ChatSpatial Genomics
Natural language-driven spatial transcriptomics analysis via MCP. Integrates 60+ methods for preprocessing, visualization, spatial statistics, cell communication, deconvolution, and trajectory analysis.
What is ChatSpatial Genomics?
ChatSpatial Genomics is a Model Context Protocol (MCP) server that allows AI assistants like Claude, Cursor, and VS Code to natural language-driven spatial transcriptomics analysis via mcp. integrates 60+ methods for preprocessing, visualization, spatial statistics, cell communication, deconvolution, and trajectory analysi...
Natural language-driven spatial transcriptomics analysis via MCP. Integrates 60+ methods for preprocessing, visualization, spatial statistics, cell communication, deconvolution, and trajectory analysis.
This server falls under the Data Science & ML category on MCPgee, the world's largest MCP server directory with 33,000+ servers.
Features
- Natural language-driven spatial transcriptomics analysis via
Use Cases
Maintainer
Works with
Installation
PIP
pip install chatspatialManual Installation
pip install chatspatialConfiguration
Configuration Details
claude_desktop_config.json
Performance
Response Metrics
Resource Usage
How to Set Up and Use ChatSpatial Genomics
ChatSpatial is a Python MCP server that brings natural language control to spatial transcriptomics analysis, connecting AI assistants like Claude to a suite of 65+ analytical methods spanning 15 biological categories. It supports major spatial platforms including 10x Visium, Xenium, Slide-seq v2, MERFISH, and seqFISH, and exposes 20 schema-validated MCP tools for workflows ranging from data loading and quality control to cell-cell communication, deconvolution, trajectory inference, and CNV analysis. Computational biologists and bioinformaticians use it to run complex multi-step analyses through plain English prompts rather than writing code.
Prerequisites
- Python 3.11, 3.12, or 3.13 installed
- pip or uv package manager
- Spatial transcriptomics data in .h5ad (AnnData) format
- An MCP-compatible client such as Claude Desktop or Claude Code
- Sufficient RAM for loading spatial datasets (16 GB+ recommended for large Visium datasets)
Install ChatSpatial from PyPI
Install the chatspatial package using pip. This pulls in all analytical dependencies including scanpy, squidpy, and spatial method libraries.
pip install chatspatialVerify the installation
Confirm the package installed correctly by checking the available entry points. The MCP server is exposed via the chatspatial command.
python -m chatspatial --helpPrepare your spatial data
Ensure your spatial transcriptomics data is available as an .h5ad file with absolute path accessible to the MCP server process. ChatSpatial needs the full path when loading data through the AI client.
Configure your MCP client
Add ChatSpatial to your claude_desktop_config.json. The server runs via stdio so no ports need to be open.
{
"mcpServers": {
"chatspatial": {
"command": "python",
"args": ["-m", "chatspatial"]
}
}
}Restart your MCP client
Restart Claude Desktop after editing the configuration. ChatSpatial's 20 tools will appear in the connected tools list, ready to accept natural language analysis requests.
ChatSpatial Genomics Examples
Client configuration
claude_desktop_config.json entry for ChatSpatial using pip-installed Python module.
{
"mcpServers": {
"chatspatial": {
"command": "python",
"args": ["-m", "chatspatial"]
}
}
}Prompts to try
Example natural language prompts to run spatial transcriptomics analyses through Claude.
- "Load /data/brain_visium.h5ad and show me the tissue structure with spatial plots"
- "Run quality control on the loaded dataset — filter low-quality cells and normalize"
- "Identify spatial domains using SpaGCN and visualize the clusters on the tissue image"
- "Analyze cell-cell communication between identified clusters using CellChat"
- "Perform deconvolution with Cell2location using the reference single-cell atlas at /data/ref.h5ad"Troubleshooting ChatSpatial Genomics
ImportError or missing method libraries on first run
Some optional analytical methods (e.g., Cell2location, STAGATE) require additional packages not installed by default. Install the optional extras: `pip install chatspatial[all]` or install specific packages like `pip install cell2location`.
Server fails to load .h5ad file
Always provide absolute paths to data files (e.g., /Users/you/data/sample.h5ad). Relative paths are resolved from the server's working directory which may differ from your project directory.
Analysis runs out of memory on large datasets
Subsample the dataset before loading — use scanpy's sc.pp.subsample() in a Python script first, or ask Claude to 'subsample to 5000 cells before running the heavy analysis'.
Frequently Asked Questions about ChatSpatial Genomics
What is ChatSpatial Genomics?
ChatSpatial Genomics is a Model Context Protocol (MCP) server that natural language-driven spatial transcriptomics analysis via mcp. integrates 60+ methods for preprocessing, visualization, spatial statistics, cell communication, deconvolution, and trajectory analysis. It connects AI assistants to external tools and data sources through a standardized interface.
How do I install ChatSpatial Genomics?
Install via pip with: pip install chatspatial. Then configure your AI client to connect to this MCP server.
Which AI clients work with ChatSpatial Genomics?
ChatSpatial Genomics works with all major MCP-compatible AI clients including Claude Desktop, Claude Code, Cursor, VS Code (GitHub Copilot), Windsurf, and Cline.
Is ChatSpatial Genomics free to use?
Yes, ChatSpatial Genomics is open source and available under the MIT License license. You can use it freely in both personal and commercial projects.
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Quick Config Preview
Add this to your claude_desktop_config.json or .cursor/mcp.json
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