Individual skill
neuropixels-analysis
Neuropixels neural recording analysis. Load SpikeGLX/OpenEphys data, preprocess, motion correction, Kilosort4 spike sorting, quality metrics, Allen/IBL curation, AI-assisted visual analysis, for Neuropixels 1.0/2.0 extracellular electrophysiology. Use when working with neural recordings, spike sorting, extracellular electrophysiology, or when the user mentions Neuropixels, SpikeGLX, Open Ephys, Kilosort, quality metrics, or unit curation.
cli-tool/components/skills/scientific/neuropixels-analysis/SKILL.md
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AI_CURATION.mddoc · 8,657 bytesANALYSIS.mddoc · 9,869 bytesAUTOMATED_CURATION.mddoc · 10,033 bytesLICENSE.txtdoc · 1,065 bytesMOTION_CORRECTION.mddoc · 8,670 bytesPREPROCESSING.mddoc · 6,696 bytesQUALITY_METRICS.mddoc · 9,454 bytesSKILL.mdcore · 11,340 bytesSKILL.mdcore · 11,340 bytesSKILL.mdcore · 11,340 bytesSKILL.mdcore · 11,340 bytesSKILL.mdcore · 11,340 bytesSKILL.mdcore · 11,340 bytesSKILL.mdcore · 11,340 bytesSKILL.mdcore · 11,340 bytesSKILL.mdcore · 11,340 bytesSKILL.mdcore · 11,340 bytesSKILL.mdcore · 11,340 bytesSKILL.mdcore · 11,340 bytesSKILL.mdcore · 11,340 bytesSKILL.mdcore · 11,340 bytesSKILL.mdcore · 11,340 bytesSKILL.mdcore · 11,340 bytesSKILL.mdcore · 11,340 bytesSKILL.mdcore · 11,340 bytesSKILL.mdcore · 11,340 bytesSPIKE_SORTING.mddoc · 7,918 bytesassets/analysis_template.pyruns · 9,014 bytesreferences/api_reference.mddoc · 8,175 bytesreferences/plotting_guide.mddoc · 10,837 bytesreferences/standard_workflow.mddoc · 8,646 bytesscripts/compute_metrics.pyruns · 5,226 bytesscripts/explore_recording.pyruns · 5,529 bytesscripts/export_to_phy.pyruns · 2,477 bytesscripts/neuropixels_pipeline.pyruns · 13,286 bytesscripts/preprocess_recording.pyruns · 4,235 bytesscripts/run_sorting.pyruns · 2,573 bytes
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# 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)