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Clickup id: 86acd9txj

This PR adds support for OME-Zarr labels. In particular, we now check for the presence of labels in the labels group in both Zarr v2 and v3. If labels are found, they are a) shown in the metadata table, and b) added to Neuroglancer state (when state generation is not disabled in preferences).

Due to current limitations in Neuroglancer's NGFF support (outlined in issues 869 and 870), we need to go back to generating the full Neuroglancer state for the OME-Zarr. Therefore, as part of this PR I revisited the "legacy" processing, updated it to match the new native multichannel loading, and renamed it (the preference is still named "legacy" for backwards compatibility). For now I'm only using this method when there are labels present, and using the default NGFF support otherwise.

I also did some code clean up around typing and other minor issues in the related files.

@JaneliaSciComp/fileglancer @StephanPreibisch

@krokicki krokicki changed the title Support OME-Zarr labels metadata feat: support OME-Zarr labels metadata Dec 14, 2025
@allison-truhlar
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Looks good to me!

@krokicki krokicki merged commit 9ad8551 into main Dec 17, 2025
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@krokicki krokicki deleted the support-segmentations branch December 17, 2025 12:25
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3 participants