I am performing immunofluorescence assays in my lab. I would like to study protein expression of different glial markers, and so its possible variation among my experimental groups. So, I am trying to find the correct method to analyze flourescence intensity of my samples (I downloaded the program fiji and cell profiler). I would be grateful if somebody could clear me what are the steps to follow for a correct analysis, what data I could get from my images?
Two example images are attached below (They represents AQP4 in red and GFAP in green, two common astrocytic markers. Cell nuclei are blue). The entire picture represents the region of interest.
Thank you for time spent!