Help Creating a Pipeline

Hi all,

I’m fairly new to CellProfiler and am self-teaching myself the software and its various modules. I’ve been practicing with different brain slice images and was wondering if someone would be kind enough to help me construct a pipeline for this brain slide that I am practicing with.

Here is the practice tissue sample image:

What I am attempting to achieve is:
(1) quantitate the number of fluorescent green neurons (size does not matter).
(2) quantitate the number of fluorescent red neurons (only the one’s with an evident, bold cell body; NOT the lines [axons] nor dots [dendrites/branches].

I have no idea where to begin - since the sample is meshed and not as determinate as the tutorials on CellProfiler’s webpage. I’d sincerely appreciate any and all help.


Attached is a pipeline which should get you started. Hope this is helpful!

Thank you very much Mark! This is very helpful.

I sincerely appreciate your time and efforts in helping me with this. :smiley: