"Problems with pipeline"

I’m working with a CellProfiler pipeline we recreated from version 1.0 to 2.1. It works, but it throws the following warning before starting the workflow:

We do use the ImageMath module in this pipeline but I’m not seeing any variables in that module (or any other) that would have to do with ExecutionTime. What do I need to do to prevent this warning from popping up? Thanks in advance for any advice you might have, I appreciate it!


Execution Time statistics are kept for all modules. There is something wrong with the new pipeline, and/or in the Preferences, and/or the Default Input or Default Output directories. It’s possible that our upgrade path didn’t catch an old case. Would you check your:
(1) File > Preferences – all paths legal?
(2) ImageMath – possibly simplest to just delete and recreate from scratch in 2.1.1.
(3) Output – click the “View Output Settings” button at the bottom of your pipeline and double-check the paths in the input/output settings are valid.

If all these fail, then you can also post your 1.0 pipeline here and we can try upgrading it ourselves.


Hello David,

Thank you for your response! I should clarify: when I say the pipeline was “recreated from 1.0 to 2.1” I mean re-wrote the pipeline in 2.1.1, rather than bringing it through as a legacy file. We had thought that might have been the problem as well.

The paths for your points (1) and (3) are all valid. As this is a pipeline we are going to describe in a manuscript, I am not able to share the details here. I realize that doesn’t help you to help me. Other than the three possibilities you’ve raised, is there anything else, even incredibly unlikely, I could check?

Thank you again for your help with this, I’m very grateful.

Hi Alison,

This issue can be “fixed” by doing the following:

  • Go to ExportToSpreadsheet

  • Press the “Press to select measurements” button that goes with measurement export setting.

  • In the dialog box that appears, simply press ‘OK’ to dismiss it. No need to change anything.

  • Save/export the pipeline

  • Re-open it by dragging/dropping it into the pipeline panel, or selecting File > Import > Pipeline from file.

A bug report has been filed here: github.com/CellProfiler/CellPro … ssues/1213