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neuropixels-analysis

Analyze Neuropixels recordings into curated spike-sorting units with Kilosort4.

Updated May 24, 2026
Search Tags:#quality metrics#SpikeInterface#spike sorting#neuropixels#motion correction#unit curation
One-click install
npx skills add https://github.com/Estrella-231/Mathematical_modeling_tongmeng --skill neuropixels-analysis-estrella-231
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: neuropixels-analysis
Source: https://github.com/Estrella-231/Mathematical_modeling_tongmeng/tree/main/.agents/skills/neuropixels-analysis
Command: npx skills add https://github.com/Estrella-231/Mathematical_modeling_tongmeng --skill neuropixels-analysis-estrella-231

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes scripts (resource) and references (resource) and assets (resource) components.

What problem does it solve?

Neuropixels extracellular recordings are complex to process end-to-end, especially when you need reliable preprocessing, motion/drift handling, spike sorting, and unit curation that meets common QC standards.

Core Features & Use Cases

  • Full spike-sorting workflow: load SpikeGLX/Open Ephys/NWB data, preprocess, estimate/correct motion, run spike sorting (e.g., Kilosort4), and compute standard postprocessing outputs.
  • Quality metrics + curation: calculate quality metrics (SNR, ISI violations, presence ratio, drift metrics, isolation measures) and apply Allen/IBL/strict curation logic.
  • AI-assisted visual review: use AI to inspect waveform/correlogram plots and help decide borderline unit classifications.
  • Export for manual review: export to Phy and optionally NWB to support publication-grade review and iteration.

Quick Start

Use the neuropixels-analysis skill to run the full pipeline on your Neuropixels recording and produce curated units with quality metrics exported to an output directory.

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?▼

To run spike sorting on Neuropixels recordings, you can load SpikeGLX, Open Ephys, or NWB data and use SpikeInterface to preprocess, estimate motion, run Kilosort4, and generate curated units.

What quality metrics are calculated for unit curation in extracellular electrophysiology?▼

Quality metrics for unit curation include SNR, ISI violations, presence ratio, drift metrics, and isolation measures, which are evaluated using Allen, IBL, or strict curation logic standards.

Can I process data from both SpikeGLX and Open Ephys formats in the same spike-sorting workflow?▼

Yes, the spike-sorting workflow supports loading raw data from SpikeGLX, Open Ephys, and NWB formats to preprocess recordings and apply probe-appropriate corrections like phase shift for Neuropixels 1.0.

How does motion correction handle drift estimation in Neuropixels data?▼

Motion correction handles drift by estimating and correcting motion within the SpikeInterface preprocessing pipeline before running spike sorting to ensure accurate unit separation.

Does AI visual assistance help with deciding borderline unit classifications?▼

Yes, AI visual assistance inspects waveform and correlogram plots to help you decide borderline unit classifications during the curation process after computing quality metrics.

What is the best way to export curated spike-sorting units for publication-ready review?▼

To export curated units for publication-ready review, generate outputs in Phy and optionally NWB formats to support manual inspection and iterative evaluation.

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