Problems about strange interface when using Cellprofiler

Recently I’m analyzing the results of Oil Red O Staining using the Cellprofiler. I tested it by the example provided. However, when it came to the Untangle, correct, and straighten worm clusters step, there was something wrong with my interface and I can’t find solution by clicking help. The problems are listed below.


Can you tell me what version of CP and what OS version you’re using? Are you making the pipeline from scratch or is this an example pipeline, and if so which exact one?

I don’t run Mac but on PC I’ve noticed some of the example pipelines that are SUPER old (which many of the worm examples are) EditObjectsManually behaves poorly or won’t start at all- between 2.0 and 2.1/2.2 it was upgraded a lot so it works much better overall but some of the backwards compatibility was lost. For me creating a new “EditObjectsManually” step with the same settings as the included one and then deleting the original fixes it. Can you try that and let me know whether or not it fixes your issue?

I tried to create a new “EditObjectsManually” step as you said but the problems are still there – no colored outlines or [done] button ( but I can use other buttons on the interface after clicking the mouse with [control] this time).

It is Mac ( OS X EI Capitan, Version 10.11 ) and the example pipeline ( CellProfiler 2.1 pipeline: Pipeline4_ManuallyCorrectStraighten.cppipe ) I’am using now. I’m not sure which part is wrong.

Thanks for your help.

I think the missing “Done” button may be a window width thing- can you try manually dragging the window wider and see if it appears?

I tried but couldn’t replicate this error on my PC nor find anything about it in the forum or the github; I can try to get my hands on a Mac in the next couple of days but it sounds like this may be a very specific thing so I’m not sure I can replicate it (and therefore fix it) even if I do. Things I’d recommend in the meantime:
-Upgrade from 2.1 to 2.2 or 2.3. This may be a bug that’s already been fixed.
-Make sure your Worm objects were created correctly in the first pipeline- one explanation for there being no outlines is that there aren’t any objects to display. Probably the easiest way to do this is to go back to the Images module and double clicking on one of the worm_objects.tif files; CP should pop up a window that shows the file. If it’s all black, then that’s the reason you’re not seeing any outlines.
-If this is super urgent, either create a windows VM on your machine or find a lab computer that runs Windows or a different Mac OS and see if that works better for you.

  • The version of the Cellprofiler I’m using is 2.2
  • I checked the worm_objects.tif files and found out they were all black. But I used the example pipeline-1, example images and DefaultWormModel downloaded at the website to run the program. I didn’t change anything (except the training set file location). Thus I couldn’t figure out what is wrong with my pipeline-1.
  • Also I used the lab computer that runs Windows and the same problem happens ( the worm_objects.tif files are all black).

Thanks for your help.

If the worm_objects.tif are all black (when opened in CellProfiler or in ImageJ and contrast adjusted, it’ll appear black no matter what in most non-scientific image programs) then the problem is definitely in pipeline 1.

When you look at the second IdentifyPrimaryObjects in pipeline 1, are objects getting created? What about in the UntangleWorms? If those both look fine, double check the settings on the SaveImages module that makes the worm_objects.tif (the last one). If all else fails, delete the copies of all the downloaded files and download new ones, maybe something got corrupted or accidentally overwritten.

Beyond that, I’m not sure what to do without being able to physically operate your computer- that pipeline generates the worm_objects.tif correctly in CellProfiler2.2 on my PC. If you want to play with pipeline4, I can zip and email you the worm_objects files.



I tried all the methods you provided and all of them failed. Please sent me the worm_objects files.


Shiyi Zhou

The object files are attached below. Good luck! (2.0 MB)