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It enables efficient annotation workflows using a task-based approach with small, manageable volumes, implementing the \"small-and-many\" proofreading strategy described in [Bishop et al. (2020)](https://ieeexplore.ieee.org/document/9630109/).\n\n![image](https://github.com/user-attachments/assets/9750ac0a-b76a-4333-a6f7-bf7544b93369)\n\n![image](https://github.com/user-attachments/assets/1105642e-99ea-4933-a129-d94fbf9fb820)\n\n![image](https://github.com/user-attachments/assets/7ba452fc-4d70-401b-9cd5-1efa48fe66d1)\n\n\n\n## Features\n\n-   **🎨 Interactive 3D Painting**: Intuitive lasso-based annotation tools for volumetric data\n-   **📊 BossDB Integration**: Native support for [BossDB](https://bossdb.org/) cloud storage and retrieval\n-   **⚡ Collaboration**: Task-based workflow with user assignment and progress tracking\n-   **🔄 Multi-resolution Support**: Efficient rendering across different zoom levels\n-   **💾 Automatic Checkpointing**: Save progress incrementally with background processing\n-   **🎯 Neuroglancer Integration**: Generate links to view annotations in [Neuroglancer](https://github.com/google/neuroglancer)\n-   **📱 Touch Support**: Optimized for both desktop and tablet workflows\n\n## Architecture\n\nBossyPaints consists of two main components:\n\n-   **Frontend**: SvelteKit-based web application with TypeScript\n-   **Backend**: FastAPI server with Python for data processing and task management\n\n### Frontend Stack\n\n-   [SvelteKit](https://kit.svelte.dev/) - Web framework\n-   [TypeScript](https://www.typescriptlang.org/) - Type safety\n-   [p5.js](https://p5js.org/) - Canvas rendering and interaction\n-   [Tailwind CSS](https://tailwindcss.com/) - Styling\n\n### Backend Stack\n\n-   [FastAPI](https://fastapi.tiangolo.com/) - API framework\n-   [uvicorn](https://www.uvicorn.org/) - ASGI server\n-   [intern](https://github.com/jhuapl-boss/intern) - BossDB Python client\n-   [zmesh](https://github.com/seung-lab/zmesh) - 3D mesh generation\n\n## Development\n\n### Prerequisites\n\n-   Python 3.11 or higher\n-   Node.js 18 or higher\n-   [uv](https://docs.astral.sh/uv/) (recommended Python package manager)\n\n### Installation\n\n1. **Clone the repository**\n\n    ```bash\n    git clone https://github.com/aplbrain/bossypaints.git\n    cd bossypaints\n    ```\n\n2. **Set up the backend**\n\n    ```bash\n    cd server\n    # Install uv if not already installed\n    curl -LsSf https://astral.sh/uv/install.sh | sh\n\n    # Install dependencies and run server\n    uv run uvicorn server:app --reload\n    ```\n\n3. **Set up the frontend** (in a new terminal)\n\n    ```bash\n    cd bossypaints\n    npm install\n    npm run dev\n    ```\n\n4. **Access the application**\n\n    Open your browser and navigate to `http://localhost:5173`\n\n### Docker Deployment\n\nFor production deployment, use the provided Docker configuration:\n\n```bash\ndocker-compose up -d\n```\n\n## 📖 Usage\n\n### Getting Started\n\n1. **Obtain BossDB API Token**: Visit [BossDB Token Management](https://api.bossdb.io/v1/mgmt/token) to generate your API token\n\n2. **Create a Task**:\n\n    - Navigate to \"Create New Task\"\n    - Enter your BossDB collection, experiment, and channel details\n    - Define the region of interest (ROI) for annotation\n    - Specify destination collection for storing annotations\n\n3. **Start Annotating**:\n    - Use the paint brush tool to create regions\n    - Hit backspace to subtract from regions\n    - Use keyboard shortcuts for efficient workflow\n\n### Keyboard Shortcuts\n\n| Key                 | Action                             |\n| ------------------- | ---------------------------------- |\n| **Space**           | Toggle between paint and pan modes |\n| **Backspace**       | Subtract current annotation        |\n| **,** / **.**       | Navigate between Z layers          |\n| **n** / **b**       | Next/previous segment ID           |\n| **d**               | Delete current annotation          |\n| **ESC**             | Reset view to task center          |\n| **Alt + S**         | Save checkpoint                    |\n| **Alt + Shift + S** | Final submission                   |\n\n### API Endpoints\n\nThe backend provides a RESTful API for task management:\n\n-   `GET /api/tasks` - List all tasks\n-   `POST /api/tasks/create` - Create new annotation task\n-   `GET /api/tasks/{task_id}` - Get specific task details\n-   `POST /api/tasks/{task_id}/checkpoint` - Save annotation checkpoint\n-   `POST /api/tasks/{task_id}/save` - Final task submission\n\n## 🔧 Configuration\n\n### Environment Variables\n\nCreate a `.env` file in the server directory:\n\n```env\nKEYCLOAK_URL=\u003cyour-keycloak-url\u003e\nKEYCLOAK_CLIENT_ID=\u003cyour-client-id\u003e\n#KEYCLOAK_CLIENT_SECRET=\u003cyour-client-secret\u003e\nPUBLIC_BOSSYPAINTS_API_URL=\"\"\n```\n\n### Frontend Configuration\n\nModify `bossypaints/src/lib/webpaint/config.ts` for application settings:\n\n```typescript\nexport default {\n    debug: false,\n    fixedChunkSize: {\n        width: 512,\n        height: 512,\n        depth: 16,\n    },\n    chunkLoading: {\n        radius: 2,\n        prioritizeCenter: true,\n    },\n};\n```\n\n### Development Setup\n\n1. Fork the repository\n2. Create a feature branch (`git checkout -b feature/amazing-feature`)\n3. Make your changes\n4. Add tests if applicable\n5. Commit your changes (`git commit -m 'Add amazing feature'`)\n6. Push to the branch (`git push origin feature/amazing-feature`)\n7. Open a Pull Request\n\n### Code Style\n\n-   Frontend: Follow Prettier and ESLint configurations\n-   Backend: Follow PEP 8 with Black formatting\n-   Use TypeScript for all frontend code\n-   Include type hints for Python functions\n\n## Issue Reporting\n\nFound a bug? Please report it on our [Issues page](https://github.com/aplbrain/bossypaints/issues) with:\n\n-   Operating system and browser version\n-   Steps to reproduce the issue\n-   Expected vs actual behavior\n-   Screenshots if applicable\n\n## 🙏 Acknowledgments\n\n-   [Bishop et al. (2020)](https://ieeexplore.ieee.org/document/9630109/) for the small-and-many proofreading methodology\n-   [BossDB](https://bossdb.org/) team for cloud infrastructure\n-   [Neuroglancer](https://github.com/google/neuroglancer) for visualization integration\n-   The neuroscience open-source community\n\n## 📄 License\n\nThis project is licensed under the Apache License 2.0 - see the [LICENSE](LICENSE) file for details.\n\n\u003cp align='center'\u003e\u003csmall\u003eMade with 💙 at \u003ca href='http://www.jhuapl.edu/'\u003e\u003cimg alt='JHU APL' align='center' src='https://user-images.githubusercontent.com/693511/62956859-a967ca00-bdc1-11e9-998e-3888e8a24e86.png' height='42px'\u003e\u003c/a\u003e\u003c/small\u003e\u003c/p\u003e\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Faplbrain%2Fbossypaints","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Faplbrain%2Fbossypaints","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Faplbrain%2Fbossypaints/lists"}