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neuropixels-analysis

Automate end-to-end Neuropixels electrophysiology analysis from raw data to curated results.

1|Updated Mar 12, 2026
Search Tags:#data analysis#spike sorting#electrophysiology#neuropixels#spikeinterface#neural recording
One-click install
npx skills add https://github.com/yf8578/clawomics --skill neuropixels-analysis-yf8578
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: neuropixels-analysis
Source: https://github.com/yf8578/clawomics/tree/main/skills/neuropixels-analysis
Command: npx skills add https://github.com/yf8578/clawomics --skill neuropixels-analysis-yf8578

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

This Skill automates the complex and time-consuming process of analyzing Neuropixels neural recordings, from raw data to curated, publication-ready results.

Core Features & Use Cases

  • End-to-End Workflow: Handles preprocessing, motion correction, spike sorting, quality metrics, and curation.
  • Best Practices: Implements current standards from SpikeInterface, Allen Institute, and IBL.
  • Use Case: Analyze a Neuropixels recording session by providing the raw data path, and receive sorted units, quality metrics, and curated labels.

Quick Start

Use the neuropixels-analysis skill to run a full analysis pipeline on the provided Neuropixels 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 and curation for Neuropixels electrophysiology recordings?▼

Yes, you can analyze NWB format data alongside SpikeGLX and OpenEphys recordings. The pipeline supports these three input formats for end-to-end processing, allowing you to run preprocessing and spike sorting directly on your NWB files.

Does this analysis pipeline support data recorded in the NWB format?▼

Yes, you can analyze NWB format data alongside SpikeGLX and OpenEphys recordings. The pipeline supports these three input formats for end-to-end processing, allowing you to run preprocessing and spike sorting directly on your NWB files.

What is the best way to run Kilosort4 and SpykingCircus2 for neural recording analysis?▼

To start end-to-end electrophysiology analysis, provide the path to your raw neural recording data. The pipeline will automatically execute preprocessing, motion correction, spike sorting, and quality metric computation to deliver publication-ready curated results.

How do I start end-to-end electrophysiology analysis from raw data to curated units?▼

To start end-to-end electrophysiology analysis, provide the path to your raw neural recording data. The pipeline will automatically execute preprocessing, motion correction, spike sorting, and quality metric computation to deliver publication-ready curated results.

Can I use SpikeInterface for automated quality metric computation and curation?▼

Spike sorting requires careful motion correction and preprocessing beforehand to handle drift in Neuropixels recordings. This pipeline automates those necessary preliminary steps before running Kilosort4 or SpykingCircus2 to ensure accurate unit separation.

Why does spike sorting require motion correction for Neuropixels data?▼

Spike sorting requires careful motion correction and preprocessing beforehand to handle drift in Neuropixels recordings. This pipeline automates those necessary preliminary steps before running Kilosort4 or SpykingCircus2 to ensure accurate unit separation.

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