Cell-GPS documentation

Cell-GPS is the reference implementation for Cophenetic Spatial Topology Embedding (COSTE), a framework for analyzing multiscale tissue architecture in spatial omics data. These docs cover both the installable Python package and the manuscript companion code.

Contents:

• Cell-GPS
  • Package names
  • Key features
  • Installation
  • Reviewer note
• Manuscript Overview
  • Preprint
  • What the Manuscript Shows
  • Repository Companion Code
  • Citation
• Reproducing Manuscript Code
  • Quick Start
  • Data Availability and Paths
  • Recommended Reading Order
  • Core Package Entry Points
  • Reproducibility Status
  • Validation
• Figure and Table Code
  • Main Figures
  • Supplementary Figures
  • Supplementary Tables
  • Detailed Provenance
• Reviewer Guide
  • Package naming
  • Suggested reading order
  • Repository map
  • Minimal install
  • Manuscript validation scope
  • Input contract
  • Reproducibility note
• Installation
  • From PyPI
  • From conda-forge
  • From GitHub
  • For local inspection
  • Requirements
  • Optional extras
  • Related Packages
• Usage
  • From a coordinate table
  • From Xenium output
  • Large datasets
• API reference
  • Core COSTE and StructureMap functions
  • Topology extensions
  • Preprocessing and input helpers
  • Plotting
• Contributing
  • Types of Contributions
  • Get Started!
  • Pull Request Guidelines
  • Tips
  • Deploying
  • Code of Conduct
• Authors
  • Project and corresponding authors
  • Code repository maintainers
• History
  • Unreleased
  • 0.0.6 (2026-05-30)
  • 0.0.5 (2026-05-30)
  • 0.0.2 (2026-04-02)
  • 0.1.0 (2025-01-03)

Indices and tables

• Index

• Module Index

• Search Page