CellProfiler 2.1.1 won't start after changing maximum memory


I’ve been having some issues with memory in CellProfiler 2.1.1 (latest revision). The images I was trying to analyze seemed to be too large so I tried changing the maximum amount of memory in Preferences (I’m working on a Mac). After doing that and closing CellProfiler, if I try to open it again, the logo flashes quickly and the program does not open.

I’ve read several other posts and it seems that clearing the config files might solve the issue but I couldn’t open the link that was posted in all of those posts with instructions to do so.

Does this seem like it might solve my issue? If yes, where would I find instructions to clear the CellProfiler config files? If not, is there something else that might help?

Thank you in advance!


Hi Jessie,
Sorry about the link problem, as this is another unfortunate casualty of migration to our new forum. I rewrote the instructions for this here: CellProfiler 2.0 FAQ
I suspect this will help based on others’ experiences. Let us know how it goes!

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Yes, thank you, it worked!

So it seems that it would not start after I tried to increase the memory in Preferences from the default 512mb, closed CellProfiler, and then tried to reopen. Do you have any idea why this might be? I’m trying to analyze some larger images and without increasing the memory, I would usually get an error in NamesAndTypes and if I expanded to see the details in the error message, the last line said “Memory Error.”

I could possibly break up the image into smaller ones but if I could avoid doing that, that would be ideal.

Good - glad that fix worked.

Please note that the memory in the Prefs only affect the Java allocation, and not the standard image processing. If you have a huge number of images, and not simply big individual images, then that Java memory allocation should be increased, but for most cases this won’t help. What will help is either:

The 64-bit processing aspect allows more RAM to be utilized during processing. And we’re pretty confident now in the nightly build, so I’d say give it a shot. But note that pipelines are not backwards-compatible, so you can’t then run any newly created pipelines on an older version of CP. Hope that helps!

Oh okay, I didn’t realize that! Thank you for explaining!

Once I downloaded the nightly build and tried to open it I got a pop-up box that said “CellProfiler Error” and the program would not open. Do you know what this might occur? Will there be a regular 64 bit option for Mac at some point?

Did you try clearing the prefs again?

Yes, just did that and still have the same error. Once the error box comes up, it asks whether to open console or whether to terminate. When I opened the console, it seems that this is the most common error:

3/1/16 3:00:41.317 PM CellProfiler[4225]: Could not find Java JRE compatible with x86_64 architecture

Does this mean that I might not have the correct version of Java installed?

Yes, please see this for some requirements and instructions for getting the Beta or Nightly to run.