CellProfiler
RunCellPose Error
Error while processing RunCellpose:
(Worker) FileNotFoundError [Errno 2]
No such file or directory: '/Users/eweisbar/Documents/CPoutput/.cellprofiler_temp/c564a507-17e5-4256-837d-6e1d59892524/img/c564a507-17e5-4256-837d-6e1d59892524_seg.npy
Cellpose built 4.2.6 on OS Sonoma and 4.2.5 built on OS Ventura Latest CellProfiler-plugins commit https://github.com/CellProfiler/CellProfiler-plugins/commit/f5139bf4a0094ec4bac648bf35c10fa910652d42
Run CellPose in Docker, cellprofiler/runcellpose_with_pretrained:0.1
The first image in my run completes but on all subsequent images I get this error.
My output folder does have .cellprofiler_temp in it and it is filling up with HASH/img/ folders with HASH_seg.npy and HASH.tiff files.
I'm guessing it has something to do with Run CellPose in Docker because when I run the same pipeline (in docker) with Run Cellpose in local Python environment then it runs just fine.
This issue has been mentioned on Image.sc Forum. There might be relevant details there:
https://forum.image.sc/t/runcellpose-not-working-with-docker/95013/6
This issue has been mentioned on Image.sc Forum. There might be relevant details there:
https://forum.image.sc/t/running-cellpose-with-cell-profiler-using-docker/96022/2
This issue has been mentioned on Image.sc Forum. There might be relevant details there:
https://forum.image.sc/t/install-and-run-runcellpose-on-cellprofiler/96536/4
Error while processing RunCellpose: (Worker) FileNotFoundError [Errno 2] No such file or directory: '/Users/eweisbar/Documents/CPoutput/.cellprofiler_temp/c564a507-17e5-4256-837d-6e1d59892524/img/c564a507-17e5-4256-837d-6e1d59892524_seg.npyCellpose built 4.2.6 on OS Sonoma and 4.2.5 built on OS Ventura Latest CellProfiler-plugins commit f5139bf
Run CellPose in Docker, cellprofiler/runcellpose_with_pretrained:0.1
The first image in my run completes but on all subsequent images I get this error. My output folder does have
.cellprofiler_tempin it and it is filling up with HASH/img/ folders with HASH_seg.npy and HASH.tiff files.
I am having exactly the same issue. Have you figured out how to solve it? Thank you!
Apparently what happens is that Docker containers ungracefully crash when you exceed the CPU and/or memory usage available for Docker, so no .npy file is created and the module crashes because it doesn't find it.
In general, for the pipeline not to crush, you should run it with number of workers <= number of cores. If the pipeline still crashes, it's likely that container memory usage is higher than allocated memory to Docker. This can be increased within Docker Desktop from Settings > Resources:
