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.
npx skills add BioTender-max/awesome-bio-agent-skills --skill neuropixels-analysis --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# 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 |
- Overview
- When to Use This Skill
- Supported Hardware & Formats
- Quick Start
- Basic Import and Setup
- Loading Data
- Complete Pipeline (One Command)
- Standard Analysis Workflow
- 1. Preprocessing
- 2. Check and Correct Drift
- 3. Spike Sorting
- 4. Postprocessing
- 5. Curation
- 6. AI-Assisted Curation (For Uncertain Units)
python scripts/preprocess_recording.py /path/to/data --output preprocessed/ python scripts/run_sorting.py preprocessed/ --sorter kilosort4 --output sorting/ python scripts/compute_metrics.py sorting/ preprocessed/ --output metrics/ --curation allen python scripts/export_to_phy.py metrics/analyzer --output phy_export/ cp assets/analysis_template.py my_analysis.py Edit parameters and run python my_analysis.py Core packages pip install spikeinterface[full] probeinterface neo Spike sorters
What does the neuropixels-analysis skill do?
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.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill neuropixels-analysis --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.