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CHANGELOG.md

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Changelog

All notable changes to the QuPath Cohort Metadata Extractor will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

[2.0.0] - 2025-06-02

Added

  • QuPath 0.6+ Compatibility: Full support for QuPath 0.6.0-rc3 and later versions
  • Enhanced Metadata Extraction: Now captures 50+ metadata fields including:
    • Detailed scanner information (scanner type, ScanScope ID, apparent magnification)
    • Comprehensive timing data (scan date, time, timezone)
    • Acquisition settings (exposure scale, exposure time, gamma, filtering)
    • Stage position data (left, top coordinates)
    • Technical specifications (stripe width, compression details, tile organization)
    • Quality indicators (scan warnings, BigTIFF support, ICC profiles)
  • Improved Error Handling: Better exception management and detailed error logging
  • Performance Monitoring: Execution time tracking and performance statistics
  • Quality Control Metrics: Automated quality assessment for each image
  • Analysis Recommendations: Optimal pyramid level suggestions for analysis

Changed

  • API Compatibility: Updated method calls for QuPath 0.6+ (getImageClass() instead of getImageType())
  • Enhanced CSV Output: Expanded from 4 to 50+ columns of metadata
  • Improved Documentation: Comprehensive field descriptions and usage examples
  • Better File Handling: More robust path and URI processing

Fixed

  • Method Signature Issues: Resolved getImageType() compatibility errors in QuPath 0.6+
  • JSON Dependencies: Removed unsupported Groovy JSON libraries
  • Memory Management: Improved handling of large image collections
  • Error Recovery: Better graceful handling of corrupted or inaccessible images

[1.1.0] - 2025-06-01

Added

  • Menu Integration: Added QuPath menu integration for easier access
  • Configuration Options: Customizable settings for output directories and formats
  • Batch Processing: Support for processing entire projects automatically
  • Multiple Export Formats: CSV and summary text file outputs

Changed

  • User Interface: Simplified workflow with menu-driven operations
  • Output Organization: Better structured output directory and file naming

[1.0.0] - 2025-05-30

Added

  • Initial Release: Basic metadata extraction functionality
  • Core Features:
    • Image dimension and property extraction
    • Basic pixel calibration data
    • File format and size information
    • Simple scanner metadata detection
  • CSV Export: Basic CSV output format
  • QuPath Integration: Compatible with QuPath 0.3.x and later

Known Issues

  • Limited metadata extraction (only basic fields)
  • JSON export dependency issues
  • API compatibility issues with QuPath 0.6+

[Unreleased]

Planned Features

  • Extended Scanner Support: Better support for additional scanner manufacturers
  • Machine Learning Integration: Automated image quality assessment using ML models
  • Cloud Storage Support: Direct integration with cloud storage platforms
  • Real-time Processing: Live metadata extraction as images are imported
  • Advanced Filtering: More sophisticated cohort selection tools
  • Integration APIs: REST API for integration with LIMS and other systems

Migration Guide

From v1.x to v2.0

If you're upgrading from version 1.x:

  1. Update QuPath: Ensure you're using QuPath 0.6.0+ for best compatibility
  2. Replace Scripts: Use the new QuPath_v06_Compatible.groovy script
  3. Review Output: The new CSV format has significantly more columns
  4. Update Analysis Code: Field names may have changed - review your downstream analysis scripts

Compatibility Matrix

Version QuPath Compatibility Features
2.0.0 0.6.0+ Full feature set, 50+ metadata fields
1.1.0 0.3.0 - 0.5.x Basic features, menu integration
1.0.0 0.3.0 - 0.5.x Basic metadata extraction only

For detailed upgrade instructions and breaking changes, see the Migration Guide.