mag. If you have an extremely large number of cell counts, it might be useful to type in a Mag that is less than 1. The Mag can also be changed at a later point. Mag: DTI Array Comment: 0.05 M0.050000; 0.5 M0.500000 1 Default - No comment 2 M2.000000; 3 M3.000000;
Plus any user customized magnitude. Position: Left Center Right
DTI Array Comment: P2; Default - No comment P1;
Page 7-41
Color: Blue Red Pink Light Green Light Blue Light Yellow Dark Grey Dark Blue Brown Dark Purple Dark Green Teal Black Light Grey
1. 2. 3.
DTI Array Comment: Outline Color No comment C2; C3; C4; C5; C6; C7; C8; C9; C10; C11; C12; C13; C14;
Fill Color No comment F2; F3; F4; F5; F6; F7; F8; F9; F10; F11; F12; F13; F14;
PROCEDURE: MODIFY SHIFT DISTANCE BETWEEN CONTOUR OUTLINES

On Select Arrays, in the Available Arrays box, click to highlight the Contour=D# array. On Select Arrays, click the Expand menu to display the Name and Comment fields. On Select Arrays, in the Comment Field for the Contour=D# Array, modify the S=#; comment. Increase the number to increase the distance between the contour outlines. Decrease the number to decrease the distance between the contour outlines. If the S=#; comment does not exist, add it.
Shift: Line Array Comment: 1 Default - No comment 2 S=2; 3 S=3; Plus any user defined shift value. The greater the number, the greater the shift.
4. 5. On the Atlas Viewers system tool bar, click the Redraw with the new parameters. button to update the converted atlas display
Continue with Step 3: Saving a Parameters File (page 7-42).

RELATED TOPICS
MODIFY CONVERTED ATLAS PARAMETERS IN THE ATLAS SHOP

DTI cell and Contour array parameters may be modified by returning to the Atlas Shop and choosing different parameters on the Contour Conversion dialog box. 1. In the Atlas Viewer, on the Select Arrays dialog box, de-select the Contour=D# array, then select the original raw data Topo array. BIOQUANT Topographer Handbook: Planar & Contour Conversion
Page 7-42
2. 3. 4. 5. On the Atlas Viewers system tool bar, click the Redraw original atlas. Click the Atlas Shop Section Mode active. button to update the Atlas window with the
button (or choose File> Atlas Shop on the menu bar). The Atlas Shop will open with
In the Atlas Shop, from the Tools menu, choose Contour Conversion to open the Contour dialog box. The previously generated DTI arrays are listed. Change any of the following parameters: DO NOT reset fiduciary markers or re-convert data. a. b. c. d. Choose an alternate Symbol Shape. Choose an alternate Position (left, center, right). Choose a different Fill color. Change the Shift value (Tools>Shift menu).
6. 7. 8.
Close the Contour dialog box (without resetting fiduciary markers or re-converting the atlas). From the File menu, choose Exit Atlas Shop to return to the Atlas Viewer to see the results of the changes. Continue with Step 3: Saving a Parameters File (page 7-42).

RELATED TOPICS
STEP 3: SAVING A PARAMETERS FILE

After the conversion parameters have been set or adjusted to produce a satisfactory atlas, the way the converted atlas looks in the Atlas window can be adjusted using options on Atlas Viewers Parameters dialog box. After an ideal view of the atlas is established, the display parameters can be saved to a Parameters file. Parameter files save the zoom, pan, orientation, and rotation of an atlas, as well as the selected array list.
PROCEDURE
1. 2. 3. Make sure that the Contour=D# array is selected and that the currently displayed view of the atlas is the one you wish to save. From the File menu, choose Save Parameters to open the Save Parameter file dialog box. The Parameters file is a *.set file type. The default Save in location is BQOSTEO\Topographer or BQLifescience\Topographer. For ease of finding the parameters file again, it is recommended that you create a subdirectory in the Topographer folder that is named the same as your Data Volume and Data Set. Then when you later need to find and open the parameter files for a particular Data Set you can easily navigate to them. Type a file name into the File Name: text box. Click the OK button to save the Parameters file. Continue with Step 4: Loading a Parameters File (page 7-43).
4. 5. 6.
Page 7-43 DISPLAYING AND MODIFYING THE CONTOUR CONVERSION PROTOCOL:

RELATED TOPICS
STEP 4: LOADING A PARAMETERS FILE

Once a data set is opened, any Parameter file for it can be loaded. The Parameter file automatically selects the arrays and sets the zoom, pan, and orientation settings for an Atlas. 1. 2. From the File menu, choose Load Parameters to open the Open Parameter File box. The default location for saving parameter files is BQOSTEO\Topographer or BQLifescience\Topographer. If you created a subdirectory associated with your Data Volume and Data Set as recommended in the Save Parameters procedure, it will be listed there. Navigate to the folder that contains the Parameter file for the current data set. Click to highlight the Parameter file to be opened. Click the OK button. The view of the atlas will change to reflect the loaded parameters
3. 4.
ADDITIONAL OUTPUT NOTES

The Converted Atlas Display can also be printed and/or saved as a Bitmap or Metafile. See Printing, Copying, or Exporting an Atlas on 5-34.

RELATED TOPICS
Page 7-44
Page index--i
Index
A
add interior object to selection 6-9 add/delete topo arrays in Atlas Viewer 5-43 align sections automatically 3-33 manually 3-33 Aligning Fiduciary Planar Conversion 7-15 alignment problems, correcting 3-9 Atlas Modeler auto rotate 4-13 load model parameters file 4-18 pan model 4-5 print model 4-23 record and play AVI movie 4-14 rotate model 4-5 save model parameters file 4-18 set color parameters 4-7 set lighting parameters 4-9 set movie parameters 4-11 use ideal forms to set lighting 4-6 view surface as points 4-3 view surface as solid 4-2 view surface as wire frame 4-2 atlas parameters colors/symbols tab 5-10 perspective tab 5-7 rotation tab 5-25 Atlas Shop align sections 6-35 Atlas Shop interface 6-2 auto redraw 6-24 close polygon 6-40 combine two objects 2-32 delete objects 2-34 internal copy 6-28 internal cut 6-28 internal paste 6-28 line editing tools 2-30, 3-24 numeric transform 3-54, 6-41 open polygon 6-39 overlay sections 6-20 redefine edge 2-34 resolution 6-36 rotate section or object 6-53 straighten edge 2-31 undo 6-27 z sort 6-37 Atlas Viewer add/delete topo arrays 5-43 center atlas 5-6 open data set 3-2 play AVI movie 5-28 record AVI movie 5-27 redraw 5-6 resize to fit 5-4 rotate atlas continuously 5-26 rotate xyz perspectives 5-9 save atlas parameters file 5-31 set atlas parameters 5-7 show control bar 5-2 symbols 5-20 thick tracings 5-30 zoom 5-4 auto movie rotate 4-13 auto redraw in Atlas Shop 6-24 auto rotate model 4-13 AV_F1_SAVE_DATA_SET 5-45 AVI movie play in Atlas Viewer 5-28 record and play in Atlas Modeler 4-14 record in Atlas Viewer 5-27
B
background color change in Atlas Modeler 4-5 change in Atlas Viewer 5-29 backup original 2D map data 2-19 Bitmap Export 5-36 BMP Export 5-36 bounding box 4-15 branched structures changing color of one branch 3-30 closing gap after color change 3-31 identifying 3-11 improve surface rendering of 3-11
C
cap object 6-46, 6-68
Index
Page index--ii
center in Atlas Shop 6-18, 6-45 in Atlas Viewer 5-6 change color of background in Atlas Modeler 4-5 of background in Atlas Viewer 5-29 of branched structure 3-30, 6-67 of section, object, or points 6-57 of tracings or symbols 5-13 wire frame fill color 5-16 change resolution to speed rendering 6-36 change z offset 6-63 close atlas window in Atlas Viewer 5-3 close ends of rendered model 6-46, 6-68 close polygon 6-40 Color Contour Conversion 7-30 Planar Conversion 7-9 color index verses color shown 4-8 color palette 6-47 color parameters of model hide objects of particular color 4-8 make surface transparent 4-8 color problems, correcting 3-8 combine two objects 2-32 conjoint sections,dealing with 3-42 Connect Fiduciaries 7-18 Contour Conversion 7-25 backing up raw topo data 7-27 Color 7-30 Converting 7-36 customizing DTI arrays 7-29 data collection strategies 7-3 define Fiduciaries 7-31 delete Fiduciaries 7-33 displaying in Topographer 7-37 Fill 7-31 guidelines for data set 7-2 Loading a Parameters file 7-43 Mag 7-30 modifying the DTI using Select Arrays 7-39 move Fiduciaries 7-33 opening Atlas Shop 7-26 Position 7-30 Ratio 7-30 Saving a Parameters file 7-42 Shift Value 7-35 symbol shape 7-29 understanding the basics 7-2
Index
convert OS/2 data 5-46 copy to clipboard surface rendered model 4-24
D
data deleting from topo array 5-42 list in Atlas Viewer 5-40 OS/2 convert 5-46 print in Atlas Viewer 5-41 save 5-45 save data set 5-45 understand topo data 6-23 view in Atlas Shop 6-22 view in Atlas Viewer 5-40 data set open in Atlas Viewer 3-2 delete objects in Atlas Shop 2-34 DTI Array parameters 7-8 dual label color in Atlas Viewer 5-14 duplicate a section map 6-31
E
end of object 6-46, 6-68 Export to BMP 5-36 Export to SVG 5-37
F
Fiduciaries Defining for Planar Conversion 7-10 Fill Contour Conversion 7-31 Planar Conversion 7-9 fill color in Atlas Viewer 5-14 flash section 6-18, 6-45 format rendered model cap ends 3-51 create transparent window 3-51 remove format 3-52
H
help files 6-47 how do I? 6-47
I
internal copy 6-28
Page index--iii
internal cut 6-28 internal paste 6-28
O
object mode 6-11, 6-45 open atlas window in Atlas Viewer 5-3 open data set in Topographer 3-2 open polygon 6-39 open window in model 6-46 orientation of atlas in Atlas Viewer 5-7 overlay sections for reference 6-20
L
landmark show in Atlas Shop 6-22 leave open 6-46, 6-68 lighting parameters of model global ambient light 4-10 set first on ideal test forms 4-6 spotlight on camera 4-10 surrounding light 4-10 line edit tools combine two objects 3-25, 6-59 delete object 3-26, 6-62 redefine edge (tracing) 3-25, 6-61 separate two objects 3-25, 6-60 straighten edge 3-24, 6-59 list data 5-40
P
pan in Atlas Modeler 4-5 in Atlas Shop 6-17, 6-48 in Atlas Viewer 5-5 perspective tab 5-7 Planar Conversion Aligning Fiduciary 7-15 backing-up raw topos 7-6 Color 7-9 Connect Fiduciaries 7-18 Converting 7-16 data collection strategies 7-3 Define Fiduciaries 7-10 Delete Fiduciary 7-12 displaying the Planar histogram 7-17 DTI Array parameters 7-8 edit DTI using comments 7-21 Fill 7-9 guidelines for data set 7-2 Mag 7-9 Move Fiduciary 7-12 Opening the Atlas Shop 7-4 Position 7-9 Ratio 7-9 retrieving parameters file 7-24 saving parameters file 7-24 setting up for conversion 7-7 Shift Value 7-14 Symbol 7-8 Topographer Procedure 7-4 understanding the basics 7-2 point mode 6-11, 6-45 Position Contour Conversion 7-30 Planar Conversion 7-9 print rendered model 4-23 topo data 5-41
Index
M
Mag Contour Conversion 7-30 Planar Conversion 7-9 measuring the atlas area of object 6-72 count objects in area 6-74 count objects in volume 6-75 counts per volume 6-71 distance 6-76 region of interest area 6-71 volume 6-70 messages to save data 6-6 middle of object 6-46, 6-69 movie parameters auto movie rotate 4-13 bounding box 4-15 video compression 4-15
N
Numeric Transform resize 3-56 rotate 3-57 translate 3-55 numeric transform 6-41
Page index--iv
problem section map, eliminate 6-29
R
Ratio Contour Conversion 7-30 Planar Conversion 7-9 redefine edge (tracing) 2-34 redraw in Atlas Shop 6-23, 6-45 in Atlas Viewer 5-6 remove surface format 6-46, 6-69 rename an array 5-39 resize section or object with numeric transform 6-43 with resize tool 6-55 resize to fit in Atlas Shop 6-16, 6-46 in Atlas Viewer 5-4 resolution of atlas surface 6-36 restore color and symbol defaults 5-17 rotate by numeric transform 6-44 model perspective 4-5 model, continuously 4-13 section or object in Atlas Shop 6-53 specify "rotate around" point 5-10 wire frame, continuously 5-26 wire frame, xyz perspectives 5-9
S
sample maps and models 1-5 save atlas parameters in Atlas Shop 5-12 atlas to new topo array 3-6 edits in Atlas Shop 6-2 save data 5-45 save data messages 6-6 save data set 5-45 saving Atlas Shop edits save 6-3 save as 6-3 save selection as 6-4 Scalable Vector Graphic (SVG) Export 5-37 section mode 6-10, 6-45 select arrays in Atlas Viewer 5-38 select objects in Atlas Shop all section maps in atlas 6-9
Index
by adding interior objects 6-9 by color 6-8, 6-52 by selecting next 6-13, 6-45 by selecting previous 6-13, 6-45 from goto list 6-14 in same area on all sections 6-12 select none, deselect all 6-10 using polygon tool 6-8, 6-49 using rectangle tool 6-7, 6-49 Shift Value Contour Conversion 7-35 Planar Conversion 7-14 show aligning landmark in Atlas Shop 6-22 all sections in Atlas Shop 6-20 data in Atlas Shop 6-22 data in Atlas Viewer 5-40 larger objects as symbols 5-21 only selected items in Atlas Shop 6-19 small objects as symbols 5-20 Show Start Point 6-21 sort sections by z offset 3-40 Start Point 6-21 straighten edge tool in Atlas Shop 2-31 surface render enhancements cap open ends of model 3-51 create transparent window 3-51 remove 3-52 surface rendered model special formatting options 4-19 surface rendering parameters file 4-17 SVG Export 5-37 Symbol Planar Conversion 7-8 symbol Contour Conversion 7-29 symbols change shape 5-22 change size 5-23 fill some, do not fill others 5-19 hide some, show others 5-18 reduce number of 5-24 show larger objects as 5-21 show small objects as 5-20
T
test isohedron 4-6 test plane 4-6 test sphere 4-6
Page index--v
thick tracings in Atlas Viewer 5-30 topo arrays adding in Atlas Viewer 5-43 deleting from data set 5-44 print data 5-41 show data in Atlas Shop 6-22 show data in Atlas Viewer 5-40 tracings change color 5-10 make thicker 5-30 translate by numeric transform 6-42 translate section or object 6-54 transparent window in model 6-46, 6-68
U
undo last atlas edit 6-27, 6-66
W
Windows Media Player 4-15
X
x perspective 6-26, 6-46 xyz rotation of wire frame 5-9
Y
y perspective 6-25, 6-46
Z
z axis spacing problems, correcting 3-9 z offset change 3-38, 6-35, 6-63 z perspective 6-25, 6-46 z shift for wire frame atlas 5-9 z sort 3-40, 6-37 zoom in Atlas Shop 6-17, 6-48 in Atlas Viewer 5-4 zoom factor 5-8
Index
Page index--vi
Index

BIOQUANT Topographer Handbook

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BIOQUANT Topographer

Copyright 2010, 2011

2D Mapping - Review & Optimize - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 2-1

3D Modeling - Review & Optimize the 3D Data - - - - - - - - - - - - - - - - - - - - 3-1

3D Modeling: Surface Rending in the Atlas Modeler - - - - - - - - - - - - - - - - 4-1

The Atlas Viewer in Detail - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 5-1

The Atlas Shop in Detail - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 6-1

Planar & Contour Conversion - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 7-1

BIOQUANT Topographer Handbook

THE TOPOGRAPHER THREE WORK AREAS

BIOQUANT Topographer Handbook: Topographer Introduction

BIOQUANT Topographer Handbook: Topographer Introduction

Page 1-4 RELATED TOPICS

GENERAL STEPS REQUIRED TO CREATE A 2D MAP

GENERAL STEPS REQUIRED TO CREATE A 3D MODEL

BIOQUANT Topographer Handbook: Topographer Introduction

Page 1-5 3D MODELING INSTRUCTIONS

ADDITIONAL TOPOGRAPHER FEATURES

VIEWING BIOQUANT SAMPLE 2D MAPS AND 3D MODELS

SAMPLE 2D MAPS LIST

SAMPLE 3D MODELS LIST

TO OPEN THE SAMPLES, CONTINUE TO

PROCEDURES FOR VIEWING SAMPLE RECONSTRUCTIONS

PROCEDURE 1 - OPEN THE GENERAL ATLAS SET

BIOQUANT Topographer Handbook: Topographer Introduction

PROCEDURE 2 - CHOOSE AND DISPLAY THE DESIRED ATLAS

BIOQUANT Topographer Handbook: Topographer Introduction

Repeat from step 2 to resize and display the new atlas.

PROCEDURE 3 - SURFACE RENDER A 3D ATLAS

BIOQUANT Topographer Handbook: Topographer Introduction

HAND ROTATING TIPS

BIOQUANT Topographer Handbook: Topographer Introduction

BIOQUANT Topographer Handbook

2D Mapping - Review & Optimize

2D Mapping Review & Optimize

ENTERING THE TOPOGRAPHER

THE ATLAS VIEWER

BIOQUANT Topographer Handbook: 2D Mapping - Review & Optimize

Page 2-3 RELATED TOPICS

PART 1-OPEN THE DESIRED DATA SET

BIOQUANT Topographer Handbook: 2D Mapping - Review & Optimize

MORE 2-D MAP REVIEW & OPTIMIZING TOPICS

PART 2-SELECT AND DISPLAY THE 2D MAP

BIOQUANT Topographer Handbook: 2D Mapping - Review & Optimize

DATA CORRECTIONS ARE DONE IN THE ATLAS SHOP

DISPLAY ENHANCEMENTS ARE DONE IN THE ATLAS VIEWER

MORE 2-D MAP REVIEW & OPTIMIZING TOPICS

PRINT THE MAP

Adjust any printing options. Click the OK button.

Page 2-7 2-D MAP REVIEW & OPTIMIZING TOPICS

EXPORT THE MAP TO A FILE

2-D MAP REVIEW & OPTIMIZING TOPICS

EXPORT TO BMP PROCEDURE

2-D MAP REVIEW & OPTIMIZING TOPICS

EXPORT TO SVG PROCEDURE

BIOQUANT Topographer Handbook: 2D Mapping - Review & Optimize

2-D MAP REVIEW & OPTIMIZING TOPICS

COPY AND PASTE THE MAP INTO A DIFFERENT PROGRAM

BIOQUANT Topographer Handbook: 2D Mapping - Review & Optimize

Page 2-10 2-D MAP REVIEW & OPTIMIZING TOPICS

PART 3-OPTIMIZE THE MAP DISPLAY

MORE 2-D MAP REVIEW & OPTIMIZING TOPICS

MANIPULATING THE MAP