Borrowing it
Nothing to install: this file belongs to Rebell-Leader/SpatialAI_MCP. Take a copy, put it at the same path in your own repository, and replace the rules that are about this project with yours.
curl -O https://raw.githubusercontent.com/Rebell-Leader/SpatialAI_MCP/main/AGENTS.mdgit clone --depth 1 https://github.com/Rebell-Leader/SpatialAI_MCPWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/instructions/rebell-leader/spatialai_mcp/agents-md)<a href="https://agentmods.dev/instructions/rebell-leader/spatialai_mcp/agents-md"><img src="https://agentmods.dev/badge/instructions/rebell-leader/spatialai_mcp/agents-md.svg" alt="Measured on agentmods" height="20"></a>What it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5.1 | $0.01373 | $0.01373 |
| Opus 5 | $0.00687 | $0.00687 |
| Sonnet 5 | $0.00275 | $0.00275 |
| Haiku 4.5 | $0.00137 | $0.00137 |
Grade A, and why
SpatialAI_MCP AGENTS.md scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 7d ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Nothing flagged
None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.
How it starts
The opening of the file, as written. The whole thing — 106 lines — stays where its author put it; the contents beside it link to each section on GitHub.
AGENTS.md — OpenProblems Spatial Transcriptomics Co-pilot
Canonical, provider-neutral instructions for any AI coding agent working in this repository (Claude Code, OpenAI Codex, Cursor, GitHub Copilot, and others). This is the single source of truth. Tool-specific files (
CLAUDE.md,.cursor/rules/,.github/copilot-instructions.md) are generated from this file and theskills/directory byinstaller/— do not edit them by hand.
What this project is
A co-pilot for computational biologists working on the OpenProblems spatial transcriptomics benchmarks. It ships two things:
- An MCP server (
src/openproblems_mcp/) — domain-aware validation and analysis tools for spatial data and bioinformatics workflows, exposed over the Model Context Protocol so any MCP-capable agent can call them. - A provider-agnostic skill installer (
skills/,context/,installer/) — author rules/skills/context once here, then project them into whichever agent the user runs.
Ground truth: which MCP tools actually exist
Only call tools that are registered. As of now the server is read-only analysis — it validates and inspects, it does not execute pipelines.
Available now:
health_check, list_tools_status, get_server_info,
validate_spatial_data, validate_multiple_spatial_files,
analyze_spatial_metadata, check_spatial_data_compatibility,
extract_bioinformatics_metadata, analyze_workflow_configuration,
assess_data_quality, analyze_workflow_dependencies.
Roadmap — NOT implemented, do not call:
run_nextflow_workflow, run_viash_component, build_docker_image,
run_nf_test, analyze_nextflow_log, create_spatial_component,
setup_spatial_environment, and the OpenProblems build/benchmark/submission
tools. For these actions, drive the user's local nextflow / viash / docker
CLIs directly via the terminal instead, and say so plainly.
Domain rules (spatial transcriptomics)
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 7d ago First seen · 106 lines · 1,373 tokens per session scan A 946ffac560a4
SpatialAI_MCP AGENTS.md is an instructions file published in the GitHub repository Rebell-Leader/SpatialAI_MCP (4 stars, last pushed 2mo ago), licensed Apache-2.0. It adds 1,373 tokens to every session, about $0.0069 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-31.
Other instructions, from other repositories
codex AGENTS.md
AGENTS.md instructions for openai/codex, covering rust/codex-rs, the codex-core crate, code review rules, crate api surface and model visible context.
vscode buildNext.instructions.md
Working notes and architecture documentation for the new esbuild-based build system in build/next. Use when making changes to the new build pipeline (transpile/bundle commands, NLS plugin, source-map handling, resource copying, or self-hosting watch tasks).
next.js AGENTS.md
AGENTS.md instructions for vercel/next.js, covering next.js development guide, codebase structure, monorepo overview, core package: packages/next and other important packages.
langchain AGENTS.md
AGENTS.md instructions for langchain-ai/langchain, covering global development guidelines for the langchain monorepo, corridor security analysis, project architecture and context, monorepo structure and development tools & commands.
vscode oss-third-party-notices.instructions.md
Instructions for microsoft/vscode, covering vs code oss third-party-notices pipeline, architecture, pipeline flow in ci, applying the notice (cutover) and fallback chain (never fail the build).
spec-kit AGENTS.md
AGENTS.md instructions for github/spec-kit, covering agents.md, about spec kit and specify, quickstart — add a new integration in 5 steps, integration architecture and integrationmanifest — file tracking.