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.
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 serverWorks 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.
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
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, 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 |
| 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) |
| Guide | Description |
|---|---|
| Installation | Virtual environment setup, all platforms |
| Quick Start | 5-minute first analysis |
| Examples | Step-by-step workflows |
| Methods Reference | All 20 tools with parameters |
| Full Docs | Complete reference |
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.
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.