If I take multiple images in different fluorescent channels (after staining the cells with some antibody/maker), how can I automatically quantitate the fraction of cells positive for each marker? Has anyone done something like this in Python?
I can already use Fiji (ImageJ) to count the cells containing only one staining type, but I can't make it run a selective count on merged images which contain two staining types. Since Fiji interacts well with python, I was thinking of writing a script that looks at each respective image containing only one staining type and then obtain the x-y coordinates of the respective image and check for matches between. I am not sure if that's a good idea though and I was wondering, if anyone has done something similar or has a more efficient way of getting the task done?
Thanks for your help!
You could use cont = cv2.findcontours to find the almost round shaped cells and count them 
with len(cont).
Cell Counting: Selective; Only count cells positive for all stainings