I am currently extracting some measurements from masked images of a densely packed tissue. Among the several parameters I am interested into, I would like to count the number of neighbour nuclei per nucleus. This is an example of a frame from a masked stack (so the nuclei are in 3D actually):
I am using Python to analyse these images and I would like to know whether it already exists a function that has been implemented for this task. On this forum, I found questions and solution regarding solely CellProfiler. Is there something also in Python?
Otherwise, is there a way to do it ? Maybe expanding the 3D surface area until objects touch? Do you know a similar script I can use as a basis to try out this?
Thank you a lot!