Soft agar colony size

I am trying to quantify the size and number of colonies grown on soft agar. I tried to use the FindEdeges module followed by IdentifyPrimAutomatic (I attach the pipeline), however, it seems that I have three main problems which I didnt manage to solve:

  1. The colonies are dark gray on a light gray background. I tried inverting the picture with ImageMath module, however it didnt help much.
  2. The colonies size is very variable between treatments (see attached images).
  3. The surface of the agar is not uniform which result with shaded areas. I tried to correct it with CorrectIllumination_Calculate followed by CorrectIllumination_Apply, but it was not successful.

I would appreciate your help in solving these problems,
colonyPIPE.mat (1.26 KB)


Have you tried the Classified Colonies example & tutorial? The example sounds very similar to the images you’re describing (though I couldn’t see the attachments, for some reason).



Hi Gur,

Attached is a pipeline that does a decent job of subtracting out the background and identifying the colonies. The idea is basically the same as the colonies example- split into component colors, create an illumination function representative of the background variation & subtract this off, and identify the colonies.

Let me know how that works!

softagarPIPE.mat (1.11 KB)