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.

Some screenshots from Volumest plugin:

Install and requirements

Download latest Volumest_*.jar file and copy it to ImageJ plugins folder. Volumest needs java version 1.5 or greater. Volumest is tested with ImageJ 1.35 and 1.38. Latest version (Volumest_20101017.jar) is briefly tested with ImageJ version 1.43u.

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!

Download Volumest.

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.

Questions and suggestions to Markko Merzin <markko.merzin@ut.ee>.

Volumest has been cited by:
Caleb A. Doll and Kendal Broadie. Activity-dependent FMRP requirements in development of the neural circuitry of learning and memory. © 2015. Published by The Company of Biologists Ltd | Development (2015) 142, 1346-1356 doi:10.1242/dev.117127.
Fischer S, Hirche C, Reichenberger MA, et al. Silicone Implants with Smooth Surfaces Induce Thinner but Denser Fibrotic Capsules Compared to Those with Textured Surfaces in a Rodent Model. Rubino C, ed. PLoS ONE. 2015;10(7):e0132131. doi:10.1371/journal.pone.0132131.
Lina, Ioan A. BS; Puvanesarajah, Varun BS; Liauw, Jason A. MD; Lo, Sheng-fu L. MD; Santiago-Dieppa, David R. MD; Hwang, Lee MD; Mao, Annie; Bydon, Ali MD; Wolinsky, Jean-Paul MD; Sciubba, Daniel M. MD; Gokaslan, Ziya MD; Holmes, Christina PhD; Witham, Timothy F. MD. Quantitative Study of Parathyroid Hormone (1-34) and Bone Morphogenetic Protein-2 on Spinal Fusion Outcomes in a Rabbit Model of Lumbar Dorsolateral Intertransverse Process Arthrodesis. DOI: 10.1097/BRS.0000000000000169
Stacey Adjei, Alexandra L. Houck, Katherine Ma, Daniel W. Wesson. Age-dependent alterations in the number, volume, and localization of islands of Calleja within the olfactory tubercle. DOI: 10.1016/j.neurobiolaging.2013.05.014.
Boulland, Jean-Luc; Leung, Doreen S. Y.; Thuen, Marte; Vik-Mo, Einar; Joel, Mrinal; Perreault, Marie-Claude; Langmoen, Iver A.; Haraldseth, Olav; Glover, Joel C. Evaluation of Intracellular Labeling With Micron-Sized Particles of Iron Oxide (MPIOs) as a General Tool for In Vitro and In Vivo Tracking of Human Stem and Progenitor Cells. Cell Transplantation, Volume 21, Number 8, 2012, pp. 1743-1759(17) DOI: http://dx.doi.org/10.3727/096368911X627598
Paula Vickerton, Jonathan C. Jarvis, James A. Gallagher, Riaz Akhtar, Hazel Sutherland, and Nathan Jeffery. Morphological and histological adaptation of muscle and bone to loading induced by repetitive activation of muscle Proc. R. Soc. B August 7, 2014 281 1788 20140786; doi:10.1098/rspb.2014.0786 1471-2954
Tamori Y, Deng WM. Tissue repair through cell competition and compensatory cellular hypertrophy in postmitotic epithelia. Dev Cell. 2013 May 28;25(4):350-63. doi: 10.1016/j.devcel.2013.04.013. Epub 2013 May 16.
Vega-Zuniga T, Medina FS, Fredes F, Zuniga C, Severın D, et al. (2013) Does Nocturnality Drive Binocular Vision? Octodontine Rodents as a Case Study. PLoS ONE 8(12): e84199. doi:10.1371/journal.pone.0084199
Mahmoud Mageed, Dagmar Berner, Henriette Jülke, Christian Hohaus, Walter Brehm, Kerstin Gerlach1. Is sheep lumbar spine a suitable alternative model for human spinal researches? Morphometrical comparison study. Lab Anim Res. 2013 December; 29(4): 183–189. Published online 2013 December 20. doi: 10.5625/lar.2013.29.4.183
Valle-Leija P, Blanco-Hernández E, Drucker-Colín R, Gutiérrez-Ospina G, Vidaltamayo R (2012) Supernumerary Formation of Olfactory Glomeruli Induced by Chronic Odorant Exposure: A Constructivist Expression of Neural Plasticity. PLoS ONE 7(4): e35358. doi:10.1371/journal.pone.0035358
Anna Ligasová, Jana Bulantová, Ondřej Šebesta, Martin Kašný, Karel Koberna1 and Libor Mikeš. Secretory glands in cercaria of the neuropathogenic schistosome Trichobilharzia regenti - ultrastructural characterization, 3-D modelling, volume and pH estimations. Parasites & Vectors 2011, 4:162 doi:10.1186/1756-3305-4-162
Thomas Kaindl. Control of Specific Cell Response with Strongly Correlated Functional Domains Embedded in Supported Membranes. Ruperto-Carola University of Heidelberg, Germany. PhD thesis. 2011.

Last updated 24.08.2015