Take long time to get results

Hello,

I am using CellProfiler (ver.4.0.6) for counting two primary objects. After setting pipeline and starting analysis, it has been taking lots of time (more than three hours) to get results from only 12 pictures. I am not sure how long it actually takes because I stop the analysis every time it takes longer. It seems to be weird because we had been able to get results more quickly.

Has anyone faced the same issue? If you know how to solve this issue, please tell me. I attached screenshot which shows what is happening now.

Best,

Hiro

Hi @hirom,

It looks like CellProfiler probably ran into a problem with writing to the results file. You might want to check that the program has write access to the directory specified in ExportToSpreadsheet.

It may also be worth upgrading to version 4.0.7, in which a few bugs have been fixed.

Could I also check whether this is a packaged version or if you compiled from source?

Hope that helps

Hello David,

Thank you for your advice, David.
I downloaded the new version (4.0.7). It seems not all file cannot be processed.
When error comes out, the attached “error” popup appears.
I do not understand what this means.
Could you tell me how to solve that?

Best,

hiro

Hi @hirom,

If you’re using a version downloaded as a .app executable, would you be able to send a copy of the pipeline and an example image set that triggers this?

Otherwise, if you installed this from the command line with pip, would you be able to send the results of running pip freeze? If your installation is built from source you may need to upgrade cellprofiler-core as well.

Hi David,

I separated the number of files to small, then everything went well.
Other files could be operated normally, so I guess the files might be damaged when uploaded or downloaded.

I appreciate your advices and I will follow your advice when that happens again.
Thank you and happy new year!

Best,

hirom

Glad to hear you got it working @hirom,

Would you still be able to confirm whether you downloaded a build or installed with pip? The second error you saw suggests that the built-in error handler is not working properly, so we’d like to fix that.

Thanks!

Hi David,

Thank you for your response. If I am correct, I downloaded a build from this website (Download | CellProfiler). I hope it will be fixed.
Thank you,

hirom