Cellprofiller not saving or exporting files


Hi. At the end of the analysis, the option “ExportToSpreadSheet” is selected, where files .csv should be exported.
However, no files are saved in the folder selected nor anywhere else in the computer. Am I doing something wrong?


Is ‘Export all measurement types?’ set to ‘No’ by any chance? See here for more details.


Hi. Thanks for the quick reply :slight_smile:
In “Export all mearurements types” the option was “Yes”. So shouldn’t all files be exported?
I changed to “No” and selected the files I wanted to be saved. Still no files saved in the folder.


If it’s set to yes, then you’re right that there should be CSVs created- it’s just the most common cause of that issue, so it was a good first thing to rule out :slight_smile: Definitely set it back to “Yes” before continuing.

Other common causes-

  1. You’ve double checked what folder it should be writing to- ie if you have it set to write to DefaultOutputFolder, you’ve checked what that’s set to that you’re looking in the right place?
  2. Do you have write permissions for the folder that you’re trying to write to?
  3. Are you in TestMode? (You’d be able to tell by the fact that rather than two buttons on the bottom left corner saying ‘Start Test Mode’ and ‘Analyze Images’, you’d have 4-5 saying things like ‘Step’, ‘Run’, ‘Exit Test Mode’). Spreadsheets are not made in Test Mode, only in analysis mode.

If neither of those are the issues, you should upload your pipeline for troubleshooting.


1- the folder is correct
2-yes, I have write permissions in this computer
3-I’m not in test mode. I was running the "Analyze Images"
I’m attaching the pipeline for troubleshooting, if that’s ok.
BestTbrucei.cppipe (17.0 KB)


Hmmm, everything looks configured correctly in ExportToSpreadsheet, so I’m still not sure what the issue might be.

Is it saying that it has completed successfully, or is it returning an error? If the latter, can you post the error message?

The only non-standard thing that I’m seeing is your CalculateStatistics module, which seems to be set up a bit strangely- if you try omitting that, do you get files?


Hi. I do get an error message (Image attached). This error only appear in the end, afterthe window “ExportToSpreadSheet” pops up.
Even if I omit the Calculate Statistics module, and leaving only the Identify Primary, Secondary and Terciary objects, I still get the error and the files are not saved. I have already deleted the images and replace them with new ones, and I still get the same problem.


If you’re getting an error, it’s not surprising that the files aren’t being saved. The error you posted is specific to CalculateStatistics- if you disable or delete that module, what’s the error message you’re getting instead?


Hi. It’s working now. So even if the eye is closed the module will still interfere with the analysis?
Thanks a lot for your help :slight_smile:


The eye being closed just means you won’t see the output window the module generates- it has nothing to do with whether or not the module is being run. If you DO want to stop a module from being run, clicking on the green checkmark next to the module name so that it ‘fades out’ will keep the module from executing during the pipeline.

Glad we got it sorted out for you!