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neuropixels-analysis

Automate Neuropixels analysis from raw recordings to curated units.

4|1|Updated Jun 18, 2025
Search Tags:#data-analysis#quality-metrics#neuropixels#spikeinterface#spike-sorting#drift-correction#ai-curation
One-click install
npx skills add https://github.com/HolobiomicsLab/Toolomics --skill neuropixels-analysis-holobiomicslab
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: neuropixels-analysis
Source: https://github.com/HolobiomicsLab/Toolomics/tree/main/mcp_host/skills/scientific-skills/scientific-skills/neuropixels-analysis
Command: npx skills add https://github.com/HolobiomicsLab/Toolomics --skill neuropixels-analysis-holobiomicslab

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

Analyzing Neuropixels data is a complex, multi-step workflow that takes raw recordings through preprocessing, drift correction, spike sorting, quality assessment, and curated unit labeling, all while requiring reproducible configuration and clear outputs.

Core Features & Use Cases

  • End-to-end Neuropixels workflow: load data from SpikeGLX or Open Ephys, preprocess, correct motion, sort spikes, compute quality metrics, and curate units.
  • AI-assisted curation: integrate AI-based visual analysis to assist unit labeling and decision making.
  • Export-ready results: supports outputs such as Phy exports, NWB, and analysis reports for publication.

Quick Start

Run the Neuropixels analysis pipeline on your dataset to obtain preprocessed data, sorted units, and quality metrics.

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 recordings?▼

You can run spike sorting and drift correction on Neuropixels recordings by loading SpikeGLX or Open Ephys data into SpikeInterface, then applying the automated preprocessing, motion correction, and sorting workflow to generate curated units.

What is the best way to analyze Neuropixels 2.0 data end-to-end?▼

The best way to analyze Neuropixels 2.0 data end-to-end is using an automated pipeline that handles preprocessing, motion correction, spike sorting, and quality metrics computation to produce export-ready curated units and analysis reports.

Can I use SpikeInterface for AI-assisted curation of sorted units?▼

Yes, SpikeInterface can be combined with AI-assisted visual analysis to help label sorted units and support curation decisions, streamlining the manual review process typically done in Phy.

Does this Neuropixels analysis pipeline support Open Ephys data formats?▼

Yes, the pipeline supports loading raw recordings directly from Open Ephys as well as SpikeGLX, allowing you to preprocess and spike sort data acquired from either system.

How do I export spike sorting results to NWB and Phy?▼

You can export spike sorting results to NWB and Phy formats using the pipeline's export-ready outputs, which also generate analysis reports for publication directly from the curated units.

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