Utilities for accessing N5 data through zarr v3.
Project description
zarr-python-n5
N5 utilities for zarr-python.
- Documentation: https://zarr-python-n5.readthedocs.io
Codecs
N5 Default Codec
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.
Release history Release notifications | RSS feed
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