Starspace defines a basic, minimal, proof of concept schema for gene or protein expression data containing spatially localized information. Specifically, it:
- Defines a standard schema to describe spots, spatial matrices, and cell regions
- Implements a library that reads and writes files in the defined schema, leveraging the zarr container to ensure scalability.
- To demonstrate the flexibility of the schema, converts data from a variety of published assay types, including Spatial Transcriptomics, CODEX, In-situ Sequencing, MERFISH, osmFISH, and starMAP
- Demonstrates how to visualize and interact with these data using common analysis packages, and convert the formats into loom and anndata objects, for downstream analysis in R and Python.
See the documentation for more information.