Release v1.0.0

This release merge several fork and add new functionality to Biom3d.

New funtionalities

• 2D images can be taken as input
• OMERO training data (same way as the prediction does)
• Easier to install with our brand new installers (Windows and macOS)
• Remote mode on macOS
• Official Docker images
• Automated deployment pipeline
• Metal (Applie Silicon) compatibility, due to us not having Macs with Apple Silicon, it may still be unstable, contact us if you encounter a problem
• New DataHandler system that abstract image loading/saving and allow to easily implement new image format
• HDF5 files are now supported

Changes

• Documentation :
  • Documentation structure has changed
  • Documentation now have a Developper part where the API and the whole deployment scripts are described
  • Installation documentation updated
  • New Docker documentation
  • New Server/Client documentation
  • New Config documentation
  • New Dataset documentation
  • New DataHandler documentation
  • Almost all classes and functions are now documented, exception are:
    • FileHandler and HDF5Handler, refer to DataHandler doc
    • gui.py, because it's a mess
• Bug fix
  • Added a new safegard in auto_config.py that prevent None element in spacings list and empty spacings, preventing a numpy.median(spacings) error
  • Fixed semseg_torchio to ensure extracted foreground are casted to numpy.ndarray
  • Added roll_stride option to models and utils to make retrocompatibility with model trained before commit f2ac9ee (August 2023)
  • Fixed error in Google Collab
  • Added missing doc dependencies in pyproject.toml
• Code
  • Simples refactorings and code cleaning
  • versus_one() doesn't load images by himself, you need to provide it with the images to compare, you can use eval() from biom3d.eval to do that automatically
  • Everywhere an image was loaded/saved, we now use a Datahandler that abstract the logic and allow to easily implement new formats. Sole exceptions are old predictions function.
  • Almost every variable refering to directory for image have been renamed to emphasize the new DataHandler system (except in GUI).
  • Biom3d.utils has been shattered to multiple files to ease reading and modification. The namespace hasn't changed.
  • Methods to read and save images has been moved to utils.data_handler.file_handler in the class ImageManager. The old path biom3d.utils still work but has been marked as deprecated.
  • Added condition if not REMOTE to display start locally button in GUI
  • Put constant initialization before imports in gui.py
• Miscellaneous
  • Added CHANGELOG.md file
  • Now using semantic versionning
  • Biom3d version and date time (UTC) of training are stored in model config.yaml

Still in progress

• Integration in Bacmman
• Bioimage Model Zoo model exportation
• DockerHub link to include

Knwown issues

• On Windows, the omero_preprocess_train will crash trying to export model. You will need to manually export it to your Project