Index

C

clr_normalize_each_cell() (in module COSIE.data_preprocessing) cluster_and_visualize() (in module COSIE.downstream_analysis) cluster_and_visualize_superpixel() (in module COSIE.downstream_analysis) combine_mask() (in module COSIE.image_preprocessing) compute_joint() (in module COSIE.loss) compute_knn_graph() (in module COSIE.utils) compute_linkages() (in module COSIE.linkage_construction) compute_linkages_per_subgraph() (in module COSIE.linkage_construction) compute_neighborhood_embedding() (in module COSIE.utils) construct_knn_graph_hnsw() (in module COSIE.utils) construct_metacell_data_dict() (in module COSIE.data_preprocessing) COSIE module COSIE.configure module COSIE.COSIE_framework module

COSIE.data_preprocessing module COSIE.downstream_analysis module COSIE.image_preprocessing module COSIE.linkage_construction module COSIE.loss module COSIE.model_component module COSIE.utils module COSIE_model (class in COSIE.COSIE_framework) create_model() (in module COSIE.image_preprocessing) create_normalized_adata() (in module COSIE.downstream_analysis) crossview_contrastive_Loss() (in module COSIE.loss)

D

decoder() (GraphAutoencoder method)

E

encoder() (GraphAutoencoder method)

extract_features() (in module COSIE.image_preprocessing)

F

forward() (GraphAutoencoder method) (Prediction_mlp method)

G

generate_homograph() (in module COSIE.image_preprocessing) generate_pxl_location_from_mask() (in module COSIE.image_preprocessing)

get_default_config() (in module COSIE.configure) get_white_superpixel_centers() (in module COSIE.image_preprocessing) GraphAutoencoder (class in COSIE.model_component)

H

highlight_joint_clusters_all_sections() (in module COSIE.downstream_analysis)

I

image_feature_extraction() (in module COSIE.image_preprocessing)

L

load_data() (in module COSIE.data_preprocessing) load_image() (in module COSIE.image_preprocessing)

load_pickle() (in module COSIE.image_preprocessing) load_protein_gene_mapping() (in module COSIE.linkage_construction)

M

merge_clusters_to_new_ids() (in module COSIE.downstream_analysis) metacell_construction_optimized() (in module COSIE.data_preprocessing) mkdir() (in module COSIE.image_preprocessing) module COSIE COSIE.configure COSIE.COSIE_framework COSIE.data_preprocessing COSIE.downstream_analysis COSIE.image_preprocessing COSIE.linkage_construction COSIE.loss COSIE.model_component COSIE.utils

N

nn_approx() (in module COSIE.utils)

P

PatchDataset (class in COSIE.image_preprocessing) perform_prediction() (in module COSIE.downstream_analysis) perform_strong_linkage_knn() (in module COSIE.linkage_construction) perform_weak_linkage_knn() (in module COSIE.linkage_construction) plot_histology_clusters() (in module COSIE.downstream_analysis)

plot_marker_comparison() (in module COSIE.downstream_analysis) plot_marker_comparison_superpixel() (in module COSIE.downstream_analysis) Prediction_mlp (class in COSIE.model_component) prepare_image() (in module COSIE.downstream_analysis) preprocess_adata() (in module COSIE.data_preprocessing) preprocess_data_for_subgraphs() (in module COSIE.linkage_construction)

R

reconstruct_metacell_to_original() (in module COSIE.data_preprocessing)

relabel_clusters_sequentially() (in module COSIE.downstream_analysis) rescale_image() (in module COSIE.image_preprocessing)

S

save_jpg() (in module COSIE.image_preprocessing) save_pickle() (in module COSIE.image_preprocessing)

setup_seed() (in module COSIE.utils) split_into_subgraphs() (in module COSIE.linkage_construction) split_raw_data() (in module COSIE.linkage_construction)

T

to_device() (COSIE_model method) train_model() (COSIE_model method)

transform_coordinates() (in module COSIE.image_preprocessing) truncate_gene_expression_smartclip() (in module COSIE.downstream_analysis)

V

visualize_global_cluster_centroid_dendrogram() (in module COSIE.downstream_analysis)

visualize_section_cluster_centroids_dendrogram() (in module COSIE.downstream_analysis)