alterlab-neuropixels

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Analyze Neuropixels 1.0/2.0 extracellular electrophysiology with SpikeInterface — load SpikeGLX/Open Ephys recordings, preprocess and motion-correct, run Kilosort4 spike sorting, compute quality metrics, apply Allen/IBL curation, and do AI-assisted visual inspection. Use when working with neural recordings, spike sorting, or extracellular electrophysiology, or when the user mentions Neuropixels, SpikeGLX, Open Ephys, Kilosort, quality metrics, or unit curation. Part of the AlterLab Academic Skills suite.

AI & Automation 66 stars 13 forks Updated 1 weeks ago MIT

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Skill Content

# Neuropixels Data Analysis ## Overview Comprehensive toolkit for analyzing Neuropixels high-density neural recordings using current best practices from SpikeInterface, Allen Institute, and International Brain Laboratory (IBL). Supports the full workflow from raw data to publication-ready curated units. ## When to Use This Skill This skill should be used when: - Working with Neuropixels recordings (.ap.bin, .lf.bin, .meta files) - Loading data from SpikeGLX, Open Ephys, or NWB formats - Preprocessing neural recordings (filtering, CAR, bad channel detection) - Detecting and correcting motion/drift in recordings - Running spike sorting (Kilosort4, SpykingCircus2, Mountainsort5) - Computing quality metrics (SNR, ISI violations, presence ratio) - Curating units using Allen/IBL criteria - Creating visualizations of neural data - Exporting results to Phy or NWB ## Supported Hardware & Formats | Probe | Electrodes | Channels | Notes | |-------|-----------|----------|-------| | Neuropixels 1.0 | 960 | 384 | Requires phase_shift correction | | Neuropixels 2.0 (single) | 1280 | 384 | Denser geometry | | Neuropixels 2.0 (4-shank) | 5120 | 384 | Multi-region recording | | Format | Extension | Reader | |--------|-----------|--------| | SpikeGLX | `.ap.bin`, `.lf.bin`, `.meta` | `si.read_spikeglx()` | | Open Ephys | `.continuous`, `.oebin` | `si.read_openephys()` | | NWB | `.nwb` | `si.read_nwb()` | ## Quick Start ### Basic Import and Setup ```python import spikeinterface.full as...

Details

Author
AlterLab-IEU
Repository
AlterLab-IEU/AlterLab-Academic-Skills
Created
5 months ago
Last Updated
1 weeks ago
Language
Python
License
MIT

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Anthropic · AI

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AlterLab-Academic-Skills

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