I have been using CellProfiler 3.0.0 on Mac. I have a simple pipeline that identifies nuclei from HCS Cellmask/Hoechst staining in IDPrimaryObjects, propagates that out to the cell body in IDSecondaryObjects, then quantifies intensities from several channels in each objects. Before updating to Mac OS Mojave (10.14) from High Sierra (10.13) I did not have any issues. Now, when I run test mode with the eyeball on so I can check the segmentation, I get an error message that reads:
Error while processing IdentifyPrimaryObjects: C++ assertion “cgContext” failed at ./src/osx/window_osx.cpp(1631) in MacPaintBorders(): Do you want to stop processing?
Meanwhile, the IDPrimaryObjects window pops up, but with a doubled tool bar. As soon as I drag the window somewhere else, the second toolbar disappears.
The window functions normally otherwise, but regardless of whether I choose cancel or continue, test mode quits out and I cannot continue. On some googling, I’ve seen people can resolve this error by turning off visualization. This does work for me, but it kind of defeats the purpose of test mode if I can’t visualize the results. The actual image analysis seems to run fine.
I had also seen elsewhere that this problem was resolved in 3.1.5. Indeed, test mode works fine in the new version of the software, which is great. However, analysis fails as I have been having the same problem as here Index is out of bounds error!, where I get several errors during analysis that object indices are out of bounds. The solution to this seems to be to use an older version of CP…which I can’t use test mode in. It’s oddly circular…
Is there a better solution to this than me having to use 3.1.5 to test analysis then manually re-enter the pipeline into 3.0.0 to do the actual run (manually since there appear to be version incompatibilities for importing a pipeline or project made in 3.1.5 into 3.0.0 directly…).