Starspace

Starspace defines a basic, minimal, proof of concept schema for gene or protein expression data containing spatially localized information. This project consists of the following:

1. Defines a standard schema to describe spots, spatial matrices, and cell regions
2. Implements a library that reads and writes files in the defined schema, leveraging the zarr container to ensure scalability.
3. 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
4. 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.

Contents

• Schema
  • Spots
  • Regions
  • Matrix
• Working with Data
• Matrix
  • Serialization options
  • Extracting column or row metadata
• Spots
• Regions
• Conversion Scripts
• Analysis Examples
• Contributing