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zarr

The Zarr :ref:`data format driver<data-formats>` provides access to Zarr version 2 and Zarr version 3 arrays, and OME-Zarr multiscale v4.0 and v5.0 arrays.

URL syntax

Specifying an :file:`{additional/path/}` after the zarr URL scheme is currently equivalent to including it in the :file:`{KVSTORE-URL/}`, but may be preferred for distinguishing the root of a zarr hierarchy from the path within it, and may be necessary to support group-level storage transformers which may be added to the specification in the future.

For zarr v2 only, if a dimension separator of / is used but not indicated in the metadata, it must be specified using the :file:`#dimension_separator=/` syntax.

The :file:`{KVSTORE-URL/}` must refer to a directory, and the combination of :file:`{KVSTORE-URL/}` and any :file:`{additional/path/}` after the zarr URL scheme must specify either a Zarr array or a Zarr group with OME-Zarr multiscale metadata.

Data types

Supported data types:

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

Coordinate spaces

Units specified by OME-Zarr multiscale metadata are supported.

Additionally, as a Neuroglancer-specific 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 features

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 features

Supported codecs:

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

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