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:
- The colonies are dark gray on a light gray background. I tried inverting the picture with ImageMath module, however it didnt help much.
- The colonies size is very variable between treatments (see attached images).
- 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)