├── Dockerfile ├── LICENSE ├── README.md ├── config.py ├── deeperhistreg ├── __init__.py ├── dhr_creators │ └── __init__.py ├── dhr_datasets │ └── __init__.py ├── dhr_deformation │ ├── __init__.py │ └── apply_deformation.py ├── dhr_evaluation │ ├── __init__.py │ └── evaluation.py ├── dhr_experiments │ └── __init__.py ├── dhr_input_output │ ├── __init__.py │ ├── dhr_loaders │ │ ├── __init__.py │ │ ├── cucim_loader.py │ │ ├── displacement_loader.py │ │ ├── loader.py │ │ ├── openslide_loader.py │ │ ├── pair_full_loader.py │ │ ├── pil_loader.py │ │ ├── simple_loader.py │ │ ├── sitk_loader.py │ │ ├── tiff_loader.py │ │ └── vips_loader.py │ ├── dhr_parsers │ │ └── __init__.py │ ├── dhr_savers │ │ ├── __init__.py │ │ ├── displacement_saver.py │ │ ├── pair_full_saver.py │ │ ├── pil_saver.py │ │ ├── results_saver.py │ │ ├── saver.py │ │ ├── sitk_saver.py │ │ ├── tiff_saver.py │ │ ├── vips_saver.py │ │ └── warping_params_saver.py │ └── input_output.py ├── dhr_networks │ ├── __init__.py │ ├── superglue.py │ └── superpoint.py ├── dhr_paths │ ├── __init__.py │ ├── general_paths.py │ └── model_paths.py ├── dhr_pipeline │ ├── __init__.py │ ├── full_resolution.py │ ├── patch_based.py │ └── registration_params.py ├── dhr_postprocessing │ ├── __init__.py │ └── postprocessing.py ├── dhr_preprocessing │ ├── __init__.py │ ├── general_preprocessing.py │ ├── images_preprocessing.py │ ├── landmarks_preprocessing.py │ └── preprocessing.py ├── dhr_registration │ ├── __init__.py │ ├── dhr_building_blocks │ │ ├── __init__.py │ │ ├── bsplines.py │ │ ├── cost_functions.py │ │ ├── instance_optimization.py │ │ └── regularizers.py │ ├── dhr_initial_alignment │ │ ├── __init__.py │ │ ├── exhaustive_rigid_search.py │ │ ├── feature_combination.py │ │ ├── io_affine.py │ │ ├── multi_feature.py │ │ ├── sift_ransac.py │ │ ├── sift_superglue.py │ │ ├── superpoint_ransac.py │ │ └── superpoint_superglue.py │ ├── dhr_nonrigid_registration │ │ ├── __init__.py │ │ ├── io_bsplines.py │ │ └── io_nonrigid.py │ ├── initial_alignment_methods.py │ └── nonrigid_registration_methods.py ├── dhr_runners │ └── __init__.py ├── dhr_training │ └── __init__.py ├── dhr_utils │ ├── __init__.py │ ├── utils.py │ └── warping.py ├── dhr_visualization │ └── __init__.py └── run.py ├── deeperhistreg_examples ├── affine_registration.py ├── apply_deformation.py ├── example_notebook.ipynb ├── nonrigid_registration.py ├── run_registration.sh └── run_registration_docker.sh ├── deeperhistreg_params ├── default_initial.json ├── default_initial_fast.json ├── default_initial_nonrigid.json ├── default_initial_nonrigid_fast.json ├── default_initial_nonrigid_high_resolution.json ├── default_nonrigid.json ├── default_nonrigid_fast.json └── default_nonrigid_high_resolution.json ├── figures ├── Overview.png └── SoftwareXVis.png ├── pyproject.toml └── requirements.txt /Dockerfile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MWod/DeeperHistReg/HEAD/Dockerfile 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