What is flowreg-agent-skills?

A collection of coding-agent skills for planning, running, and checking dense motion correction in microscopy images. Microscopy is the use of microscopes to record biological samples, often over time or in three dimensions.

Use it to plan motion correction, process microscopy recordings, align sessions, correct movement along depth, register volumes, and check results.

It brings related workflows together for different kinds of image movement, so a developer can choose an appropriate process for 2D, multi-session, depth-drift, or 3D data.

flowreg-agent-skills — Plugin for Claude Code by FlowRegSuite

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/FlowRegSuite/flowreg-agent-skills

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/flowregsuite/flowreg-agent-skills/flowreg-agent-skills/github.svg)](https://agentmods.dev/plugins/flowregsuite/flowreg-agent-skills/flowreg-agent-skills)

Your own site

<a href="https://agentmods.dev/plugins/flowregsuite/flowreg-agent-skills/flowreg-agent-skills"><img src="https://agentmods.dev/badge/plugins/flowregsuite/flowreg-agent-skills/flowreg-agent-skills/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/flowregsuite/flowreg-agent-skills/flowreg-agent-skills"><img src="https://agentmods.dev/badge/plugins/flowregsuite/flowreg-agent-skills/flowreg-agent-skills.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 The manifest loads nothing itself; its 7 skills cost 583 tokens a session between them.

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

flowreg-agent-skills 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.

.claude-plugin/plugin.json · 19 lines

What it actually says

{
  "name": "flowreg-agent-skills",
  "displayName": "FlowRegSuite Agent Skills",
  "version": "0.1.0",
  "description": "FlowRegSuite Agent Skills: plan, execute and quality-control dense Flow-Registration motion correction for 2D, multi-session, axial z-drift and volumetric 3D microscopy data.",
  "author": { "name": "Philipp Flotho" },
  "homepage": "https://github.com/FlowRegSuite/flowreg-agent-skills",
  "repository": "https://github.com/FlowRegSuite/flowreg-agent-skills",
  "license": "MIT",
  "keywords": [
    "microscopy",
    "motion-correction",
    "optical-flow",
    "two-photon",
    "flowreg"
  ],
  "skills": "./skills/"
}

Contents

What it installs

The manifest is a name and a version. 7 skills travel with it, and installing the plugin installs all of them — 583 tokens a session between them. Each is measured on its own page, and each can be installed alone.

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 · 19 lines scan A 907f6e4dd2fa

Subscribe to this mod's changes

flowreg-agent-skills is a plugin published in the GitHub repository FlowRegSuite/flowreg-agent-skills (2 stars, last pushed 3mo ago), licensed MIT. 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 2026-08-31.

Scientific

flowreg-agent-skills next to 6 plugins from other repositories
Mod	Type	Stars	Last push	Licence	Scan	Tokens	Works with
flowreg-agent-skillsFlowRegSuite/flowreg-agent-skills	Plugin	2	3mo ago	MIT	A	—	Claude Code
antimicrobial-resistance-scientistK-Dense-AI/scientific-agents	Plugin	237	1mo ago	MIT	A	—	Claude Code
catalysis-scientistK-Dense-AI/scientific-agents	Plugin	237	1mo ago	MIT	A	—	Claude Code
hyphamycelium-cmbse/mycelium-hypha	Plugin	12	yesterday	Apache-2.0	A	—	Claude Code
r2g-skillsShenShan123/r2g-skills	Plugin	44	8d ago	MIT	B	—	Claude Code
aremaballarin/ccplugins	Plugin	4	11d ago	MIT	A	—	Claude Code
physical-sciencesKalarisLabs/research-agent-skills	Plugin	105	today	none	A	—	Claude Code