Index

_

__init__() (AugmentedDeepFeatureExtractor method) (BaseCAM method) (BaseExplainer method) (BaseGraphBuilder method) (BaseGraphGradCAMExplainer method) (BaseGraphVisualization method) (BaseImageVisualization method) (BaseModel method) (BatchPipelineRunner method) (BNReLU method) (CellGraphModel method) (ColorMergedSuperpixelExtractor method) (Conv2dWithActivation method) (Decoder method) (DeepFeatureExtractor method) (DenseBlock method) (DenseGINLayer method) (Encoder method) (ExplainerModel method) (GaussianTissueMask method) (GINLayer method) (GraphPruningExplainer method) (GridAugmentedDeepFeatureExtractor method) (GridDeepFeatureExtractor method) (GridPatchDataset method) (HACTModel method) (HACTVisualization method) (HoverNet method) (ImageToPatchDataset method) (InstanceMapPatchDataset method) (KNNGraphBuilder method) (MacenkoStainNormalizer method) (MergedSuperpixelExtractor method) (MLP method) (MultiLayerGNN method) (NucleiConceptExtractor method) (NucleiExtractor method) (OverlayGraphVisualization method) (PatchFeatureExtractor method) (PipelineRunner method) (PipelineStep method) (PNALayer method) (RAGGraphBuilder method) (ResidualBlock method) (SLICSuperpixelExtractor method) (StainNormalizer method) (SuperpixelExtractor method) (TissueGraphModel method) (Upsample2x method) (VahadaneStainNormalizer method)

A

adj_to_dgl() (in module histocartography.utils.graph) adj_to_networkx() (in module histocartography.utils.graph) aggregate_max() (in module histocartography.ml.layers.constants) aggregate_mean() (in module histocartography.ml.layers.constants) aggregate_min() (in module histocartography.ml.layers.constants)

aggregate_std() (in module histocartography.ml.layers.constants) aggregate_var() (in module histocartography.ml.layers.constants) AnnotationPostProcessor (class in histocartography.preprocessing.tissue_mask) AssignmnentMatrixBuilder (class in histocartography.preprocessing.assignment_matrix) AugmentedDeepFeatureExtractor (class in histocartography.preprocessing.feature_extraction)

B

BaseCAM (class in histocartography.interpretability.grad_cam) BaseExplainer (class in histocartography.interpretability.base_explainer) BaseGraphBuilder (class in histocartography.preprocessing.graph_builders) BaseGraphGradCAMExplainer (class in histocartography.interpretability.grad_cam) BaseGraphVisualization (class in histocartography.visualization.visualization)

BaseImageVisualization (class in histocartography.visualization.visualization) BaseModel (class in histocartography.ml.models.base_model) BatchPipelineRunner (class in histocartography.pipeline) BNReLU (class in histocartography.ml.models.hovernet) buffer_plot_and_get() (in module histocartography.utils.io)

C

CellGraphModel (class in histocartography.ml.models.cell_graph_model) check_for_dir() (in module histocartography.utils.io) clear_hooks() (BaseCAM method) ColorMergedSuperpixelExtractor (class in histocartography.preprocessing.superpixel)

ConfusionMatrixMetric (class in histocartography.metrics.metrics) Conv2dWithActivation (class in histocartography.ml.models.hovernet) copy_graph() (in module histocartography.utils.graph) crop_op() (in module histocartography.ml.models.hovernet)

D

Decoder (class in histocartography.ml.models.hovernet) DeepFeatureExtractor (class in histocartography.preprocessing.feature_extraction) DenseBlock (class in histocartography.ml.models.hovernet) DenseGINLayer (class in histocartography.ml.layers.dense_gin_layer) DGLGraphLoader (class in histocartography.preprocessing.io) Dice (class in histocartography.metrics.metrics) distillation_loss() (ExplainerModel method) download_box_link() (in module histocartography.utils.io) download_example_data() (in module histocartography.utils.io) download_test_data() (in module histocartography.utils.io) draw_circle() (in module histocartography.utils.draw_utils) draw_edges() (BaseGraphVisualization method) (OverlayGraphVisualization method)

draw_ellipse() (in module histocartography.utils.draw_utils) draw_instances() (BaseGraphVisualization method) (BaseImageVisualization method) (InstanceImageVisualization method) (OverlayGraphVisualization method) draw_large_circle() (in module histocartography.utils.draw_utils) draw_line() (in module histocartography.utils.draw_utils) draw_nodes() (BaseGraphVisualization method) (OverlayGraphVisualization method) draw_poly() (in module histocartography.utils.draw_utils) dynamic_import_from() (in module histocartography.utils)

E

Encoder (class in histocartography.ml.models.hovernet)

ExplainerModel (class in histocartography.interpretability.graph_pruning_explainer) extract_patches_from_image() (in module histocartography.utils.image)

F

fast_confusion_matrix() (in module histocartography.metrics.metrics) fast_histogram() (in module histocartography.preprocessing.utils) FeatureExtractor (class in histocartography.preprocessing.feature_extraction) FileLoader (class in histocartography.preprocessing.io) fit() (MacenkoStainNormalizer method) (StainNormalizer method) (VahadaneStainNormalizer method) forward() (BaseModel method) (BNReLU method) (CellGraphModel method) (Conv2dWithActivation method) (Decoder method) (DenseBlock method) (DenseGINLayer method) (Encoder method) (ExplainerModel method) (GINLayer method) (HACTModel method) (HoverNet method) (MLP method) (MultiLayerGNN method) (PNALayer method) (PNATower method) (ResidualBlock method) (SamepaddingLayer method) (TissueGraphModel method) (Upsample2x method)

G

GaussianTissueMask (class in histocartography.preprocessing.tissue_mask) get_filename() (in module histocartography.utils.io) get_last_steps() (in module histocartography.utils.image) get_number_of_classes() (in module histocartography.ml.models.base_model) get_tissue_mask() (in module histocartography.preprocessing.tissue_mask) GINLayer (class in histocartography.ml.layers.gin_layer) GradCAM (class in histocartography.interpretability.grad_cam) GradCAMpp (class in histocartography.interpretability.grad_cam) graph_preprocessing() (BaseGraphVisualization method) (OverlayGraphVisualization method)

GraphDiameter (class in histocartography.preprocessing.stats) GraphGradCAMExplainer (class in histocartography.interpretability.grad_cam) GraphGradCAMPPExplainer (class in histocartography.interpretability.grad_cam) GraphLRPExplainer (class in histocartography.interpretability.lrp_gnn_explainer) GraphPruningExplainer (class in histocartography.interpretability.graph_pruning_explainer) GridAugmentedDeepFeatureExtractor (class in histocartography.preprocessing.feature_extraction) GridDeepFeatureExtractor (class in histocartography.preprocessing.feature_extraction) GridPatchDataset (class in histocartography.preprocessing.feature_extraction)

H

h5_to_numpy() (in module histocartography.utils.io) h5_to_tensor() (in module histocartography.utils.io) H5Loader (class in histocartography.preprocessing.io) HACTModel (class in histocartography.ml.models.hact_model) HACTVisualization (class in histocartography.visualization.visualization) HandcraftedFeatureExtractor (class in histocartography.preprocessing.feature_extraction) histocartography module histocartography.interpretability module histocartography.interpretability.base_explainer module histocartography.interpretability.grad_cam module histocartography.interpretability.graph_pruning_explainer module histocartography.interpretability.lrp_gnn_explainer module histocartography.metrics module histocartography.metrics.metrics module histocartography.ml module histocartography.ml.layers module histocartography.ml.layers.constants module histocartography.ml.layers.dense_gin_layer module histocartography.ml.layers.gin_layer module histocartography.ml.layers.mlp module histocartography.ml.layers.multi_layer_gnn module histocartography.ml.layers.pna_layer module histocartography.ml.models module histocartography.ml.models.base_model module histocartography.ml.models.cell_graph_model module histocartography.ml.models.hact_model module histocartography.ml.models.hovernet module

histocartography.ml.models.tissue_graph_model module histocartography.ml.models.zoo module histocartography.pipeline module histocartography.preprocessing module histocartography.preprocessing.assignment_matrix module histocartography.preprocessing.feature_extraction module histocartography.preprocessing.graph_builders module histocartography.preprocessing.io module histocartography.preprocessing.nuclei_concept_extraction module histocartography.preprocessing.nuclei_extraction module histocartography.preprocessing.stain_normalizers module histocartography.preprocessing.stats module histocartography.preprocessing.superpixel module histocartography.preprocessing.tissue_mask module histocartography.preprocessing.utils module histocartography.utils module histocartography.utils.draw_utils module histocartography.utils.graph module histocartography.utils.image module histocartography.utils.io module histocartography.utils.torch module histocartography.visualization module histocartography.visualization.visualization module HoverNet (class in histocartography.ml.models.hovernet)

I

ImageLoader (class in histocartography.preprocessing.io) ImageToPatchDataset (class in histocartography.preprocessing.nuclei_extraction) InstanceImageVisualization (class in histocartography.visualization.visualization) InstanceMapPatchDataset (class in histocartography.preprocessing.feature_extraction) IoU (class in histocartography.metrics.metrics) is_better() (Dice static method) (IoU static method) (Metric static method)

is_box_url() (in module histocartography.utils.io) is_per_class (Dice property) (IoU property) (MeanDice property) (MeanIoU property) (Metric property)

K

KNNGraphBuilder (class in histocartography.preprocessing.graph_builders)

L

link_output() (BatchPipelineRunner method) load_image() (in module histocartography.preprocessing.utils) load_json() (in module histocartography.utils.io) logs_model (Dice property) (IoU property) (Metric property)

loss() (ExplainerModel method) lrp() (CellGraphModel method) (GINLayer method) (MLP method) (MultiLayerGNN method) (TissueGraphModel method)

M

MacenkoStainNormalizer (class in histocartography.preprocessing.stain_normalizers) map_value_to_color() (in module histocartography.utils.draw_utils) MeanDice (class in histocartography.metrics.metrics) MeanIoU (class in histocartography.metrics.metrics) MergedSuperpixelExtractor (class in histocartography.preprocessing.superpixel) message_func() (PNATower method) Metric (class in histocartography.metrics.metrics) min_nodes() (in module histocartography.ml.layers.constants) mkdir() (AnnotationPostProcessor method) (FileLoader method) (StatsComputer method) MLP (class in histocartography.ml.layers.mlp) module histocartography histocartography.interpretability histocartography.interpretability.base_explainer histocartography.interpretability.grad_cam histocartography.interpretability.graph_pruning_explainer histocartography.interpretability.lrp_gnn_explainer histocartography.metrics histocartography.metrics.metrics histocartography.ml histocartography.ml.layers histocartography.ml.layers.constants histocartography.ml.layers.dense_gin_layer histocartography.ml.layers.gin_layer histocartography.ml.layers.mlp histocartography.ml.layers.multi_layer_gnn histocartography.ml.layers.pna_layer histocartography.ml.models histocartography.ml.models.base_model histocartography.ml.models.cell_graph_model histocartography.ml.models.hact_model histocartography.ml.models.hovernet histocartography.ml.models.tissue_graph_model histocartography.ml.models.zoo histocartography.pipeline histocartography.preprocessing histocartography.preprocessing.assignment_matrix histocartography.preprocessing.feature_extraction histocartography.preprocessing.graph_builders histocartography.preprocessing.io histocartography.preprocessing.nuclei_concept_extraction histocartography.preprocessing.nuclei_extraction histocartography.preprocessing.stain_normalizers histocartography.preprocessing.stats histocartography.preprocessing.superpixel histocartography.preprocessing.tissue_mask histocartography.preprocessing.utils histocartography.utils histocartography.utils.draw_utils histocartography.utils.graph histocartography.utils.image histocartography.utils.io histocartography.utils.torch histocartography.visualization histocartography.visualization.visualization

msg_fn() (GINLayer method) MultiLayerGNN (class in histocartography.ml.layers.multi_layer_gnn)

N

name2rgb() (in module histocartography.utils.draw_utils) node_update_fn() (GINLayer method)

NucleiConceptExtractor (class in histocartography.preprocessing.nuclei_concept_extraction) NucleiExtractor (class in histocartography.preprocessing.nuclei_extraction)

O

OverlayGraphVisualization (class in histocartography.visualization.visualization)

P

pad_image() (in module histocartography.utils.image) PatchFeatureExtractor (class in histocartography.preprocessing.feature_extraction) PipelineRunner (class in histocartography.pipeline) PipelineStep (class in histocartography.pipeline) PNALayer (class in histocartography.ml.layers.pna_layer) PNATower (class in histocartography.ml.layers.pna_layer) posttrans_nodes() (PNATower method) precompute() (BaseGraphBuilder method) (BatchPipelineRunner method) (FeatureExtractor method) (NucleiExtractor method) (PipelineRunner method) (PipelineStep method) (StainNormalizer method) (StatsComputer method) (SuperpixelExtractor method) (TissueMask method)

pretrans_edges() (PNATower method) process() (PipelineStep method) process_and_save() (StainNormalizer method) process_instance() (in module histocartography.preprocessing.nuclei_extraction) process_np_hv_channels() (in module histocartography.preprocessing.nuclei_extraction)

R

RAGGraphBuilder (class in histocartography.preprocessing.graph_builders) reduce_fn() (GINLayer method) reduce_func() (PNATower method) reduce_max() (in module histocartography.ml.layers.constants) reduce_min() (in module histocartography.ml.layers.constants)

ResidualBlock (class in histocartography.ml.models.hovernet) rgb() (in module histocartography.utils.draw_utils) rlp() (HACTModel method) run() (BatchPipelineRunner method) (PipelineRunner method)

S

SamepaddingLayer (class in histocartography.ml.models.hovernet) save_image() (in module histocartography.preprocessing.utils) scale_amplification() (in module histocartography.ml.layers.constants) scale_attenuation() (in module histocartography.ml.layers.constants) scale_identity() (in module histocartography.ml.layers.constants) set_forward_hook() (BaseModel method) set_graph_on_cpu() (in module histocartography.utils.graph) set_graph_on_cuda() (in module histocartography.utils.graph) set_lrp() (CellGraphModel method) (GINLayer method) (MLP method) (MultiLayerGNN method) (TissueGraphModel method)

set_rlp() (HACTModel method) (PNALayer method) sigmoid() (ExplainerModel static method) signal_last() (in module histocartography.utils) SLICSuperpixelExtractor (class in histocartography.preprocessing.superpixel) StainNormalizer (class in histocartography.preprocessing.stain_normalizers) StatsComputer (class in histocartography.preprocessing.stats) SuperpixelCounter (class in histocartography.preprocessing.stats) SuperpixelExtractor (class in histocartography.preprocessing.superpixel)

T

TissueGraphModel (class in histocartography.ml.models.tissue_graph_model) TissueMask (class in histocartography.preprocessing.tissue_mask) to_cpu() (in module histocartography.utils.graph)

to_device() (in module histocartography.utils.graph) torch_to_numpy() (in module histocartography.utils.torch) two_hop_neighborhood() (in module histocartography.preprocessing.graph_builders)

U

Upsample2x (class in histocartography.ml.models.hovernet)

V

VahadaneStainNormalizer (class in histocartography.preprocessing.stain_normalizers)

W

write_json() (in module histocartography.utils.io)