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neuropixels-analysis

Automate Neuropixels electrophysiology analysis from SpikeGLX, OpenEphys, and NWB data.

Updated Mar 10, 2026
Search Tags:#data processing#spike sorting#electrophysiology#neuropixels#neural data analysis#brain science
One-click install
npx skills add https://github.com/Yezez9/Research-Agent --skill neuropixels-analysis-yezez9
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: neuropixels-analysis
Source: https://github.com/Yezez9/Research-Agent/tree/main/scientific-skills/neuropixels-analysis
Command: npx skills add https://github.com/Yezez9/Research-Agent --skill neuropixels-analysis-yezez9

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

This Skill streamlines the complex process of analyzing Neuropixels neural recordings, from raw data to publication-ready curated units, saving researchers significant time and effort.

Core Features & Use Cases

  • End-to-End Workflow: Supports loading, preprocessing, motion correction, spike sorting, quality assessment, and curation.
  • Advanced Tools: Integrates Kilosort4, SpikeInterface, and AI-assisted curation for robust analysis.
  • Use Case: Analyze a Neuropixels recording to identify and classify single neurons, assess their firing properties, and visualize their activity patterns across different brain regions.

Quick Start

Run the full neuropixels analysis pipeline on the provided recording data.

Frequently Asked Questions about neuropixels-analysis

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

FAQPage Schema
How do I automate spike sorting for Neuropixels recordings from SpikeGLX or OpenEphys?▼

Yes, you can load OpenEphys and SpikeGLX data directly. This Skill automates the extracellular electrophysiology pipeline by handling format ingestion, preprocessing, and motion correction before running spike sorting.

What is the best way to curate sorted units and compute quality metrics for neural data analysis?▼

The best way to curate sorted units is using automated and AI-assisted curation. This Skill computes quality metrics and analyzes waveforms to help you assess firing properties and refine neural data analysis outputs.

Does this electrophysiology pipeline support exporting results to Phy and NWB formats?▼

Yes, this electrophysiology pipeline supports exporting to Phy and NWB formats. It visualizes activity patterns and exports the final curated units from your Neuropixels recordings for downstream analysis.

Can I use SpikeInterface and Kilosort4 for end-to-end brain science data processing?▼

You can use SpikeInterface and Kilosort4 for brain science data processing. This Skill integrates these frameworks to manage the entire workflow from raw data loading to automated curation of neural recordings.

What are the limitations of AI-assisted curation in extracellular electrophysiology analysis?▼

While the Skill provides AI-assisted curation to streamline extracellular electrophysiology analysis, limitations include relying on computed quality metrics and waveform analysis, requiring manual review in Phy for complex borderline units.

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