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RamanEbrahimi
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neuropixels-analysis

Automate Neuropixels neural recording analysis with spike sorting and quality metrics.

3|Updated Apr 17, 2026
Search Tags:#quality metrics#spike sorting#neuropixels#neural recording#AI curation
One-click install
npx skills add https://github.com/RamanEbrahimi/raman-marketplace --skill neuropixels-analysis-ramanebrahimi
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: neuropixels-analysis
Source: https://github.com/RamanEbrahimi/raman-marketplace/tree/main/plugins/agentic-research/skills/scientific-skills/neuropixels-analysis
Command: npx skills add https://github.com/RamanEbrahimi/raman-marketplace --skill neuropixels-analysis-ramanebrahimi

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

This Skill automates the complex process of analyzing Neuropixels neural recordings, including preprocessing, spike sorting, quality metrics, and AI-assisted curation, saving researchers significant time and reducing human error.

Core Features & Use Cases

  • Preprocessing: Highpass filter, phase shift correction, common reference, and bad channel removal.
  • Spike Sorting: Kilosort4, SpykingCircus2, Mountainsort5, and Tridesclous2 sorters supported.
  • Quality Metrics: Computes SNR, ISI violations, presence ratio, and more.
  • AI-Assisted Curation: Uses Claude Code to analyze visualizations and provide expert curation decisions.
  • Use Case: Imagine you have hours of Neuropixels data to analyze. Use this Skill to automatically preprocess the data, run spike sorting, compute quality metrics, and apply AI-assisted curation, resulting in curated units ready for further analysis.

Quick Start

Load your neuropixels data into the neuropixels-analysis skill.

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 high-density extracellular electrophysiology data?▼

To automate spike sorting and curation, this Skill preprocesses binary neural recordings, runs sorters like Kilosort4 or Mountainsort5, and applies AI-assisted curation using Claude Code to yield curated units ready for downstream analysis.

What preprocessing steps are needed for Neuropixels neural recordings before spike sorting?▼

Preprocessing Neuropixels neural recordings requires highpass filtering, phase shift correction, applying a common reference, and bad channel removal. These steps prepare the binary recording data for accurate spike sorting and subsequent quality metrics computation.

Which spike sorting algorithms are supported for high-density extracellular electrophysiology analysis?▼

Supported spike sorting algorithms include Kilosort4, SpykingCircus2, Mountainsort5, and Tridesclous2. These sorters process the preprocessed neural recordings to detect and cluster spike events for downstream quality metric evaluation.

Can I use AI to assist with neural recording curation and unit quality evaluation?▼

AI-assisted curation uses Claude Code to analyze visualizations and provide expert curation decisions for neural recordings. It evaluates computed quality metrics like SNR and ISI violations to help curate the sorted units.

Does this spike sorting workflow support parallel processing for large neural recordings?▼

The spike sorting workflow supports parallel processing to improve performance on large neural recordings. This allows researchers to process extensive high-density extracellular electrophysiology datasets more efficiently using SpikeInterface and related libraries.

What quality metrics are computed during Neuropixels data analysis?▼

Quality metrics computed during Neuropixels data analysis include signal-to-noise ratio (SNR), ISI violations, and presence ratio. These metrics evaluate the reliability of sorted units before AI-assisted curation finalizes the results.

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