Volume Browser - User's Guide
This PSC Volume Browser User's Guide includes introductory material, an overview of the dialog boxes, and descriptions of common procedures.
The Visible Female cryosection dataset is a rectangular volume of RGB (red, green, and blue) values, each representing the color and brightness of a particular sample from the volume. Each of these samples is called a voxel, or Volume Element. In the full resolution Visible Female voxels are spaced at regular 1/3 mm intervals in all 3 principle directions. In navigation mode, the PSC Volume Browser allows you to view a 2D slice through this or any other 3D volume, and move the slice in any direction or orientation. The browser produces the slice image view from the voxels which intersect the current view plane. In segmentation mode, the browser also allows you to trace sections of each slice to create your own 3D sub-volumes (for example, the kidneys) by segmenting a number of sections next to each other.
Getting Started
To get started with the PSV Volume Browser, you must :
Installing the PSC Volume Browser
The PSC Volume Browser is available for Windows 95, Windows 98, Windows ME, Windows 2000, Linux, and Mac OS X.
Microsoft Windows 95, Windows 98, Windows ME, Windows 2000/XP
- Download the file vbxxx.exe, where xxx is the version number of the browser. This is a compressed archive that contains the Volume Browser program.
- Double-click on this file, select the directory where you want to install the browser, then choose Extract. The program file, vb.exe, and a .dll file are placed in the directory.
- Double-click on vb.exe to start the Volume Browser.
Linux
For these UNIX versions:
- Download the file vbxxx_linux, where xxx is the version number of the browser.
- At the command prompt, type "vbxxx_linux."
Macintosh OS X
- Download the file vbxxx.app.tar.gz, where xxx is the version number of the browser. This is a compressed archive that contains the volume browser program.
- If your browser does not automatically open this file, double-click on the file to extract it. By default, the software will extract to your desktop.
- The Volume Browser is the file called vb. Double click on the icon to run it.
Starting the PSC Volume Browser
To start the PSC Volume Browser:
- In Microsoft Windows, double-click on vb.exe
- In Linux , at the command prompt, type "vbxxx_linux."
- In Macintosh OS X, double-click on vbxxx.
The Volume Browser windows appear on the display. The window on the left (the Volume Browser window) is the one in which you view the current slice, and the window on the right (the Context window) shows the position of the slice in the entire volume. Since you have not yet loaded any data, the windows are empty.
To load the Visible Human dataset, choose "Dataset > VHF - RGB." The female model appears in both windows.
To close the Volume Browser, choose "Dataset > Exit."
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The Visible Human (female) data set is a "brick" of data made up of RGB (red, green, blue) values each representing the color of a small portion, a 1/3 mm cube, of the volume. Each RGB value is called a voxel, or Volume Element.
PVB has two main windows ? the left window is the view window, and displays the 2D slice information, while the right window is the context window, and presents the 2D slice in the proper scale and orientation within the 3D context. The 3D display includes anatomical structure surfaces, including the overlying skin. The intersection of surfaces and the slicing plane can be viewed in both the 2D and 3D windows. Surfaces, represented as meshes, are retrieved for display using HTTP. Windows are empty until you open a dataset.
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Opening a Dataset
To open a dataset, choose "Dataset > VHF - RGB." Note that the cursor in the volume browser is a "+" rather than an arrow.
The Visible Human Female dataset is automatically loaded into the volume browser:
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As the Volume Browser starts up, or if it needs to request more data from the server, you might notice regions which you know are inside the body but are colored black. Depending on the speed of your network connection, the black colored regions may fill themselves in quickly or it may take a few minutes.
View Angles
You are automatically placed in navigation mode when you start the Volume Browser, and the default view is a sagittal view, from the side. There are three standardized viewing angles: sagittal, coronal (from the front), and transverse (from above):
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Sagittal View |
Coronal View |
Transverse View |
Exiting the Volume Browser
To exit the PSC Volume Browser, either press "Esc" or click on the view window to activate it, then choose "Dataset > Exit."
Navigating through the 3D Volume
In navigation mode, the PSC Volume Browser allows you to view a 2D slice of a 3D dataset, and move the slice in any direction or orientation. Use the Volume Browser window to navigate through the Visible Human data.
In general, use the following methods to change the position of the slice:
Zooming
When you first load the Visible Female dataset into the PSC Volume Browser, the zoom ratio is at 10%, which displays the entire Visible Human height in both the Volume Browser and Context windows. (The zoom ratios are the same for both windows.) At 100% zoom you are viewing the most detailed data available, the actual unreduced voxels, of the Visible Human dataset. At 200% you are still seeing the 100% data, but magnified, so it may look blocky.
To change the zoom ratio, do one of the following:
- Slide the bar to the zoom ratio you want. The current zoom field on the left is updated.
- Click the cursor in the current zoom field, type the zoom ratio you want, and press Enter.
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Clicking on one of the numbers in the toolbar will provide you with clear results more easily, since these are at the actual dataset resolutions. If the selected view resolution does not match any dataset resolution, press "i" to interpolate between voxels in the current view. |
The display is updated to the requested zoom ratio. The image below is of a 100% zoom.
The image is centered on the green cross in the center of the view window, in the same region as the initial view, only magnified. The cross is located at the same voxel in each of the sagittal, transverse, and coronal views. By switching views, you can look at this voxel from three different viewpoints.
Dragging
Use the Drag button from the view window to center the view on a different section of the dataset, and to move the slice toward and away from the current plane of view.
To drag the image:
- Select the Drag button from the Volume Browser window (the yellow menu button in the example below).
- Place the cursor on the feature on which you're interested.
- Hold down the left mouse button (the right mouse button moves the slice toward and away from you).
- Move the mouse to the new position.
The image moves to follow the cursor.
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Notice that if you drag the image in one view and switch to a different one, the green cross is located at the same voxel in each of the sagittal, transverse, and coronal views. By switching views, you can look at this voxel from three different viewpoints.
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Moving the Slice
Use the Drag button from the Volume Browser window to move the slice toward and away from the current plane of view. When you are in Navigation mode, you can also use the Home key to move the slice toward you, and the End key to move it away.
To move the slice:
- Select the Drag button from the Volume Browser window (the yellow menu button in the example below).
- Place the cursor in the Volume Browser window.
- Hold down the right mouse button.
- Drag the mouse up to move the volume away, or down to move the volume closer.
Note that the plane stays in the same place, while the volume moves around it. In the example below, the cursor was moved down. This is because the context window was set so that the viewpoint was set to Center on Plane. Other viewpoint settings will have a different effect.
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So, although the volume (depicted by the skin display) moved down, the slice moved up (away) relative to the volume.
Rotating and Free Mode
"Free" means not constrained to an orthogonal view; in free mode the slice can be rotated to any angle. You can drag the image while in free mode; however, you must be in free mode to rotate the image; in fact, the Volume Browser changes to free mode when you select the Rotate button.
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To rotate the image, select the Rotate button from the Volume Browser window (the yellow menu button in the example below). The Free button is then also activated (the green menu button):
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There is a small delay between starting rotation with the mouse and the display rotating on the screen, intended to help you rotate about a single axis when you can't move the mouse exactly the distance you want.
Using Tick Marks
The tick marks provide a guide for your rotation angle.
- Click the left mouse button on the top or bottom tick to rotate your current x-axis by 45 degrees.
- Click the left mouse button on the left or right tick to rotate your current y-axis by 45 degrees.
- Drag the right mouse button from the center cross to any of the tick marks to rotate your view about the x-axis. Dragging the right mouse button from the tick mark on one edge of the window to a tick mark on an adjacent edge rotates the view 90 degrees.
Optic Nerve Example
As an instance of why arbitrary rotation is important, the optic nerve cannot be completely seen in the coronal, transverse, or sagittal views. However, if you rotate a transverse view a few degrees you'll be able to see the optic nerve completely:
A transverse view of
the optic nerve.A rotated view so the
entire optic nerve appears.
Navigation Mode Keybindings
The following keybindings are available in Navigation mode:
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shift + Q |
Exits the Volume Browser. |
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l |
(lower-case "L") Displays the label associated with the current cursor position. |
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c |
Centers the view on the cursor position. |
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Moves the slice closer. |
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Moves the slice away. |
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Moves the image up within the current view plane. |
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Moves the image down within the current view plane. |
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Moves the image to the left within the current view plane. |
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Moves the image to the right within the current view plane. |
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Rotates the slice 90 degrees counter-clockwise around the x-axis. |
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Rotates the slice 90 degrees clockwise around the x-axis. |
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Rotates the slice 90 degrees clockwise around the y-axis. |
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Rotates the slice 90 degrees counter-clockwise around the y-axis. |
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Rotates the plane 5 degrees in the same directions as the Ctrl+arrows keybindings. |
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i |
If the selected view resolution does not match any dataset resolution, this interpolates between voxels in the current view. |
Segmentation and Surface Mesh Construction
Image segmentation classifies voxels into categories such as "fat," "muscle,""bone," and so forth. Use points and curves in the PSC Volume Browser to segment images.
The PVB labeling and segmentation tools are used by expert anatomists to trace and capture anatomical structures. Arbitrary slice navigation allows you to create segments in the natural plane of an object rather than the one defined by the original imaging technique. You can save multiple curves in the volume, and points marked in the volume can be displayed in a 3D color cube to visualize the effectiveness of color segmentation settings. These tools can be used to transform raw volume data into the comprehensive anatomical directory needed for teaching anatomy students.
Spline Tracing of Liver and Kidneys
Some structures do not exist as objects than can be easily segmented in an automated process. For example, at a sufficient level of detail a single bone may have different names applied to regions which seamlessly merge into other parts of the same bone. The segmentation tools in the Volume Browser are intended to be guides for automated segmentation, rather than a complete segmentation solution. However, nearly all structures have large regions that have image characteristics that can be segmented automatically. In these instances, a sparse set of manually placed segmentation points can be used to seed automated segmentation without requiring you to completely trace an object in three dimensions or even as a complete 2D contour.
To enter points and curves into the volume dataset, choose a "Segmentation > Points" or a "Segmentation > Curves" option. You are put into Segmentation mode, and can then use the mouse to indicate points in the model. You can also use the Ctrl+m keybinding to toggle between Segmentation mode and Navigation mode.
Segmentation Mode Keybindings
Many commands in the Volume Browser can only be accessed with keybindings. The following keybindings are available in either Segmentation mode or Navigation mode:
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shit + Q |
Exits the Volume Browser. |
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Ctrl+m |
Toggles between Segmentation mode and Navigation mode. |
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l |
(lower-case "L") Displays the label associated with the current cursor position. |
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c |
Centers the view on the cursor position. |
The following keybindings are also available in Segmentation mode:
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Selects the previous control point. (doesn't presently work with Windows) |
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Selects the next control point. |
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m |
Loads the surface associated with the currently selected control point. |
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Displays information associated with the currently selected control point. |
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Inserts a new control point. (doesn't presently work with Windows) |
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Deletes the currently selected control point. (doesn't presently work with Windows) |
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(exclamation point) Snaps curve control points to a color template. |
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Snaps the curve to the currently selected control point. |
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Snaps the curve to the currently selected control point's tangent |
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Moves the currently selected control point up one voxel. |
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Moves the currently selected control point up one voxel. |
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Moves the currently selected control point up one voxel. |
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Moves the currently selected control point up one voxel. |
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Saves segmentation data. |
Entering Points
Use the "Segmentation > Points" menu to enter points in the volume.
The points are green, and the closer they are on the z-axis, the brighter they appear. The points are not displayed if they are too far or too close.
To place a point in the volume:
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Move through the volume until you have displayed the plane in which you want to draw the point.
- Choose "Segmentation > Points > Mark." The browser enters segmentation mode, and the cursor changes to an arrow. In the Volume Browser window, you can click for individual points, or click and drag for a string of points. The faster you drag, the farther apart the points will be.
- Choose "Segmentation > Points > Undo" to undo the last point entered. Repeat this command to remove points in the order that they were placed in the volume.
- Choose "Segmentation > Points > Undo All" to remove all the points entered since entering segmentation mode.
You can also use points to visualize the distribution of dataset colors in the color cube.
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If points or curves are not appearing, choose "Display > Segmentation Data." |
Entering Curves
Curves in the PSC Volume Browser are defined by Catmul-Rom splines. A spline is a mathematical curve whose position in space is defined by control points. For Catmul-Rom splines, the curve always goes through the control points. If you move a control point, the curve will change shape in order to pass through the control point. In addition, if you move a single control point in a Catmul-Rom spline, the curve will only change shape near that point. Thus, if a curve is not initially correct, you only need to change a few points, rather than considering the entire curve.
The volume browser allows you to draw and edit any number of curves in arbitrary planes. You can create two types of curves: closed and open. A closed curve has no end points, and an open curve has two end points.
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A closed curve. |
The same closed curve |
An open curve. |
Once a set of curves is created, they can be formed into a surface mesh that represents a 3D sub-volume in the dataset. The surfaces supplied for the PSC Volume Browser are created from such segmentations.
Drawing Curves
To draw a curve:
- Move through the volume until you have displayed the plane in which you want to draw the curve.
- Choose "Segmentation > New Closed Curve" or "Segmentation > New Open Curve".
- Draw the curve in the Volume Browser window with the left mouse button.
- Click the right mouse button to complete the curve.
A green curve and its control points appear. The curve is given a number, with the first one you create starting at 0.
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A closed curve. |
The same closed curve |
An open curve. |
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If points or curves are not appearing, choose "Display > Segmentation Data." |
Once you have created a curve, you can edit it to be closer to the desired shape. Also use the editing tools to create many similar curves.
Editing Curves
After you have created a curve, it is likely that some further shape refinements will be needed. Before you edit a curve, you must select the curve or its control points.
You can only operate on one curve at a time. The "current curve", the one you are working with, is drawn in green and its control points are displayed. All other curves are drawn in yellow and their control points are not displayed.
- Choose "Segmentation > Curves > Select." A window appears, allowing you to select the curve by number. Specify the curve in one of the following ways:
- Enter the curve number in the number box and press Enter.
- Move the slider to the correct curve number.
- Click the arrows on the number box to reach the correct curve number.
The selected curve turns green, and its control points are displayed.
To display only the current curve:
- Choose "Segmentation > Curves > Show Current Curve Only."
Snapping Control Points to a Color Template
By selecting a control point as a template for an accurate transition border between two colors, you can outline a region of a given color.
To snap control points to a template:
- Select a control point on the border of two regions of different color that you would like the curve to try and approximate.
- Press "!"
The volume browser will attempt to fit the control points based on those regions of different color. If any control points pass through a region which is very different from that of the selected control point, they will not be moved.
Copying Curves
In some situations, contours may not change much from layer to layer. Rather than redrawing a very similar contour repeatedly, you can copy a curve which has already been defined.
To copy a curve:
- Move through the volume until you have displayed the plane in which you want to place the new curve.
- Select the curve you want to copy.
- Choose "Segmentation > Curves > Copy."
- Choose "Segmentation > Curves > Paste."
The curve will be copied into the current plane.
Using the Curves to Change the Display
Since you are working in a 3D environment, it is possible at any time to rotate the view to see the results of the segmentation from another angle. This can help you tell how your segments look in space rather than in a plane.
To return to the plane in which you were segmenting:
- Select a curve you have already defined.
- Choose "Segmentation > Curves > Snap to Curve."
The viewing plane is now aligned with the plane of that curve.
You can also select control points to center and rotate the viewpoint:
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Snap to Selected Control Point |
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Snap to Selected Control Point Tangent |
Deleting Curves
To delete a curve:
- Select the curve.
- Choose "Segmentation > Curves > Delete."
To delete multiple curves:
- Choose "Segmentation > Curves > Delete Range." A window appears, allowing you to enter the start and end of the range. Remember that curve numbering starts at 0.
- Choose "Delete." The curves disappear.
Saving and Loading Segments
Generally, creating segments is time-consuming work, and you should save segmentation data regularly.
To save segments:
- Choose "Segmentation > Save & Load" or press Ctrl+s. The "Save & Load Segmentation Data" window appears.
- Type the path in the Path field, and the name of the file in the Filename field.
- Choose Save. The data is saved in the specified file, with numbered extensions as applicable.
If you save data with the same filename more than once during a session, the Volume Browser will back up your current file by giving it a numbered extension, starting at 000. If you save to a new filename, the numbering process begins again at 000. However, if you start with a filename (such as "ulna.seg"), change to a new one (such as "tibia.seg"), then revert to "ulna.seg", the numbering would restart at 000, not where it left off.
To load segmentation data:
- Choose "Segmentation > Save & Load." The "Save & Load Segmentation Data" window appears.
- Type the path in the Path field, and the name of the file in the Filename field.
- By default, the Volume Browser replaces any segments currently loaded with the new segments. If you want to add this information to the current segmentation data, select "Merge Curves on Load." (This option is not yet implemented.)
- Curves that have been created in other software packages may have extra control points (sometimes many extra control points). The PSC Volume Browser can simplify the curves by removing redundant control points. If you want this option, select "Filter Curves through Simplifier."
- Choose Load.
The segments appear in the Volume Browser window, replacing any that were originally there.
Hints and Tips
The following tips can make the Volume Browser easier to use:
Zooming
- Clicking on one of the numbers in the toolbar will provide you with clear results more easily, since these are at the actual dataset resolutions. If the selected view resolution does not match any dataset resolution, press "i" to interpolate between voxels in the current view.
Rotating
- Use the tick marks to provide a guide for your rotation angle.
Scrolling through the Volume
- To quickly scroll within the view plane, place the cursor over the position that you would like to slide to the center of the slice window and press the 'c' key on your keyboard. You do have to click the mouse. If you have not moved the mouse your cursor will now be over a new position. Therefore, if you repeat the 'c' centering operation without moving the cursor you will slide through the the volume towards the direction of the cursor.
Switch Between Drag and Rotate
- Note that you can switch between dragging and rotating by clicking the middle mouse button.
Points or Curves Don't Appear
- If points or curves are not appearing, choose "Display > Segmentation Data."
PSC Volume Browser Window
This window shows a 2D slice of the dataset, with commands for orienting the slice, creating segments (that can later be labeled) by entering points and lines in the dataset, collaborating with other people using the browser, and saving bookmarks to return to a particular viewpoint. The slice is also displayed in the VB Context window, in the context of the entire 3D dataset.
Segmentation
Dataset
Display
Collaborate
- Transmit/Receive
- Receive Only
- Chat
- Disconnect
Bookmarks
Import
Buttons
Displaying Navigation Aids
The PSC Volume Browser provides several ways to mark where you are in the dataset, return to saved viewpoints, identify areas for segmentation, and measure angles and distances. These navigation aids are accessed from the PSC Volume Browser "Display" menu.
Ball Indicator
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The ball indicator is an orienting display that shows your 3D position in either the PSC Volume Browser or the VB Context windows. It includes R (right), L (left), H (head), and F (foot) markers, to show the orientation of the Visible Human dataset. Choose "Display > Ball Indicator" from either Volume Browser window to toggle the ball on and off. |
Displaying Segmentation Data
If you are entering a large number of points or curves, they may be confusing when you navigate through the dataset.
- Choose "Display > Segmentation Data" to toggle the point and curve display on and off.
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If points or curves are not appearing as you enter them, choose "Display > Segmentation Data." |
Display controls for PSC Volume Browser window only:
Go To
This command allows you to enter point coordinates on which to center the slice, and a normal vector for the slice. When you first choose "Display > Go" from the PSC Volume Browser window, a toolbar appears with the current display values.
To move by an absolute position, enter the new coordinates in the fields, or click on the direction arrows to change the value of the coordinate. This is an easy way to move incrementally through the volume, for example, when you are segmenting for a 3D surface.
To change the angle of the slice, change the values of the vector normal to that slice. Thus, to align the plane with the yz plane, enter "1" in the nX field, and "0" in the nY and nZ fields.
Scale Indicator
The scale indicator shows the distance, in centimeters, spanned by the indicator. If the distance is less than one centimeter, it is given in fractions of a centimeter.
Choose "Display > Scale Indicator" from the PSC Volume Browser window to toggle its display on and off.
Displaying Surface Cross-Sections
When you have displayed a surface (sectioned model), you can also display the cross-section of that surface in your current plane.
To display a cross-section:
- Choose "Display > Sectioned Models" from the PSC Volume Browser window.
If any surfaces are displayed in the context window, and intersect the viewing plane, the cross-section is outlined in the browser window.
Color Cube
Use points to visualize the distribution of dataset colors in the color cube. To do this:
- Enter points in the volume.
- Choose "Display > Color Cube" from the PSC Volume Browser window. The color cube window appears, showing the points in their color positions.
You can rotate the cube by clicking and dragging on the cube.
Points that are far apart are colored very differently, and automatic segmentation may be possible. Points that are close together either belong to very similar anatomical structures, or will need to be segmented at least partially using hand tracing.
Using Bookmarks
PVB bookmarks allow you to save viewpoints, name them, and return to them.
Add Bookmark
To add a bookmark:
- Choose "Bookmarks > Add Bookmark." A window appears, allowing you to enter the bookmark name.
- Click in the "Bookmark name" field, type a name, and press Enter. Note that you can name more than one bookmark with the same name.
The bookmark name appears at the center of the view in both windows. The bookmark is also given a number, starting with 0.
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Displaying Bookmarks
You can turn on bookmark names to display information about a view, or turn them off if they are intrusive.
- To turn off all bookmarks, choose "Display > Bookmarks > None."
- To turn on only the currently selected bookmark, choose "Display > Bookmarks > Current." The bookmark name appears, although the view will not change to match the bookmark view.
- To turn on all bookmarks, choose "Display > Bookmarks > All." If there are bookmarks located at the same place (for example, different angles of the same voxel), the names will appear on top of each other.
Select
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In order to display the viewpoint associated with a bookmark, you need to select that bookmark. When bookmarks are loaded, their names appear in the display, but the viewpoint is not changed. |
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To display a bookmark's viewpoint (select a bookmark):
The viewpoint associated with the bookmark appears in the PSC Volume Browser window. |
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Edit
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To edit bookmark properties:
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Saving and Loading Bookmarks
Once you have created your bookmarks, you can save them in a file for reuse.
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To save bookmarks:
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To load bookmarks:
The loaded bookmarks replace any that you have previously created or loaded. The last created bookmark appears in both windows, and you can now select any of the bookmarks. |
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VB Context Window
This window shows the 3D dataset, with commands for orienting and changing the display. The slice in the PSC Volume Browser window is displayed in the context of the entire 3D dataset.
ViewpointDisplaySurfacesButtons |
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Navigation tools specific to the context window:
Arrow and Plane Indicators
The arrow and plane indicators show the orientation of the slice relative to the rest of the 3D dataset. The arrow and the plane both appear in the VB Context window.
- Choose "Display > Arrow Indicator" from the VB Context window to toggle the arrow display on and off. The arrow is perpendicular to the slice, and points along the x-direction.
- Choose "Display > Plane Indicator" from the VB Context window to toggle the plane display on and off. The plane is concurrent with the slice, and contains it.
Viewpoint
The Viewpoint menu in the VB Context window applies constraints to the 3D view as you move through the volume. The image below was moved using different viewpoint settings:
- Fix at Center: the center of the volume is always in the center of the image window.
- Center at Plane: the center of the plane is always in the center of the image window.
- Moves with Plane: the 3D volume is always oriented so that the plane is facing out.
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original view |
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Fix at Center |
Center at Plane |
Moves With Plane |
Displaying Surfaces
The PSC Volume Browser provides many surfaces of anatomical sections, a library which is constantly increasing. These surfaces are made from 2D segments created by expert anatomists.
To toggle surface display:
- Choose "Surfaces > [surface name]."
Changing Surface Appearance
You can change the opacity of the surface, view it as a wireframe or a solid, and clip it with the view plane.
To change surface appearance:
- Choose "Display > Options" from the VB Context window. The Model Options window appears. Change any of the model options. The display is updated as you make the changes:
- Select Surface or Wireframe.
- Type an opacity or select it with the slider.
- Select one of the "Clip plane" options. If you clip the surfaces with the normal, portions on the arrow side of the plane are displayed. If you clip the surfaces against the normal, portions below the arrow side of the plane are displayed.
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Solid Skin and Liver Surfaces |
Wireframe Skin and Liver Surfaces |
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Opacity of Liver Set at 80% |
Liver Clipped with the Plane's Normal |
Many commands in the Volume Browser, particularly those associated with control points, can only be accessed with keystrokes.
Esc
Exits the Volume Browser.
l
(lower-case "L") Displays the label associated with the current cursor position.
c
Centers the view on the cursor position.
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