Neuropixels Analysis

Handles the full Neuropixels pipeline from raw SpikeGLX or Open Ephys recordings through Kilosort4 spike sorting to curated units. Wraps SpikeInterface with opinionated workflows from Allen Institute and International Brain Laboratory, including motion correction, quality metrics computation, and automated curation. The AI-assisted visual analysis is clever: Claude can examine waveform plots directly to help classify borderline units that fall between your metric thresholds. Best for electrophysiology labs running Neuropixels 1.0 or 2.0 probes who want current best practices without reinventing preprocessing chains. Assumes you understand the neuroscience but saves you from stitching together fragmented documentation across five different packages.

skills.sh installs: 217
GitHub stars: 33.2K
last updated: Aug 21, 2026

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Install

$ npx -y skills add davila7/claude-code-templates --skill neuropixels-analysis --agent claude-code

Installs into .claude/skills of the current project.

Files

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