What is flowreg-register-3d?

A workflow for aligning 3D microscopy volumes, which are image data containing width, height, and depth, using a displacement for each point in three directions. It is marked experimental and requires careful result validation.

Use it for pairs or time series of volumetric microscopy recordings when the motion is genuinely three-dimensional.

It handles movement or deformation that cannot be represented by aligning individual 2D image slices, while making its unfinished interface and limitations explicit.

flowreg-register-3d — 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-3d

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-3d/github.svg)](https://agentmods.dev/skills/flowregsuite/flowreg-agent-skills/flowreg-register-3d)

Your own site

<a href="https://agentmods.dev/skills/flowregsuite/flowreg-agent-skills/flowreg-register-3d"><img src="https://agentmods.dev/badge/skills/flowregsuite/flowreg-agent-skills/flowreg-register-3d/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-3d"><img src="https://agentmods.dev/badge/skills/flowregsuite/flowreg-agent-skills/flowreg-register-3d.svg" alt="Reviewed on agentmods" width="80" height="20"></a>

Per session 77 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.

When invoked 1,817 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	$0.00077	$0.01817
Opus 5.5	$0.00031	$0.00727
Sonnet 5.5	$0.00015	$0.00363
Haiku 4.5	$0.00008	$0.00182

Measured 2mo ago against content hash 11e9288b9ddf, 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-3d 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-3d/SKILL.md · 148 lines

How it starts

The opening of the file, as written. The whole thing — 148 lines — stays where its author put it; the contents beside it link to each section on GitHub.

Native volumetric (3D) registration

This capability is experimental. The solver runs, but the surrounding interface is unfinished: there is no motion-correction command line, no backend selector, no test pins the displacement component order, several documented options are silently inert, and every CPU-versus-GPU parity test is skipped upstream. Say this to the user before running anything, and validate results rather than trusting them.

1. Purpose

Register volumes to volumes with a dense three-component displacement field, for moving volumes and time-resolved volumetric microscopy.

2. Use this skill when

The moving data are volumes: a volume pair, or a time series of volumes.
Deformation is genuinely three-dimensional and cannot be captured slice-wise.

3. Do not use this skill when

A single 2D imaging plane is drifting through a reference stack → flowreg-correct-z-drift. A z stack in the problem does not make it a 3D registration problem.
You want independently acquired 2D slices mutually aligned. That is not a supported capability.
The data are a 2D time series → flowreg-register-2d.
Several 2D recordings need shared coordinates → flowreg-register-session.

4. Required inputs and metadata

Volumes with explicit axis order. The canonical layout is (T, Z, Y, X, C) for a series and (Z, Y, X, C) for one volume — z first, channels last.
Channel count and meaning.
Physical voxel spacing and its unit. The runtime has no voxel-spacing parameter; you record spacing for interpretation, and you must not pretend the solver used it.
Volume dimensions, dtype and volume count.
Available RAM, free disk, CPU count, and GPU model and memory if a GPU is intended.
A new run directory outside the source data.

There is no motion-correction command line. The flowreg3d console script provides only data preparation (tiff-reshape, concat-tiffs). Registration is Python-API-only.

5. Preflight checks

Read the full file on GitHub · 148 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 · 148 lines · 77 tokens per session scan A 11e9288b9ddf

Subscribe to this mod's changes

flowreg-register-3d is a skill published in the GitHub repository FlowRegSuite/flowreg-agent-skills (2 stars, last pushed 3mo ago), licensed MIT. It adds 77 tokens to every session and 1,817 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-3d next to 6 skills from other repositories
Mod	Type	Stars	Last push	Licence	Scan	Tokens	Works with
flowreg-register-3dFlowRegSuite/flowreg-agent-skills	Skill	2	3mo ago	MIT	A	77	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