Erro message C++ assertion



I am using Cellprofiler(3.0.0) to analyze my images now.But when I analyzed almost 200 images, it came with an error message like this. Picture1

Can someone help me to fix the problem? The problem is coming with my images or not? Thanks a lot!


We’d love to help but need more information- can you tell us what OS you’re using? Were you in test mode or analysis mode? Can you attach the pipeline and a set of images? When did the error come up, right away, in the middle or near the end of the image set? Can you analyze smaller sets successfully without the error?


Thanks a lot for your replying. I am using PC with windows7. I meet this problem in analysis mode, and in test mode I have no error. I attached the pipeline and some images. I tried to analysis 2000 images, the error came at around 180 images. when I analysis 200images, the error came around 120images. When I test to analysis 10images is fine, without any errors.

HTC assay.cpproj (1.6 MB)

The format of my images is FLEX. I can’t upload images…
I upload 10 images to


Hmmm- can you try to run it with the eyes closed by going to Window->Hide All Windows On Run on your set of 200 and see if it works for you? I’m wondering if there’s an issue with one of your display windows along the way. If you don’t get the error with 10 images, likely I won’t either.

Otherwise, is it at all possible that one (or a small number) of your images is corrupted/not loading properly? One way to check of this would be to a) check all your file sizes to make sure one isn’t suspiciously small and b) try running the pipeline a couple times and see if CP always fails at the same place or not.

Error message while running analysis in Cell Profiler

Great, now it’s running well without error message when I run it with eyes closed. Thank you very much!


I was getting the same error on a mac and found that the eyes closed trick solved the problem for me as well.