I am very new in using cellprofiler and I got some problem with analyzing some staining. I stained my samples for CD31 and a second protein. I would like to quantify the intensity of my second protein only in the areas, that are overlapping with my CD31 postitive cells. By doing that I would like to see the expression of my second protein in endothelial cells (CD31+ cells).
So far I was only able to get good quantifications of my separated staining with the IdentifyPrimaryObject tool. I also figured out, that I can relate my objects. I chose CD31 as parent and the second protein as child. I continued using the FilterObjects tool to measure the Slit2, that are overlapping with the CD31. My problem is, that the quantification really doesn't give the results, that I am aiming for. Cellprofiler seems to count the cells, that are overlapping. But what I want is: to substrate all the areas of my second protein, that don't overlap with CD31 and quantify the expression of the protein in the overlapping areas.
Did somebody tried to do the same before or has ideas how to solve that problem?