Im trying to find an available software that can help me quantify the process thickness of microglia in images I have. I have previously used NeuronJ through Image J to measure their length, but I do not believe I can measure thickness through this method. Is anyone aware of a software package that can manage this?
Imaris, however, is too expensive. You may find it in the University's core facility.
For thickness measurements you need to have both a skeleton and a distance map of the binary mask. To my knowledge, both Imaris and Amira can do it, and Amira is a less expensive option. We have recently used Amira in a such way for the vasculature analysis, so you can check out some details here: https://www.nature.com/articles/s42003-021-02275-y.