CorrectIlluminationCalculate and LoadImages bugs


I’ve run into a bug in CorrectIlluminationCalculate and LoadImages which has reared its ugly head when trying to analyse a large set of images (1536x2 16-bit TIF images). The problem is that neither CorrectIlluminationCalculate nor LoadImages seem to release file handles when they have finished loading images. This results in a “Too many files open” error and the analysis crashing after a while. I’ve had a look at the processes using “Process Explorer” under Windows XP, and it is obvious that Cellprofiler just creates more and more file handles until it hit the ceiling of 512 (minus STDERR, STDIN, STDOUT) open file handles allowed per process. LoadImages even creates two file handles per opened image for some reason. The use of ConserveMemory does not remedy the problem as it only seems to release the images from memory, not the file handles.

I’m using Cellprofiler version 11248.

Could you guys please have a look into this, as it is preventing me from running my analysis?


HI Karl,

This sounds like an issue we encountered previously with .flex files. If you’re willing, could you try running our latest trunk build (note the caveats therein) and see if it solves your problem?