Counting red particles only in the green channel


Hello everyone,

I would like to ask you a suggestion on how to solve this problem: I have the green and the red channel of motor neurons photos and I am interested in knowing how many red particles I have within the green channel.

I would be very grateful if someone could write an example pipeline to solve this problem.

Thank you in advance,



Hi Chiata,

I’ve attached a pipeline for you to try. The gist of it is to mask the red image with the green image. (175.5 KB)

P.S. Avoid using JPG image format for image analysis. Since JPG does not use a lossless compression algorithm, artifacts can be introduced into your images that impact segmentation and quantification. If you need compression use PNG instead.