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@ktsitsi ktsitsi commented Dec 15, 2025

This PR:

  • Removes the pin versions of tifffile and its dependencies zarr, ome-zarr.
  • Fixes the typo issue with Zarr3.
  • Removes the support for both python3.9 and python3.12 at the same time. OME-Zarr API has changed enough to justify this and this will be a breaking change for the users.
  • Support same format Ingestion/Extraction roundtrip. V04 Images will be ingested as such and then extracted back to the same format using a reader_kwargs. Same applies for V05. Until full migration the default is FormatV04 (Zarr<3) for backwards-compatibility.
  • New test image https://uk1s3.embassy.ebi.ac.uk/ebi-ngff-challenge-2024/4ffaeed2-fa70-4907-820f-8a96ef683095.zarr for FormatV05
  • Default compressor for FormatV05 is ZSTD, still no full support from our ome-zarr dependency to pass the compressor and some other metadata keys. Full migration to Zarr3 will require keys like chunks_grid and some others to be migrated as well.

@ktsitsi ktsitsi force-pushed the kt/support-zarr3-in-tiledb-bioimg branch 2 times, most recently from 116b191 to d4c3a45 Compare December 15, 2025 17:11
@ktsitsi ktsitsi force-pushed the kt/support-zarr3-in-tiledb-bioimg branch from d4c3a45 to 710d19e Compare December 15, 2025 17:18
@ktsitsi ktsitsi force-pushed the kt/support-zarr3-in-tiledb-bioimg branch 3 times, most recently from f43e7d5 to f3682db Compare December 16, 2025 19:55
@ktsitsi ktsitsi force-pushed the kt/support-zarr3-in-tiledb-bioimg branch from f3682db to 4bf8cee Compare December 16, 2025 20:13
@ktsitsi ktsitsi changed the title Fixing typo error for Zarr 3 Preliminary support for Zarr 3 Dec 16, 2025
@ktsitsi ktsitsi force-pushed the kt/support-zarr3-in-tiledb-bioimg branch from 0d3c39a to ea7b865 Compare December 16, 2025 20:35
@ktsitsi ktsitsi force-pushed the kt/support-zarr3-in-tiledb-bioimg branch from f78fd42 to 3e12634 Compare December 16, 2025 21:08
@ktsitsi ktsitsi force-pushed the kt/support-zarr3-in-tiledb-bioimg branch from d722d70 to 5bde107 Compare December 17, 2025 14:08
@ktsitsi ktsitsi requested a review from jp-dark December 17, 2025 15:01
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2 participants