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Documentation Changelog

[2024-12-19] - Documentation Improvements

Added

  • Detailed documentation for load_image: Added comprehensive descriptions of parameters, return values, usage examples, and notes
  • New "Image Segmentation" page: Created a dedicated page with complete documentation of all segmentation functions
  • Updated main page: Transferred information from README.md with improved structure and navigation
  • Usage examples: Added practical examples for all main functions

Changed

  • Enhanced load_image function documentation:
  • Added detailed parameter and return value descriptions
  • Included usage examples for OME-TIFF and OME-ZARR formats
  • Added notes about supported formats and implementation details
  • Updated navigation: Added link to segmentation page in main menu

Documentation Structure

docs/
├── index.md              # Main page with library overview
├── segmentation.md       # Detailed segmentation documentation
├── api.md               # Complete API documentation
└── CHANGELOG.md         # Change history

Supported Image Formats

  • OME-TIFF (.ome.tiff, .ome.tif) - Primary format for multi-channel images
  • OME-ZARR (.zarr) - Modern format for large datasets
  • TIFF - Standard image format (with limited metadata support)

Segmentation Functions

  • load_image - Image loading with automatic dimension handling
  • cellpose_cellseg - Cell segmentation using deep learning
  • stardist_cellseg - Star-convex object-based segmentation
  • watershed_classic - Classical watershed segmentation
  • median_denoise, nlm_denoise - Noise filtering
  • background_subtract - Background subtraction
  • Postprocessing functions: rescue_cells, remove_small_objects, remove_large_objects
  • feature_extraction_adata - Feature extraction to AnnData format