neuropixels-analysis
Analyze Neuropixels extracellular recordings end-to-end with SpikeInterface. Covers loading SpikeGLX/Open Ephys/NWB data, preprocessing, drift/motion correction, Kilosort4 (and CPU) spike sorting, quality metrics, and unit curation (threshold-based, model-based UnitRefine, and AI-assisted visual review). Use when working with Neuropixels 1.0/2.0 recordings, spike sorting, or extracellular electrophysiology analysis.
npx skills add K-Dense-AI/scientific-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 Toolkit for analyzing Neuropixels high-density neural recordings using current best practices from [SpikeInterface](https://spikeinterface.readthedocs.io/), the Allen Institute, and the International Brain Laboratory (IBL). It covers the full workflow from raw data to publication-ready curated units. All examples use the real SpikeInterface API (`spikeinterface.full as si`) plus the companion curation module (`spikeinterface.curation as sc`). The skill ships runnable scripts in `scripts/` and a copy-and-edit template in `assets/` that implement this workflow directly on top of SpikeInterface — there is no separate package to install beyond the dependencies listed under [Installation](#installation). ## 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, common reference, bad-channel detection) - Detecting and correcting motion/drift - Running spike sorting (Kilosort4, SpykingCircus2, Mountainsort5, Tridesclous2) - Computing quality metrics (SNR, ISI violations, pr
- Overview
- When to Use This Skill
- Supported Hardware & Formats
- Quick Start
- Import and configure parallel processing
- Loading data
- Full pipeline (bundled script)
- Standard Analysis Workflow
- 1. Preprocessing
- 2. Check and correct drift
- 3. Spike sorting
- 4. Postprocessing
- 5. Curation by metric thresholds
- 6. Model-based curation (UnitRefine)
python scripts/neuropixels_pipeline.py /path/to/spikeglx/data output/ --sorter kilosort4 --curation allen python scripts/explore_recording.py /path/to/data 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 the PARAMETERS section, then run python my_analysis.py Core packages (SpikeInterface bundles the curation/model tooling)
What does the neuropixels-analysis skill do?
Analyze Neuropixels extracellular recordings end-to-end with SpikeInterface. Covers loading SpikeGLX/Open Ephys/NWB data, preprocessing, drift/motion correction, Kilosort4 (and CPU) spike sorting, quality metrics, and unit curation (threshold-based, model-based UnitRefine, and AI-assisted visual review). Use when working with Neuropixels 1.0/2.0 recordings, spike sorting, or extracellular electrophysiology analysis.
How do I install it?
Run `npx skills add K-Dense-AI/scientific-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 K-Dense-AI/scientific-agent-skills, a repository with 32,619 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.