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)