Volume measurement of 3D object using imageJ


I previously used imageJ to measure volumes of Drosophila larval ovaries. I used the analysis, thresholding and the measurement stacks plug-in. For some reason, I can no longer use that plug-in. I tried to download it again, but it did not work.

I tried the 3D object counter, but I am not sure that is giving me the right calculation. Is that an accurate way to get a volume of a whole organ? The images are z-stacks.

I appreciate any assistance anyone can provide.



for similar topics I use the following script (require fijipytools.py, which can be found on the same Github repo):

and I also converted this script into an APEER module, which can be found here:

3D Segmentation and Analysis

The code is public and can be downloaded.


Maybe it helps.

If you calibrate your image (Image>Properties) well (x, y and z), 3D object counter should give the correct

Thank you very much for your suggestions. I am still working on it. Plug-ins are missing on my program and I am not able to download some of what I need.

Thanks again!

are you using Fiji, right?

Yes, I am using Fiji. I used it before and it worked well, but now I am having challenges with it. My “compile and run” plug in is not “supported” so not working. I tried to download it, but the message box says it may damage my computer, so I don’t think I want to try that. From there I used measure stacks, etc., to calculate volumes of the whole organ, but of can’t even get to that function without the compiler. I tried to download the measure stacks plug-ins but was unsuccessful with those.
Frustrating for me at this point and data at a standstill.



And did you test the alternatives? Do they work for you?

Dear Tammara,
not clear to me which plugins you are missing.
and which plugin you are trying to compile an run.