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>
- Add comprehensive BRENDA database skill with API integration
- Include enzyme data retrieval, pathway analysis, and visualization
- Support for enzyme queries, kinetic parameters, and taxonomy data
- Add visualization scripts for enzyme pathways and kinetics
- Convert uniprot_client.py to use argparse module
- Convert peds_client.py to use argparse module
- Convert trademark_client.py to use argparse module
- Add mutually exclusive argument groups for better UX
- Implement comprehensive help text with examples
- Add short and long argument options for all commands
- Improve error handling with proper parser.error() calls
Replaces error-prone manual sys.argv parsing with robust
argparse implementation for better user experience and
input validation.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
