Add neuropixels-analysis skill for extracellular electrophysiology

Adds comprehensive toolkit for analyzing Neuropixels high-density neural
recordings using SpikeInterface, Allen Institute, and IBL best practices.

Features:
- Data loading from SpikeGLX, Open Ephys, and NWB formats
- Preprocessing pipelines (filtering, phase shift, CAR, bad channel detection)
- Motion/drift estimation and correction
- Spike sorting integration (Kilosort4, SpykingCircus2, Mountainsort5)
- Quality metrics computation (SNR, ISI violations, presence ratio)
- Automated curation using Allen/IBL criteria
- AI-assisted visual curation for uncertain units
- Export to Phy and NWB formats

Supports Neuropixels 1.0 and 2.0 probes.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

scientific-skills/neuropixels-analysis/scripts/export_to_phy.py

@@ -0,0 +1,79 @@
+#!/usr/bin/env python
+"""
+Export sorting results to Phy for manual curation.
+
+Usage:
+    python export_to_phy.py metrics/analyzer --output phy_export/
+"""
+
+import argparse
+from pathlib import Path
+
+import spikeinterface.full as si
+from spikeinterface.exporters import export_to_phy
+
+
+def export_phy(
+    analyzer_path: str,
+    output_dir: str,
+    copy_binary: bool = True,
+    compute_amplitudes: bool = True,
+    compute_pc_features: bool = True,
+    n_jobs: int = -1,
+):
+    """Export to Phy format."""
+
+    print(f"Loading analyzer from: {analyzer_path}")
+    analyzer = si.load_sorting_analyzer(analyzer_path)
+
+    print(f"Units: {len(analyzer.sorting.unit_ids)}")
+
+    output_path = Path(output_dir)
+
+    # Compute required extensions if missing
+    if compute_amplitudes and analyzer.get_extension('spike_amplitudes') is None:
+        print("Computing spike amplitudes...")
+        analyzer.compute('spike_amplitudes')
+
+    if compute_pc_features and analyzer.get_extension('principal_components') is None:
+        print("Computing principal components...")
+        analyzer.compute('principal_components', n_components=5, mode='by_channel_local')
+
+    print(f"Exporting to Phy: {output_path}")
+    export_to_phy(
+        analyzer,
+        output_folder=output_path,
+        copy_binary=copy_binary,
+        compute_amplitudes=compute_amplitudes,
+        compute_pc_features=compute_pc_features,
+        n_jobs=n_jobs,
+    )
+
+    print("\nExport complete!")
+    print(f"To open in Phy, run:")
+    print(f"  phy template-gui {output_path / 'params.py'}")
+
+
+def main():
+    parser = argparse.ArgumentParser(description='Export to Phy')
+    parser.add_argument('analyzer', help='Path to sorting analyzer')
+    parser.add_argument('--output', '-o', default='phy_export/', help='Output directory')
+    parser.add_argument('--no-binary', action='store_true', help='Skip copying binary file')
+    parser.add_argument('--no-amplitudes', action='store_true', help='Skip amplitude computation')
+    parser.add_argument('--no-pc', action='store_true', help='Skip PC feature computation')
+    parser.add_argument('--n-jobs', type=int, default=-1, help='Number of parallel jobs')
+
+    args = parser.parse_args()
+
+    export_phy(
+        args.analyzer,
+        args.output,
+        copy_binary=not args.no_binary,
+        compute_amplitudes=not args.no_amplitudes,
+        compute_pc_features=not args.no_pc,
+        n_jobs=args.n_jobs,
+    )
+
+
+if __name__ == '__main__':
+    main()