When I run CellProfiler 2.0 on a Windows 7 system with 12GB of RAM the program will give a MemoryError whenever it reaches 1GB of RAM usage even when there are still 10GB of RAM available on the system. CellProfiler 2.0 never seems to go above this 1GB level, whereas I can run CellProfiler 1.0 in MATLAB and utilize up to 8GB of RAM on the same computer. Has anybody else run into this problem or been able to use CellProfiler 2.0 in Windows with more than 1GB of RAM? Is there some setting in CellProfiler or in Windows that I need to adjust to allow the program to use more RAM? I also tried CellProfiler 2.0 on a Windows Vista system and ran into the same problem. Can I get around this by running in Linux?
This is a limitation of the current Windows release. We are working on a 64-bit build that we hope to release soon. In the meantime, the easiest way to reduce memory consumption is to keep figure windows closed during analysis (we have some fixes for this that will be in the next beta release, as well). If that’s not sufficient, the ConserveMemory module can be used to free up images that are no longer needed in the pipeline.
The new Beta (r9777) has a 64-bit windows version, and should use less memory when module output windows are displayed, as well.