Hello everybody,

I am trying to compute the volumes of some nuclei I have segmented, together with other measures such as the centroid position, for example. The problem is that I have a stack and so far I can only extract 2D data from each frame using skimage.measure.regionprops(). I would like to continue the image analysis in Python, therefore the question:

How can I calculate 3D measurements starting from this stack?

I do know the pixel size in xy and z, but I am not sure that simply computing that for the number of frames is correct. I was trying therefore to use skim age.measure.marching_cubes_lewiner, which computed the 3D surface area. But again, it is the area and I do not know how to translate this in the volume and other measurements.

### Sample image and/or code

This is only one frame of the masked stack. I have just opened in Fiji and it appears that all nuclei have the same value. Actually, in the stack I have every nucleus is labeled with a unique integer value so I can recognise them through the stackâ€¦ anyway, this is just to give an idea.

S16-20200805_30hpf_LM1_eGFP-LAP2B_H2B-RFP_40X_E7_processed_crop-2.tif (1.2 MB)

Please, if you know how I can solve this problem let me know!

Thanks,

Lucrezia