What is flowreg-register-2d?

A workflow for correcting left-right and up-down movement in one 2D microscopy time series. A time series is a sequence of images recorded over time; it may contain one or several image channels.

Use it on one recording, including multichannel data, narrow regions such as dendrites or vessels, recordings with large drift, and cases where the motion field should be saved for later analysis.

It removes in-plane movement that can make cells, vessels, or other structures appear in different locations from frame to frame.

flowreg-register-2d — Skill 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.

Any agent

npx skills add FlowRegSuite/flowreg-agent-skills --skill flowreg-register-2d

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.

README.md

[![agentmods](https://agentmods.dev/badge/skills/flowregsuite/flowreg-agent-skills/flowreg-register-2d/github.svg)](https://agentmods.dev/skills/flowregsuite/flowreg-agent-skills/flowreg-register-2d)

Your own site

<a href="https://agentmods.dev/skills/flowregsuite/flowreg-agent-skills/flowreg-register-2d"><img src="https://agentmods.dev/badge/skills/flowregsuite/flowreg-agent-skills/flowreg-register-2d/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/skills/flowregsuite/flowreg-agent-skills/flowreg-register-2d"><img src="https://agentmods.dev/badge/skills/flowregsuite/flowreg-agent-skills/flowreg-register-2d.svg" alt="Reviewed on agentmods" width="80" height="20"></a>

Per session 85 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.

When invoked 1,853 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.

Model	Per session	Once invoked
Fable 5.1	$0.00085	$0.01853
Opus 5.5	$0.00034	$0.00741
Sonnet 5.5	$0.00017	$0.00371
Haiku 4.5	$0.00009	$0.00185

Measured 2mo ago against content hash 60a24c5c6ea0, method: parsed. Prices are Anthropic first-party input rates as of 2026-10-07, from the pricing page.

Security

Grade A, and why

flowreg-register-2d 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.

skills/flowreg-register-2d/SKILL.md · 153 lines

How it starts

The opening of the file, as written. The whole thing — 153 lines — stays where its author put it; the contents beside it link to each section on GitHub.

Dense 2D motion correction

1. Purpose

Correct in-plane motion in one logical two-dimensional time series, and keep the dense displacement field as a scientific output rather than a disposable intermediate.

2. Use this skill when

One recording (possibly split across files that are chunks of the same acquisition) shows x-y motion.
The data are single- or multichannel, with or without a stable structural channel.
The region of interest is narrow (a dendrite, a vessel) and needs careful pyramid handling.
Large bulk drift suggests rigid pre-alignment before the variational stage.

3. Do not use this skill when

Several recordings must end up in a shared coordinate system → flowreg-register-session.
The imaging plane is drifting axially through a reference volume → flowreg-correct-z-drift.
The moving data are volumes → flowreg-register-3d.
The run has already finished and needs assessment → flowreg-qc-and-audit.

4. Required inputs and metadata

Input path or in-memory array, and its explicit axis order. Frames are (T, H, W, C).
Channel count and what each channel is. Structural and functional channels behave differently.
Pixel spacing and frame rate, for interpretation and for the manifest.
A writable new run directory, outside the source data directory.
Free disk at least the estimated output size, with margin.

There is no command-line interface for 2D correction. This capability is Python-API-only. Any command purporting to run 2D compensation from a shell is fabricated.

5. Preflight checks

Read references/runtime-capability.md for verified entry points and the exact output names.
Import the runtime and record its version into the manifest. Do not install anything.
Confirm the axis order from metadata or from the user — never from rank.
Confirm the output directory exists, is writable, and is not inside the source directory.
If a GPU backend was requested, confirm the GPU exists and the runtime can use it. Do not fall back silently in either direction.

Read the full file on GitHub · 153 lines

Files

What ships with it

3 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.

2mo ago First seen · 153 lines · 85 tokens per session scan A 60a24c5c6ea0

Subscribe to this mod's changes

flowreg-register-2d is a skill published in the GitHub repository FlowRegSuite/flowreg-agent-skills (2 stars, last pushed 3mo ago), licensed MIT. It adds 85 tokens to every session and 1,853 once invoked, about $0.0003 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.

Scientific

flowreg-register-2d next to 6 skills from other repositories
Mod	Type	Stars	Last push	Licence	Scan	Tokens	Works with
flowreg-register-2dFlowRegSuite/flowreg-agent-skills	Skill	2	3mo ago	MIT	A	85	Claude Code
instrument-data-to-allotropeanthropics/knowledge-work-plugins	Skill	35k	3d ago	Apache-2.0	A	123	Claude Code
exploratory-data-analysisK-Dense-AI/scientific-agent-skills	Skill	56k	4d ago	MIT	A	83	Claude Code
matlabK-Dense-AI/scientific-agent-skills	Skill	56k	4d ago	MIT	A	44	Claude Code
phylogeneticsK-Dense-AI/scientific-agent-skills	Skill	56k	4d ago	MIT	A	71	Claude Code, Codex
research-engineerdavila7/claude-code-templates	Skill	33k	yesterday	MIT	A	43	Claude Code, Codex
mapping-to-snomedmaziyarpanahi/openmed	Skill	5.8k	yesterday	Apache-2.0	A	205	Claude Code