API Reference

• core
  • Public API
• Preprocessing
  • adjust_gamma()
  • extract_tissue_masks()
  • gamma_corrections()
  • load_slide()
  • load_wsi_images()
  • pad_images_np()
  • pad_single()
  • pad_to_same_size()
  • preprocess_images()
  • process_nuclei_patch()
  • resize_and_compute_translation()
  • scale_transformation_matrix()
  • FlorenceTissueMaskExtractor
  • UNetTissueMaskExtractor
  • create_nuclei_dataframe_from_points()
  • detect_nuclei_patch_watershed()
  • extract_nuclei_points()
  • extract_patches_from_wsi()
  • load_nuclei_coordinates()
  • process_fixed_patch()
  • process_moving_patch()
  • process_nuclei_in_patches()
  • save_nuclei_data_to_csv()
  • subsample_nuclei()
  • StainNormalizer
  • apply_padding_landmarks()
  • calculate_pad_value()
  • pad_image_src()
  • pad_images()
  • pad_landmarks()
  • remove_padding()
• Registration
  • convert_4x4_to_3x3_transform()
  • create_displacement_field()
  • find_mutual_nearest_neighbors()
  • perform_cpd_registration()
  • perform_icp_registration()
  • perform_rigid_registration()
  • perform_shape_aware_registration()
  • ShapeAwarePointSetRegistration
  • Trimorph
  • XFeatReg
  • extract_corresponding_tiles()
  • perform_shape_aware_registration()
  • register_wsi_with_fine_tuning()
  • rigid_registration()
  • apply_deformation_field()
  • build_reference_coordinate_system()
  • compute_deformation_and_apply()
  • compute_normalized_cross_correlation()
  • compute_smoothness_regularization()
  • convert_image_to_tensor()
  • create_multiscale_representation()
  • elastic_image_registration()
  • gaussian_smoothing()
  • initialize_deformation_field()
  • prepare_image_tensors()
  • scale_deformation_field()
  • scale_tensor_to_dimensions()
  • CPD
• Evaluation
  • apply_displacement_field_to_points()
  • evaluate_nonrigid_registration()
  • evaluate_registration_tre()
  • load_evaluation_landmarks()
  • load_landmark_points()
  • ngf_metric()
  • rtre()
  • transform_points_homogeneous()
  • tre()
• Utilities
  • apply_affine_transformation()
  • apply_deformation_to_points()
  • apply_displacement_field()
  • calculate_resample_size()
  • combine_deformation()
  • compute_center_of_mass()
  • convert_pytorch_checkpoint()
  • create_deform()
  • create_deformation_field()
  • create_displacement_field_for_wsi()
  • create_nonrigid_mha()
  • create_pyramid()
  • deform_conversion()
  • dice()
  • find_scale()
  • gamma_corrections()
  • gaussian_filter()
  • load_image()
  • load_image_as_grayscale()
  • load_landmarks()
  • load_landmarks_no_header()
  • matchpoints()
  • matrix_df()
  • matrix_mha()
  • mse()
  • normalize()
  • pad_landmarks()
  • phase_correlation()
  • plot_landmarks()
  • print_rtre()
  • resample()
  • resample_both()
  • resample_displacement_field()
  • rotate_point()
  • round_up_to_odd()
  • rtre()
  • save_landmarks()
  • scale_coordinates()
  • scale_transformation_matrix()
  • skip_subsample()
  • sort_coordinates()
  • tensor_to_rgb_numpy()
  • to_image()
  • transform_landmarks()
  • tre()
  • warp_image()
  • apply_displacement_field()
  • array_to_vips()
  • get_image_shape()
  • load_mha_displacement()
  • register_wsi_with_mha()
  • resize_displacement_field()
  • save_displacement_as_mha()
  • vips_to_array()
• Visualization
  • create_detailed_nuclei_plot_with_colormaps()
  • create_method_comparison_plot()
  • create_nuclei_overlay_plot()
  • create_registration_comparison_plot()
  • setup_bokeh_notebook()
  • show_plot()
  • visualize_cluster_alignment()
  • visualize_overlays()
  • visualize_patches()
  • visualize_shape_aware_registration()
  • visualize_transformed_image()