Neuropixels Analysis

This is a complete pipeline for analyzing Neuropixels neural recordings, from loading raw SpikeGLX or Open Ephys data through spike sorting with Kilosort4 and unit curation using Allen Institute or IBL criteria. It wraps SpikeInterface with sensible defaults for preprocessing (highpass filtering, bad channel detection, common average referencing), motion correction, and quality metrics computation. The AI-assisted curation feature is genuinely useful for borderline units where SNR sits in that awkward 3-8 range. Built for both Neuropixels 1.0 and 2.0 probes. If you're doing extracellular electrophysiology and tired of stitching together preprocessing scripts, this gives you a tested workflow that matches what major neuroscience labs actually use. The documentation is thorough about pitfalls like remembering phase shift correction for 1.0 probes.

skills.sh installs: 2K
GitHub stars: 56.6K
last updated: Aug 21, 2026

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Install

$ npx -y skills add k-dense-ai/scientific-agent-skills --skill neuropixels-analysis --agent claude-code

Installs into .claude/skills of the current project.

Files

Neuropixels Data Analysis

Overview

Toolkit for analyzing Neuropixels high-density neural recordings using current best practices from SpikeInterface, the Allen Institute, and the International Brain Laboratory (IBL). It covers the full workflow from raw data to reviewed, curated units. Targets SpikeInterface 0.105.0, ProbeInterface 0.4.0 and Neo 0.14.5 (reviewed 2026-10-01). Synthetic tests cover recording contracts, preprocessing, analyzers, metrics and exports; real acquisition files, native sorters, GPU execution and pretrained models remain illustrative.

All examples use the real SpikeInterface API (spikeinterface.full as si) plus the companion curation module (spikeinterface.curation as sc). The skill ships runnable scripts in scripts/ and a copy-and-edit template in assets/ that implement this workflow directly on top of SpikeInterface — there is no separate package to install beyond the dependencies listed under Installation.