Tissue DAPI channel quantification



Hey there!

I just started out a new project where I need to identify certain cell populations in mouse long bone sections. After sectioning and staining for different markers, we use IF microscopy and scan the entire section. As a result, we get huge pictures (11000x11000).

So far everything was going pretty well, but the analysis is a little bit trickier than I thought. My first intention was to use basic image software like ImageJ/Fiji to count my cells of interest (which are stained with a specific antibody, therefore are in a separate channel) and then normalize it using the total cells count from the DAPI channel.

With a lot of hassle, I was able to get the right parameter for my cells of interest, which are now so frequent. However, since it is a picture from a tissue, there is a high density of cells, thus the DAPI staining looks pretty packed. After sometime trying ,I kind of gave up on trying to quantify all the DAPI cells and did some digging on the internet finding Cellprofiler.

Apparently is an extremely powerful tool for all kinds of image processing. I´m trying to go through as fast as I can on learning how the program works, but I´m having some trouble.

Is anyone have any suggestion how could I assemble a pipeline (or just a stating point) which can give a fair DAPI count in such huge tissue image?

It would extremely helpful!

Thanks a lot,



Hi Arthur,

Thanks for giving CellProfiler a try! I highly recommend that you visit our “Before Posting: Tips page” (link below). This will optimize your post so that we can best assist you.