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Volumest (VOLUMe ESTimation) is a ImageJ plugin for volume estimation using stereological method. Volumest is published under GPL free software license. Source code is packaged with binaries to jar files.

• JavaDoc
• Browsable source code. Start from Volumest class.

Some screenshots from Volumest plugin:

• Setup dialog.
• Results in main window.
• Grid and input setup.
• One help window.

Install and requirements

There were confirmed user reports that Volumest does not work with some newer (since versions 1.39) ImageJ version. Fixed version of Volumest plugin is available for download!

Quickstart for DICOM images from CT.

1. Select from ImageJ main menu: File / Import / Image Sequence ...
2. Navigate to folder with .dcm images and select one (any).
3. When importing, mark "Convert to RGB" button.
4. Select from ImageJ menu: Plugins / Volumest.
5. Note that "Slice thickness" field is already filled. It is extracted from first image of stack.
6. Using scrollbar below image window or mousewheel, find object of interest.
7. Count the number of slices where object or objects appear. Look at the upper left corner of the image window. There are two numbers separated with slash (like 34/83). First number shows the number of visible slice, second number shows count of slices.
8. Answer 4 to "slices to be estimated".
9. Press "Pilot". Volumest suggests grid width for pilot measurement. Default grid width is one tenth of picture width. One may change this ratio by pointing mouse to "Pilot" button and scrolling mouse wheel. Choose ratio which suggests grid width roughly same as measured objects largest width.
10. Choose appropriate object type: irregular or ellipsoide-like.
11. Press "OK" to start measurement.
12. Navigate to the first slice with grid when object of interest is visible (using "prev. grid" or "next grid" buttons or mouse wheel).
13. Using left mouse button, drag around the borders of object of interest. Objects border appears in yellow crosses, objects interior with red dots or angles.
14. Press "next grid" and repeat until whole object of interest is measured. Read results.
15. CE of pilot measurement should be about 0.3 to 0.5. Press "Again".
16. When object is ellipsoid like: Answer 4 to "Slices to estimated" and 50 to "Points to be counted".
17. When object is irregular: Answer 10 to "Slices to estimated" and 250 to "Points to be counted".
18. Repeat measurement. This time CE should be 0.02 to 0.05.
19. Is object of interest clearly visible under the grid? If using Volumest first time on CT images then probably not. Press "setup" button. Select "Grid Setup" tab and mark "Grid type" to "right angles". Decrease "Angle arm length" until object of interest become clearly visible. Setting that to 5% is often good. When necessary change grid color also. Setting it to some dark color is often good. Sometimes is nessesary to switch grid display off completely. Press "apply" button.

Cite volumest as: Merzin, Markko. "Applying stereological method in radiology. Volume measurement." Bachelor's thesis. University of Tartu. 2008.

For theoretical background see article by N. Roberts, M.J. Puddephat and V. McNulty, The benefit of stereology for quantitative radiology, The British Journal of Radiology, 73 (2000), 679-697.

Last updated 28.03.2012