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LeonChaoX
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neuropixels-analysis

Preprocess, drift-correct, sort, and curate Neuropixels recordings with Kilosort4.

783|65|Updated Feb 27, 2026
Search Tags:#quality metrics#spike sorting#AI-assisted review#neuropixels#spikeinterface#motion correction#unit curation
One-click install
npx skills add https://github.com/LeonChaoX/qinyan-academic-skills --skill neuropixels-analysis-leonchaox
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: neuropixels-analysis
Source: https://github.com/LeonChaoX/qinyan-academic-skills/tree/main/skills/07-%E4%B8%B4%E5%BA%8A%E5%8C%BB%E5%AD%A6%E4%B8%8E%E7%B2%BE%E5%87%86%E5%8C%BB%E7%96%97/neuropixels-analysis
Command: npx skills add https://github.com/LeonChaoX/qinyan-academic-skills --skill neuropixels-analysis-leonchaox

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires spikeinterface[full], probeinterface, neo, kilosort, spykingcircus, mountainsort5, anthropic, ibl-neuropixel, ibllib, and includes scripts (resource) and references (resource) and assets (resource) components.

What problem does it solve?

Neuropixels users need a reliable, publication-grade pipeline that converts raw extracellular recordings into quality-assessed and curated single units, including preprocessing, drift correction, spike sorting, metrics, and optional AI-assisted review. This Skill eliminates fragmented, error-prone workflows by coordinating the end-to-end analysis steps required for spike sorting and unit curation on Neuropixels 1.0/2.0 data.

Core Features & Use Cases

  • End-to-end Neuropixels workflow: preprocess, motion/drift handling, spike sorting (e.g., Kilosort4), postprocessing, and export-ready outputs.
  • Quality metrics + automated curation: compute core ephys QC metrics (e.g., SNR, ISI violations, presence ratio, amplitude cutoff) and apply Allen/IBL/strict labeling rules.
  • AI-assisted visual curation: use a vision-language model to review borderline units using waveform/ACG style plots for good/mua/noise decisions.
  • Exports for downstream review: prepare outputs for Phy and NWB, plus generate analysis reports and figures.

Quick Start

Run the full pipeline on a Neuropixels recording with Kilosort4 and Allen-style curation to produce curated unit labels and publication-ready exports.

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 on Neuropixels recordings from SpikeGLX or Open Ephys?▼

AI-assisted visual curation reviews borderline units by feeding waveform and autocorrelogram plots to a vision-language model. The model analyzes the visual data to classify units into good, mua, or noise categories, automating borderline unit decisions.

Does this pipeline support phase-shift correction for Neuropixels 1.0?▼

Automated unit curation applies Allen, IBL, or strict labeling rules to the computed quality metrics. Additionally, an AI-assisted visual review uses waveform and autocorrelogram plots to classify borderline units as good, mua, or noise.

Does the workflow handle phase-shift correction for Neuropixels 1.0 data?▼

Export-ready outputs are prepared for downstream review in Phy and NWB formats. The pipeline also generates analysis reports and figures summarizing the spike sorting and unit curation results.

Does the workflow handle phase-shift correction for Neuropixels 1.0 data?▼

Export-ready outputs are prepared for downstream review in Phy and NWB formats. The pipeline also generates analysis reports and figures summarizing the spike sorting and unit curation results.

Does the workflow handle phase-shift correction for Neuropixels 1.0 data?▼

Export-ready outputs are prepared for downstream review in Phy and NWB formats. The pipeline also generates analysis reports and figures summarizing the spike sorting and unit curation results.

Does the workflow handle phase-shift correction for Neuropixels 1.0 data?▼

Export-ready outputs are prepared for downstream review in Phy and NWB formats. The pipeline also generates analysis reports and figures summarizing the spike sorting and unit curation results.

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