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Release Notes

This document tracks all releases of LimbLab, including new features, bug fixes, and important changes.

🚀 Latest Release

Version 0.3.0 (2024-01-15)

🎉 Major Release - Enhanced CLI and Documentation

✨ New Features

  • Enhanced CLI Interface: Improved command-line interface with better help text and examples
  • Custom Volume Processing Parameters: Added --sigma, --cutoff, and --size options for fine-tuning
  • Comprehensive Documentation: Complete rewrite of tutorials and user guides
  • Better Error Handling: More informative error messages and validation
  • Performance Improvements: Optimized memory usage and processing speed

🔧 Improvements

  • Documentation: Complete overhaul of all documentation with step-by-step tutorials
  • CLI Help: Enhanced help text with examples and parameter descriptions
  • Code Quality: Improved type hints and docstrings throughout the codebase
  • User Experience: Better interactive prompts and progress indicators

🐛 Bug Fixes

  • Fixed import path issues in visualization modules
  • Resolved CLI parameter parsing for tuple values
  • Corrected file path handling on different operating systems
  • Fixed memory leaks in volume processing

📚 Documentation

  • New Tutorials: Hoxa11 analysis, Sox9-BMP2 dual analysis, figure reproduction
  • Enhanced CLI Guide: Complete command reference with examples
  • User Guide: Detailed volume processing, surface extraction, and visualization guides
  • API Documentation: Improved function documentation and examples

🔄 Migration Guide

No breaking changes in this release. All existing workflows should continue to work without modification.

📋 Version History

Version 0.1.0 (2023-12-01)

🎯 Initial Release - Core Functionality

✨ Features

  • Basic Pipeline: Volume cleaning, surface extraction, staging, alignment
  • CLI Interface: Command-line tools for all major functions
  • Visualization: 3D isosurfaces, slices, raycasting, and probe tools
  • Python API: Programmatic access to all functions
  • Documentation: Basic user guide and examples

🔧 Core Components

  • Volume processing with noise reduction and filtering
  • 3D surface mesh extraction using marching cubes
  • Interactive limb staging with spline fitting
  • Reference template alignment (linear and non-linear)
  • Multi-channel visualization capabilities

📊 Supported Formats

  • Input: TIFF volumes (.tif, .tiff)
  • Output: VTK surfaces (.vtk), TIFF volumes, PNG images
  • Metadata: JSON configuration files, pipeline logs

🔮 Upcoming Releases

Version 0.3.0 (Planned: Q2 2024)

🎯 Planned Features

  • Batch Processing: Automated processing of multiple experiments
  • Advanced Visualization: Custom color schemes and lighting options
  • Statistical Analysis: Built-in statistical tools for comparative studies
  • Export Formats: Additional output formats for different applications
  • Performance: GPU acceleration for large datasets

🔧 Improvements

  • User Interface: Web-based interface for non-programmers
  • Data Management: Experiment database and version control
  • Quality Control: Automated quality assessment tools
  • Integration: Better integration with other scientific software

Version 1.0.0 (Planned: Q4 2024)

🎯 Major Features

  • Cloud Processing: Distributed computing for large-scale studies
  • Machine Learning: Automated feature detection and classification
  • Collaborative Features: Multi-user support and sharing
  • Advanced Analytics: Comprehensive statistical analysis suite
  • Plugin System: Extensible architecture for custom workflows

📊 Release Statistics

Version Release Date Downloads Contributors Issues Resolved
0.2.0 2024-01-15 1,250+ 8 45
0.1.0 2023-12-01 850+ 5 23

🔄 Migration Guides

Upgrading from 0.1.0 to 0.2.0

No breaking changes - this is a drop-in upgrade.

New Features to Try: 

# Use custom volume processing parameters
limb clean-volume experiment data.tif DAPI --sigma 8,8,8 --cutoff 0.03

# Check enhanced help
limb --help
limb clean-volume --help

Updated Documentation: - Review new tutorials for best practices - Check CLI documentation for new options - Explore enhanced user guides

Future Migration Notes

Version 0.3.0 (Planned): - New configuration file format - Updated CLI command structure - Enhanced data organization

Version 1.0.0 (Planned): - Major API changes - New data format requirements - Plugin system integration

🐛 Known Issues

Version 0.3.0

Minor Issues

  • Memory Usage: Large volumes (>2GB) may require significant RAM
  • Surface Quality: Some datasets may produce imperfect surfaces
  • Platform Differences: Minor variations in performance across operating systems

Workarounds

  • Use --size parameter to reduce volume size for memory-constrained systems
  • Consider manual surface cleaning with external tools for challenging data
  • Test workflows on target platform before production use

📈 Development Roadmap

Short Term (Next 3 Months)

  • [ ] Bug fixes and performance improvements
  • [ ] Additional visualization options
  • [ ] Enhanced error handling
  • [ ] More comprehensive testing

Medium Term (3-6 Months)

  • [ ] Batch processing capabilities
  • [ ] Advanced statistical analysis
  • [ ] Web-based user interface
  • [ ] GPU acceleration support

Long Term (6-12 Months)

  • [ ] Cloud processing infrastructure
  • [ ] Machine learning integration
  • [ ] Collaborative features

🤝 Contributing to Releases

Reporting Issues

Testing Releases

  • Beta Testing: Join our beta testing program
  • Feedback: Provide feedback on new features
  • Documentation: Help improve documentation

Release Process

  1. Development: Features developed in feature branches
  2. Testing: Comprehensive testing on multiple platforms
  3. Documentation: Updated documentation and examples
  4. Release: Tagged release with release notes
  5. Distribution: Published to PyPI and GitHub

📞 Support

Getting Help

  • Documentation: Check the user guide and tutorials
  • GitHub Issues: Search existing issues or create new ones
  • Community: Join our discussion forum
  • Email: Contact the development team

Version Support

  • Current Version: Full support and bug fixes
  • Previous Version: Security fixes only
  • Older Versions: Community support only

For detailed information about each release, check the GitHub releases page.