This would be a great question to post in our new free medical imaging question and answer forum ( www.imagingQA.com ), there are a number of digital pathology and image processing experts in the community. If useful, please feel free to open a new topic at the link below :

https://community.imagingqa.com/c/questions/5

You can use the Volume Calculator plugin. Users may measure volumes directly from a 3D picture with the Volume Calculator plugin. The plugin is set up to function best with photos that the Skeleton 3D and Analyze 3D plugins can read and analyze. The Volume Calculator makes use of three Fiji plugins: Skeletonize3D for skeletonization, AnalyzeSkeleton for analysis, and 3D Viewer for visualization.

Hi there,

It's always easier if you share the pictures...

To add to Shamim Ahmed response:

Depending on the quality of your images you can use the 3D object counter plugin and the 3D ROI manager

https://imagejdocu.tudor.lu/plugin/analysis/3d_object_counter/start

https://imagejdocu.tudor.lu/plugin/stacks/3d_roi_manager/start

The only problem is that working with those two you will get only the information concerning to your signal, eg: if you have a membrane staining, you won't get the volume information of the volume bounded by the membrane, but only the volume of the stained regions. However, by looping over the 3D ROI manager and using binary operators (Binary>Close and Binary>Fill holes, basically) you should be able to easily get a 3D binary mask corresponding to your cell volume (by filling the gaps),

Cheers,

J

J. Ramirez-Franco. If you share your email id with me I can mail you my problem. I need to solve this problem.