Slide Collection **************** Overview ======== The :class:`SlideCollection ` is the central controller of CuBATS. It organizes and manages a collection of whole-slide images (WSIs), with each WSI being implemented by the :class:`Slide ` class. The :class:`SlideCollection` class loads and stores processing results, the status of the pipeline. It wraps all functional processing stages of CuBATS: 1. Image Registration 2. Tumor Segmentation 3. Quantification of Staining Intensities 4. Combinatorial Analysis of Antigen Co-Expression Each stage is implemented as a separate module and called internally by the `SlideCollection` class. .. note:: You can still run individual modules separately, particularly the registration and segmentation modules. However, the quantification and combinatorial analysis modules are tightly integrated into the :class:`SlideCollection` class and cannot be run independently. Classes ======== Slide Collection ------------------ .. autoclass:: cubats.slide_collection.slide_collection.SlideCollection :members: __init__, register_slides, tumor_segmentation, extract_mask_tile_coordinates, quantify_all_slides, quantify_single_slide, generate_antigen_pair_combinations, generate_antigen_triplet_combinations, evaluate_antigen_pair, evaluate_antigen_triplet Slide ------ .. autoclass:: cubats.slide_collection.slide.Slide :members: __init__, quantify_slide, summarize_quantification_results, reconstruct_slide