# ChatSpatial

> 🧬 Analyze spatial transcriptomics data through natural language conversation. Stop writing code, start having conversations with your data. MCP server for Claude Code and Codex.

- **URL**: https://www.freshcrate.ai/projects/ChatSpatial
- **Author**: cafferychen777
- **Category**: MCP Servers
- **Latest version**: `v1.2.10` (2026-05-21)
- **License**: MIT
- **Source**: https://github.com/cafferychen777/ChatSpatial
- **Homepage**: http://cafferyang.com/ChatSpatial/
- **Language**: Python
- **GitHub**: 30 stars, 8 forks
- **Registry**: github
- **Tags**: `agentic-ai`, `bioinformatics`, `cell-communication`, `claude-desktop`, `computational-biology`, `deconvolution`, `genomics`, `llm-agent`, `python`

## Description

🧬 Analyze spatial transcriptomics data through natural language conversation. Stop writing code, start having conversations with your data. MCP server for Claude Code and Codex.

## Recent releases

| Version | Date | Urgency | Changes |
| --- | --- | --- | --- |
| `v1.2.10` | 2026-05-21 | High | **Full Changelog**: https://github.com/cafferychen777/ChatSpatial/compare/v1.2.8...v1.2.10 |
| `v1.2.8` | 2026-05-12 | High | **Full Changelog**: https://github.com/cafferychen777/ChatSpatial/compare/v1.2.7...v1.2.8 |
| `v1.2.7` | 2026-05-11 | High | **Full Changelog**: https://github.com/cafferychen777/ChatSpatial/compare/v1.2.6...v1.2.7 |
| `v1.2.6` | 2026-05-02 | High | **Full Changelog**: https://github.com/cafferychen777/ChatSpatial/compare/v1.2.5...v1.2.6 |
| `v1.1.6` | 2026-02-28 | Low | ## What's Changed * perf: memory/speed consistency improvements across core tools and wrappers by @cafferychen777 in https://github.com/cafferychen777/ChatSpatial/pull/19   **Full Changelog**: https://github.com/cafferychen777/ChatSpatial/commits/v1.1.6 |
| `v0.3.0-data` | 2025-10-28 | Low | Sample datasets for testing ChatSpatial functionality:  📊 **Included Datasets:** - **card_reference_filtered.h5ad**: Single-cell reference data (1,782 cells × 19,736 genes, 36MB)   - 9 cell types including cancer clones and ductal cells   - Pancreatic tissue from cancer research    - **card_spatial.h5ad**: Spatial transcriptomics data (428 spots × 25,753 genes, 7.7MB)   - Clear spatial domain structure (3 distinct regions)   - Includes spatial coordinates  🎯 **Perfect for testing:** - ✅ Spatia |
| `v0.2.0-data` | 2025-09-23 | Low | Sample datasets for testing ChatSpatial functionality:  📊 **Included Datasets:** - **destvi_reference_small.h5ad**: Single-cell reference data (598 cells × 300 genes, 7.8MB) - **destvi_spatial_small.h5ad**: Spatial transcriptomics data (200 spots × 300 genes, 10MB)  🎯 **Perfect for testing:** - Spatial deconvolution with Cell2location/DestVI - Cell type annotation  - Spatial domain identification - Cell communication analysis  📥 **Usage:** ```bash curl -L -o reference_data.h5ad https://github |
| `v0.2.0` | 2025-08-26 | Low | # 🧬 ChatSpatial MCP Server v0.2.0  **Production-ready Model Context Protocol server for spatial transcriptomics analysis**  ## 🎯 **What's New**  ### 📚 **Documentation & CI Improvements** - **FIXED**: All broken documentation links in README.md - **ALIGNED**: Feature descriptions with actual code implementation - **UPDATED**: Installation guides and dependency configuration - **ENHANCED**: CI workflow with Python 3.10/3.11 testing matrix - **IMPROVED**: Code quality checks and automated testin |
| `v0.1.2` | 2025-08-26 | Low | **Full Changelog**: https://github.com/cafferychen777/ChatSpatial/compare/v0.1.0...v0.1.2 |
| `v0.1.1` | 2025-08-26 | Low | ## 🚀 Release v0.1.1  ### 🛠 GitHub Actions Improvements - ✅ Fixed all GitHub Actions workflows - ✅ Resolved dependency resolution issues   - ✅ Added minimal test workflow for quick validation - ✅ Improved CI/CD pipeline reliability  ### 📊 Current Status All workflows now passing with **100% success rate**: - CI ✅ - Tests ✅ - Code Quality ✅ - ChatSpatial Test Suite ✅ - Minimal Test ✅  ### 🐛 Bug Fixes - Fixed missing `requirements.txt` references - Fixed `pip install` dependency resolution dept |

## Dependency audit

- **Score**: 40/100
- **Total deps**: 73
- **Resolved**: 43
- **Unresolved**: 30
- **License conflicts**: 0
- **Warnings**: 26
- **Scanned**: 2026-04-27

## Citation

- HTML: https://www.freshcrate.ai/projects/ChatSpatial
- Markdown: https://www.freshcrate.ai/projects/ChatSpatial.md
- Dependencies JSON: https://www.freshcrate.ai/api/projects/ChatSpatial/deps

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