neuropixels-analysis
Neuropixels Analysis
Overview
Neuropixels probes record extracellular voltage from 384 (NP 1.0) or 192 (NP 2.0) simultaneously recorded channels at 30 kHz. Analysis follows a canonical pipeline: raw data → spike sorting (Kilosort) → quality curation → unit analysis. SpikeInterface (Python) provides a unified API across 10+ spike sorters, handles data loading from multiple formats (SpikeGLX, OpenEphys, NWB), computes quality metrics, and exports sorted results. ProbeInterface manages probe geometry and channel maps. Post-sort analysis (PSTHs, firing rate, decoding) uses standard Python scientific stack.
When to Use
- Spike-sorting Neuropixels recordings from SpikeGLX (
.bin) or OpenEphys (.dat) to extract single-unit activity - Applying automatic quality control metrics (ISI violations, SNR, firing rate) to curate sorted units
- Computing peristimulus time histograms (PSTHs) locked to experimental events
- Analyzing population coding: decoding stimulus or behavioral variables from firing rates
- Converting sorted data to NWB (Neurodata Without Borders) format for sharing
- Comparing multiple spike sorters on the same dataset for method validation
- Visualizing unit waveforms, auto-correlograms, and spatial distribution across probe channels
- Use SpikeInterface instead for a unified framework that supports 10+ spike sorters with a common API and comparison tools
Prerequisites
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