Issue after MIP: Images shown empty in napari

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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Issue after MIP: Images shown empty in napari #735

Closed jluethi closed 2 months ago

jluethi commented 2 months ago

Are we missing important metadata after the MIP task? The OME-Zarr image is fine and has the correct metadata. But it's not displayed in napari anymore when loading it as a whole plate.

Also reproducible with example 01: I can load the 3D plate & 3D image. I can load the 2D image. But trying to load the 2D plate finds the channel, but shows a black image:

jluethi commented 2 months ago

The issue turned out to be: Rows & columns are switched in the plate .zattrs metadata and somehow that passed all the tests. I'll be creating a quick fix and deploying it soon.

jluethi commented 2 months ago

If you have an OME-Zarr file that was created by the 1.0.0 or 1.0.1 version of this task and want to fix it without rerunning the workflow, switch the rows & columns in the plate .zattrs file: