What is SpatialAI_MCP copilot-instructions.md?

Project instructions for SpatialAI_MCP, a co-pilot for spatial transcriptomics—the study of where gene activity occurs inside tissue. They document its analysis tools and coding rules.

Use them when developing or using the project’s spatial-data and bioinformatics analysis tools, or updating its agent instructions.

They tell coding agents which tools actually exist and clarify that the server inspects and validates data rather than running analysis pipelines.

How Rebell-Leader/SpatialAI_MCP configures GitHub Copilot

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/.github/copilot-instructions.md

Clone the repo

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

Made for: GitHub Copilot.

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/copilot-instructions.svg)](https://agentmods.dev/instructions/rebell-leader/spatialai_mcp/copilot-instructions)

Your own site

<a href="https://agentmods.dev/instructions/rebell-leader/spatialai_mcp/copilot-instructions"><img src="https://agentmods.dev/badge/instructions/rebell-leader/spatialai_mcp/copilot-instructions.svg" alt="Measured on agentmods" height="20"></a>

Per session 3,776 This file is loaded in full into every session.

When invoked 3,776 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	$0.03776	$0.03776
Opus 5	$0.01888	$0.01888
Sonnet 5	$0.00755	$0.00755
Haiku 4.5	$0.00378	$0.00378

Measured 7d ago against content hash e1f3b2205fc3, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-07, from the pricing page.

Security

Grade A, and why

SpatialAI_MCP copilot-instructions.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.

Origin

Copies of this mod

1 near-identical copy found in the catalogue:

SpatialAI_MCP GEMINI.md — 100% identical, 0 lines differ

.github/copilot-instructions.md · 349 lines

How it starts

The opening of the file, as written. The whole thing — 349 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.

Read the full file on GitHub · 349 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.

7d ago First seen · 349 lines · 3,776 tokens per session scan A e1f3b2205fc3

Subscribe to this mod's changes

SpatialAI_MCP copilot-instructions.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 3,776 tokens to every session, about $0.0189 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.

Scientific

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.

openai/codex · 5,182 tokens

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).

microsoft/vscode · 6,785 tokens

SpatialAI_MCP: Instructions file for GitHub Copilot