FIJI (ImageJ): Bone Analysis with BoneJ2 [Trabecular Bone]

Learn how to use FIJI (ImageJ) to analyze bone images using a collection of plugins from BoneJ2. This tutorial focuses on trabecular bone analysis. Measurement parameters for trabeculae include area/volume fraction, surface area, surface fraction, connectivity, thickness, purify, particle analysis, and skeleton analysis.
Image credit (image stack of trabecular bone from condyle,Talpa europeae):
Doube, Michael; Kłosowski, Michał M; Hutchinson, John; J. Shefelbine, Sandra (2018). X-ray microtomography images of trabecular bone from the femoral head and condyle of 18 avian, 72 mammalian and one crocodilian species.. figshare. Dataset. doi.org/10.608...
BoneJ2 - Domander, R., Felder, A. A., & Doube, M. (2021). BoneJ2 - refactoring established research software. Wellcome Open Research, 6, 37. doi:10.12688/wellcomeopenres.16619.2
Sample macro for saving BoneJ Resuluts table:
setBatchMode(true);
directory = getDir("Choose a Directory");
run("Table... ", "writecolheaders=true writerowheaders=true columndelimiter=, outputfile=["+directory+"results.csv]");
run("Clear BoneJ results");
SUBSCRIBE to have first access to new video tutorials: / @johanna.m.dela-cruz

[@simonediana1958]

Hi Johanna, good video. For the next exam we have to prepare a presentation on a specific ImageJ Plug-in. I chose levan. what do you think about it?

[@johanna.m.dela-cruz]

Hi @simonediana1958. Thanks for watching. I have not tried the Levan plugin, unfortuantely. I'm sure it serves its purpose in terms of image analysis. Good luck on your presentation.

[@simonediana1958]

@@johanna.m.dela-cruz thank you!

[@mericdumbek8239]

Hi Johanna, thanx for this video. I have micro CT images. I want to crop the areas where the trabeculae are located. Do you have any suggestions regarding this? Do you have an e-mail address I can contact you? Thank you so much.

[@johanna.m.dela-cruz]

Hi! Thanks for watching. You can draw a region around the trabecular and then Crop. My email should be available in my channel description.