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https://github.com/K-Dense-AI/claude-scientific-skills.git
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312f18ae60
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>
80 lines
2.4 KiB
Python
80 lines
2.4 KiB
Python
#!/usr/bin/env python
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"""
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Export sorting results to Phy for manual curation.
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Usage:
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python export_to_phy.py metrics/analyzer --output phy_export/
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"""
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import argparse
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from pathlib import Path
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import spikeinterface.full as si
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from spikeinterface.exporters import export_to_phy
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def export_phy(
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analyzer_path: str,
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output_dir: str,
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copy_binary: bool = True,
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compute_amplitudes: bool = True,
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compute_pc_features: bool = True,
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n_jobs: int = -1,
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):
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"""Export to Phy format."""
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print(f"Loading analyzer from: {analyzer_path}")
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analyzer = si.load_sorting_analyzer(analyzer_path)
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print(f"Units: {len(analyzer.sorting.unit_ids)}")
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output_path = Path(output_dir)
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# Compute required extensions if missing
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if compute_amplitudes and analyzer.get_extension('spike_amplitudes') is None:
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print("Computing spike amplitudes...")
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analyzer.compute('spike_amplitudes')
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if compute_pc_features and analyzer.get_extension('principal_components') is None:
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print("Computing principal components...")
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analyzer.compute('principal_components', n_components=5, mode='by_channel_local')
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print(f"Exporting to Phy: {output_path}")
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export_to_phy(
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analyzer,
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output_folder=output_path,
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copy_binary=copy_binary,
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compute_amplitudes=compute_amplitudes,
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compute_pc_features=compute_pc_features,
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n_jobs=n_jobs,
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)
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print("\nExport complete!")
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print(f"To open in Phy, run:")
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print(f" phy template-gui {output_path / 'params.py'}")
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def main():
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parser = argparse.ArgumentParser(description='Export to Phy')
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parser.add_argument('analyzer', help='Path to sorting analyzer')
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parser.add_argument('--output', '-o', default='phy_export/', help='Output directory')
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parser.add_argument('--no-binary', action='store_true', help='Skip copying binary file')
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parser.add_argument('--no-amplitudes', action='store_true', help='Skip amplitude computation')
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parser.add_argument('--no-pc', action='store_true', help='Skip PC feature computation')
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parser.add_argument('--n-jobs', type=int, default=-1, help='Number of parallel jobs')
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args = parser.parse_args()
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export_phy(
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args.analyzer,
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args.output,
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copy_binary=not args.no_binary,
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compute_amplitudes=not args.no_amplitudes,
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compute_pc_features=not args.no_pc,
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n_jobs=args.n_jobs,
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)
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if __name__ == '__main__':
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main()
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