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 stack… anyway, this is just to give an idea.
Please, if you know how I can solve this problem let me know!