zarr-n5 0.2.0

Utilities for accessing N5 data through zarr v3.

zarr-python-n5

N5 utilities for zarr-python.

• Documentation: https://zarr-python-n5.readthedocs.io

Codecs

N5 Default Codec

As described here.

Only whole-chunk reading is supported.

N5 Compressor support

N5 compressor	Supported	Zarr bytes-to-bytes codec	Notes
raw	yes	n/a	Equivalent to omitted bytes-to-bytes codec
blosc	yes	blosc
gzip	yes	gzip
zstd	yes	zstd
lz4	no		Incompatible codecs
xz	no		No equivalent Zarr codec
jpeg	no		Needs N5 documentation, Zarr codec
bzip2	no		No equivalent Zarr codec

Stores

N5WrapperStore allows reading N5 data with DEFAULT-mode blocks through any Zarr store by converting metadata on the fly. By default, this does not replicate the N5 behaviour of inferring an empty group where a metadata document does not exist. To achieve this, wrap it in the provided ImplicitGroupWrapperStore.

Tools

This package provides n5tozarr, a command-line interface for converting N5 data to Zarr in-place. The N5 metadata are left untouched, and no chunk data is altered, moved, or copied. A zarr.json file is simply added to each Zarr node.

N5 attributes are extracted and added to the zarr.json attributes.

The full N5 metadata document is accessible inside the zarr.json in an attribute called _n5. If a directory/prefix was empty and the existence of an N5 group was inferred, the zarr.json attribute _implicit will be true.

Contributing

Use uv for project management.

Use just for common development tasks.