zarr¶

The Zarr data format driver provides access to Zarr version 2 and Zarr version 3 arrays, and OME-Zarr multiscale v4.0 and v5.0 arrays.

URL syntax¶

• KVSTORE-URL/|zarr: (auto-detect zarr version)

• KVSTORE-URL/|zarr2: (v2 only)

• KVSTORE-URL/|zarr3: (v3 only)

• KVSTORE-URL/|zarr:additional/path/

• KVSTORE-URL/|zarr2:additional/path/

• KVSTORE-URL/|zarr3:additional/path/

• KVSTORE-URL/|zarr:#dimension_separator=/

• KVSTORE-URL/|zarr2:#dimension_separator=/

Specifying an additional/path/ after the zarr URL scheme is currently equivalent to including it in the 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 #dimension_separator=/ syntax.

The KVSTORE-URL/ must refer to a directory, and the combination of KVSTORE-URL/ and any 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

Auto detection¶

• Zarr v2 is detected automatically based on the presence of the .zarray and .zattrs files.

• Zarr v3 is detected automatically based on the presence of the zarr.json file.