Which Neuropixels probes are supported by this skill?

The skill supports Neuropixels 1.0 and Neuropixels 2.0 (both single-shank and 4-shank versions), including specific corrections like phase_shift for 1.0 probes.

How does the AI-assisted curation feature work?

When running in Claude Code, Claude can analyze waveform plots and quality metrics to provide expert reasoning for unit classification, specifically helping with borderline 'good' vs 'mua' decisions.

What data formats can I import?

It natively supports SpikeGLX (.ap.bin, .lf.bin, .meta), Open Ephys (.continuous, .oebin), and NWB (.nwb) file formats.

Does it handle drift correction?

Yes, it includes specialized routines for drift estimation and correction, which is critical for long-term recordings where the probe may move relative to the brain tissue.

Can I run Kilosort4 directly through this workflow?

Yes, the skill provides wrappers for SpikeInterface to run Kilosort4, though it requires a compatible GPU for optimal performance.

Neuropixels Neural Analysis

Name: Neuropixels Neural Analysis
Author: Yezez9

byYezez9

0•

Data Science & ML

Streamlines the analysis of Neuropixels high-density neural recordings using SpikeInterface and industry-standard curation workflows.

This skill provides a comprehensive toolkit for processing Neuropixels 1.0 and 2.0 extracellular electrophysiology data. It enables Claude to guide users through the entire neural analysis pipeline, including raw data loading from SpikeGLX or Open Ephys, sophisticated preprocessing, motion and drift correction, and high-performance spike sorting via Kilosort4. By integrating quality metrics from the Allen Institute and International Brain Laboratory (IBL), it facilitates rigorous unit curation and AI-assisted visual analysis, helping researchers move from raw recordings to publication-quality results efficiently.

Key Features

01Full pipeline support for Neuropixels 1.0 and 2.0 (single and 4-shank) recordings.

02AI-assisted visual curation for resolving borderline neural unit classifications.

030 GitHub stars

04Integrated motion estimation and drift correction using non-rigid accurate presets.

05Standardized quality metric calculation including SNR, ISI violations, and presence ratio.

06Automated spike sorting management for Kilosort4, SpykingCircus2, and Mountainsort5.

Use Cases

01Processing large-scale extracellular recordings for systems neuroscience research.

02Automating quality control and curation for high-density silicon probe data.

03Converting raw SpikeGLX or Open Ephys data into curated NWB or Phy-compatible formats.

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add yezez9/research-agent neuropixels-analysis

For use in Claude.ai and ChatGPT

Key Features

01Full pipeline support for Neuropixels 1.0 and 2.0 (single and 4-shank) recordings.

02AI-assisted visual curation for resolving borderline neural unit classifications.

030 GitHub stars

04Integrated motion estimation and drift correction using non-rigid accurate presets.

05Standardized quality metric calculation including SNR, ISI violations, and presence ratio.

06Automated spike sorting management for Kilosort4, SpykingCircus2, and Mountainsort5.

Use Cases

01Processing large-scale extracellular recordings for systems neuroscience research.

02Automating quality control and curation for high-density silicon probe data.

03Converting raw SpikeGLX or Open Ephys data into curated NWB or Phy-compatible formats.