search

CellProfiler / CellProfiler-plugins

Community-contributed and experimental CellProfiler modules.
http://plugins.cellprofiler.org/
54 stars 65 forks source link

RunCellPose plugin script leads to not adding a working module #247

Closed MikeLippincott closed 2 months ago

MikeLippincott commented 2 months ago

I was having issues getting RunCellPose to work in an existing pipeline. Upon further investagation with @jenna-tomkinson we found that the runcellpose.py script in the CellProfiler-plugins/active_plugins directory seems to be the culprit.

We found that the pipeline runs with the runcellpose.py script from commit 7bfb39005da6717595b9349f320397b4e2ca50ba but fails to load with the runcellpose.py script from the main branch at the time of opening this issue. Commit f0e4db193c1fc82cc5bd81844cc2ce307e307442.

I am attaching screen shots to show what we see on our end:

Example of a pipeline that works usually with RunCellPose that is no longer working: f0e4db193c1fc82cc5bd81844cc2ce307e307442

Example of a pipeline that works usually with RunCellPose that is working: 7bfb39005da6717595b9349f320397b4e2ca50ba

Thank you for your help and continuous support on CellProfiler and CellProfiler-plugins! :)

jenna-tomkinson commented 2 months ago

To provide some more context, this is using CellProfiler v4.2.6 installed from a conda environment.

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/discrepancies-in-results-from-base-cellpose-vs-plugin-in-cellprofiler/95466/8

bethac07 commented 2 months ago

Sorry, syntax error, fixed now, please pull.

MikeLippincott commented 2 months ago

This fixed the module error! Thank you! :D