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Zarr, N5 support#3

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clbarnes wants to merge 10 commits into
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Zarr, N5 support#3
clbarnes wants to merge 10 commits into
mainfrom
zarr

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@clbarnes

@clbarnes clbarnes commented Jun 15, 2022

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Not working yet, but unsure whether this should go in at all, as it's counter to the idea of one universal workflow. These files will almost certainly go through another round of processing (alignment, contrast correction etc.) which would be a more appropriate time for such an export.

Other points to consider:

  • Raw header and footer bytes are hex-encoded to fit into JSON metadata. Base64 would be more efficient but possibly less easy to introspect.
  • NestedDirectoryStore by default in zarr, as this plays nicer with some HPC file systems

@clbarnes

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N5 doesn't have the same flexibility as zarr for endianness and array order, which makes the roundtripping a bit more complicated.

@clbarnes

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Tests are extremely heavy on storage and RAM which causes problems.

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