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Fix: update _auto_chunking in zarr tile writer to not chunk in Z#723

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jdeschamps merged 4 commits into
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jd/fix/zarr_z_chunk
Feb 3, 2026
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Fix: update _auto_chunking in zarr tile writer to not chunk in Z#723
jdeschamps merged 4 commits into
mainfrom
jd/fix/zarr_z_chunk

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@jdeschamps jdeschamps commented Feb 3, 2026

Description

3D microscopy images are most often accessed on a slice-by-slice basis, so when saving to zarr we should avoid making chunks that are min(128, z_dim) since extracting any slice will require loading the entire data into memory...

This PR treats Z as the other dimensions when no chunking is given (chunking along Z is 1).

Closes #658

@jdeschamps jdeschamps marked this pull request as ready for review February 3, 2026 14:26
@jdeschamps jdeschamps requested a review from a team February 3, 2026 14:27
@jdeschamps jdeschamps removed the request for review from a team February 3, 2026 14:58
@jdeschamps jdeschamps requested a review from a team February 3, 2026 15:26
@jdeschamps jdeschamps merged commit b6182b0 into main Feb 3, 2026
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@jdeschamps jdeschamps deleted the jd/fix/zarr_z_chunk branch February 3, 2026 20:01
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Zarr tile prediction writer: chunks along Z

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