fractal-analytics-platform / fractal-tasks-core

Main tasks for the Fractal analytics platform
https://fractal-analytics-platform.github.io/fractal-tasks-core/
BSD 3-Clause "New" or "Revised" License
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Fix for yx images in Cellpose task #789

Closed jluethi closed 4 months ago

jluethi commented 4 months ago

Closes #788

This PR contains a small special case handling to enable the Cellpose task to process yx images. Given the current generalizations we've already made, only the channel selection during dask image loading and the metadata updating needed minor adjustment.

With this PR, there are 2 additional checks for those 2 parts that then handle the yx case. It's working well in my local tests on yx data, but we don't currently have yx testing data available.

A cleaner implementation and better testing will come with the ngio work here, I'll already merge this now to unblock user workflows though.

Checklist before merging

github-actions[bot] commented 4 months ago

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  fractal_tasks_core/tasks
  cellpose_segmentation.py 320-322, 380
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