What is SpatialAI_MCP GEMINI.md?

Repository instructions for an AI coding agent working on OpenProblems, a project that validates and analyzes spatial transcriptomics data from tissue samples.

They guide work on the read-only MCP server, spatial-data validation, bioinformatics analysis, and the installer that shares rules across coding agents.

They define the project’s scientific context, available analysis tools, and limits, reducing the risk of calling tools that do not exist or treating analysis as pipeline execution.

How Rebell-Leader/SpatialAI_MCP configures Gemini CLI

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/GEMINI.md

Clone the repo

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

Made for: Gemini CLI.

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/gemini-md/github.svg)](https://agentmods.dev/instructions/rebell-leader/spatialai_mcp/gemini-md)

Your own site

<a href="https://agentmods.dev/instructions/rebell-leader/spatialai_mcp/gemini-md"><img src="https://agentmods.dev/badge/instructions/rebell-leader/spatialai_mcp/gemini-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/gemini-md"><img src="https://agentmods.dev/badge/instructions/rebell-leader/spatialai_mcp/gemini-md.svg" alt="Reviewed on agentmods" width="80" 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 100% copy Near-identical to another mod 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 5.5	$0.01510	$0.01510
Sonnet 5.5	$0.00755	$0.00755
Haiku 4.5	$0.00378	$0.00378

Measured 2mo ago against content hash e1f3b2205fc3, 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 GEMINI.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.

Origin

This is a copy

100% identical to SpatialAI_MCP copilot-instructions.md — 0 lines differ, which has more behind it and is treated as the original. This page carries a canonical link to it rather than competing with it.

GEMINI.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.

2mo ago First seen · 349 lines · 3,776 tokens per session scan A e1f3b2205fc3

Subscribe to this mod's changes

SpatialAI_MCP GEMINI.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 3,776 tokens to every session, about $0.0151 per session on Opus 5.5. A static security scan graded it A with 0 findings. It is 100% identical to SpatialAI_MCP copilot-instructions.md, differing in 0 lines, and is treated as a copy.

Scientific

SpatialAI_MCP GEMINI.md next to 6 instructions from other repositories
Mod	Type	Stars	Last push	Licence	Scan	Tokens	Works with
SpatialAI_MCP GEMINI.mdRebell-Leader/SpatialAI_MCP	Instructions file	4	4mo ago	Apache-2.0	A	3,776	Gemini CLI
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
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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 Gemini CLI