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Imaris import support #57

Merged
merged 17 commits into from
Feb 3, 2025
Merged

Imaris import support #57

merged 17 commits into from
Feb 3, 2025

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akhanf
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@akhanf akhanf commented Jan 30, 2025

Adds import support for Imaris prestitched files. Uses zarr to read each channel directly from ims (hdf5) to zarr zipstore, then converts those to ome zarr.

This also updates in-place creation of the ome-zarr zipstore (if zipstores are enabled), instead of writing to a DirectoryStore then using 7zip to make it a zipstore.

akhanf and others added 17 commits January 12, 2025 21:56
TODO:
  - get metadata from the ims file
  - make the intermediate zarr another rule perhaps
also testing new spimprep-deps container with this dependency added
Had issues with some of the non-serializable datasets (like metadata
strings) but those don't need to be copied here..
I compared with rechunking at the copy stage, but that was much slower..
better for parallelization
note: need to enable this for non-imaris files too
also, some of the remote storage features may be broken
@akhanf akhanf merged commit 1bc5084 into main Feb 3, 2025
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@akhanf akhanf deleted the imaris branch February 3, 2025 17:58
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