Install¶

pip install zarr-vectors-tools
zvtools --version          # prints e.g. zvtools (zarr-vectors-tools 0.3.0)

This needs Python 3.11 or newer. It installs the zvtools command and the core package, zarr-vectors.

Optional extras¶

The base install converts CSV point tables (csv, table), line CSVs (lines), edge-list CSVs (edgelist), SWC, OBJ and STL. Other formats and features need an extra:

pip install "zarr-vectors-tools[trk]"         # one extra
pip install "zarr-vectors-tools[trk,h5ad]"    # several
pip install "zarr-vectors-tools[all]"         # every extra except gpu

Extra	Enables	Installs
`trk`	TRK and TCK ingest; TRK export	nibabel
`trx`	TRX ingest and export	trx-python
`streamlines`	`trk` and `trx` together	nibabel, trx-python
`surfaces`	GIFTI and FreeSurfer ingest; GIFTI export; CIFTI through `zvtools attach`	nibabel
`las`	LAS and LAZ ingest	laspy, lazrs
`ply`	PLY ingest and export	plyfile
`h5ad`	AnnData `.h5ad` ingest and export	anndata
`graph`	GraphML ingest; per-node metrics in Python `ingest_edgelist`	networkx
`points-enrichment`	`--knn-distance-k` on point ingest	scipy
`mesh`	mesh decimation for mesh pyramids	pyfqmr, scipy
`precomputed`	Neuroglancer precomputed skeleton and mesh ingest; precomputed export	cloud-volume, mapbuffer, cloud-files
`parallel`	`--workers-backend dask`	dask[distributed]
`recipes`	YAML recipes for `zvtools run`	pyyaml
`gpu`	GPU CSV reading in Python `ingest_edgelist(..., use_cudf=True)`. Install RAPIDS first	cudf
`all`	every extra above except `gpu`

If an extra is missing, the command stops with an error that names it, e.g. laspy is required for LAS/LAZ ingest. Install with: pip install 'zarr-vectors-tools[las]'.

The core package¶

This package builds on zarr-vectors, which defines the Zarr Vectors format and reads and writes stores. It needs a core that writes Zarr Vectors format 0.9 and has the zarr_vectors.building API; zarr-vectors 0.9.2 on PyPI has both, and pip installs it for you. If an older zarr-vectors is already installed, run pip install -U zarr-vectors.

Install from GitHub¶

# unreleased changes
pip install "git+https://github.com/AllenInstitute/zarr-vectors-tools"
pip install "zarr-vectors-tools[trk] @ git+https://github.com/AllenInstitute/zarr-vectors-tools"
pip install "git+https://github.com/AllenInstitute/zarr-vectors-py"   # core, if you need its latest changes