ChatSpatial
ChatSpatial
MCP server for spatial transcriptomics analysis via natural language
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.
ChatSpatial exposes 20 schema-validated MCP tools that orchestrate 65 spatial transcriptomics methods across 15 analytical categories. The tools are the stable natural-language interface; the methods are the analysis backends selected through tool parameters.
Start Here
Install ChatSpatial — Installation Guide for Python/uv setup, or Docker Guide for the GHCR image
Configure your MCP client — Configuration Guide
Run your first analysis — Quick Start
Docker quick start:
docker pull ghcr.io/cafferychen777/chatspatial:v1.2.10Minimal example prompt:
Load /absolute/path/to/spatial_data.h5ad and show me the tissue structureIf 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.
Capabilities
Current coverage includes 65 methods across 15 analytical categories, exposed through 20 MCP tools. Supports 10x Visium, Xenium, Slide-seq v2, MERFISH, seqFISH.
Category | Example methods |
Data Loading & Preprocessing | Scanpy I/O, QC, Normalization, HVG, PCA, Neighbors |
Visualization | Spatial plots, Embedding plots, Gene expression overlays |
Spatial Domain Identification | SpaGCN, STAGATE, GraphST, BANKSY, Leiden, Louvain |
Deconvolution | FlashDeconv, Cell2location, RCTD, DestVI, Stereoscope, SPOTlight, Tangram, CARD |
Cell-Cell Communication | LIANA+, CellPhoneDB, CellChat ( |
Cell Type Annotation | Tangram, scANVI, CellAssign, mLLMCelltype, scType, SingleR |
Differential Expression | Wilcoxon, t-test, Logistic Regression, pyDESeq2 |
Trajectory Inference | CellRank, Palantir, DPT |
RNA Velocity | 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 Analysis | GSEA, ORA, Enrichr, ssGSEA, Spatial EnrichMap |
Spatially Variable Genes | SpatialDE, SPARK-X, FlashS |
Multi-sample Integration | Harmony, BBKNN, Scanorama, scVI |
CNV Analysis | InferCNVPy, Numbat |
Spatial Registration | PASTE, STalign |
Documentation
Guide | Use this when... |
You need to install ChatSpatial in a Python environment | |
You want a reproducible container runtime or local dependency resolution fails | |
You need exact MCP client syntax or the runtime path model | |
ChatSpatial is installed and you want the first successful analysis | |
You need to choose an analysis strategy from a biological question | |
You want copy-pasteable natural-language workflow prompts | |
You need canonical tool names, method names, parameters, and defaults | |
Setup, data loading, or analysis behavior is not working | |
You want the 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.
Maintenance
Latest Blog Posts
MCP directory API
We provide all the information about MCP servers via our MCP API.
curl -X GET 'https://glama.ai/api/mcp/v1/servers/cafferychen777/ChatSpatial'
If you have feedback or need assistance with the MCP directory API, please join our Discord server