What is flowreg-correct-z-drift?

A microscopy workflow that estimates where each pixel in a 2D recording sits along the depth axis of a known 3D image stack. It can also correct movement through that depth.

Use it to measure per-pixel, per-frame depth positions or create a recording corrected for axial, or z-axis, drift.

It addresses recordings where structures fade in and out because the imaging plane moves up or down, rather than shifting left or right.

flowreg-correct-z-drift — 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-correct-z-drift

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

Your own site

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

Per session 79 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.

When invoked 1,971 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	$0.00079	$0.01971
Opus 5.5	$0.00032	$0.00788
Sonnet 5.5	$0.00016	$0.00394
Haiku 4.5	$0.00008	$0.00197

Measured 2mo ago against content hash 713c35ddebd8, method: parsed. Prices are Anthropic first-party input rates as of 2026-10-07, from the pricing page.

Security

Grade A, and why

flowreg-correct-z-drift 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-correct-z-drift/SKILL.md · 158 lines

How it starts

The opening of the file, as written. The whole thing — 158 lines — stays where its author put it; the contents beside it link to each section on GitHub.

Axial (z) drift estimation and correction

1. Purpose

Estimate, per pixel and per frame, where in a reference volume the imaging plane actually was, and optionally correct the recording for that axial displacement.

The output is an axial position field, not a displacement field. It says which reference slice each pixel best matches.

2. Use this skill when

A 2D recording drifts along z through tissue for which a reference z stack exists.
Structures fade in and out rather than translating within the plane.
You need a z-shift field as a measurement, a z-corrected recording, or both.

3. Do not use this skill when

The motion is in-plane → flowreg-register-2d. Axial correction does not fix x-y motion, and in-plane correction does not fix axial motion. Recordings often need both.
You are registering volume to volume → flowreg-register-3d.
You want to align independently acquired 2D slices to each other. That is not a supported capability; say so rather than improvising.
You already corrected a 3D acquisition and simply want one plane out of it. That is plane extraction from a register-3d result, a different operation with different failure modes.
No reference volume exists. This capability requires one; there is no substitute.

4. Required inputs and metadata

The recording, with explicit axis order (T, H, W, C).
A reference volume, with explicit axis order (Z, H, W, C) — or a source recording from which one can be built.
Channel correspondence between recording and volume. Mismatched channels produce a confident, meaningless z field.
z spacing and its physical unit. The runtime works in slice indices; converting to micrometres is your responsibility, and the manifest must carry the spacing.
x-y spacing.
The nominal imaging plane, if known — useful for sanity-checking the estimated anchor.
The intended z search half-width, patch size and patch overlap.
Whether in-plane pre-alignment of the recording is needed first.
What is wanted: a z-shift field, a corrected recording, or both.

Read the full file on GitHub · 158 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 · 158 lines · 79 tokens per session scan A 713c35ddebd8

Subscribe to this mod's changes

flowreg-correct-z-drift is a skill published in the GitHub repository FlowRegSuite/flowreg-agent-skills (2 stars, last pushed 3mo ago), licensed MIT. It adds 79 tokens to every session and 1,971 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-correct-z-drift next to 6 skills from other repositories
Mod	Type	Stars	Last push	Licence	Scan	Tokens	Works with
flowreg-correct-z-driftFlowRegSuite/flowreg-agent-skills	Skill	2	3mo ago	MIT	A	79	Claude Code
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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