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CellProfiler / CellProfiler-plugins

Community-contributed and experimental CellProfiler modules.
http://plugins.cellprofiler.org/
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RunCellPose Error #243

Open ErinWeisbart opened 3 months ago

ErinWeisbart commented 3 months ago 
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.

ErinWeisbart commented 3 months ago

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.

imagesc-bot commented 3 months ago

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

imagesc-bot commented 2 months ago

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

imagesc-bot commented 1 month ago

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

YunxiaoWangwww commented 1 month ago 
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 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_temp in 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!