neuropixels-analysis

SKILL.md

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