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Fix/ome zarr omero metadata v05#886

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r2dliu wants to merge 5 commits intogoogle:masterfrom
r2dliu:fix/ome-zarr-omero-metadata-v05
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Fix/ome zarr omero metadata v05#886
r2dliu wants to merge 5 commits intogoogle:masterfrom
r2dliu:fix/ome-zarr-omero-metadata-v05

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@r2dliu
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@r2dliu r2dliu commented Feb 19, 2026

I noticed channel names weren't loading correctly from the metadata in my OME-Zarr 0.5 datasets so found a couple of bugs.

  1. Fixed omero metadata load
  2. When metadata loads, parseOmeroChannel fires (was being skipped before since metadata wasn't being read) and crashes on parseRGBColorSpecification. Made more defensive to prevent this

@chrisj
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chrisj commented Feb 27, 2026

Looks good! Could you add/update the zarr tests to demonstrate/prevent regression?

@r2dliu r2dliu force-pushed the fix/ome-zarr-omero-metadata-v05 branch from 6b4ac87 to 8fe6dad Compare March 6, 2026 21:46
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r2dliu commented Mar 6, 2026

I added omero data to both datasets. Validated that removing the fix caused the regression and broke the existing tests

@jbms
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jbms commented Mar 13, 2026

Please also update the generate_ome_zarr.py script rather than manually editing the generated examples.

@r2dliu
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r2dliu commented Mar 17, 2026

Missed that somehow, sorry
Updated the generate_ome_zarr.py script

@fcollman
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@jbms can you we get the workflows enabled for this PR?

@chrisj
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chrisj commented Mar 25, 2026

@jbms should we remove these generated files from vsc and have it run JIT? Or a warning to manually run it if the files are missing?

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4 participants