Running pipelines in parallel on Cell Profiler

IHC_Cell_Counts.cpproj (418.8 KB)

Hi! I need to run several sets of images through different pipelines on cell profiler, which are essentially the same as the one I have posted, only with little bits tweaked for each one. I am wondering if I can set up several pipelines in parallel, which will all run different sets of images? For example: 5 images in sample A run with pipeline A and a different 5 images in sample B run with pipeline B etc.

Hi @ABarry,

Generally you’ll need to run these separately. You can run multiple instances of CellProfiler at the same time, but you should take care to not be running more worker processes in total than the number of physical cores your system has (otherwise the instances will compete for resources).

No problem, thank you for the help!