zarrs_n5

N5 support for the zarrs ecosystem.

Limitations

• Read-only
• No partial chunk reading
• "default" chunk mode (i.e. not varlen or object)
• Compression support:
  • N5 core
    • gzip
    • bzip2
    • lz4
    • xz
  • N5 extensions
    • zstd https://github.com/JaneliaSciComp/n5-zstandard
    • blosc https://github.com/saalfeldlab/n5-blosc
    • jpeg is implemented in java but not well documented
      • PRs welcome but I'm unlikely to prioritise this unless a Zarr JPEG codec were stabilised
• The handling of edge chunks is quite inefficient
• Zarr groups must have metadata documents, but N5 groups may not. This may lead to unexpected behaviour when discovering hierarchy structure. This library allows inferring a group with empty attributes when a metadata document is missing.
• N5 hierarchies have a root (metadata contains the "n5" key), but Zarr hierarchies do not; in practice this doesn't matter much

Prior art

• constantinpape/z5: C++/Python reader over a common subset of Zarr and N5
• aschampion/rust-n5: rust implementation of N5
• zarr-developers/zarr-python: Zarr v2's N5 support
• zarr-developers/n5py: python plugins for reading N5 through Zarr v3
• saalfeldlab/n5-zarr: Java implementation reading zarr data through the N5 interface