Implementations

Software that represents the abstract data model in memory: its elements, coordinate systems, instances and annotation tables. Which software reads and writes the storage format is listed in Storage format implementations.

Implementations of the data model

Each has its own in-memory format of the whole data model.

• spatialdata: Python (documentation).

• SpatialData: R, Bioconductor.

• SpatialData.js: JavaScript and TypeScript.

Software built on the data model

These packages work with datasets of the data model through the in-memory format of spatialdata:

• spatialdata-io: reads the output of spatial omics technologies into datasets of the data model (documentation).

• spatialdata-plot: static plots (documentation).

• napari-spatialdata: interactive exploration and annotation in napari (documentation).

• Sopa: a technology-invariant pipeline for spatial omics analysis.

• Harpy: spatial transcriptomics and proteomics analysis.

• Celldega: spatial omics analysis and visualization.