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flowreg-plan

flowreg-plan is a skill for Claude Code from FlowRegSuite/flowreg-agent-skills. It costs 90 tokens per session (2,014 once invoked), scanned A, original, MIT.

A planning workflow for choosing how to correct movement in microscopy data. It checks the data, available methods, computing resources, a small trial run, and rules for deciding whether the result is acceptable.

In plain words
What is it for?
Use it before correcting 2D recordings, aligning several recordings, correcting depth drift, or registering 3D volumes when the workflow is not yet clear.
Why use it?
It prevents choosing the wrong correction method or promising a capability before checking axes, channels, voxel spacing, reference images, and available hardware.

Skill for Claude Code

Written for Claude Code: shipped in a Claude Code plugin.

Part of the flowreg-agent-skills plugin — 7 skills shipped together

not rated 2repo 3mo ago A scan 90 tokens original MIT

Good fit Use it before correcting 2D recordings, aligning several recordings, correcting depth drift, or registering 3D volumes when the workflow is not yet clear.

Compare 6 skills from other repositories ↓
Install with agentmods
npx agentmods add skills/flowregsuite/flowreg-agent-skills/flowreg-plan
View source ↗ FlowRegSuite/flowreg-agent-skills
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.

Any agent
npx skills add FlowRegSuite/flowreg-agent-skills --skill flowreg-plan
Clone the repo
git clone --depth 1 https://github.com/FlowRegSuite/flowreg-agent-skills

Made for: Claude Code.

Or install flowreg-agent-skills, the plugin that ships this one along with the rest of its 7 skills.

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.

agentmods badge for flowreg-plan

README.md
[![agentmods](https://agentmods.dev/badge/skills/flowregsuite/flowreg-agent-skills/flowreg-plan/github.svg)](https://agentmods.dev/skills/flowregsuite/flowreg-agent-skills/flowreg-plan)
Your own site
<a href="https://agentmods.dev/skills/flowregsuite/flowreg-agent-skills/flowreg-plan"><img src="https://agentmods.dev/badge/skills/flowregsuite/flowreg-agent-skills/flowreg-plan/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.

agentmods 80×15 button for flowreg-plan

Your own site · 80×15
<a href="https://agentmods.dev/skills/flowregsuite/flowreg-agent-skills/flowreg-plan"><img src="https://agentmods.dev/badge/skills/flowregsuite/flowreg-agent-skills/flowreg-plan.svg" alt="Reviewed on agentmods" width="80" height="20"></a>
Per session 90 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 2,014 The whole file, excluding the scripts and references it only reads on demand.
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.

ModelPer sessionOnce invoked
Fable 5.1 $0.00090 $0.02014
Opus 5.5 $0.00036 $0.00806
Sonnet 5.5 $0.00018 $0.00403
Haiku 4.5 $0.00009 $0.00201

Measured 2mo ago against content hash 16bb7064a22b, method: parsed. Prices are Anthropic first-party input rates as of 2026-10-07, from the pricing page.

Security

Grade A, and why

flowreg-plan 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.

The scan reads SKILL.md. This mod also ships 1 executable file (scripts/inspect_input.py), listed below but not scanned — reading those needs a real analyzer, not pattern matching.

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.

skills/flowreg-plan/SKILL.md · 167 lines

How it starts

The opening of the file, as written. The whole thing — 167 lines — stays where its author put it; the contents beside it link to each section on GitHub.

FlowRegSuite planning and routing

1. Purpose

Turn a vague request about "fixing motion" into one explicitly chosen capability, a runtime that is verified to exist, a reference strategy, a small pilot, a resource estimate, and quality-control gates that decide in advance what would count as failure.

This skill produces a plan. It does not run a full registration.

2. Use this skill when

  • The user asks to correct, stabilise, register or align microscopy data and the workflow is not already settled.
  • Axes, channel meaning, voxel spacing, reference availability or hardware are uncertain.
  • More than one recording may need to share coordinates.
  • You need to know whether a capability is even available before promising anything.

3. Do not use this skill when

  • The workflow is already chosen and a plan exists — go straight to the execution skill.
  • A run has finished and needs assessment — use flowreg-qc-and-audit.
  • The request is about one-dimensional signals or evoked responses. That is flowreg1D, which ships no skill in this release; report the capability status instead.

4. Required inputs and metadata

Collect all of the following. Where something is unavailable, record it as an unresolved question rather than guessing.

Group Items
Data file format, array shape, named axis order, dtype, value range, frame/volume count, approximate size
Semantics which axis is time, which is z, which is channel, and what each channel is (structural vs functional)
Physical pixel and voxel spacing with units, frame or volume rate
Reference is a reference volume or reference recording available, and how was it acquired
Scope one recording, or several that must share coordinates
Resources free disk, RAM, CPU count, GPU model and memory, whether the runtime can use that GPU
Location local, network mount, or cluster

Never infer axis meaning from array rank or from which dimension is longest. A 4-D array may be TZYX, TYXC or ZYXC. Getting this wrong silently registers the wrong thing. Axis order must come from file metadata, acquisition software, or an explicit statement by the user, and the plan must record which of those it was.

Read the full file on GitHub · 167 lines

Files

What ships with it

5 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.

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.

  1. 2mo ago First seen · 167 lines · 90 tokens per session scan A 16bb7064a22b

Subscribe to this mod's changes

flowreg-plan is a skill published in the GitHub repository FlowRegSuite/flowreg-agent-skills (2 stars, last pushed 3mo ago), licensed MIT. It adds 90 tokens to every session and 2,014 once invoked, about $0.0004 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.

PlanningScientific
Related

flowreg-plan compared with skills from other repositories

flowreg-plan next to 6 skills from other repositories
ModTypeStarsLast pushLicenceScanTokensWorks with
flowreg-planFlowRegSuite/flowreg-agent-skillsSkill23mo agoMITA90Claude Code
instrument-data-to-allotropeanthropics/knowledge-work-pluginsSkill35k3d agoApache-2.0A123Claude Code
exploratory-data-analysisK-Dense-AI/scientific-agent-skillsSkill56k4d agoMITA83Claude Code
matlabK-Dense-AI/scientific-agent-skillsSkill56k4d agoMITA44Claude Code
phylogeneticsK-Dense-AI/scientific-agent-skillsSkill56k4d agoMITA71Claude Code, Codex
research-engineerdavila7/claude-code-templatesSkill33kyesterdayMITA43Claude Code, Codex
mapping-to-snomedmaziyarpanahi/openmedSkill5.8kyesterdayApache-2.0A205Claude Code