├── .idea ├── .gitignore ├── CODA.iml ├── inspectionProfiles │ └── profiles_settings.xml ├── misc.xml ├── modules.xml └── vcs.xml ├── CODA Visium integration scripts 05-07-2024 ├── HE_cell_count_visium.m ├── README.txt └── register_CODA_segmentation_to_visium_slide.m ├── original upload version ├── HE_cell_count.m ├── base │ ├── annotation_bounding_boxes.m │ ├── bpassW.m │ ├── calculate_elastic_registrationC.m │ ├── calculate_elastic_registrationS.m │ ├── calculate_global_reg.m │ ├── calculate_tissue_space_082.m │ ├── calculate_transform.m │ ├── colordeconv2pw4_log10.m │ ├── combine_tiles_big.m │ ├── deeplab_classification.m │ ├── detect_scales.m │ ├── edit_individual_classes_082.m │ ├── fill_annotations_file.m │ ├── find_tissue_area.m │ ├── gcnt.m │ ├── getImLocalWindowInd_rf.m │ ├── get_ims.m │ ├── image_preprocessing_global.m │ ├── invert_D.m │ ├── load_xml_file.m │ ├── make_final_grids.m │ ├── make_rgb_kmeans_90.m │ ├── mskcircle2_rect.m │ ├── pad_im.m │ ├── pad_im_both.m │ ├── pad_im_both2.m │ ├── pkfndW.p │ ├── plot_settings.m │ ├── preprocessing.m │ ├── random_augmentation.m │ ├── reg_ims_EL.m │ ├── reg_ims_ELS.m │ ├── reg_ims_com.m │ ├── register_cell_coordinates_1type.m │ ├── register_cell_coordinates_list.m │ ├── register_cell_coordinates_new.m │ ├── register_global_im.m │ ├── register_images_2E.m │ ├── rescale_ims.m │ ├── save_images_global.m │ ├── save_inverted_Ds.m │ ├── train_deeplab.m │ ├── xcorrf2.m │ └── xml2struct2.m ├── make_training_deeplab.m ├── normalize_HE.m ├── plot_3D_tiss.m ├── register_cell_coordinates.m ├── register_images.m ├── save_cell_coordinates_registered.m └── save_images_elastic2.m └── update 12-13-2023 ├── README.txt ├── apply_image_registration.m ├── build_cell_volume.m ├── build_tissue_volume.m ├── calculate_image_registration.m ├── calculate_tissue_ws.m ├── cell_detection.m ├── cell_detection_base_functions ├── calculate_optimal_vals.m ├── cell_cell_dist.m ├── colordeconv_log10.m ├── im2mat.p └── pkfndW.p ├── combine_z_projections.m ├── create_downsampled_tif_images.m ├── deconvolve_histological_images.m ├── get_mpp_of_image.m ├── get_nuclear_detection_parameters.m ├── image registration base functions ├── bpassW.m ├── calculate_elastic_registration.m ├── calculate_global_reg.m ├── calculate_global_reg_IHC.m ├── calculate_transform.m ├── find_tissue_area.m ├── gcnt.m ├── getImLocalWindowInd_rf.m ├── get_ims.m ├── group_of_reg.m ├── im2mat.p ├── invert_D.m ├── make_final_grids.m ├── mskcircle2_rect.m ├── pad_im_both2.m ├── preprocessing.m ├── reg_ims_ELS.m ├── reg_ims_com.m ├── register_global_im.m └── xcorrf2.m ├── make_cell_detection_mosaic.m ├── manual_cell_count.m ├── register_cell_coordinates.m ├── segmentation base functions ├── build_model_tiles.m ├── calculate_tissue_space.m ├── combine_tiles_density_shuffle.m ├── deeplab_classification.m ├── fill_annotations_file.m ├── load_xml_file.m ├── load_xml_loop.m ├── make_check_annotation_classified_image.m ├── make_cmap_legend.m ├── 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