User interface corruption in CP 2.1


I encounter problems with the user interface of version 2.1.
After using the test mode for a while, user interface parts fall off and become unreadable (see screenshot appendix). The program is then hard to use and must be restarted. It appears in both the beta version of 13 November as the 16 December release.

I’m using Windows 7 Professional SP1 on a 64 -bit Intel Xenon CPU -1245 V2 @ 3,40 GHz, 20.0 GB of RAM memory.
Do others have this problem ?


Thanks for your report, Peter. I’m trying to recreate this and I’m not having any success yet. Do you see any unusual log output in the console window? Are you rerunning the same module over and over or are you running through the entire pipeline? Stepping or running? If you’re editing one module (e.g. trying to get the settings right for IdentifyPrimaryObjects), which module and what are you doing?

It’s really good for you to have reported this - I’ll keep trying to recreate this on my own, but if you have steps that let me reproduce the problem it would help me a lot.


Hi Lee, thanks you for your fast responce!

To reproduce the GUI problems I now used one of your CP examples: Yeast colony classification and converted it to a CP2.1 version.

  • When I used the stepmode and opened and closed the images output: nothing happened./*]
  • I changed settings during the step mode and rerun the same module: nothing happened.
  • I zoomed in and out an output image ImageMath moduie), enlarged the window several times and then I got problems. The Log window appeared to be above the normal window (see attaced file). But it was like a screenshot. When I tried to get the contents of the real Log window it totally crashed. I attached all files I used.


ExampleYeastColonies_BT 1a.cpproj (385 KB)

Peter, I’ve found the problem and it’s THANK YOU! This would have gone out in the release if you hadn’t reported it and the problem would have been magnified. I don’t like getting bug reports, if you know what I mean, but considering the alternative, a well documented bug report and a persistent but cheerful user, those are the sorts of things that keep us on track.

Happy new year - release will be publicly available shortly after Jan 1.

The details would make your eyes glaze over, if you care, you can follow them at


This issue has been resolved in CellProfiler 2.1 and later, new releases of which can now be downloaded from