CellProfiler 3.1 MySQL Error: maximum columns reached


I am running CellProfiler 3.1.8 on Windows 10 with a published pipeline (Singh S, Bray MA, Jones TR, Carpenter AE (2014).) When running the ExportToDatabase module, an error message showed up as the following:
Encountered unrecoverable error in ExportToDatabase during startup:
MySQL Error: maximum columns reached.
Try exporting a single object per table.
Probleatic table: Analysis_WithICFs_PerImage

I also tried exporting a single object per table, but the same error persisted. I ran the same pipeline using CellProfiler 2.2 without any problem.

I’m unable to upload files at this time, but I can send you the corresponding pipelines for both versions if necessary.

Thank you!


My guess is the MeasureTexture module is the culprit- far more texture features are extracted in CP3 than CP2, which might be pushing you over the column limit. Can you try disabling that module and seeing if that fixes the issue?

Yes, I verified that MeasureTexture module caused the problem. I also tried to extract texture measurements from objects only, but still too long. Do you recommend separate MeasureTexture to the next pipeline? But then I have to manually merge two database files. What would be the best solution in CellProfiler 3.1?

I’d personally consider just skipping MeasureTexture until we can get a new implementation published (we’re working on it!), but it ultimately depends on how important texture features are to your analysis. Running them separately would also be an option.

Look forward to new releases! Thanks a lot