Since I am new with image analysis and Cell profiler I would appreciate a bit of help.
In the three images that I have uploaded I have three different states of neurons after treatment. My imaging is not neurite targeted (simple alive cell staining) but the difference by eye is obvious I just can not put it to numbers.
I would like to measure the Neuron body numbers and the total axon length and the branches. I went through all the instructions and the forum with the related topics but I can not solve my problem.
I am using Cell Profiler v4. but I can not see the measure neuron module, I know that I have to do Morph and or Morphological Skeleton but I do not obtain any result either with grayscale images or with binary mask. Although in the pipeline that I have uploaded by Identify Secondary Objects I can detect the axons in grayscale images
I guess I am missing something fundamental.
Thank you in advance