I have brightfield images of cells and floruoscent images as well (these fluoroscent channels shows the proteins the cells have in the.There are three channels-red, blue and green hence 3 proteins). . How can I count number of cells that have these proteins. The other issue I am facing is if you see the brghtfield image, the cells are very oddly shaped, have different levels of grey in them and some cross over the other, when I try to threshold them to binarize, some of them appear broken and I cannot use imfill directly( If I could use imfill, I would just intersect them and find overlapping area). Is there any solution to finding the number of cells that have the three proteins given these concerns?