A plugin that provides tools for analysing spatial proteomics data, which shows where proteins are located within tissue samples.

Correcting uneven lighting, aligning images, separating tissue microarray samples, segmenting images, measuring results, and grouping similar samples.

It brings several image-analysis steps into tools that an AI assistant can use, reducing the need to run each step separately.

spmind — Plugin for Claude Code by tomtommyyuan

Install

Getting it into your agent

One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.

Clone the repo

git clone --depth 1 https://github.com/tomtommyyuan/spmind

Made for: Claude Code.

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/plugins/tomtommyyuan/spmind/spmind-plugin/github.svg)](https://agentmods.dev/plugins/tomtommyyuan/spmind/spmind-plugin)

Your own site

<a href="https://agentmods.dev/plugins/tomtommyyuan/spmind/spmind-plugin"><img src="https://agentmods.dev/badge/plugins/tomtommyyuan/spmind/spmind-plugin/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/plugins/tomtommyyuan/spmind/spmind-plugin"><img src="https://agentmods.dev/badge/plugins/tomtommyyuan/spmind/spmind-plugin.svg" alt="Reviewed on agentmods" width="80" height="20"></a>

Per session not measured What this adds to a session before it is invoked.

When invoked not measured Not applicable: nothing here is loaded into a session.

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.

Security

Grade A, and why

spmind 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 1mo 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.

spmind-plugin/.claude-plugin/plugin.json · 13 lines

What it actually says

{
  "name": "spmind",
  "version": "1.0.0",
  "description": "Spatial proteomics analysis tools (illumination correction, registration, TMA dearraying, segmentation, quantification, clustering) exposed as MCP tools.",
  "author": {
    "name": "SP-Mind Team",
    "email": "[email protected]",
    "url": "https://github.com/tomtommyyuan/spmind"
  },
  "homepage": "https://github.com/tomtommyyuan/spmind",
  "repository": "https://github.com/tomtommyyuan/spmind"
}

Contents

What it installs

The manifest is a name and a version. 1 MCP server travel with it, and installing the plugin installs all of them. Each is measured on its own page, and each can be installed alone.

MCP server spmind A not measured

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.

1mo ago First seen · 13 lines scan A 990b0fa3aea3

Subscribe to this mod's changes

spmind is a plugin published in the GitHub repository tomtommyyuan/spmind (280 stars, last pushed 12d ago), licensed Apache-2.0. Its token cost is not measured: this kind of file is read by the harness, not the model. 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 2026-08-30.

Scientific ai-agents ai4science benchmark bioinformatics biomedical-ai icml-2026

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