Cell Profiler crash


I can’t run cell profiler on my computer.
When I try to run an IdentifyPrimaryObjects in test mode it crashes when it tries to display the result window. If I run the test without displaying the result it runs fine.
Attached I send a crash report.


System Profile:
Model: iMac7,1, BootROM IM71.007A.B03, 2 processors, Intel Core 2 Duo, 2 GHz, 5 GB, SMC 1.20f4
Graphics: ATI Radeon HD 2400 XT, ATI,RadeonHD2400, PCIe, 128 MB
Memory Module: BANK 0/DIMM0, 1 GB, DDR2 SDRAM, 667 MHz
Memory Module: BANK 1/DIMM1, 4 GB, DDR2 SDRAM, 667 MHz
CellProfiler_2015-04-13-120958_a180-mac8.crash.zip (29 KB)


It’s not quite clear from this crash report, but some aspect of Java is the culprit. You can change a couple settings in the preferences and see if it helps. Click CellProfiler menu->Preferences, change these below, and restart CellProfiler:
(1) Maximum memory for Java (MB). It defaults to 512 I believe, so up it to 1024 or 2048.
(2) Maximum number of workers: defaults to total # of CPUs detected on your computer (2), but you could try setting it to 1 and see if it helps.

If those don’t work, some other thoughts:
(1) Is your image list very long? Does it happen with only one small image set loaded?
(2) Disable viewing any other module windows. Or are there many thousands of objects in the IDPrimary window?
(3) Does one of the example pipelines run for you in the Help Window?

Let us know how it goes.

Hi David,

The suggestions you gave me didn’t work. Actually if I set Java (MB) memory to 2048 Cell Profiler doesn’t even start. I had to delete the CellProfilerLocal.cfg file to put it running again.

Regarding your questions:
(1) The image list is 1 image (Tiff, 16bit, 1004x1002, 2MB)
(2) IDPrimary is the only module in the pipeline. There are 15 objects in this picture but Cell Profiler is not even able to display the module window, it crashes before the results are shown. If I disable the view option it doesn’t crash but I’m not able to see the results and optimize the module parameters.
(3) The example pipelines also don’t run.

Thanks for your help,

Hi ricardo,

So even after removing the cfg file, CellProfiler doesn’t run? If not, please try these suggestions carefully: viewtopic.php?f=14&t=3783&p=10952&hilit=CellProfilerLocal.cfg#p109

Did CP ever run on this computer?

If these above don’t work either, what version of Java do you have? At a terminal, type


after renovated cfg file Cell Profiler didn’t work. I already tried the suggestions of the topic you mentioned before I posted this topic. nothing works.

CP never run on this computer. In the beginning I could not even start it up after installing CP 2.1. I had to install CP 2.0 and then 2.1 over it to get it started. Now it starts but can not do anything. The IT people of my institute are also trying to figure out what is going on but since they are not so familiar with CP I thought it was better to ask for help here too.

My java version is:
java version "1.6.0_65"
Java™ SE Runtime Environment (build 1.6.0_65-b14-466.1-11M4716)
Java HotSpot™ 64-Bit Server VM (build 20.65-b04-466.1, mixed mode)


Thanks for the responses and for asking here – hmm, that is odd! I will create a Github issue on our bug tracking system and see if anybody else here can figure this out. Our lead developer is away until next week unfortunately.

Another thing to try is to download and install a “trunk build”, one of our new versions of CP. They are here: github.com/CellProfiler/CellPro … TrunkBuild
I’m not sure why it would work, but it would be instructive if it did. You can also rename the .app when you install, and it won’t overwrite the standard “release” version (even though the release doesn’t work for you anyway!).


same problem with the “trunk build”.

Not an answer yet (but a hint).
FYI: Github issue here: github.com/CellProfiler/CellPro … ssues/1342


Hmm, the error indicates a problem with a font you’re using. Our lead developer says:

I know you said you did this, but can you again:
(1) Uninstall CP (all versions!)
(2) Delete the file ~/Library/Preferences/CellProfilerLocal.cfg
(3) Empty your Mac Trash
(4) Re-install CP and try it out.


I did the uninstall, delete .cfg, empty trash, reinstall again, and still doesn’t work. And I didn’t change any default font or anything in 2.0.

With the IT people from the institute we checked if there is any problem with the memory but everything appears to be fine.

Thanks a lot for the help, any more ideas?

Hmm, darn. Can you upload the Console crash log again, just so we can crosscheck it with the last one?

sure, here it goes.
CellProfiler_2015-04-21-162556_a180-mac8.crash.zip (29.8 KB)


Can you please try a new trunk build here? Our lead engineer says that upgrading our freetype to 2.5.5 (a font library) might help, which he has done.


Tried it and same problem…

here goes the crash log

Thanks a lot for your time on this!
CellProfiler_2015-04-29-104133_a180-mac8.crash.zip (31.1 KB)