{"name":"napari-nifti-viewer","display_name":"NIfTI Viewer","visibility":"public","icon":"","categories":[],"schema_version":"0.2.1","on_activate":null,"on_deactivate":null,"contributions":{"commands":[{"id":"napari-nifti-viewer.make_widget","title":"Open NIfTI Viewer","python_name":"napari_nifti_viewer._widget:NiftiViewerWidget","short_title":null,"category":null,"icon":null,"enablement":null}],"readers":null,"writers":null,"widgets":[{"command":"napari-nifti-viewer.make_widget","display_name":"NIfTI Viewer","autogenerate":false}],"sample_data":null,"themes":null,"menus":{},"submenus":null,"keybindings":null,"configuration":[]},"package_metadata":{"metadata_version":"2.4","name":"napari-nifti-viewer","version":"0.1.2","dynamic":["author","home-page","requires-python"],"platform":null,"supported_platform":null,"summary":"A comprehensive napari plugin for NIfTI file analysis and visualization","description":"# napari-nifti-viewer\n\nA powerful napari plugin for comprehensive NIfTI file analysis and visualization.\n\n[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)\n[![Python](https://img.shields.io/badge/python-3.8+-blue.svg)](https://www.python.org/downloads/)\n[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-nifti-viewer)](https://napari-hub.org/plugins/napari-nifti-viewer)\n\n## Overview\n\nnapari-nifti-viewer is a comprehensive napari plugin specifically designed for reading, analyzing, and visualizing NIfTI (.nii/.nii.gz) files. It provides detailed metadata extraction, intelligent label detection, and seamless integration with napari's visualization capabilities.\n\n## Features\n\n### 🔍 **Complete NIfTI Support**\n- Read .nii and .nii.gz format files\n- Support for NIfTI-1 standard\n- Compatible with both image and label data\n\n### 📊 **Comprehensive Metadata Analysis**\n- Extract complete NIfTI header information (40+ fields)\n- Display affine transformation matrices\n- Show coordinate system information\n- Analyze voxel spacing and orientation\n\n### 🏷️ **Intelligent Label Detection**\n- Automatic label image detection\n- Statistical analysis of label distributions\n- Label value counting and percentage calculations\n\n### 📈 **Data Statistics**\n- Complete data shape and type information\n- Statistical measures (min, max, mean, std)\n- Non-zero voxel counting\n- Unique value analysis\n\n### 💾 **Export Capabilities**\n- Export complete metadata as JSON\n- Preserve all numerical precision\n- Human-readable format\n\n### 🎨 **User-Friendly Interface**\n- Clean, organized tabbed interface\n- Real-time data loading\n- Seamless napari integration\n\n## Interface\n\nThe plugin provides a clean, organized interface with three main tabs:\n\n### 📋 File Overview Tab\nDisplays basic file information and data statistics including file size, format, data shape, and statistical measures.\n\n### 📊 Detailed Information Tab  \nShows complete NIfTI header fields and metadata in an organized table format, alongside full JSON metadata export.\n\n### 🏷️ Label Analysis Tab\nProvides intelligent label detection and statistical analysis with automatic identification of label images and distribution analysis.\n\n## Installation\n\n### From PyPI (Recommended)\n```bash\npip install napari-nifti-viewer\n```\n\n### From Source\n```bash\ngit clone https://github.com/yohanchiu/napari-nifti-viewer.git\ncd napari-nifti-viewer\npip install -e .\n```\n\n## Quick Start\n\n1. **Launch napari** with the plugin installed\n2. **Open the plugin** from the Plugins menu → napari-nifti-viewer\n3. **Load a file** by clicking \"Browse...\" and selecting a .nii/.nii.gz file\n4. **Explore the data** across three informative tabs:\n   - **File Overview**: Basic information and statistics\n   - **Detailed Info**: Complete NIfTI headers and metadata\n   - **Label Analysis**: Label detection and analysis\n5. **Visualize in napari** by clicking \"Load to Napari\"\n\n## Usage Examples\n\n### Loading a Medical Image\n```python\nimport napari\nfrom napari_nifti_viewer import NiftiViewerWidget\n\n# Create napari viewer\nviewer = napari.Viewer()\n\n# The plugin will be available in the Plugins menu\n# Or you can add it programmatically:\nwidget = NiftiViewerWidget(viewer)\nviewer.window.add_dock_widget(widget, name=\"NIfTI Viewer\")\n```\n\n### Exporting Metadata\nThe plugin allows you to export complete metadata including:\n- File information (size, format, version)\n- NIfTI header fields (all 40+ standard fields)\n- Data statistics (shape, type, value ranges)\n- Coordinate system information\n- Affine transformation matrices\n\n## Requirements\n\n- **napari** >= 0.4.18\n- **nibabel** >= 5.2.1\n- **numpy** >= 1.21.0\n- **qtpy** >= 2.0.0\n- **magicgui** >= 0.7.0\n- **Python** >= 3.8\n\n## Supported File Formats\n\n- `.nii` - Uncompressed NIfTI files\n- `.nii.gz` - Compressed NIfTI files\n- Compatible with NIfTI-1 standard\n- Support for both neuroimaging and medical imaging data\n\n## Development\n\n### Setting up Development Environment\n\n```bash\n# Clone the repository\ngit clone https://github.com/yohanchiu/napari-nifti-viewer.git\ncd napari-nifti-viewer\n\n# Create virtual environment\npython -m venv venv\nsource venv/bin/activate  # On Windows: venv\\Scripts\\activate\n\n# Install in development mode\npip install -e \".[dev]\"\n\n# Run tests\npython -m pytest\n```\n\n### Running Tests\n\n```bash\n# Basic functionality test\npython test_plugin.py\n\n# Test with napari interface\npython test_plugin.py --napari\n```\n\n## Contributing\n\nWe welcome contributions! Please see our [Contributing Guidelines](CONTRIBUTING.md) for details.\n\n### Ways to Contribute\n- 🐛 Report bugs\n- 💡 Suggest new features\n- 📝 Improve documentation\n- 🔧 Submit pull requests\n\n## License\n\nThis project is licensed under the MIT License - see the [LICENSE](LICENSE) file for details.\n\n## Citation\n\nIf you use this plugin in your research, please consider citing:\n\n```bibtex\n@software{napari_nifti_viewer,\n  title={napari-nifti-viewer: Comprehensive NIfTI Analysis for napari},\n  author={Qiu Yuheng},\n  year={2024},\n  url={https://github.com/yohanchiu/napari-nifti-viewer}\n}\n```\n\n## Acknowledgments\n\n- Built with [napari](https://napari.org/) - a fast, interactive, multi-dimensional image viewer\n- Uses [nibabel](https://nipy.org/nibabel/) for NIfTI file handling\n- Inspired by the neuroimaging and medical imaging communities\n\n## Support\n\n- 📖 [Documentation](https://github.com/yohanchiu/napari-nifti-viewer/wiki)\n- 🐛 [Issue Tracker](https://github.com/yohanchiu/napari-nifti-viewer/issues)\n- 💬 [Discussions](https://github.com/yohanchiu/napari-nifti-viewer/discussions)\n\n---\n\nMade with ❤️ for the napari and neuroimaging communities \n","description_content_type":"text/markdown","keywords":"napari,nifti,neuroimaging,medical imaging,visualization,plugin","home_page":"https://github.com/yohanchiu/napari-nifti-viewer","download_url":null,"author":"Yohanchiu","author_email":"Yohanchiu <qyhohh@163.com>","maintainer":null,"maintainer_email":"Yohanchiu <qyhohh@163.com>","license":"MIT","classifier":["Development Status :: 4 - Beta","Framework :: napari","Intended Audience :: Science/Research","Intended Audience :: Healthcare Industry","License :: OSI Approved :: MIT License","Operating System :: OS Independent","Programming Language :: Python :: 3","Programming Language :: Python :: 3.8","Programming Language :: Python :: 3.9","Programming Language :: Python :: 3.10","Programming Language :: Python :: 3.11","Programming Language :: Python :: 3.12","Topic :: Scientific/Engineering :: Medical Science Apps.","Topic :: Scientific/Engineering :: Image Processing","Topic :: Scientific/Engineering :: Visualization","Topic :: Software Development :: Libraries :: Python Modules"],"requires_dist":["napari>=0.4.18","numpy>=1.21.0","nibabel>=5.2.1","qtpy>=2.0.0","magicgui>=0.7.0","pytest>=7.0; extra == \"dev\"","pytest-cov; extra == \"dev\"","black; extra == \"dev\"","isort; extra == \"dev\"","flake8; extra == \"dev\"","pre-commit; extra == \"dev\"","pytest>=7.0; extra == \"test\"","pytest-cov; extra == \"test\""],"requires_python":">=3.8","requires_external":null,"project_url":["Homepage, https://github.com/yohanchiu/napari-nifti-viewer","Bug Tracker, https://github.com/yohanchiu/napari-nifti-viewer/issues","Documentation, https://github.com/yohanchiu/napari-nifti-viewer/wiki","Source Code, https://github.com/yohanchiu/napari-nifti-viewer","Changelog, https://github.com/yohanchiu/napari-nifti-viewer/blob/main/CHANGELOG.md"],"provides_extra":["dev","test"],"provides_dist":null,"obsoletes_dist":null},"npe1_shim":false}