|Volume Calculator (Fiji)|
|Author||Peter C Marks (firstname.lastname@example.org)|
|Maintainer||Peter C Marks (email@example.com)|
|Latest version||December 5th, 2012|
The Volume Calculator plugin is designed to let users measure the volumes of arbitrary segments of blood vessels by selecting them directly from a 3D image. Although Volume Calculator was developed for quantification in a mouse hindlimb ischemia experiment, it should be useful for the volume measurement of any network. This possibility is determined by the following requirement: the plugin is configured to work best with images that can be read and analyzed by the Skeleton 3D and Analyze 3D plugins. Hence, it is suggested that users first check their images with these two plugins.
Volume Calculator uses three Fiji plugins:
- Skeletonize3D for performing the skeletonization,
- AnalyzeSkeleton for the analysis and
- 3D Viewer for display.
The section explains how to use Volume Calculator. A Magnetic Resonance Angiogram  (MRA) is used as an example image. This MRA is of the hindlimb vasculature of a mouse and was performed in vivo.
If your image is not binary then it must be thresholded in order for the first stage in the Volume Calculator to work. These settings are often determined by the nature of the image, for example, its noisiness, or by what features you wish to retain. You can pretest this image by running the image through the Skeletonize3D plugin. A second test can be performed by taking this skeleton image and applying to the AnalyzeSkeleton plugin to see if it can be analyzed. If it can not be analyzed then oftentimes adjusting the threshold can make it "analyzable".
The Volume Calculator is located at Plugins>Analyze in the Fiji menu. When run, it will take the current image as input. Processing begins immediately; its progress is shown in the status bar. After a successful run, the plugin will display the Volume Calculator window (Figure 2.) This window is actually the 3D Viewer plugin. Volume Calculator has taken its final result - a Java 3D representation of the analyzed image - and asked the 3D Viewer to display it.
Because the 3D Viewer plugin is used for display, its menu is available at the top of the window. Below this menu line is the image area where the image can be manipulated with all of the available 3D Viewer commands. At the bottom of the window is an additional area that Volume Calculator uses to display volume results. It will be discussed in more detail in the next section. Below this area are two check boxes. These check boxes alter the display and behavior of the 3D Viewer. Checking the Bounding Box will cause the 3d Viewer boundary box to be displayed. Checking Key Nav. Only allows you to perform 3d transformations such as rotation with the just the directional keys.
The selection of the lines (vessel segments in a vasculature) is performed entirely with mouse clicks. For the purpose of selection, lines (segments) are delimited by the end of a line and/or a line branching from it.
Selected lines are shown in the current measurement color; double clicking a line will change the color of that line and measure the volume based its corresponding voxels in the original, thresholded image (Figure 3). The voluem is shown next to the measurement color. The unit of measurement can be seen at the bottom of the image. Volume Calculator will attempt to find unit information in the image. If that is not possible, the unit of measurement is in voxels. Often a measurement will appear to be too short but rotating the image will show that selection stopped at a branch point - possibly very small. The algorithm used to calculate the volume is a variation of dilation (reverse skeletonization) that is bound by the voxels in the original image. Bifurcations and such are dealt with by sharing the voxels at the junctions.
The "C" button next to a color is used to reset all of that color's lines to white. The volume is set to zero.
Another form of selection is to click a ponit on a line once and then click another line, elsewhere, once. The Volume Calculator will attempt to find a connected path between the two points. If that is possible, the path is changed to the measurement color and the volume of the entire path is calculated. If there is no connected path, a warning is displayed.
The Volume Calculator keeps track of the what measurements are associated with a color. If you select a line with a color different from the measurement color, the volume of that line is subtracted from the original color total and added to the measurement color total.
The Volume Calculator plugin uses the following plugins:
- Skeletonize3D for performing the skeletonization,
- AnalyzeSkeleton for the analysis. Also tree traversal to create the Java 3D image is based on the one in this plugin.
- 3D Viewer for display and image manipulation.
Copyright (c) 2012, Peter C Marks and Maine Medical Center Research Institute All rights reserved.
Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
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