ChatSpatial

Overview

ChatSpatial is a specialized MCP server designed for spatial transcriptomics analysis, replacing ad-hoc LLM code generation with schema-enforced orchestration. It exposes 20 schema-validated MCP tools that orchestrate 65 spatial transcriptomics methods across 15 analytical categories. The project provides a stable natural-language interface where users can work with spatial data through simple prompts rather than writing complex scripts, making spatial transcriptomics workflows more reproducible across sessions and clients.

Try asking AI

After installing, here are 5 things you can ask your AI assistant:

• load_data

  Load spatial transcriptomics data from files like h5ad

  Try:Load /absolute/path/to/spatial_data.h5adTry:Load my spatial data from the desktop
• show_tissue_structure

  Visualize tissue structure of loaded spatial data

  Try:Show me the tissue structureTry:Display spatial layout of the data
• spatial_domain_identification

  Identify spatial domains using methods like SpaGCN, STAGATE

  Try:Find spatial domains in the tissueTry:Identify tissue regions using SpaGCN
• deconvolution

  Perform cell type deconvolution using methods like Cell2location

  Try:Deconvolve cell types in my dataTry:Run Cell2location to estimate cell proportions
• cell_cell_communication

  Analyze cell-cell communication with LIANA+ or CellPhoneDB

  Try:Find communicating cells in the tissueTry:Run CellPhoneDB to identify ligand-receptor pairs
• cell_type_annotation

  Annotate cell types using methods like scANVI or SingleR

  Try:Annotate cell types in my dataTry:Use scType to identify cell types
• differential_expression

  Find differentially expressed genes across conditions

  Try:Find genes that differ between tissue regionsTry:Run differential expression analysis
• trajectory_inference

  Perform trajectory inference with CellRank or Palantir

  Try:Find cell trajectories in my dataTry:Run CellRank to identify differentiation paths
• spatial_statistics

  Calculate spatial statistics like Moran's I or co-occurrence

  Try:Calculate Moran's I for gene expressionTry:Find spatially variable genes
• enrichment_analysis

  Perform gene set enrichment analysis like GSEA

  Try:Run GSEA on my differentially expressed genesTry:Find enriched pathways in my data
• visualization

  Create spatial plots, embedding plots, and expression overlays

  Try:Create a spatial plot of gene expressionTry:Show UMAP embedding colored by cell type
• multi_sample_integration

  Integrate multiple samples using Harmony or BBKNN

  Try:Integrate my 10 spatial samples togetherTry:Run Harmony to batch correct my data

Comparable tools

Installation

pip install chatspatial

docker pull ghcr.io/cafferychen777/chatspatial:v1.2.9

{
  "mcpServers": {
    "chatspatial": {
      "command": "python",
      "args": ["-m", "chatspatial", "run"]
    }
  }
}

FAQ

What spatial transcriptomics platforms does ChatSpatial support?

ChatSpatial supports 10x Visium, Xenium, Slide-seq v2, MERFISH, and seqFISH platforms.

How do I load my spatial data?

Simply provide a natural language prompt like 'Load /absolute/path/to/spatial_data.h5ad and show me the tissue structure'. ChatSpatial will handle the data loading internally.

Compare ChatSpatial with