# Raman Spectroscopy Analysis Application Documentation

```{only} html
[![License: MIT](https://img.shields.io/badge/License-MIT-blue.svg)](https://github.com/zerozedsc/Raman-Spectroscopy-Analysis-Application/blob/main/LICENSE)
[![Python 3.12+](https://img.shields.io/badge/python-3.12+-blue.svg)](https://www.python.org/downloads/)
[![Read the Docs](https://readthedocs.org/projects/raman-spectroscopy-analysis-application/badge/?version=latest)](https://raman-spectroscopy-analysis-application.readthedocs.io/en/latest/)
```

```{only} not html
- License: MIT
- Python 3.12+
- Read the Docs: https://raman-spectroscopy-analysis-application.readthedocs.io/en/latest/
```

Welcome to the comprehensive documentation for the **Raman Spectroscopy Analysis Application**, a state-of-the-art desktop software for real-time Raman spectral classification and disease detection.

## 🎯 Quick Navigation

::::{grid} 2
:gutter: 3

:::{grid-item-card} 🚀 Getting Started
:link: getting-started
:link-type: doc

Installation guides, quick start tutorials, and first steps with the application.
:::

:::{grid-item-card} 📚 User Guide
:link: user-guide/index
:link-type: doc

Comprehensive tutorials for data import, preprocessing, analysis, and machine learning.
:::

:::{grid-item-card} 🔬 Analysis Methods
:link: analysis-methods/index
:link-type: doc

Detailed documentation of all preprocessing and analysis algorithms with parameter guidance.
:::

:::{grid-item-card} 💻 API Reference
:link: api/index
:link-type: doc

Complete API documentation for developers and advanced users.
:::

::::

## 📖 About This Project

The Raman Spectroscopy Analysis Application is an **open-source**, **cross-platform** desktop software designed for **real-time classification and disease detection** using Raman spectroscopy. Developed at the **University of Toyama** under the **Laboratory for Clinical Photonics and Information Engineering** (臨床光情報工学研究室).

### Key Features

- **40+ Preprocessing Methods**: Research-validated algorithms including baseline correction, smoothing, and normalization
- **Real-Time Analysis**: Interactive PCA, UMAP, t-SNE, clustering, and statistical tests
- **Machine Learning**: Complete ML pipeline with SVM, Random Forest, XGBoost, and interpretability via SHAP
- **Modern GUI**: Intuitive PySide6/Qt6 interface with multi-language support (English/Japanese)
- **Production Ready**: Portable executables and installers for clinical deployment
- **Open Source**: MIT License, contributions welcome

## 🌐 Language Support

This documentation is available in:

- **English** (You are here)
- **日本語** (Japanese) - [Switch to Japanese](https://raman-spectroscopy-analysis-application.readthedocs.io/ja/latest/)

## 📋 Table of Contents

```{toctree}
:maxdepth: 2
:caption: Getting Started

getting-started
installation
quick-start
```

```{toctree}
:maxdepth: 2
:caption: User Guide

user-guide/index
user-guide/interface-overview
user-guide/data-import
user-guide/preprocessing
user-guide/analysis
user-guide/machine-learning
user-guide/best-practices
```

```{toctree}
:maxdepth: 2
:caption: Analysis Methods

analysis-methods/index
analysis-methods/preprocessing
analysis-methods/exploratory
analysis-methods/statistical
analysis-methods/machine-learning
```

```{toctree}
:maxdepth: 2
:caption: API Documentation

api/index
api/core
api/pages
api/components
api/functions
api/widgets
```

```{toctree}
:maxdepth: 2
:caption: Development

dev-guide/index
dev-guide/architecture
dev-guide/contributing
dev-guide/build-system
dev-guide/testing
```

```{toctree}
:maxdepth: 1
:caption: Additional Resources

changelog
troubleshooting
faq
glossary
references
```

## 🔬 Research Context

**Project Title:** Real-Time Raman Spectroscopy Classification Software for Disease Detection  
**Institution:** University of Toyama (富山大学)  
**Laboratory:** [Clinical Photonics and Information Engineering](http://www3.u-toyama.ac.jp/medphoto/)

**Developer:** Muhammad Helmi bin Rozain (12270294)  
**Program:** BSc Information Intelligence Engineering (工学部の知能情報工学コース、4年生、学部生)  
**Supervisors:** 大嶋 佑介 (Oshima Yusuke), 竹谷 皓規 (Taketani Akinori)

## 🤝 Contributing

We welcome contributions from the community! See our [Contributing Guide](dev-guide/contributing.md) for details on:

- Reporting bugs and requesting features
- Submitting pull requests
- Code style guidelines
- Documentation standards

## 📞 Support & Contact

- **Issues**: [GitHub Issues](https://github.com/zerozedsc/Raman-Spectroscopy-Analysis-Application/issues)
- **Discussions**: [GitHub Discussions](https://github.com/zerozedsc/Raman-Spectroscopy-Analysis-Application/discussions)
- **Email**: [@zerozedsc](https://github.com/zerozedsc)

## 📄 License

This project is licensed under the MIT License. See the [LICENSE](https://github.com/zerozedsc/Raman-Spectroscopy-Analysis-Application/blob/main/LICENSE) file for details.

---

**Note**: This software is intended for **research use only** and is not approved for clinical diagnostic purposes.