Chatspatial
About
Natural language-driven spatial transcriptomics analysis via MCP. Integrates 60+ analytical methods across 15 categories including preprocessing, visualization, spatial statistics, cell communication, deconvolution, and trajectory analysis.
Details
- Author
- cafferychen777
- Downloads
- 236
- Categories
- Other, Developer Tools
Jump to
- 75+ analysis methods across 12 categories (cell annotation, spatial domains, deconvolution, etc.)
- Supports 10x Genomics Visium, Xenium, Slide-seq v2, MERFISH, seqFISH, and standard formats (H5AD, MTX, CSV)
- Natural language interface for data loading, analysis, and visualization
- Publication-ready visualizations (spatial plots, heatmaps, communication networks)
- Optional GPU acceleration for deep learning methods
- MIT licensed for academic and commercial use
Setting up with Highlight
This MCP is not yet compatible with Highlight’s one-click setup. However, you can still use it with Highlight by following these steps:
- Download and install Highlight from highlightai.com/download
- Navigate to the plugins tab and select "Add Custom Plugin"
-
Configure the plugin with the settings below
Plugin Name
ChatspatialCommand (node, npx, python, etc.)Please refer to the README for specific instructions on how to obtain API keys or other required environment variables.
- Enable "Start Automatically" if you want the plugin to start when Highlight launches
From the repository
Create a Python 3.10+ virtual environment, install the package with pip install -e ".[full]", then configure Claude Desktop by adding an MCP server entry to claude_desktop_config.json or Claude Code with the claude mcp add command. Download sample data and load it using absolute paths (e.g., /Users/yourname/Downloads/card_spatial.h5ad). After setup, simply type natural language requests in Claude chat to analyze spatial transcriptomics data—no coding required.
Claude Desktop / Cursor
Paste into your MCP client config file to install this server.
{
"mcpServers": {
"chatspatial": {
"ChatSpatial": {
"command": "python",
"args": [
"--version",
"#",
"Should",
"be",
"3.10+"
]
}
}
}
}McpServers
{
"ChatSpatial": {
"command": "python",
"args": [
"--version",
"#",
"Should",
"be",
"3.10+"
]
}
}ChatSpatial
Agentic Workflow Orchestration for Spatial Transcriptomics Analysis
</div> Eliminate the implementation tax. Focus on biological insight. ChatSpatial is an agentic workflow orchestration platform that integrates 60 state-of-the-art methods from fragmented Python and R ecosystems into a unified conversational interface. Built on the Model Context Protocol (MCP), it enables human-steered discovery through natural language in Claude Desktop or Claude Code, eliminating the need for manual data conversion and complex programming. 🎯 Example: Analyze spatial transcriptomics data through conversation with Claude ``text
👤 "Load my 10x Visium dataset and identify spatial domains"
🤖 ✅ Loaded 3,456 spots, 18,078 genes
✅ Identified 7 spatial domains using SpaGCN
✅ Generated spatial domain visualization
👤 "Find marker genes for domain 3 and create a heatmap"
🤖 ✅ Found 23 significant markers (adj. p < 0.05)
✅ Top markers: GFAP, S100B, AQP4 (astrocyte signature)
✅ Generated expression heatmap
`
👤 = You chatting with Claude | 🤖 = ChatSpatial MCP executing analysis
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🚀 Why Researchers Choose ChatSpatial
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<tr>
<td width="50%" valign="top">
Before: Traditional Analysis
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