Problem: Cell Profiler gets stuck during analysis

Hi!

I’ve been using Cell Profiler for a while now and it always worked fine. However I wanted to make a more complex analysis (including filtering Objects) and now the program just halts somewhere during analysis. There is no error message; it’s just stuck on the “Load Image” in a random cycle. I’ve tried this several times and it always gets stuck in a different cycle.
The computer it’s running on is a MacPro4,1 with a Quad-Core Intel Xeon 2.66 GHz and 6GB RAM. At first I thought it could be a memory problem, but Cell Profiler only uses approximately 1.8 GB of RAM during this analysis. Any thoughts would be helpful.

Hi,

Could you post your pipeline plus an image so we could take a look? Also, if possible, could you post a screenshot of your terminal/console screen, i.e., the screen that opens with CellProfiler and shows the module-by-module execution times and status as a pipeline is running?

Regards,
-Mark

Hi,

Sorry for the delay, here are the pipeline and the picture. Unfortunately no console window is opened when I run Cell Profiler, so I can’t post a screenshot.

Cheers!








020511_20XgfpCM.cp (12.2 KB)

Hi,

My turn to apologize for the delay. I wonder whether calculating the illumination correction function with “All: First cycle” might be the problem? Even though this option is available, we typically use “All: Across cycles”, use SaveImages to to save it as a .mat file on the last cycle, then use a 2nd pipeline that contains LoadSingleImage to load the illumination correction function and apply it to the image with CorrecIllumApply. Perhaps you can give that a try and see if it solves your problem.
Regards,
-Mark