ChatSpatial

MCP server for spatial transcriptomics analysis via natural language

Paper MLGenX @ ICLR 2026 ENAR 2026 IBC 2026 PyPI Python 3.11-3.13 License: MIT Docs

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.

Start Here

Install ChatSpatial — Installation Guide
Configure your MCP client — Configuration Guide
Run your first analysis — Quick Start

Minimal example prompt:

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

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

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)

Documentation

Guide	Owns
Installation	Environment setup, package install, platform notes
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

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.

Contributing

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

MIT License · GitHub · Issues

ChatSpatial

ChatSpatial

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Capabilities

Documentation

Citation

Contributing

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