Cell Profiler Crew -
I’m a new cell profiler user that would like to identify objects and retrieve data from the objects. I am trying to identify microbial colonies growing on agar. I have been using IdentifyPrimAutomatic and EdgeFind, but can’t seem to identify the objects. I have had mild success from EdgeFind, but no success from IdentifyPrimAutomatic. I have been manipulating ApplyThresh to get a better contrast between objects and the background, but this hasn’t seemed to help.
I also closely followed your speckles example, without success.
My typical Pipeline:
- Apply threshold - make colonies darker
- apply theshold - make background darker (Essentially I have binarized the image)
Do you have any suggestions?
Here is the picture I am trying to analyze.