ChatSpatial MCP Server
by cafferychen777MCP server for spatial transcriptomics analysis through natural language interfaces.
ChatSpatial is an open-source mcp server by cafferychen777, written mainly in Python, with 45 GitHub stars and the MIT license. Its code was last updated Oct 20, 2026.
Scan summary: scanned Nov 5, 2026 at commit 30eb958. Seen able to read environment and secrets. Scan policy
ScannedScanned. The automated checks below ran on the commit shown. Read each line for what was and was not covered.
Full scan at
30eb958 · Nov 5, 2026 ScannedStatic, secrets and dependency checks completed with no critical findings. BuildsIt installed from a fresh machine.
Passed. This check ran and found nothing it flags.Static code scanpassPassed. This check ran and found nothing it flags.
Passed. This check ran and found nothing it flags.Secrets scanpassPassed. This check ran and found nothing it flags.
Passed. This check ran and found nothing it flags.Dependency audit0 known vulnerabilitiespassPassed. This check ran and found nothing it flags.
Passed. This check ran and found nothing it flags.Manifestserver.jsonpassPassed. This check ran and found nothing it flags.
Passed. This check ran and found nothing it flags.BuildpassPassed. This check ran and found nothing it flags.
Flagged. This check found an issue. See the findings below.Boot & handshakefailFlagged. This check found an issue. See the findings below.
Not applicable. This check does not apply to this kind of project, or it was not run in this scan.Network egressn/aNot applicable. This check does not apply to this kind of project, or it was not run in this scan.
Not applicable. This check does not apply to this kind of project, or it was not run in this scan.Reproducible (×3)n/aNot applicable. This check does not apply to this kind of project, or it was not run in this scan.
Findings (2)
- mediumMedium. Worth checking, often a vulnerable dependency or a setup problem.MCP server didn't complete the protocol handshakeserver exited early with code 2
- lowLow. Minor, or common in normal tools. Shown for information.Reads environment variables not listed in the manifestCHATSPATIAL_OUTPUT_DIR, CHATSPATIAL_CACHE_DIR, LOCALAPPDATA, XDG_CACHE_HOME, TQDM_DISABLE, CHATSPATIAL_SCTYPE_R_DIR, CHATSPATIAL_EXPORT_RESULTS, SPHINX_LANGUAGE, CHATSPATIAL_ENABLE_LANGUAGE_SWITCHER, GEMINI_API_KEY, ANTHROPIC_API_KEY, OPENAI_API_KEY, OPENAI_API_URL, CHATSPATIAL_REPRO_DATA_DIR, PYTHO…
Network activity
During install
files.pythonhosted.orgpypi.org
While running
Not run — the code wasn't started in this scan
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