Code

Imaris import support#57

Code

Merged

akhanf merged 17 commits intomainkhanlab/SPIMprep:mainfrom imariskhanlab/SPIMprep:imarisCopy head branch name to clipboardFeb 3, 2025

+2,262-1,951

Commits

Commits on Jan 13, 2025

• initial (working) version of imaris import

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• refactored, and added new metadata extraction

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• updates to chunking, only copy 1st level data

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• updated to read chunk-by-chunk

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• add print

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• fix issue with lz4 using hdf5plugins

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• update deps to match spimprep-deps

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Commits on Jan 14, 2025

• much more efficient copying with zarr copy()

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• add rechunking

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• refactor to copy channel in separate rule

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Commits on Jan 15, 2025

• enable writing directly to zipstore

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• forgot to bundle with last commit

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Commits on Jan 16, 2025

• separate rules for imaris copy and ome zarr write

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Commits on Jan 30, 2025

• update README

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• add back dryrun samples

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• revert spaces to tabs

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• snakefmt, update container

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