ChatSpatial replaces ad-hoc LLM code generation with schema-enforced orchestration. Instead of generating arbitrary scripts, the LLM selects tools and parameters from a curated registry, making spatial transcriptomics workflows more reproducible across sessions and clients.

It exposes 60+ spatial transcriptomics methods as MCP tools, so any MCP-compatible client can analyze data through natural language.

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Start Here

1. Install ChatSpatial — Installation Guide for Python/uv setup, or Docker Guide for the GHCR image
2. Configure your MCP client — Configuration Guide
3. Run your first analysis — Quick Start

Docker quick start:

docker pull ghcr.io/cafferychen777/chatspatial:latest

Minimal example prompt:

Load /absolute/path/to/spatial_data.h5ad and show me the tissue structure

If you use Docker, mount host data to /data and prompt with the container path, for example /data/spatial_data.h5ad.

ChatSpatial works with any MCP-compatible client — Claude Code, Claude Desktop, Codex, OpenCode, and other MCP-capable tools.

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Capabilities

60+ methods across 11 categories. Supports 10x Visium, Xenium, Slide-seq v2, MERFISH, seqFISH.

Category	Methods
Spatial Domains	SpaGCN, STAGATE, GraphST, BANKSY, Leiden, Louvain
Deconvolution	FlashDeconv, Cell2location, RCTD, DestVI, Stereoscope, SPOTlight, Tangram, CARD
Cell Communication	LIANA+, CellPhoneDB, CellChat (cellchat_r), FastCCC
Cell Type Annotation	Tangram, scANVI, CellAssign, mLLMCelltype, scType, SingleR
Differential Expression	Wilcoxon, t-test, Logistic Regression, pyDESeq2
Trajectory & Velocity	CellRank, Palantir, DPT, scVelo, VeloVI
Spatial Statistics	Moran's I, Local Moran, Geary's C, Getis-Ord Gi*, Ripley's K, Co-occurrence, Neighborhood Enrichment, Centrality Scores, Local Join Count, Network Properties
Enrichment	GSEA, ORA, Enrichr, ssGSEA, Spatial EnrichMap
Spatial Genes	SpatialDE, SPARK-X, FlashS
Integration	Harmony, BBKNN, Scanorama, scVI
Other	CNV Analysis (InferCNVPy, Numbat), Spatial Registration (PASTE, STalign)

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Documentation

Guide	Owns
Installation	Environment setup, package install, platform notes
Docker	GHCR image, volume mounts, and container-backed MCP setup
Quick Start	First successful analysis after setup
Concepts	Method selection and analysis reasoning
Examples	Prompt recipes and workflow examples
Configuration	Exact MCP client configuration syntax
Troubleshooting	Symptom → fix guidance
Methods Reference	Canonical tool parameters and defaults
Full Docs	Complete documentation site

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Citation

If you use ChatSpatial in your research, please cite:

@article{Yang2026.02.26.708361,
  author = {Yang, Chen and Zhang, Xianyang and Chen, Jun},
  title = {ChatSpatial: Schema-Enforced Agentic Orchestration for Reproducible and Cross-Platform Spatial Transcriptomics},
  elocation-id = {2026.02.26.708361},
  year = {2026},
  doi = {10.64898/2026.02.26.708361},
  publisher = {Cold Spring Harbor Laboratory},
  URL = {https://www.biorxiv.org/content/early/2026/03/01/2026.02.26.708361},
  journal = {bioRxiv}
}

ChatSpatial orchestrates many excellent third-party methods. Please also cite the original tools your analysis used.

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Contributing

Documentation improvements, bug reports, and new analysis methods are all welcome. See CONTRIBUTING.md.