Multiple image analysis fails on Linux

Hi, we would welcome help how to run CellProfiler2 on Linux. We have CellProfiler running. Can load images (cannot drag and drop). Test mode work just fine. If there is only one single set of images, analysis runs. However, with more images, we constantly have an error message. Thanks in advance for help. Cheers,

Hi Gyula,

Could you post your pipeline along with the error message that you receive so we can take a look?


Hi Mark,

I opened CellProfiler on Linux remotely using a Mac. I was taking some screenshots, some of which I will upload now. The pipeline run just fine the first time when I used a single image set. However, there are a few errors that appear in terminal already at the startup of CellProfiler. The startup in the terminal is in the pictures named “LINUX 1-3”. One of the errors appears to be: Ilastic_pixel_classification is not loaded. Then some error messages are in the files named “Error”. I do not have on this computer the pipline, I only took a screenshot of CP with the pipline loaded. If you need the pipeline, I can get it tomorrow. I hope this helps a bit. Let me know what other information may help resolve this problem.



Your errors relate to Java memory allocation and also possibly too many ‘workers’/threads. I would open CellProfiler menu-> Preferences, scroll down to some of the last settings, and
(1) Increase the “Maximum memory for Java” to > 512 which is the default. Maybe try 2048.
(2) Change the “Maximum number of workers” to say, 8. Your errors say that worker 21 or 22 failed, implying that you have many CPUs and/or cores on your machine, which in principle is fine, but the memory allocation is probably not keeping up with your CPU demands.
(3) Click OK and restart CellProfiler to be sure the settings are saved and applied.

Let us know if that helps.