Images load as black in test run, program closes in real run


I just started building a pipeline to count bacterial colonies plated on agar from a 96 well format. Yesterday while testing the pipeline images loaded fine. Today when trying to test and fine tune the pipeline, images wouldn’t load and came up as black squares. It was suggested I try running the pipeline in a real run and the cell profiler closes itself and I then get a message that cell profiler quit unexpectedly. The images are fine and not corrupted and open fine in ImageJ and other image software.

I’ve attached a screenshot of the error as well as one of the images I was working on trying to analyze. I have also attached the pipeline.

Any idea what could be happening? No changes were made to the pipeline or images since yesterday when it was working fine.
test.cp (5.83 KB)


It looks like the last setting in DefineGrid is set to “Leave blank”. If you change it to “cfu plate” is displays and you can use the manual mouse method. Does that help?

Other suggestions:

  • The image file is big. If you can image in grayscale (I don’t see anything biologically relevant in a particular color channel, so I suspect this is ok, but you would know best), that would reduce your file size by ~3x and avoid memory issues and speed up processing a lot.
  • Any skew to the image plane may cause problems with DefineGrid. Try and shoot straight down onto the plate (sorry if that was obvious)
  • Avoid saving as JPG as some image information is lost. Try PNG or TIF instead