Mammalian cell colony counting


I need to count colonies on 6cm dish. The colonies are stained blue but I take pictures of black and white (background is white). Do you have a pipeline available? I tried to modify the pipeline of counting yeast colonies, but couldn’t make it work.

Thank you very much for the help.

Hi Rong,

Please post an image example of your colonies as well as your pipeline attempt, and we’ll see if we can help.


Hi, David,

Thank you. Please find the attached pic. My purpose is to count the number of colonies using same settings for my over 200 plates.
I don’t think my modified pipeline will help because I am confused by those settings and didn’t make much effort. Thank you for the help.


Trying to post the pic again.


I am new to this but I am having problems with the pipeline to count mammalian cells stained in blue on 10cm plate. It keeps picking up light outside the plate.
Does anyone know how to correct this?
Here is a photo and pipeline- the pipeline was from the yeast counting examples online

Thanks so much

COUNT COLONI.mat (14.8 KB)

Hey Kelsey,

I’ve used cellprofiler to quantify the size of yeast colonies on agar-plates and ran into a similar issue. I ended up solving the problem by using the ‘Crop’ module (it’s in the Image Processing section) to crop the image so that it only included the plate. Perhaps you could give that a shot.