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Changelog

All notable changes to mAIcrobe will be documented in this file.

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

[0.0.2] - New release

Added

  • Comprehensive documentation overhaul and updated README
  • User guide documentation
  • Tutorials and API reference documentation
  • Contributing guidelines and development setup instructions
  • Compute_label widget enhancements - pretrained models for StarDist2D and U-Net
  • Compute_cells widget enhancements - new pretrained classification model
  • Other minor improvements and bug fixes

Changed

  • README.md completely rewritten
  • Documentation structure reorganized with user-friendly navigation
  • Enhanced project description and value proposition

Documentation

  • Added getting started guide with step-by-step tutorial
  • Added generate training data documentation with screenshots
  • Added notebooks for StarDist segmentation and cell classification
  • Created comprehensive segmentation guide
  • Detailed cell analysis documentation
  • Cell classification guide with model descriptions
  • API reference
  • Basic workflow tutorial for new users

[0.0.1] - Initial Release

Added

  • Core napari plugin functionality
  • Three main widgets:
    • compute_label: Cell segmentation using StarDist2D, Cellpose, or custom U-Net models
    • compute_cells: Comprehensive cell analysis with morphological measurements and optionally deep learning classification
    • filter_cells: Interactive cell filtering based on computed statistics
  • Deep learning cell classification with 6 pre-trained TensorFlow models for cell cycle determination in S. aureus:
    • S.aureus DNA+Membrane (Epi/SIM)
    • S.aureus DNA-only (Epi/SIM)
    • S.aureus Membrane-only (Epi/SIM)
  • Sample S. aureus datasets for testing:
    • Phase contrast images
    • Membrane fluorescence (Nile Red)
    • DNA fluorescence (Hoechst)
  • Morphological analysis with scikit-image regionprops
  • Multi-channel colocalization analysis
  • HTML report generation with statistics and visualizations
  • CSV data export for further analysis
  • Support for custom Keras models for cell classification and U-Net segmentation

Features

  • Cell Segmentation: StarDist2D, Cellpose, custom U-Net and traditional thresholding methods with watershed
  • Morphometry: Comprehensive shape and size analysis
  • Classification: Single cell classification using pre-trained models (S. aureus cell cycle) or custom trained ones
  • Filtering: Interactive filtering of cell populations
  • Reporting: HTML reports and CSV exports
  • Custom Models: Support for user-trained classification models

Contributing

We welcome contributions! See CONTRIBUTING.md

Support

  • Documentation: Complete guides at mAIcrobe docs
  • Issues: Report bugs via GitHub Issues
  • Email: Contact maintainers for security issues or collaboration

This changelog is updated with each release to help users understand what has changed and how to adapt their workflows accordingly.