I am working with whole body micro-CT of mice. My goal is to segment out the entire skeleton (as best as possible) and compare grey values to that of a phantom to assess variation in bone density across experimental groups. As of right now, I highlight the bone using a manual threshold, but I can only measure the grey value in the highlighted area on one slice.
I have two questions
Is there a way to select the entire skeleton without turning it into a binary image via the threshold tools? As I understand it that would erase the underlying grey values. An automatic method would be ideal, and optimize threshold does not seem to select the bone.
How can I measure the grey values of the selected material across the entire stack?
Thank you for your help.