How do I use CellProfiler to specify cells on stained tissue sections and count them (automated method)?


I have stained embryonic mouse brain sections with (DAPI and NKX2.1). I want to quantify the number of cells expressing NKX2.1 I found that CellProfiler can do this, however I don’t know how to set up a pipeline for the tissue section images in order to count cells automatically!

Attached image of stained embryonic mouse brain section !

I need Help :frowning:



Have you searched the forum for people studying similar issues or checked out our example pipelines and tutorials? Those are often the best ways to get started- if you get stuck along the way, people are generally quite willing to help you get over specific issues here on the forum.


Most of them have counted cells manually. In my case I need an automated method to count the cells :frowning: