Index

_

__call__() (Composition method) (SpatialAutocorrelation method) __init__() (LogNormalPoisson method) (SmartLeiden method) (SmartPca method) (SmartScaler method) (SmartUmap method) (SparseImage method)

A

add_specific_args() (AnndataFolderDM class method) (BarlowModel class method) (DinoModel class method) (SimclrModel class method) (SparseSslDM class method) (VaeModel class method)

anndata (SparseImage property) anndata_from_expression_csv() (in module tissue_purifier.io.read_anndata_from_csv) anndata_to_sparseimage() (AnndataFolderDM method) AnndataFolderDM (class in tissue_purifier.data.datamodule) are_dicts_equal() (in module tissue_purifier.utils.dict_util)

B

BarlowModel (class in tissue_purifier.models.ssl_models.barlow)

BaseEstimator (class in tissue_purifier.models.classifier_regressor.scikit_learn_interface)

C

cat_raw (SparseImage property) category_to_channels (SparseImage property) cell_type_ids (GeneDataset attribute) cell_type_mapping (GeneDataset attribute) ch_in (AnndataFolderDM property) channels_to_category (SparseImage property) clear_dicts() (SparseImage method) cluster() (SmartLeiden method) Composition (class in tissue_purifier.models.patch_analyzer.patch_analyzer)

compute_distance_embedding() (in module tissue_purifier.utils.validation_util) compute_ncv() (SparseImage method) compute_patch_features() (SparseImage method) concatenate_list_of_dict() (in module tissue_purifier.utils.dict_util) configure_optimizer() (GeneRegression method) counts (GeneDataset attribute) covariates (GeneDataset attribute) cropper_test (SparseSslDM property) cropper_train (SparseSslDM property) crops() (SparseImage method)

D

describe() (GeneDataset method)

DinoModel (class in tissue_purifier.models.ssl_models.dino) download_from_bucket() (in module tissue_purifier.io.download)

E

explained_variance_ (SmartPca property) explained_variance_ratio_ (SmartPca property)

extend_train() (GeneRegression method) extend_train_and_test() (GeneRegression method)

F

fit() (MlpClassifier method) (MlpRegressor method) (SmartPca method) (SmartScaler method) (SmartUmap method)

fit_transform() (SmartPca method) (SmartScaler method) (SmartUmap method) flatten_dict() (in module tissue_purifier.utils.dict_util) from_anndata() (SparseImage class method) from_state_dict() (SparseImage class method)

G

gene_names (GeneDataset attribute) GeneDataset (class in tissue_purifier.genex.gene_utils) GeneRegression (class in tissue_purifier.genex.pyro_model) get_default_params() (BarlowModel class method) (DinoModel class method) (SimclrModel class method) (VaeModel class method) get_distances() (SmartUmap method)

get_graph() (SmartUmap method) get_metadata_to_classify() (AnndataFolderDM method) get_metadata_to_regress() (AnndataFolderDM method) get_params() (GeneRegression method) get_percentile() (in module tissue_purifier.utils.validation_util) get_state_dict() (SparseImage method) get_z_score() (in module tissue_purifier.utils.validation_util) global_size (SparseSslDM property) gready() (SparseImage method)

I

inspect() (SparseImage method) inspect_dict() (in module tissue_purifier.utils.dict_util) inverse_one_hot() (in module tissue_purifier.utils.validation_util)

is_classifier (MlpClassifier property) (MlpRegressor property) is_regressor (MlpClassifier property) (MlpRegressor property)

K

k_cell_types (GeneDataset attribute)

L

load_ckpt() (GeneRegression method)

local_size (SparseSslDM property) LogNormalPoisson (class in tissue_purifier.genex.pyro_model)

M

make_gene_dataset_from_anndata() (in module tissue_purifier.genex.gene_utils) MlpClassifier (class in tissue_purifier.models.classifier_regressor.scikit_learn_interface) MlpRegressor (class in tissue_purifier.models.classifier_regressor.scikit_learn_interface) module tissue_purifier.genex.gene_utils tissue_purifier.genex.gene_visualization tissue_purifier.genex.pyro_model tissue_purifier.io.download tissue_purifier.io.read_anndata_from_csv tissue_purifier.plots.plot_embeddings tissue_purifier.plots.plot_images tissue_purifier.plots.plot_knn tissue_purifier.plots.plot_misc tissue_purifier.utils.dict_util tissue_purifier.utils.validation_util

moran() (SparseImage method)

N

n_global_crops (SparseSslDM property)

n_local_crops (SparseSslDM property)

O

optimizer (GeneRegression property)

P

pad_and_crop_and_stack() (in module tissue_purifier.plots.plot_images) pixel_to_raw() (SparseImage method) plot_cdf_pdf() (in module tissue_purifier.plots.plot_misc) plot_clusters_annotations() (in module tissue_purifier.plots.plot_misc) plot_embeddings() (in module tissue_purifier.plots.plot_embeddings) plot_gene_hist() (in module tissue_purifier.genex.gene_visualization)

plot_knn_examples() (in module tissue_purifier.plots.plot_knn) plot_multiple_barplots() (in module tissue_purifier.plots.plot_misc) predict() (GeneRegression method) (MlpClassifier method) (MlpRegressor method) predict_log_proba() (MlpClassifier method) predict_proba() (MlpClassifier method)

R

raw_to_pixel() (SparseImage method) read_from_image_dictionary() (SparseImage method)

read_from_patch_dictionary() (SparseImage method) read_from_spot_dictionary() (SparseImage method) remove_params() (GeneRegression static method)

S

save_ckpt() (GeneRegression method) score() (MlpClassifier method) (MlpRegressor method) show_batch() (in module tissue_purifier.plots.plot_images) show_loss() (GeneRegression method) show_raw_all_channels() (in module tissue_purifier.plots.plot_images) show_raw_one_channel() (in module tissue_purifier.plots.plot_images) SimclrModel (class in tissue_purifier.models.ssl_models.simclr) SmartLeiden (class in tissue_purifier.utils.validation_util) SmartPca (class in tissue_purifier.utils.validation_util)

SmartScaler (class in tissue_purifier.utils.validation_util) SmartUmap (class in tissue_purifier.utils.validation_util) sort_dict_according_to_indices() (in module tissue_purifier.utils.dict_util) SparseImage (class in tissue_purifier.data.sparse_image) SparseSslDM (class in tissue_purifier.data.datamodule) SpatialAutocorrelation (class in tissue_purifier.models.patch_analyzer.patch_analyzer) SslDM (class in tissue_purifier.data.datamodule) SslModelBase (class in tissue_purifier.models.ssl_models._ssl_base_model) subset_dict() (in module tissue_purifier.utils.dict_util) subset_dict_non_overlapping_patches() (in module tissue_purifier.utils.dict_util)

T

tissue_purifier.genex.gene_utils module tissue_purifier.genex.gene_visualization module tissue_purifier.genex.pyro_model module tissue_purifier.io.download module tissue_purifier.io.read_anndata_from_csv module tissue_purifier.plots.plot_embeddings module tissue_purifier.plots.plot_images module tissue_purifier.plots.plot_knn module tissue_purifier.plots.plot_misc module tissue_purifier.utils.dict_util module tissue_purifier.utils.validation_util module

to() (SparseImage method) to_anndata() (SparseImage method) to_dense() (SparseImage method) to_rgb() (SparseImage method) train() (GeneRegression method) train_and_test() (GeneRegression method) train_test_val_split() (in module tissue_purifier.genex.gene_utils) transfer_annotations_between_dict() (in module tissue_purifier.utils.dict_util) transfer_image_to_spot() (SparseImage method) transfer_patch_to_image() (SparseImage method) transfer_patch_to_spot() (SparseImage method) transform() (SmartPca method) (SmartScaler method) (SmartUmap method) trim_image_dictionary() (SparseImage method) trim_patch_dictionary() (SparseImage method) trim_spot_dictionary() (SparseImage method) trsfm_test (SparseSslDM property) trsfm_train_global (SparseSslDM property) trsfm_train_local (SparseSslDM property)

V

VaeModel (class in tissue_purifier.models.ssl_models.vae)

W

write_to_image_dictionary() (SparseImage method)

write_to_patch_dictionary() (SparseImage method) write_to_spot_dictionary() (SparseImage method)

X

x_raw (SparseImage property)

Y

y_raw (SparseImage property)