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neuropixels-analysis

Analyze Neuropixels neural recordings from raw data to curated units.

1|Updated Mar 4, 2026
Search Tags:#data-analysis#quality-metrics#neuropixels#spike-sorting#drift-correction#ai-curation#neural-data
One-click install
npx skills add https://github.com/Hung-3008/agusta --skill neuropixels-analysis-hung-3008
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: neuropixels-analysis
Source: https://github.com/Hung-3008/agusta/tree/main/.agents/skills/neuropixels-analysis
Command: npx skills add https://github.com/Hung-3008/agusta --skill neuropixels-analysis-hung-3008

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires spikeinterface, pandas, numpy, matplotlib, scipy, probeinterface, and includes scripts (resource) and references (resource) and assets (resource) components.

What problem does it solve?

Analyze Neuropixels neural recordings from raw data to curated units.

Core Features & Use Cases

  • Preprocessing: high-pass filtering, bad-channel detection, common median reference, phase shift handling.
  • Spike sorting & drift correction: run sorters (Kilosort4, SpykingCircus2, Mountainsort5) with drift mitigation and QC metrics.
  • AI-assisted curation: integrate AI visual analysis for unit-classification and batch curation.
  • Export: Phy/NWB export, quality metrics CSV, and reporting.

Quick Start

Load Neuropixels data and run the full analysis pipeline to produce a curated set of units.

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 drift correction on Neuropixels data?▼

This Skill processes raw Neuropixels recordings by applying preprocessing, drift correction, and spike sorting using SpikeInterface to output curated units.

What formats are supported for Neuropixels neural data analysis?▼

The analysis pipeline accepts SpikeGLX, Open Ephys, and NWB formats for NP1.0 and NP2.0 recordings, processing them via SpikeInterface.

Does SpikeInterface work with Kilosort4 for AI-assisted curation?▼

SpikeInterface integrates with Kilosort4 for sorting, enabling downstream AI-assisted curation modules to classify and curate units.

What is the best way to curate sorted units and export quality metrics?▼

Use this Skill's AI curation module to batch classify sorted units, generating quality metrics CSVs and exporting results to Phy or NWB formats.

How do I handle bad channels and common median reference in Neuropixels preprocessing?▼

The Skill's preprocessing step automatically applies high-pass filtering, bad-channel detection, and common median reference removal to prepare raw neural data.

Can I use Allen or IBL standards for Neuropixels data export?▼

The pipeline utilizes Allen and IBL standards during the export phase to ensure formatted NWB and Phy outputs meet recognized neuroscience benchmarks.

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