I am a new user of ImageJ and CellProfiler. I have images of human muscle sections with four staining channels:
Nuclei (with Hoechst)
Satellite cells (with pax 7)
Methylation (with 5-MeC)
The ultimate goal is to quantify the intensity of the methylation staining inside the myonuclei and inside the nuclei of the satellite cells.
After reading a lot on ImageJ I was able to already quantify the intensity of the methylation (only the stained 5-MeC that is overlapping nuclei). But now I want to do this specifically for myonuclei and nuclei from satellite cells. Myonuclei are identified based on their location: nuclei with their geometrical centre inside the inner rim of the dystrophin ring (so inside the basal lamina). So easy put: those Hoechst spots that are inside the lamina and not on top of the lamina. Satellite cells can be identified as those myonuclei that show an overlap with the pax 7 signal.
Since there will be around hundred myonuclei within one image and since I have around 500 images, I was hoping there was a way to not do this manually and build a pipeline for this. Are there existing pipelines on this topic that are reliable? Because I am not really good at programming it myself.
Can somebody help me out?