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Packages**\n\nNeuroMCP is a scalable, Pythonic framework for integrating neuroscience Python packages through the Model Context Protocol (MCP) using FastMCP. It provides a standardized way to expose neuroscience tools, ontologies, and neural device interfaces for agentic AI workflows.\n\n## Architecture\n\n```\nneuromcp/\n├── src/neuromcp/\n│   ├── __init__.py           # Package entry point\n│   ├── server.py             # Main MCP server implementation\n│   ├── registry.py           # Provider registry and discovery\n│   ├── cli.py                # Command-line interface\n│   ├── config/\n│   │   ├── __init__.py\n│   │   └── settings.py       # Configuration management\n│   ├── providers/            # Provider implementations\n│   │   ├── __init__.py\n│   │   ├── base.py                   # Base provider interface\n│   │   ├── ontology_provider.py      # Ontology & BIDS validation\n│   │   └── neural_device_provider.py # Device translation\n│   └── utils/                # Utility functions\n│       ├── __init__.py\n│       └── validation.py     # Data validation utilities\n├── tests/\n│   ├── unit/                 # Unit tests\n│   └── integration/          # Integration tests\n├── examples/                 # Usage examples\n├── pyproject.toml           # Project configuration\n└── README.md                # This file\n```\n\n## Installation\n\n### Using pip (when published)\n\n```bash\npip install neuromcp\n```\n\n## Quick Start\n\n### Using the CLI\n\n```bash\n# List available providers\nneuromcp list-providers\n\n# Run the server with auto-discovery\nneuromcp run\n\n# Run with custom configuration\nneuromcp run --config config.yaml\n\n# Run with specific options\nneuromcp run --log-level DEBUG --auto-discover true\n```\n\n\n## Built-in Providers\n\n### Ontology Provider\nThe Ontology Provider offers comprehensive support for neuroscience standards and ontologies through specialized subproviders:\n\n#### BIDS (Brain Imaging Data Structure)\n- Brain Imaging Data Structure validation\n- Quality control for neuroimaging datasets\n- Upload readiness checks for OpenNeuro and other databases\n- Comprehensive dataset structure analysis\n- Example prompts for scientists\n- See [Quality Control Guide](docs/QUALITY_CONTROL.md) for details\n\n#### NWB (Neurodata Without Borders)\n- NWB format information and best practices\n- Data structure validation\n- File organization guidance\n- Integration examples for electrophysiology, imaging, and behavior data\n\n#### NBO (Neuro Behavior Ontology)\n- Behavioral term search and validation\n- Semantic annotation for behavioral experiments\n- Ontology-driven data validation\n- Support for owlready2 and rdflib\n\n#### HED (Hierarchical Event Descriptors)\n- Event annotation and validation\n- HED tag string validation\n- Schema version management\n- Best practices for experimental event tagging\n\n#### General Ontology Tools\n- Neuroscience term standardization\n- Ontology validation\n- Format translation (abbreviated ↔ standard)\n\n### Neural Device Provider\n- Device specifications and metadata\n- Data format translation\n- Recording parameter validation\n\n\n## License\n\nMIT License - see LICENSE file for details\n","readmeFilename":"README.md"}