ChatSpatial

MCP server for spatial transcriptomics analysis with 60+ integrated methods

GitHub

ChatSpatial

MCP server for spatial transcriptomics analysis via natural language

Paper MLGenX @ ICLR 2026 CI PyPI Python 3.11+ License: MIT Docs

ChatSpatial Overview

ChatSpatial replaces ad-hoc LLM code generation with schema-enforced orchestration — the LLM selects methods and parameters from a curated registry instead of writing arbitrary code, ensuring reproducible results across sessions and platforms. It exposes 60+ spatial transcriptomics methods as MCP tools that any compatible client can call.

Quick Start

Using Claude Code / Codex / OpenCode? Just paste this:

Install ChatSpatial following https://github.com/cafferychen777/ChatSpatial/blob/main/INSTALLATION.md
Manual installation 
# Install uv (recommended - handles complex dependencies)
curl -LsSf https://astral.sh/uv/install.sh | sh

# Create environment and install
python3 -m venv venv && source venv/bin/activate
uv pip install chatspatial

# Configure (use your venv Python path)
claude mcp add chatspatial /path/to/venv/bin/python -- -m chatspatial server

Works with any MCP-compatible client — not just Claude. Use with OpenCode, Codex, or any client supporting Model Context Protocol. Configure your preferred LLM (Qwen, DeepSeek, Doubao, etc.) as the backend.

See Installation Guide for detailed setup including virtual environments and all MCP clients.

Usage

Talk to ChatSpatial in natural language:

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

Identify spatial domains using SpaGCN

Find spatially variable genes and create a heatmap

Capabilities

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

CategoryMethods
Spatial DomainsSpaGCN, STAGATE, GraphST, BANKSY, Leiden, Louvain
DeconvolutionFlashDeconv, Cell2location, RCTD, DestVI, Stereoscope, SPOTlight, Tangram, CARD
Cell CommunicationLIANA+, CellPhoneDB, CellChat, FastCCC
Cell Type AnnotationTangram, scANVI, CellAssign, mLLMCelltype, scType, SingleR
Differential ExpressionWilcoxon, t-test, Logistic Regression, pyDESeq2
Trajectory & VelocityCellRank, Palantir, DPT, scVelo, VeloVI
Spatial StatisticsMoran's I, Local Moran, Geary's C, Getis-Ord Gi*, Ripley's K, Co-occurrence, Neighborhood Enrichment, Centrality Scores
EnrichmentGSEA, ORA, Enrichr, ssGSEA, Spatial EnrichMap
Spatial GenesSpatialDE, SPARK-X, FlashS
IntegrationHarmony, BBKNN, Scanorama, scVI
OtherCNV Analysis (InferCNVPy, Numbat), Spatial Registration (PASTE, STalign)

Documentation

GuideDescription
InstallationVirtual environment setup, all platforms
Quick Start5-minute first analysis
ExamplesStep-by-step workflows
Methods ReferenceAll 20 tools with parameters
Full DocsComplete reference

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. For example, if you ran spatial domain identification with SpaGCN, cite both ChatSpatial and SpaGCN. Each method's original publication can be found in its documentation or GitHub repository.

Contributing

ChatSpatial is open to contributions! Whether it's bug reports, new analysis methods, documentation improvements, or feature requests — all are welcome. See CONTRIBUTING.md for guidelines.

MIT License · GitHub · Issues

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