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README.md

zarr data source

The "zarr" data source allows Neuroglancer to directly read zarr format arrays, using the following data source URL syntax:

zarr://FILE_URL, where FILE_URL is a URL to the directory containing the .zarray (v2) or zarr.json (v3) metadata file using any supported file protocol.

Alternatively, FILE_URL may be a URL to the directory containing the .zattrs (v2) or zarr.json (v3) group metadata file that specifies an OME-NGFF multiscale dataset. Multiscale metadata versions 0.4, 0.5-dev and 0.5 are supported.

Supported data types (little and big endian):

  • uint8
  • int8
  • uint16
  • int16
  • uint32
  • int32
  • uint64
  • float32

As an extension, dimension units may be specified using the dimension_units user attribute. For example, to specify that the voxel size is 4x5x30nm for a 3-d array, the following attribute may be set:

{
  "dimension_units": ["4 nm", "5 nm", "30 nm"]
}

Zarr v2

If the zarr array uses / rather than the default of . as the dimension separator in chunk keys, you can either specify the separator as the dimension_separator member in the .zarray metadata file (preferred) or use a data source URL of zarr://FILE_URL?dimension_separator=/.

Supported compressors:

  • blosc
  • gzip
  • null (raw)
  • zlib
  • zstd

Filters are not supported.

Dimension names may be specified using an _ARRAY_DIMENSIONS attribute, as defined by xarray.

Zarr v3

Supported codecs:

  • crc32c (not validated)
  • blosc
  • bytes
  • gzip
  • sharding_indexed
  • transpose
  • zstd