ChatSpatial

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 66 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.

The server implements MCP `2026-07-28` through the official Python SDK v2 and

continues to serve `2025-11-25` clients through SDK-managed protocol negotiation.

STDIO remains the secure local default; Streamable HTTP is available for

explicitly configured HTTP deployments.

Start Here

Install `uv` once, then

register ChatSpatial without creating or managing a Python environment:

Codex:

codex mcp add chatspatial -- uvx --from chatspatial chatspatial server

Claude Code:

claude mcp add --scope user chatspatial -- \
  uvx --from chatspatial chatspatial server

`uvx` creates an isolated environment on first launch and reuses its cache on

later launches. Restart the MCP client after adding the server.

The command above installs the standard runtime. To make all 15 composable

Python method families available in the same isolated MCP environment, use:

uvx --from 'chatspatial[full]' chatspatial server

`full` includes CellRank, FastCCC, the maintained spatial-domain and

registration backends, annotation, enrichment, and the other portable Python

families. R bridges, AESTETIK, and rctd-py remain separate because they have

system, platform, or large-runtime requirements. See the installation guide

before enabling those families.

Then:

1. Run your first analysis — Quick Start

2. Choose optional method families or a persistent environment — Installation Guide

3. Configure another MCP client — Configuration Guide

4. Inspect or reproduce the manuscript results — Reproducibility workspace

Docker quick start:

docker pull ghcr.io/cafferychen777/chatspatial:v1.4.0

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.

Capabilities

Current coverage includes 66 methods across 15 analytical categories, exposed through 20 MCP tools. Supports 10x Visium, Xenium, Slide-seq v2, MERFISH, seqFISH.

Documentation

Reproducibility

The manuscript experiment scripts, small aggregate result tables, and

supplementary tables are versioned in `reproducibility/`.

Large datasets, raw provider checkpoints, generated analysis directories, and

manuscript source files are intentionally kept outside Git. The reproducibility

workspace documents both the manuscript-era package baseline and the

current-checkout development workflow so historical evidence is not silently

regenerated with a different ChatSpatial release.

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.