MCP.Market

ChatSpatial MCP server

by cafferychen777·io.github.cafferychen777/chatspatial·v1.6.0·45 stars
No reviews yet

Schema-enforced spatial transcriptomics analysis with 20 tools and 67 methods via MCP

A92/100grade A
Write a reviewInstall
What users say
No reviews yet
Be the first
Safety scan
A92/100

full report

Adoption
Established

45 stars162 downloads/wk

Reviews

Write one

Nobody has reviewed ChatSpatial yet.

If you have run it, two minutes of your experience saves the next person an afternoon.

ChatSpatial tools (20, 1 write)

write = sends, deletes, buys or posts

Read from the package source without running it. The installed server may list more.

  • analyze_cell_communication

    Analyze cell-cell communication and ligand-receptor interaction patterns.

  • analyze_cnv

    Analyze copy number variations (CNVs) in spatial transcriptomics data.

  • analyze_enrichment

    Perform gene set enrichment analysis.

  • analyze_spatial_statistics

    Analyze spatial statistics and autocorrelation patterns.

  • analyze_trajectory_data

    Infer cellular trajectories and pseudotime ordering.

  • analyze_velocity_data

    Analyze RNA velocity to understand cellular dynamics. Requires 'spliced' and 'unspliced' layers.

  • annotate_cell_types

    Annotate cell types in spatial transcriptomics data.

  • compare_conditions

    Compare experimental conditions using pseudobulk differential expression (DESeq2).

  • compute_embeddings

    Compute dimensionality reduction (PCA, UMAP), clustering, and neighbor graphs.

  • deconvolve_data

    Deconvolve spatial spots to estimate cell type proportions.

  • export_data

    Export dataset to disk for external script access.

  • find_markers

    Find differentially expressed genes between groups.

  • find_spatial_genes

    Identify spatially variable genes.

  • identify_spatial_domains

    Identify spatial domains and tissue architecture.

  • integrate_samples

    Integrate multiple spatial transcriptomics samples into a unified dataset.

  • load_data

    Load spatial transcriptomics data with comprehensive metadata profile.

  • preprocess_datawrite action

    Run QC, filtering, normalization, and highly variable gene selection.

  • register_spatial_data

    Register/align spatial transcriptomics data across sections

  • reload_data

    Reload dataset from disk after external script modifications.

  • visualize_data

    Visualize spatial transcriptomics data. Set plot_type and subtype in params; see VisualizationParameters schema for all options.

Public scan report

scanner v0.1.10 · 2026-11-03 · same rubric, same numbers if you re-run it

no findings
  • Code scan68 source files scanned25/25
  • –Live reliabilityno gateway calls yet and no remote to proben/a
  • –Tool poisoningtools not inspected (local package is not executed); not countedn/a
  • Auth qualitylocal package, no credentials required12/15
  • Maintenancelast push 14 days ago15/15
  • Maintainer identityregistry namespace matches repository owner; GitHub account older than a year8/10
Overall 92/100. Components that don't apply are left out of the denominator. Any critical finding is an F.RubricAppeal a findingJSON

How ChatSpatial compares

Against every graded MCP server, from our own scans and uptime checks. Updated after each scan run.

Safety score
92/100
higher than 95% of 48,255 servers
Tools
20
the typical server has 7
Tools that change things
5%
typical: 0%. Fewer write tools means less an agent can break
GitHub stars
45
more than 93% of 28,688 servers
Downloads a week
162
more than 72% of 12,191 servers with a package

What its tools let an agent do: 18 read · 1 create · 1 change

Release history: 4 versions in the registry since 2026-08-15, latest 2026-10-20, typically one every 9 days.

Install ChatSpatial in Claude Code, Cursor or VS Code

claude mcp add chatspatial -- uvx chatspatial
Add to Cursor

What the publisher says

From the ChatSpatial repository's README, as published. We do not edit it. Read it on GitHub

ChatSpatial

MCP server for spatial transcriptomics analysis via natural language

ChatSpatial replaces ad-hoc LLM code generation with schema-enforced orchestration. Instead of generating arbitrary scripts, the LLM selects tools and parameters from a curated registry, making spatial transcriptomics workflows more reproducible across sessions and clients.

ChatSpatial exposes 20 schema-validated MCP tools that orchestrate 66 spatial transcriptomics methods across 15 analytical categories. The tools are the stable natural-language interface; the methods are the analysis backends selected through tool parameters.

The server implements MCP 2026-07-28 through the official Python SDK v2 and continues to serve 2025-11-25 clients through SDK-managed protocol negotiation. STDIO remains the secure local default; Streamable HTTP is available for explicitly configured HTTP deployments.

Start Here

Install uv once, then register ChatSpatial without creating or managing a Python environment:

Codex:

codex mcp add chatspatial -- uvx --from chatspatial chatspatial server

Claude Code:

claude mcp add --scope user chatspatial -- \
  uvx --from chatspatial chatspatial server

uvx creates an isolated environment on first launch and reuses its cache on later launches. Restart the MCP client after adding the server.

The command above installs the standard runtime. To make all 15 composable Python method families available in the same isolated MCP environment, use:

uvx --from 'chatspatial[full]' chatspatial server

full includes CellRank, FastCCC, the maintained spatial-domain and registration backends, annotation, enrichment, and the other portable Python families. R bridges, AESTETIK, and rctd-py remain separate because they have system, platform, or large-runtime requirements. See the installation guide before enabling those families.

Then:

  1. Run your first analysis — Quick Start
  2. Choose optional method families or a persistent environment — Installation Guide
  3. Configure another MCP client — Configuration Guide
  4. Inspect or reproduce the manuscript results — Reproducibility workspace

Docker quick start:

docker pull ghcr.io/cafferychen777/chatspatial:v1.4.0

Minimal example prompt:

Load /absolute/path/to/spatial_data.h5ad and show me the tissue structure

Shortened. The full README is on GitHub.

Nothing above is checked by us. What we check is on the safety report.

ChatSpatial: common questions

Is ChatSpatial MCP server safe?
Yes, by our scan: it is graded A (92/100). Read the ChatSpatial safety report
How do I install ChatSpatial?
It runs on your machine. Copy the Claude Code, Cursor, VS Code or Claude Desktop config from the install section.
Does ChatSpatial need an API key?
Not as far as the registry entry and our scan can tell: no credentials are declared or required.
Is ChatSpatial maintained?
The last commit was 15 days ago (2026-10-20). The latest release is v1.6.0.
How does ChatSpatial compare with other MCP servers?
safety score 92/100 (higher than 95% of 48,255 servers); tools 20 (the typical server has 7); tools that change things 5% (typical: 0%. Fewer write tools means less an agent can break). Full comparison.