I’ve started to do medium-scale image analysis on my Mac (>50 images at a time), but I’ve encountered problems with CellProfiler crashing after 20-35 cycles of image analysis with an “Out of Memory” error. I’ve modified the pipeline to include SpeedUpCellProfiler at the end, and set it to clear the entire memory each time, but that doesn’t seem to help at all.
My computer has 2 GB of RAM, and if I watch the memory usage over time, I see I have about 1.2 GB free before I start CellProfiler. When I start the image analysis it goes down to around 800 MB, and then oscillates each cycle ending at a lower number until it finally reaches 0 MB and CellProfiler crashes. I’ve pasted the error code and my pipeline file below.
I’m using the latest Devloper’s version (7098) of MATLAB, and don’t have any windows displayed during the image processing to reduce memory usage.
Any ideas how I can fix this?
There was a problem running the image analysis. Sorry, it is unclear what the problem is. It would be wise to close the entire CellProfiler program in case something strange has happened to the settings. The output file may be unreliable as well. Matlab says the error is: Out of memory. Type HELP MEMORY for your options. in the OverlayOutlines module, which is module #09 in the pipeline.
OverlayOutlines in /Users/Chris/Documents/MATLAB/CellProfiler/Modules/OverlayOutlines.m (138)
AnalyzeImagesButton_Callback in /Users/Chris/Documents/MATLAB/CellProfiler/CellProfiler.m (4497)
gui_mainfcn in /Users/Chris/Documents/MATLAB/CellProfiler/CellProfiler.m (6257)
CellProfiler in /Users/Chris/Documents/MATLAB/CellProfiler/CellProfiler.m (55)
NucleiPIPE.mat (1.74 KB)