I am a complete novice to Cell profiler and I downloaded it because of a recommendation from the treat NMD website. I have a very large number of fluorescent images from skeletal muscle cross sections to analyse and there will be many hundreds more to come as I move forward. Therefore I am looking for a semi automated method to assess several parameters from these images which are taken sections (see attached images) stained with Lamin (red; to show the outline of the muscle fiber), Pax7 (green: to detect satellite cells) and DAPI (blue; to show nuclei). Here are the 5 parameters I would like to measure:
- Muscle fiber minimum Feret (a measure of diameter) using the lamin staining
- The number of Pax7 nuclei out of the total number of DAPI positive nuclei
- The total number of DAPI postive nuclei
- The number of fibers with a DAPI positive nuclei in the middle of the fiber (a sign of muscular regeneration)
Any help in figuring out pipelines to identify these different muscle feature (from single or multiple images) would be a massive help and I would really appreciate your advice.
Thank you in advance for your time.