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neuropixels-analysis

Analyze Neuropixels electrophysiology data with Kilosort4 and export curated units.

4|Updated Mar 2, 2026
Search Tags:#quality metrics#SpikeInterface#spike sorting#AI-assisted review#neuropixels#motion correction#unit curation
One-click install
npx skills add https://github.com/shushuzn/Rairos --skill neuropixels-analysis-shushuzn
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: neuropixels-analysis
Source: https://github.com/shushuzn/Rairos/tree/main/skills/neuropixels-analysis
Command: npx skills add https://github.com/shushuzn/Rairos --skill neuropixels-analysis-shushuzn

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires spikeinterface, neuropixels-analysis, kilosort, spykingcircus, mountainsort5, anthropic, and includes scripts (resource) and references (resource) and assets (resource) components.

What problem does it solve?

Neuropixels recordings require a complex, error-prone workflow—from loading raw data through preprocessing, drift correction, spike sorting, QC, and unit curation—so this skill streamlines the full pipeline into reproducible steps that produce publication-ready curated results.

Core Features & Use Cases

  • End-to-end Neuropixels analysis workflow: Load SpikeGLX/Open Ephys/NWB data, preprocess, correct motion/drift, run spike sorting (including Kilosort4), compute quality metrics, and curate units using Allen/IBL-style criteria.
  • Publication-ready quality assessment & curation: Generate metrics like SNR, ISI violations, presence ratio, amplitude cutoff, drift metrics, isolation measures, and support exporting for manual verification.
  • AI-assisted visual analysis for uncertain units: Use vision-language models to review waveform/correlogram plots and make curation decisions for borderline cases.
  • Export for downstream review and sharing: Export curated results to Phy for human-in-the-loop inspection and to NWB for standardized archiving.

Quick Start

Run a full Neuropixels pipeline by loading your recording data, preprocessing it, running Kilosort4 spike sorting, computing quality metrics, and curating units with an Allen-style method in one go.

Frequently Asked Questions about neuropixels-analysis

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I run spike sorting and motion correction for Neuropixels data end-to-end?▼

To run spike sorting for Neuropixels data, you can load SpikeGLX, Open Ephys, or NWB files to preprocess, apply drift correction, run Kilosort4, and compute quality metrics in a single reproducible pipeline.

What quality metrics are used for spike sorting unit curation?▼

Unit curation relies on quality metrics like SNR, ISI violations, presence ratio, amplitude cutoff, drift metrics, and isolation measures, applying Allen or IBL-style criteria to evaluate sorted units.

Does this workflow support phase-shift handling for Neuropixels 1.0 probes?▼

Yes, the workflow explicitly requires phase-shift handling for Neuropixels 1.0 probes during preprocessing to ensure accurate data alignment before drift estimation and correction.

Can I use AI to review uncertain units during spike sorting curation?▼

Yes, AI-assisted visual analysis uses vision-language models to review waveform and correlogram plots, making curation decisions for borderline or uncertain units to streamline the process.

How do I export curated spike sorting results for downstream review?▼

You can export curated results to Phy for human-in-the-loop manual inspection and to NWB format for standardized archiving, facilitating downstream analysis and data sharing.

What is the best way to handle drift correction in extracellular electrophysiology data?▼

The best way to handle drift correction is through a pipeline that performs drift estimation and motion correction before spike sorting, ensuring motion artifacts do not degrade unit separation quality.

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