What is alterlab-neuropixels?

A workflow for analyzing Neuropixels recordings, which capture electrical activity from many neurons using a high-density probe. It covers processing the recordings, identifying neuron spikes, measuring data quality, and reviewing the results.

It helps load SpikeGLX, Open Ephys, or NWB files; correct recording motion; run spike-sorting software; calculate quality measures; review units; and export results to Phy or NWB.

It organizes the work needed to turn raw neural recordings into checked, usable neuron data.

alterlab-neuropixels — Skill for Claude Code by AlterLab-IEU

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 AlterLab-IEU/AlterLab-Academic-Skills --skill alterlab-neuropixels

Clone the repo

git clone --depth 1 https://github.com/AlterLab-IEU/AlterLab-Academic-Skills

Made for: Claude Code.

Or install alterlab-bioinformatics, the plugin that ships this one along with the rest of its 38 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/alterlab-ieu/alterlab-academic-skills/alterlab-neuropixels/github.svg)](https://agentmods.dev/skills/alterlab-ieu/alterlab-academic-skills/alterlab-neuropixels)

Your own site

<a href="https://agentmods.dev/skills/alterlab-ieu/alterlab-academic-skills/alterlab-neuropixels"><img src="https://agentmods.dev/badge/skills/alterlab-ieu/alterlab-academic-skills/alterlab-neuropixels/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/alterlab-ieu/alterlab-academic-skills/alterlab-neuropixels"><img src="https://agentmods.dev/badge/skills/alterlab-ieu/alterlab-academic-skills/alterlab-neuropixels.svg" alt="Reviewed on agentmods" width="80" height="20"></a>

Per session 122 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.

When invoked 3,365 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 89% 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	$0.00122	$0.03365
Opus 5	$0.00061	$0.01682
Sonnet 5	$0.00024	$0.00673
Haiku 4.5	$0.00012	$0.00336

Measured 12d ago against content hash 244271a3a19c, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-12, from the pricing page.

Security

Grade A, and why

alterlab-neuropixels 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 12d 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

89% identical to neuropixels-analysis — 140 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.

skills/bioinformatics/alterlab-neuropixels/SKILL.md · 378 lines

How it starts

The opening of the file, as written. The whole thing — 378 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

# Bundled helper functions live in scripts/neuropixels_pipeline.py
from scripts.neuropixels_pipeline import (
    load_recording, preprocess, check_drift, correct_motion,
    run_spike_sorting, postprocess, curate_units, export_results, run_pipeline,
)

# 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 · 378 lines

Files

What ships with it

18 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.

12d ago First seen · 378 lines · 122 tokens per session scan A 244271a3a19c

Subscribe to this mod's changes

alterlab-neuropixels is a skill published in the GitHub repository AlterLab-IEU/AlterLab-Academic-Skills (66 stars, last pushed 8d ago), licensed MIT. It adds 122 tokens to every session and 3,365 once invoked, about $0.0006 per session on Opus 5. A static security scan graded it A with 0 findings. It is 89% identical to neuropixels-analysis, differing in 140 lines, and is treated as a copy.

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