CellProfiler input limitations for variable plate localization?


I’m trying to make a pipeline for automating the measurement of yeast colony sizes in 96-well format omnitrays. I’m wondering if CellProfiler has the ability to locate the plate and the colonies given the right inputs, including aligning the image, or if this would have to be done manually beforehand. I’m attaching an unedited image straight from the image acquisition setup. As you can see, the plate is not always aligned.


So the pipeline would probably be a modified version of the Yeast patch identification pipeline with some major steps required beforehand:

  1. Finding plate or 96 well grid based on spot locations
  2. Aligning plate (straightening)

Does Cellprofiler have the ability to do this automatically if the plate is in different locations/angles in the image set? If it does, what are the suggested modules?

Thank you,


Hi @RodrigoC,

I think you the modified version is from the example pipeline given here.
Please do refer to the pdf shared in the example.

Yes, CellProfiler can do this automatically and align them. Sharing your pipeline that you tried with the sample images will facilitate us to help you better.