Maximum Image Size (and other tech info) for CellProfiler 3?


#1

Maybe my Google Fu is weak, but I’m having trouble finding information about the technical requirements of CellProfiler 3. I’m looking into performing some image analysis (cell counts for histology slides, specifically) for someone, and the files we’re dealing with are apparently 100-300 MB in size. I came across another post that claimed CellProfiler 2 might choke on images bigger than 2000x2000 pixels, but I’d expect CP3 can do better.

Can anyone tell me the maximum image or file size for CP3? Also, for anyone who knows something about its architecture, is CP3 designed to use more CPU processing or GPU processing? I’m trying to figure out if I need to upgrade my GPU from the standard integrated GPU in an old 3rd gen quad core Intel Core I5 processor by getting a discrete graphics card. (The rig in question has 8 GB of DDR3 as well, fwiw.)

Thanks!


#2

Hi,

As far as I know it’s memory limited based on the particular machine and the particular pipeline, but there were no specific improvements made between 2.2 and 3 with respect to memory and large image handling (it’s still on our roadmap though) so while I’ve worked on ones that are 5000x5000, I’ve seen some issues choking (at least on my personal laptop) once you get about 7000x7000. If you want to analyze in CP, is it possible to either a) downsize the images early in the pipeline or b) work on individual tiles rather than the whole tissue section at once?

CP currently doesn’t take much/any advantage of GPUs, though that’s something we’re working on in the future!


#3

That’s great information, thank you. I’m still waiting for access to the files, so unfortunately, I can’t answer your questions yet. I’m new to automated image analysis, and of course, I’m hoping for a solution that involves as few steps as possible. :slight_smile: