update readme and contributing guide

Author: mansouralawi

CONTRIBUTING.md

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+# Contributing to ExSeq-Toolbox
+
+Thank you for your interest in contributing to ExSeq-Toolbox! We welcome contributions from researchers, developers, and the broader scientific community. This document provides guidelines to help you get started.
+
+## How to Contribute
+
+### 🐛 Reporting Bugs
+
+If you find a bug, please:
+
+1. **Check existing issues** - Search the [GitHub Issues](https://github.com/RuihanZhang2015/ExSeq-Toolbox/issues) to see if the bug has already been reported
+2. **Create a new issue** with:
+   - A clear, descriptive title
+   - Steps to reproduce the bug
+   - Expected vs. actual behavior
+   - Your system information (OS, Python version, etc.)
+   - Any error messages or logs
+
+### 💡 Suggesting Features
+
+We welcome feature suggestions! Please:
+
+1. **Search existing issues** to avoid duplicates
+2. **Create a feature request** with:
+   - A clear description of the feature
+   - Use cases and benefits
+   - Any relevant research context
+   - Implementation ideas (if you have them)
+
+### 🔧 Code Contributions
+
+#### Getting Started
+
+1. **Fork the repository** on GitHub
+2. **Clone your fork** locally:
+   ```bash
+   git clone https://github.com/your-username/ExSeq-Toolbox.git
+   cd ExSeq-Toolbox
+   ```
+3. **Create a virtual environment**:
+   ```bash
+   python -m venv venv
+   source venv/bin/activate  # On Windows: venv\Scripts\activate
+   ```
+4. **Install dependencies**:
+   ```bash
+   pip install -r requirements.txt
+   pip install -r requirements_gpu.txt  # If using GPU features
+   ```
+5. **Install in development mode**:
+   ```bash
+   pip install -e .
+   ```
+
+#### Development Workflow
+
+1. **Create a new branch** for your changes:
+   ```bash
+   git checkout -b feature/your-feature-name
+   # or
+   git checkout -b fix/your-bug-fix
+   ```
+
+2. **Make your changes** following our coding standards
+
+3. **Test your changes**:
+   ```bash
+   # Run existing tests
+   pytest tests/
+   
+   # Run with coverage
+   pytest --cov=exm tests/
+   ```
+
+4. **Update documentation** if needed
+
+5. **Commit your changes** with clear commit messages:
+   ```bash
+   git commit -m "Add feature: brief description of changes"
+   ```
+
+6. **Push to your fork**:
+   ```bash
+   git push origin feature/your-feature-name
+   ```
+
+7. **Create a Pull Request** with:
+   - A clear title and description
+   - Reference to any related issues
+   - Summary of changes
+   - Any new dependencies or requirements
+
+## Coding Standards
+
+### Python Code Style
+
+- Follow **PEP 8** style guidelines
+- Use **type hints** for function parameters and return values
+- Write **docstrings** for all public functions and classes
+- Keep functions focused and **under 50 lines** when possible
+- Use **descriptive variable names**
+
+### Documentation
+
+- **Update docstrings** for any modified functions
+- **Add examples** in docstrings for complex functions
+- **Update README.md** if adding new features
+- **Update API documentation** if changing public interfaces
+
+### Testing
+
+- **Write tests** for new functionality
+- **Ensure existing tests pass** before submitting
+- **Add integration tests** for new modules
+- **Test edge cases** and error conditions
+
+## Areas for Contribution
+
+### High Priority
+
+- **Bug fixes** and performance improvements
+- **Documentation improvements** and examples
+- **Test coverage** improvements
+- **GPU optimization** for existing functions
+
+### Medium Priority
+
+- **New analysis modules** for spatial transcriptomics
+- **Visualization tools** for ExSeq data
+- **Data format support** for additional microscopy platforms
+- **Workflow automation** and pipeline tools
+
+### Low Priority
+
+- **UI improvements** for existing tools
+- **Additional file format support**
+- **Performance optimizations** for specific use cases
+
+## Review Process
+
+1. **Automated checks** will run on your PR (tests, linting, etc.)
+2. **Maintainers will review** your code and provide feedback
+3. **Address any feedback** and update your PR
+4. **Once approved**, your PR will be merged
+
+## Getting Help
+
+- **GitHub Issues**: For bug reports and feature requests
+- **GitHub Discussions**: For questions and general discussion
+- **Documentation**: Check our [docs](https://exseq-toolbox.readthedocs.io/en/latest/)
+
+## Code of Conduct
+
+We are committed to providing a welcoming and inclusive environment for all contributors. Please:
+
+- **Be respectful** and constructive in all interactions
+- **Help newcomers** learn and contribute
+- **Give credit** to others for their contributions
+- **Focus on the science** and technical merit
+
+## Recognition
+
+Contributors will be recognized in:
+- **GitHub contributors list**
+- **Release notes** for significant contributions
+- **Documentation** where appropriate
+
+---
+
+Thank you for contributing to ExSeq-Toolbox!