Examples and validation

Resources for testing an implementation of the storage format.

Example stores

The notebook multiple_elements.ipynb in spatialdata-tutorials (formerly spatialdata-notebooks; revision fabc79a, run with spatialdata 0.7.0a1.dev2 in January 2026) writes an illustrative example store of this version, multiple_elements.zarr. The repository commits its array chunks and Parquet files but not its zarr.json metadata; run the notebook to get the complete store. The store holds 2D elements of every type: a single-scale and a multiscale image, a single-scale and a multiscale labels element, points, circles, polygons and multipolygons, and a table that annotates the labels. The labels element has identity, scale, translation, affine and sequence transformations.

The store does not cover 3D elements, mapAxis transformations, tables that annotate points or shapes, several tables, string instance identifiers or invalid stores. A reader that handles it can still fail on other stores of this version.

JSON schemas

SpatialData.validate (R package, MIT licence, author Hugo Gruson, EMBL) ships JSON schemas for the metadata of raster elements of this version, including their transformations. Porting them into this repository is planned.