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.
