What is SpatialAI_MCP AGENTS.md?

Project instructions for an OpenProblems co-pilot focused on spatial transcriptomics, a method for measuring gene activity at locations within tissue. They describe the project, its available tools, domain rules, and coding standards.

Use them when working on the MCP server, skill installer, or spatial-transcriptomics validation and analysis workflows in this repository.

They give coding agents the project's ground truth, including which tools exist and that the analysis server is read-only.

How Rebell-Leader/SpatialAI_MCP configures Codex and OpenCode

Reuse

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.

Copy the file

curl -O https://raw.githubusercontent.com/Rebell-Leader/SpatialAI_MCP/main/AGENTS.md

Clone the repo

git clone --depth 1 https://github.com/Rebell-Leader/SpatialAI_MCP

Made for: Codex, OpenCode.

Wrote 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.

README.md

[![agentmods](https://agentmods.dev/badge/instructions/rebell-leader/spatialai_mcp/agents-md/github.svg)](https://agentmods.dev/instructions/rebell-leader/spatialai_mcp/agents-md)

Your own site

<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/github.svg" alt="Measured on agentmods" height="20"></a>

Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.

Your own site · 80×15

<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="Reviewed on agentmods" width="80" height="20"></a>

Per session 1,373 This file is loaded in full into every session.

When invoked 1,373 The same file — it is already loaded in full.

Security scan A 0 findings. A grade says what 26 rules found in the file — not that it is safe.

Origin original No closer match found in the catalogue.

Token cost

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 5.5	$0.00549	$0.00549
Sonnet 5.5	$0.00275	$0.00275
Haiku 4.5	$0.00137	$0.00137

Measured 2mo ago against content hash 946ffac560a4, method: parsed. Prices are Anthropic first-party input rates as of 2026-10-07, from the pricing page.

Security

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 2mo 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.

AGENTS.md · 106 lines

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 the skills/ directory by installer/ — 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)

Read the full file on GitHub · 106 lines

Changes

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.

2mo ago First seen · 106 lines · 1,373 tokens per session scan A 946ffac560a4

Subscribe to this mod's changes

SpatialAI_MCP AGENTS.md is an instructions file published in the GitHub repository Rebell-Leader/SpatialAI_MCP (4 stars, last pushed 4mo ago), licensed Apache-2.0. It adds 1,373 tokens to every session, about $0.0055 per session on Opus 5.5. 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.

Building agents Scientific

SpatialAI_MCP AGENTS.md next to 6 instructions from other repositories
Mod	Type	Stars	Last push	Licence	Scan	Tokens	Works with
SpatialAI_MCP AGENTS.mdRebell-Leader/SpatialAI_MCP	Instructions file	4	4mo ago	Apache-2.0	A	1,373	Codex, OpenCode
vscode buildNext.instructions.mdmicrosoft/vscode	Instructions file	195k	yesterday	MIT	A	9,719	GitHub Copilot
next.js AGENTS.mdvercel/next.js	Instructions file	143k	today	MIT	A	7,461	Codex, OpenCode
langchain AGENTS.mdlangchain-ai/langchain	Instructions file	149k	yesterday	MIT	A	4,680	Codex, OpenCode
vscode oss-third-party-notices.instructions.mdmicrosoft/vscode	Instructions file	195k	yesterday	MIT	A	5,516	GitHub Copilot
vscode copilot-instructions.mdmicrosoft/vscode	Instructions file	195k	yesterday	MIT	A	3,093	GitHub Copilot
deepseek-harness AGENTS.mddeepseek-ai/deepseek-harness	Instructions file	274k	2d ago	MIT	A	4,313	Codex, OpenCode

SpatialAI_MCP: Instructions file for Codex