Note
This package is under active development.
Tools for Zarr Vectors Data
zarr-vectors-py is a Python package for reading, writing, and managing large-scale vector geometry data in the zarr vectors format — a chunked, cloud-native format built on Zarr v3 for multiscale points, lines, streamlines, graphs, skeletons, and meshes.
The package supports supervoxel-level spatial binning with separated chunk and bin sizes, per-level object sparsity for balanced multi-resolution pyramids, and OME-Zarr-compatible multiscale metadata.
Aligned to the Zarr Vectors specification by Forrest Collman, Allen Institute for Brain Sciences Link to specification GitHub
link to readthedocs: https://zarr-vectors-py.readthedocs.io/en/latest
pip install zarr-vectorsdataset.zarrvectors/
├── .zattrs # root metadata: SID, CRS, conventions, base_bin_shape
├── 0/ # full resolution (bin_ratio = 1,1,1)
│ ├── vertices/ # spatial positions (ragged per bin)
│ ├── vertex_fragments/ # per-chunk fragment index (byte ranges)
│ ├── links/ # connectivity (edges, faces, parents)
│ ├── attributes/ # per-vertex data
│ │ ├── intensity/
│ │ └── gene_expression/
│ ├── object_index/ # object ID → (chunk, fragment) mapping
│ ├── object_attributes/ # per-object metadata
│ ├── groupings/ # group ID → [object IDs]
│ ├── groupings_attributes/ # per-group metadata
│ └── cross_chunk_links/ # connectivity across chunk boundaries
├── 1/ # coarsened (bin_ratio, object_sparsity in .zattrs)
│ └── [same arrays]
├── parametric/ # algebraic objects (planes, spheres)
│ ├── objects/
│ └── object_attributes/
└── metadata.json