Error Message " C + + Assertion - Invalid ItemID Value" Mid Processing >11,000 images


I am hoping someone can help me understand there error message that has started appearing a third of the way through my large scale image analysis of >11,000 images. It’s due to take >100hrs processing so I really want processing to continue through the night but it keeps getting halted by this error message when I’m not on hand to click continue.

I have uploaded an image of the error message and my pipeline. CP is using 4 workers and I believe the error message is generated each time a worker starts a new image. I can find evidence of error message being generated in the java panel.

Any help appreciated on how to instruct to always continue processing regardless of error message OR how to fix problem causes error message, or of course any other relevant information.

Many thanks,



P.s I can see from previous threads that others have encountered this issues and fixed it by going to Windows > ‘Hide All Windows On Run’ unfortunately this hasn’t corrected my issue.

Others have suggested doing smaller batches may help. Given I’m a third of the way through I’d really love to get to the end of this one!

Hi @SAB,

Do you see an error in the console window when this first occurs? It looks like CellProfiler is running out of object identifiers to assign to GUI elements, but if displaying figures is disabled then this usually shouldn’t be an issue.

An alternative solution might be to run in headless mode. You can do this by adding a “CreateBatchFiles” module and using the output file with the command line interface.

Hi DStirling,

Thanks so much for getting back to me.

There is never an error message in the console so it’s hard to get more information. Likewise I have ‘Close all windows on run’ and all the eyes closed too.

I will try running with a “CreateBatchFiles” module. Thanks for the advice. Would you mind explaining using the command line interface - I am not sure what you mean and I’m not very experience in CellProfiler.

Thanks again!