What is neuropixels-analysis?

A scientific workflow for analysing Neuropixels neural recordings, which capture electrical activity from many brain cells at once. It covers data loading, signal cleanup, spike sorting, quality checks, and curation.

Use it with SpikeGLX, Open Ephys, or NWB recordings to correct motion, identify spikes, measure unit quality, review results, create visualisations, and export data for Phy or NWB.

It brings the stages of turning raw extracellular electrophysiology recordings into reviewed neural-cell data into one process.

neuropixels-analysis — Skill for Claude Code and Codex by magic3007

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 magic3007/dotfiles --skill neuropixels-analysis

Clone the repo

git clone --depth 1 https://github.com/magic3007/dotfiles

Made for: Claude Code, Codex.

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/magic3007/dotfiles/neuropixels-analysis.svg)](https://agentmods.dev/skills/magic3007/dotfiles/neuropixels-analysis)

Your own site

<a href="https://agentmods.dev/skills/magic3007/dotfiles/neuropixels-analysis"><img src="https://agentmods.dev/badge/skills/magic3007/dotfiles/neuropixels-analysis.svg" alt="Measured on agentmods" height="20"></a>

Per session 109 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.

When invoked 2,938 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 92% copy Near-identical to another mod 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	$0.00109	$0.02938
Opus 5	$0.00055	$0.01469
Sonnet 5	$0.00022	$0.00588
Haiku 4.5	$0.00011	$0.00294

Measured 4d ago against content hash f591f6143362, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-07, from the pricing page.

Security

Grade A, and why

neuropixels-analysis 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 4d ago.

The scan reads SKILL.md. This mod also ships 7 executable files (assets/analysis_template.py, scripts/compute_metrics.py, scripts/explore_recording.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.

Origin

This is a copy

92% identical to neuropixels-analysis — 30 lines differ, which has more behind it and is treated as the original. This page carries a canonical link to it rather than competing with it.

claude/skills/scientific-agent-skills/skills/neuropixels-analysis/SKILL.md · 350 lines

How it starts

The opening of the file, as written. The whole thing — 350 lines — stays where its author put it; the contents beside it link to each section on GitHub.

Neuropixels Data Analysis

Overview

Comprehensive toolkit for analyzing Neuropixels high-density neural recordings using current best practices from SpikeInterface, Allen Institute, and International Brain Laboratory (IBL). Supports the full workflow from raw data to publication-ready curated units.

When to Use This Skill

This skill should be used when:

Working with Neuropixels recordings (.ap.bin, .lf.bin, .meta files)
Loading data from SpikeGLX, Open Ephys, or NWB formats
Preprocessing neural recordings (filtering, CAR, bad channel detection)
Detecting and correcting motion/drift in recordings
Running spike sorting (Kilosort4, SpykingCircus2, Mountainsort5)
Computing quality metrics (SNR, ISI violations, presence ratio)
Curating units using Allen/IBL criteria
Creating visualizations of neural data
Exporting results to Phy or NWB

Supported Hardware & Formats

Probe	Electrodes	Channels	Notes
Neuropixels 1.0	960	384	Requires phase_shift correction
Neuropixels 2.0 (single)	1280	384	Denser geometry
Neuropixels 2.0 (4-shank)	5120	384	Multi-region recording

Format	Extension	Reader
SpikeGLX	`.ap.bin`, `.lf.bin`, `.meta`	`si.read_spikeglx()`
Open Ephys	`.continuous`, `.oebin`	`si.read_openephys()`
NWB	`.nwb`	`si.read_nwb()`

Quick Start

Basic Import and Setup

import spikeinterface.full as si
import neuropixels_analysis as npa

# Configure parallel processing
job_kwargs = dict(n_jobs=-1, chunk_duration='1s', progress_bar=True)

Loading Data

# SpikeGLX (most common)
recording = si.read_spikeglx('/path/to/data', stream_id='imec0.ap')

# Open Ephys (common for many labs)
recording = si.read_openephys('/path/to/Record_Node_101/')

# Check available streams
streams, ids = si.get_neo_streams('spikeglx', '/path/to/data')
print(streams)  # ['imec0.ap', 'imec0.lf', 'nidq']

# For testing with subset of data
recording = recording.frame_slice(0, int(60 * recording.get_sampling_frequency()))

Read the full file on GitHub · 350 lines

Files

What ships with it

17 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.

4d ago First seen · 350 lines · 109 tokens per session scan A f591f6143362

Subscribe to this mod's changes

neuropixels-analysis is a skill published in the GitHub repository magic3007/dotfiles (11 stars, last pushed today), licensed MIT. It adds 109 tokens to every session and 2,938 once invoked, about $0.0005 per session on Opus 5. A static security scan graded it A with 0 findings. It is 92% identical to neuropixels-analysis, differing in 30 lines, and is treated as a copy.

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