alterlab-neuropixels

# 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...