ChatSpatialBLOCK
MCP server for spatial transcriptomics analysis through natural language interfaces.
Overview
From the repository's own README, as read at the audited commit. Badges and raw HTML are left out.
MCP server for spatial transcriptomics analysis via natural language
[](https://doi.org/10.64898/2026.02.26.708361) [](https://openreview.net/forum?id=xZ814yNaUW) [](https://www.enar.org/meetings/spring2026/) [](https://www.ibc2026.org/home) [](https://github.com/cafferychen777/ChatSpatial/actions/workflows/ci.yml) [](https://pypi.org/project/chatspatial/) [](https://www.python.org/downloads/) [](https://opensource.org/licenses/MIT) [](https://docs.cafferyang.com/) [](https://github.com/users/cafferychen777/packages/container/package/chatspatial)
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 thr
902255da1782OBSERVED · 2026-10-08Connect
Built from this server's own package name, version and transport as found in its source — not copied from anyone's documentation, so it cannot drift against a page we do not control. Replace the environment placeholders with a token scoped to the least it needs.
claude mcp add chatspatial -- uvx chatspatial==1.5.4 server
Trust audit
BLOCKgrade D · trust 61/100 Do not install this without reading the findings. The audit found something that could harm you or your machine.
| Layer | What it checks | Result |
|---|---|---|
| L0 | Provenance & inventory | PASS |
| L1 | Static analysis of the code | FAIL |
| L2 | Instruction surface (what it tells the agent) | PASS |
| L3 | Class-specific surface | PASS |
| L4 | Behavioural (sandbox) | SKIPPED |
What the source does
- Filesystem
- declared (2 observation(s))
- Network
- declared (1 observation(s))
- Shell
- declared (5 observation(s))
- Dependencies
- not all pinned
- Secrets in source
- none-found
Findings (20)
eval(parse(text = install_cmd))
f" {cond}: {exec_total}/{total} exec ({exec_rate:.0%}), {len(all_artifacts)} artifacts"module = importlib.import_module(f".{config.module_name}", package=__package__)likelihood = importlib.import_module(f"{module_name}._likelihood")return importlib.import_module(module_name)
"http://127.0.0.1:*",
.pre-commit-config.yaml
.readthedocs.yaml
return __import__("sys").modules.get(name) or importlib.import_module(name)re.get_analysis_dir("dataset", "../../outside")"method": "../../outside",
Connect to `http://127.0.0.1:8000/mcp`. The MCP SDK supplies a strict loopback
--allowed-origin 'http://127.0.0.1:*'
sphinx, furo, sphinx-copybutton, sphinx-design, myst-parser, sphinx-intl
curl -LsSf https://astral.sh/uv/install.sh | sh
curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh
assets/images/chatspatial-logo.png
docs/_static/architecture.png
docs/_static/logo.png
Gates applied: no_behavioural_pass.
902255da1782full audit observations/trust-audit/mcp-server/cafferychen777__chatspatial.json · Report an issue / request a re-scanAudit history
Every audit this server has had. A grade with a past is a grade somebody is still checking.
| Date | Source | Verdict | Grade | Score | Change |
|---|---|---|---|---|---|
| 2026-10-08 | 902255da1782 | BLOCK | D | 61 | first audit |
Questions
What is the ChatSpatial MCP server?
MCP server for spatial transcriptomics analysis through natural language interfaces.
Is ChatSpatial safe to connect to an agent?
No — not without reading the findings first. The audit graded it D (61/100) and found 2 critical or high issues in the source. Each one is listed on this page with the file and line it is on.
What credentials does ChatSpatial need?
It reads ANTHROPIC_API_KEY, GEMINI_API_KEY and OPENAI_API_KEY from the environment. Give it a token scoped to the least it needs — an agent that can be talked into calling a tool can be talked into calling it with your credentials.
How does ChatSpatial run?
It speaks sse, stdio and streamable-http, so it runs as a local process your client starts. It is published on PyPI as chatspatial.
How current is this page?
The grade is for one exact copy of the source (902255da1782), read on 2026-10-08. The repository is watched and re-audited when it changes.