ChatSpatial — Claude Code MCP server for spatial transcriptomics
ChatSpatial lets an MCP client run spatial transcriptomics analyses through schema-defined tools. Use it to explore spatial data without asking a model to invent analysis scripts.
claude mcp add chatspatial -- uvx chatspatialWhat ChatSpatial does
The server exposes 20 MCP tools that cover 67 methods in 13 analytical categories. Available work includes data preparation, spatial plots, domain detection, gene expression analysis, and cell-cell communication. Supported platforms include 10x Visium, Xenium, Slide-seq v2, MERFISH, and seqFISH.
Rather than writing arbitrary code, the model picks a tool and its parameters from a curated registry. This keeps workflows more consistent across sessions and clients. STDIO is the local connection mode; Streamable HTTP requires explicit setup.
For Claude Code, register the server with claude mcp add chatspatial -- uvx chatspatial, then restart the MCP client. Some analysis methods need extra components: SpaGCN, for instance, requires the spatial-domains extra.
What it helps with
- prepare spatial data for analysis
- plot gene expression across spatial coordinates
- identify spatial domains in a tissue sample
- analyze communication between cell types
- compare gene expression across groups
Example prompts for the agent
- Load the spatial dataset and plot a gene's expression across its coordinates.
- Identify spatial domains in this dataset using Leiden.
- Analyze communication between the cell types in this sample.
How to install ChatSpatial
Platform CLI
claude mcp add chatspatial -- uvx chatspatialuvx runs the command named after the package; if the README names another one, use uvx --from chatspatial <command>
Platform CLI
codex mcp add chatspatial -- uvx chatspatialuvx runs the command named after the package; if the README names another one, use uvx --from chatspatial <command>
Config file
{
"mcpServers": {
"chatspatial": {
"command": "uvx",
"args": [
"chatspatial"
]
}
}
}uvx runs the command named after the package; if the README names another one, use uvx --from chatspatial <command>
Config file
{
"servers": {
"chatspatial": {
"type": "stdio",
"command": "uvx",
"args": [
"chatspatial"
]
}
}
}uvx runs the command named after the package; if the README names another one, use uvx --from chatspatial <command>
Platform CLI
gemini mcp add chatspatial uvx chatspatialuvx runs the command named after the package; if the README names another one, use uvx --from chatspatial <command>
Step by step, with commands for each platform: How to add an MCP server to Claude Code, Codex, Cursor, VS Code, Gemini CLI and more
Questions about ChatSpatial
How do I install ChatSpatial in Claude Code?
Run claude mcp add chatspatial -- uvx chatspatial, then restart the MCP client.
What does ChatSpatial do?
It gives an MCP client tools for spatial transcriptomics analysis. The model selects methods and parameters from defined schemas instead of writing free-form analysis scripts.
Which spatial data platforms does ChatSpatial support?
Supported platforms include 10x Visium, Xenium, Slide-seq v2, MERFISH, and seqFISH.
