Takes forever for CellProfiler 2 to analyze even 1 image

I have been using Cell Profiler for quite a while and have been very happy with it. Thank you for developing this software! It makes my life easier!

But I just changed a new laptop which runs windows 8 with a 64-bit operating system. Somehow it takes forever now for cellprofiler 2 to analyze images. I tried test mode, and it worked just fine. I also downloaded some pipeline examples (ExamplePercentPositive pipeline and ExampleColocalization pipeline) from your website and had the same problem. They all worked fine under test mode, but could never finish image analyzing under the “true” image analyzing mode. There were no error messages, but cellprofiler was just keeping on running. The longest time I waited was 30 minutes, but it could not even finish 1 image.

Would you please help me with this problem? Please let me know if you need any other information.

Thank you very much!


HI Sue,
Let’s start with the simplest solution: It may be your anti-virus software. Assuming so, would you temporarily turn off your anti-virus scanning (I suggest disconnecting from the network too) and re-run Cellprofiler?
It may very well be something else, just guessing.

Hi David,

Thank you so much for your quick response. I just did as you suggested. Unfortunately, the problem persists even after I turned the anti-virus off. Any other thoughts?

Thank you!


Sorry for the slow response - any progress on this speed issue? It sounds quite unusual.

Hi Sue,

Have you checked the resolution of the images you used on your PCs? Do they have the same sizes?


Just following up on this thread. Any solutions found? I’m currently experiencing the same issue.