ChatSpatial

MCP server for spatial transcriptomics analysis via natural language.

Analyze your spatial data by chatting with Claude. No coding required.

60+ methods across 15 analysis categories. Supports 10x Visium, Xenium, Slide-seq, MERFISH, and more.

Getting Started

Installation

Set up the environment

Install ChatSpatial and prepare your Python environment.

Installation
Quick Start

Your first analysis

Load data and start analyzing with natural language.

Quick Start
Concepts

Understand the methods

When to use which method and why.

Concepts
Examples

See what’s possible

Natural language commands for every analysis type.

Examples

Reference

Methods Reference

All 20 MCP tools with parameters

Methods Reference
Configuration

MCP client configuration

Configuration Guide
Data Management

External dataset registry and fetch workflow

Data Management
Contributing

Contributor entry point for docs and code changes

Contributing

Support