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neuropixels-analysis

Automate Neuropixels neural recording analysis with SpikeInterface preprocessing and spike sorting.

13|3|Updated Jun 10, 2026
Search Tags:#spike sorting#electrophysiology#neuropixels#spikeinterface#neural data analysis
One-click install
npx skills add https://github.com/tassiovale/claude-code-kit --skill neuropixels-analysis-tassiovale
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: neuropixels-analysis
Source: https://github.com/tassiovale/claude-code-kit/tree/main/skills/neuropixels-analysis
Command: npx skills add https://github.com/tassiovale/claude-code-kit --skill neuropixels-analysis-tassiovale

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires spikeinterface, probeinterface, neo, kilosort, spykingcircus, mountainsort, tridesclous, huggingface_hub, skops, anthropic, and includes scripts (resource) and references (resource) and assets (resource) components.

What problem does it solve?

This Skill provides a comprehensive solution for analyzing high-density neural recordings from Neuropixels probes using SpikeInterface, covering preprocessing, spike sorting, quality metrics, and unit curation.

Core Features & Use Cases

  • Data Loading: Supports loading data from various formats like SpikeGLX, Open Ephys, and NWB.
  • Preprocessing: Includes drift/motion correction, noise filtering, and bad-channel detection.
  • Spike Sorting: Integrates with Kilosort4 and other sorting algorithms.
  • Quality Metrics: Computes SNR, ISI violations, presence ratio, and amplitude cutoff.
  • Unit Curation: Offers threshold-based, model-based UnitRefine, and AI-assisted visual review.
  • Use Case: Ideal for researchers working with Neuropixels 1.0/2.0 recordings and performing extracellular electrophysiology analysis.

Quick Start

Run the provided script to analyze Neuropixels data:

python scripts/neuropixels_pipeline.py /path/to/spikeglx/data output/ --sorter kilosort4 --curation allen

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 using SpikeInterface?▼

Yes, this Skill analyzes Neuropixels data from SpikeGLX, Open Ephys, and NWB formats. It uses SpikeInterface and Neo to load these high-density extracellular electrophysiology recordings for subsequent preprocessing and spike sorting.

What spike sorting algorithms are supported for Neuropixels data analysis?▼

Yes, this Skill handles Neuropixels 2.0 recordings alongside Neuropixels 1.0 data. It applies SpikeInterface preprocessing, spike sorting, and unit curation workflows to high-density extracellular electrophysiology data from either probe version.

How do I run spike sorting on Neuropixels recordings using SpikeInterface?▼

Quality metrics computed for spike sorting include SNR, ISI violations, presence ratio, and amplitude cutoff. The Skill uses these metrics for threshold-based, model-based UnitRefine, and AI-assisted visual review to curate sorted units.

What spike sorting algorithms are supported for Neuropixels data analysis?▼

Preprocessing steps include drift and motion correction, noise filtering, and bad-channel detection. These steps prepare high-density Neuropixels extracellular electrophysiology recordings for accurate spike sorting and quality metric analysis.

Does this Skill support Neuropixels 2.0 recordings and Open Ephys data formats?▼

Yes, this Skill supports Neuropixels 2.0 and 1.0 recordings. It loads data from SpikeGLX, Open Ephys, and NWB formats using SpikeInterface and Neo for comprehensive extracellular electrophysiology analysis.

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