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Summary
#1068 adds image-pyramid generation via ome-zarr-py internals as an alternative to multiscale-spatial-image. After ome/ome-zarr-py#516 lands, we can further align and simplify our implementation.
Our pyramid tests currently permit sizable differences from label pyramids produced by multiscale-spatial-image due to mismatched downscaling:
- multiscale-spatial-image: “nearest” (for labels)
- spatialdata/ome-zarr-py: “resize” (order 0 to preserve label values)
Note: even after the ome-zarr-py PR merges, per-axis scale factors remain unsupported in ome-zarr-py. This should ideally be upstreamed. Until then, we will keep a custom downscaling function, leveraging the new ome-zarr-py APIs introduced by the PR.
Action items
- After deprecate scaler class ome/ome-zarr-py#516 is merged:
- Use “nearest” for labels and align image defaults accordingly.
- Tighten test tolerances (reduce or eliminate fraction_non_equal for i > 0).
- Adopt ome-zarr-py’s 3D downscaling APIs to minimize custom logic.
- Propose upstream support for per-axis scale factors in ome-zarr-py and simplify our code once available. Or choose to maintain this functionality in our code.
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