Individual skill

neuropixels-analysis

End-to-end Neuropixels extracellular electrophysiology analysis (SpikeGLX/Open Ephys/NWB) including preprocessing, motion correction, Kilosort4 spike sorting, QC metrics, and Allen/IBL-style curation; use when processing Neuropixels recordings or when users mention Neuropixels, SpikeGLX, Open Ephys, Kilosort, quality metrics, drift/motion correction, or unit curation.

scientific-skills/Data Analysis/neuropixels-analysis/SKILL.md

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Repository stars (not skill ratings): 2,049
Repository last updated: Sep 17, 2026
License: MIT

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bioinformatics Repository topic
computational-biology Repository topic
data-analysis Repository topic
ai Repository topic
biology Repository topic
cancer-genomics Repository topic
data-visualization Repository topic
differential-expression Repository topic
genomics Repository topic
medical Repository topic
engineering Derived category
testing Derived category
testing-browser Derived category

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Browse files

SKILL.mdcore · 9,732 bytes
SKILL.mdcore · 9,732 bytes
assets/analysis_template.pyruns · 9,285 bytes
neuropixels-analysis_audit_result_v1.jsonasset · 12,867 bytes
references/AI_CURATION.mddoc · 9,088 bytes
references/ANALYSIS.mddoc · 10,454 bytes
references/AUTOMATED_CURATION.mddoc · 10,694 bytes
references/MOTION_CORRECTION.mddoc · 9,233 bytes
references/PREPROCESSING.mddoc · 7,163 bytes
references/QUALITY_METRICS.mddoc · 10,214 bytes
references/SPIKE_SORTING.mddoc · 8,395 bytes
references/api_reference.mddoc · 8,743 bytes
references/plotting_guide.mddoc · 11,525 bytes
references/standard_workflow.mddoc · 9,161 bytes
scripts/compute_metrics.pyruns · 5,404 bytes
scripts/explore_recording.pyruns · 5,697 bytes
scripts/export_to_phy.pyruns · 2,556 bytes
scripts/neuropixels_pipeline.pyruns · 13,718 bytes
scripts/preprocess_recording.pyruns · 4,357 bytes
scripts/run_sorting.pyruns · 2,671 bytes

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> **Source**: [https://github.com/aipoch/medical-research-skills](https://github.com/aipoch/medical-research-skills)

## When to Use

Use this skill in any of the following situations:

1. **You need to load and standardize Neuropixels recordings** from SpikeGLX (`.ap.bin/.lf.bin/.meta`), Open Ephys (`.continuous/.oebin`), or NWB (`.nwb`) into a consistent analysis pipeline.
2. **You are preparing raw extracellular data for spike sorting**, including high-pass filtering, phase shift correction (NP1.0), bad channel detection/removal, and common average referencing (CAR).
3. **You suspect probe drift or tissue motion** and need to estimate and correct motion before sorting (especially when drift is > ~10 µm).
4. **You want to run spike sorting** (Kilosort4 recommended; CPU alternatives supported) and then compute post-processing products (waveforms, templates, amplitudes, correlograms, unit locations).
5. **You need quality control and curation** using Allen/IBL-style thresholds, plus optional AI-assisted visual review for borderline units, and exports to Phy/NWB.

## Key Features

- **Multi-format ingestion**: SpikeGLX, Open Ephys, and NWB readers via SpikeInterface.