How much can cell profiler handle?


We upgraded our computers to have 24GB of memory, and we are still having issues processing big files. I’m trying to identify nuclei on an image that is about 8,000 x 5,500. Is there some sort of limit to the number of objects that Cell Profiler can handle at once? It makes it all the way to the end, the finished dialog box even comes up, and then it gets sluggish and gets stuck thinking. The biggest problem is I can’t see the images in the IdentifyPrimaryObject window, and the file that is saved is only the outlines of the objects (I double checked to make sure I told it to overlay on a specific image). While looking at the task manager, only about a third of the memory is being used, and I haven’t received a memory error, it just remains stuck thinking and sometimes I get the text on the top of the window saying “Not Responding.”



Hi Arjuna,

We have an FAQ entry on this issue over here. Let us know if any of these help.


Thanks Mark! I just decided to use a smaller file.