Index

A

AbstractFeatureScaler (class in morphoclass.transforms) (class in morphoclass.transforms.scalers) (class in morphoclass.transforms.scalers.abstract_scaler) AbstractGlobalFeatureExtractor (class in morphoclass.transforms) (class in morphoclass.transforms.global_features) (class in morphoclass.transforms.global_features.abstract_global_feature_extractor) acc() (morphoclass.training.trainers.Trainer static method) accuracy() (morphoclass.models.bidirectional_net.BidirectionalNet method) (morphoclass.models.BidirectionalNet method) (morphoclass.models.multi_adj_net.MultiAdjNet method) (morphoclass.models.MultiAdjNet method) add_figure() (morphoclass.report.xai.XAIReport method) add_metadata() (in module morphoclass.utils) add_nodes() (morphoclass.transforms.AddNodesAtIntervals method) (morphoclass.transforms.augmentors.add_nodes_at_intervals.AddNodesAtIntervals method) (morphoclass.transforms.augmentors.AddNodesAtIntervals method) add_section() (morphoclass.report.xai.XAIReport method) add_split() (morphoclass.training.training_log.TrainingLog method) AddNodesAtIntervals (class in morphoclass.transforms) (class in morphoclass.transforms.augmentors) (class in morphoclass.transforms.augmentors.add_nodes_at_intervals) AddOneHotLabels (class in morphoclass.transforms) (class in morphoclass.transforms.add_one_hot_labels) AddRandomPointsToReductionMask (class in morphoclass.transforms) (class in morphoclass.transforms.augmentors) (class in morphoclass.transforms.augmentors.add_random_points_to_reduction_mask)

AddSectionMiddlePoints (class in morphoclass.transforms) (class in morphoclass.transforms.augmentors) (class in morphoclass.transforms.augmentors.add_section_middle_points) adj() (morphoclass.model_utils.HierarchicalLabels property) analysis() (in module morphoclass.cleanlab) apply_mask() (morphoclass.transforms.ApplyNodeReductionMasks static method) (morphoclass.transforms.augmentors.apply_node_reduction_masks.ApplyNodeReductionMasks static method) (morphoclass.transforms.augmentors.ApplyNodeReductionMasks static method) ApplyNodeReductionMasks (class in morphoclass.transforms) (class in morphoclass.transforms.augmentors) (class in morphoclass.transforms.augmentors.apply_node_reduction_masks) are_you_sure() (in module morphoclass.utils) ask() (in module morphoclass.training.cli) AttentionGlobalPool (class in morphoclass.layers) (class in morphoclass.layers.attention_global_pool) attribute_bytes_tree_hash() (in module morphoclass.transforms.helper) attribute_check() (in module morphoclass.data.filters) augment_persistence_diagrams() (in module morphoclass.data) augment_persistence_diagrams_v2() (in module morphoclass.data) AverageBranchOrder (class in morphoclass.transforms) (class in morphoclass.transforms.global_features) (class in morphoclass.transforms.global_features.average_branch_order) AverageRadius (class in morphoclass.transforms) (class in morphoclass.transforms.global_features) (class in morphoclass.transforms.global_features.average_radius)

B

batch_size (morphoclass.data.morphology_data_loader.MorphologyDataLoader attribute) (morphoclass.data.MorphologyDataLoader attribute) (morphoclass.training.training_config.TrainingConfig attribute) BidirectionalBlock (class in morphoclass.layers) (class in morphoclass.layers.bidirectional_block) BidirectionalNet (class in morphoclass.models) (class in morphoclass.models.bidirectional_net)

BidirectionalResBlock (class in morphoclass.layers) (class in morphoclass.layers.bidirectional_res_block) BranchingOnlyNeurites (class in morphoclass.transforms) (class in morphoclass.transforms.augmentors) (class in morphoclass.transforms.augmentors.branching_only_neurites) BranchingOnlyNeuron (class in morphoclass.transforms) (class in morphoclass.transforms.augmentors) (class in morphoclass.transforms.augmentors.branching_only_neuron)

C

Cat (class in morphoclass.layers) (class in morphoclass.layers.cat) chance_agreement() (in module morphoclass.metrics) ChebConv (class in morphoclass.layers) (class in morphoclass.layers.cheb_conv) ChebConvSeparable (class in morphoclass.layers) (class in morphoclass.layers.cheb_conv_separable) check_installed() (in module morphoclass.cleanlab) (in module morphoclass.deepwalk) check_overwrite_file() (in module morphoclass.console.cmd_xai) checkpoint_path_pretrained (morphoclass.training.training_config.TrainingConfig attribute) classification_report() (in module morphoclass.metrics) clone_obj() (morphoclass.transforms.make_copy.MakeCopy class method) (morphoclass.transforms.MakeCopy class method) cnn_model_attributions() (in module morphoclass.xai) (in module morphoclass.xai.model_attributions) cnn_model_attributions_population() (in module morphoclass.xai) (in module morphoclass.xai.model_attributions) CNNEmbedder (class in morphoclass.models) (class in morphoclass.models.cnnet) CNNet (class in morphoclass.models) (class in morphoclass.models.cnnet)

collect_duplicated_morphologies() (morphoclass.console.dataset_preprocessor.Preprocessor method) collect_metrics() (in module morphoclass.training.cli) combined_filter() (in module morphoclass.data.filters) Compose (class in morphoclass.transforms) (class in morphoclass.transforms.compose) compute_hierarchical_metric() (morphoclass.models.HBNet method) (morphoclass.models.hbnet.HBNet method) ConcateCNNet (class in morphoclass.models) (class in morphoclass.models.concatecnnet) ConcateCNNetTrainer (class in morphoclass.training.trainers) ConcateNet (class in morphoclass.models) (class in morphoclass.models.concatenet) ConcateNetTrainer (class in morphoclass.training.trainers) convert() (in module morphoclass.console.helpers) convert_morphologies() (in module morphoclass.utils) CorianderNet (class in morphoclass.models) (class in morphoclass.models.coriander_net) create_k_folds() (in module morphoclass.training) ctx2dict() (in module morphoclass.console.helpers) custom_preprocess() (morphoclass.console.dataset_preprocessor.Preprocessor method)

D

data_loader() (morphoclass.training.trainers.Trainer method) dataset (morphoclass.data.morphology_data_loader.MorphologyDataLoader attribute) (morphoclass.data.MorphologyDataLoader attribute) dataset_name (morphoclass.training.training_config.TrainingConfig attribute) DatasetStatsPlotter (class in morphoclass.console.stats_plotter) DatasetType (class in morphoclass.constants) df_stats() (morphoclass.console.stats_plotter.DatasetStatsPlotter property) dict2kwargs() (in module morphoclass.utils)

discordance() (in module morphoclass.metrics) discordance_multiclass() (in module morphoclass.metrics) download() (morphoclass.data.tns_dataset.TNSDataset method) drop_duplicate_files() (morphoclass.console.dataset_preprocessor.Preprocessor method) drop_last (morphoclass.data.morphology_data_loader.MorphologyDataLoader attribute) (morphoclass.data.MorphologyDataLoader attribute) drop_mtypes_with_one_neuron() (morphoclass.console.dataset_preprocessor.Preprocessor method) dump_morphologies() (morphoclass.data.tns_dataset.TNSDataset method)

E

embed_latent_features() (in module morphoclass.xai.embedding_visualization) EmbeddingExtractor (class in morphoclass.xai) (class in morphoclass.xai.embedding_extractor) EqualizeNodeCounts (class in morphoclass.transforms) (class in morphoclass.transforms.augmentors) (class in morphoclass.transforms.augmentors.equalize_node_counts) exclusion_filter() (in module morphoclass.data.filters) extra_repr() (morphoclass.layers.GaussianPointTransformer method) (morphoclass.layers.perslay.GaussianPointTransformer method) (morphoclass.layers.perslay.PointTransformer method) (morphoclass.layers.perslay.PointwisePointTransformer method) (morphoclass.layers.PointwisePointTransformer method) extract_edge_features() (morphoclass.transforms.edge_features.extract_distance_weights.ExtractDistanceWeights method) (morphoclass.transforms.edge_features.extract_edge_features.ExtractEdgeFeatures method) (morphoclass.transforms.edge_features.ExtractDistanceWeights method) (morphoclass.transforms.edge_features.ExtractEdgeFeatures method) (morphoclass.transforms.ExtractDistanceWeights method) (morphoclass.transforms.ExtractEdgeFeatures method) extract_global_feature() (morphoclass.transforms.AbstractGlobalFeatureExtractor method) (morphoclass.transforms.AverageBranchOrder method) (morphoclass.transforms.AverageRadius method) (morphoclass.transforms.ExtractMaximalApicalPathLength method) (morphoclass.transforms.ExtractNumberBranchPoints method) (morphoclass.transforms.ExtractNumberLeaves method) (morphoclass.transforms.global_features.abstract_global_feature_extractor.AbstractGlobalFeatureExtractor method) (morphoclass.transforms.global_features.AbstractGlobalFeatureExtractor method) (morphoclass.transforms.global_features.average_branch_order.AverageBranchOrder method) (morphoclass.transforms.global_features.average_radius.AverageRadius method) (morphoclass.transforms.global_features.AverageBranchOrder method) (morphoclass.transforms.global_features.AverageRadius method) (morphoclass.transforms.global_features.extract_maximal_apical_path_length.ExtractMaximalApicalPathLength method) (morphoclass.transforms.global_features.extract_number_branch_points.ExtractNumberBranchPoints method) (morphoclass.transforms.global_features.extract_number_leaves.ExtractNumberLeaves method) (morphoclass.transforms.global_features.ExtractMaximalApicalPathLength method) (morphoclass.transforms.global_features.ExtractNumberBranchPoints method) (morphoclass.transforms.global_features.ExtractNumberLeaves method) (morphoclass.transforms.global_features.total_path_length.TotalPathLength method) (morphoclass.transforms.global_features.TotalPathLength method) (morphoclass.transforms.TotalPathLength method) extract_node_features() (morphoclass.transforms.ExtractConstFeature method) (morphoclass.transforms.ExtractDiameters method) (morphoclass.transforms.node_features.extract_const_feature.ExtractConstFeature method) (morphoclass.transforms.node_features.extract_diameters.ExtractDiameters method) (morphoclass.transforms.node_features.extract_node_features.ExtractNodeFeatures method) (morphoclass.transforms.node_features.ExtractConstFeature method) (morphoclass.transforms.node_features.ExtractDiameters method) (morphoclass.transforms.node_features.ExtractNodeFeatures method) extract_property() (morphoclass.transforms.ExtractIsBranching method) (morphoclass.transforms.ExtractIsIntermediate method) (morphoclass.transforms.ExtractIsLeaf method) (morphoclass.transforms.ExtractIsRoot method) (morphoclass.transforms.ExtractOneHotProperty method) (morphoclass.transforms.node_features.extract_node_onehot_properties.ExtractIsBranching method) (morphoclass.transforms.node_features.extract_node_onehot_properties.ExtractIsIntermediate method) (morphoclass.transforms.node_features.extract_node_onehot_properties.ExtractIsLeaf method) (morphoclass.transforms.node_features.extract_node_onehot_properties.ExtractIsRoot method) (morphoclass.transforms.node_features.extract_node_onehot_properties.ExtractOneHotProperty method) (morphoclass.transforms.node_features.ExtractIsBranching method) (morphoclass.transforms.node_features.ExtractIsIntermediate method) (morphoclass.transforms.node_features.ExtractIsLeaf method) (morphoclass.transforms.node_features.ExtractIsRoot method) (morphoclass.transforms.node_features.ExtractOneHotProperty method) ExtractBranchingAngles (class in morphoclass.transforms) (class in morphoclass.transforms.node_features) (class in morphoclass.transforms.node_features.extract_branching_angles)

ExtractBranchingNodeReductionMasks (class in morphoclass.transforms) (class in morphoclass.transforms.augmentors) (class in morphoclass.transforms.augmentors.extract_branching_node_reduction_masks) ExtractConstFeature (class in morphoclass.transforms) (class in morphoclass.transforms.node_features) (class in morphoclass.transforms.node_features.extract_const_feature) ExtractCoordinates (class in morphoclass.transforms) (class in morphoclass.transforms.node_features) (class in morphoclass.transforms.node_features.extract_coordinates) ExtractDiameters (class in morphoclass.transforms) (class in morphoclass.transforms.node_features) (class in morphoclass.transforms.node_features.extract_diameters) ExtractDistances (class in morphoclass.transforms) (class in morphoclass.transforms.node_features) (class in morphoclass.transforms.node_features.extract_distances) ExtractDistanceWeights (class in morphoclass.transforms) (class in morphoclass.transforms.edge_features) (class in morphoclass.transforms.edge_features.extract_distance_weights) ExtractEdgeFeatures (class in morphoclass.transforms) (class in morphoclass.transforms.edge_features) (class in morphoclass.transforms.edge_features.extract_edge_features) ExtractEdgeIndex (class in morphoclass.transforms) (class in morphoclass.transforms.edge_features) (class in morphoclass.transforms.edge_features.extract_edge_index) ExtractIsBranching (class in morphoclass.transforms) (class in morphoclass.transforms.node_features) (class in morphoclass.transforms.node_features.extract_node_onehot_properties) ExtractIsIntermediate (class in morphoclass.transforms) (class in morphoclass.transforms.node_features) (class in morphoclass.transforms.node_features.extract_node_onehot_properties) ExtractIsLeaf (class in morphoclass.transforms) (class in morphoclass.transforms.node_features) (class in morphoclass.transforms.node_features.extract_node_onehot_properties) ExtractIsRoot (class in morphoclass.transforms) (class in morphoclass.transforms.node_features) (class in morphoclass.transforms.node_features.extract_node_onehot_properties) ExtractMaximalApicalPathLength (class in morphoclass.transforms) (class in morphoclass.transforms.global_features) (class in morphoclass.transforms.global_features.extract_maximal_apical_path_length) ExtractNodeFeatures (class in morphoclass.transforms.node_features) (class in morphoclass.transforms.node_features.extract_node_features) ExtractNumberBranchPoints (class in morphoclass.transforms) (class in morphoclass.transforms.global_features) (class in morphoclass.transforms.global_features.extract_number_branch_points) ExtractNumberLeaves (class in morphoclass.transforms) (class in morphoclass.transforms.global_features) (class in morphoclass.transforms.global_features.extract_number_leaves) ExtractOneHotProperty (class in morphoclass.transforms) (class in morphoclass.transforms.node_features) (class in morphoclass.transforms.node_features.extract_node_onehot_properties) ExtractPathDistances (class in morphoclass.transforms) (class in morphoclass.transforms.node_features) (class in morphoclass.transforms.node_features.extract_path_distances) ExtractRadialDistances (class in morphoclass.transforms) (class in morphoclass.transforms.node_features) (class in morphoclass.transforms.node_features.extract_radial_distances) ExtractTMDNeurites (class in morphoclass.transforms) (class in morphoclass.transforms.extract_tmd_neurites) ExtractTMDNeuron (class in morphoclass.transforms) (class in morphoclass.transforms.extract_tmd_neuron) ExtractVerticalDistances (class in morphoclass.transforms) (class in morphoclass.transforms.node_features) (class in morphoclass.transforms.node_features.extract_vertical_distances)

F

FeatureManualScaler (class in morphoclass.transforms) (class in morphoclass.transforms.scalers) (class in morphoclass.transforms.scalers.manual_scaler) FeatureMinMaxScaler (class in morphoclass.transforms) (class in morphoclass.transforms.scalers) (class in morphoclass.transforms.scalers.min_max_scaler) FeatureRobustScaler (class in morphoclass.transforms) (class in morphoclass.transforms.scalers) (class in morphoclass.transforms.scalers.robust_scaler) features_dir (morphoclass.training.training_config.TrainingConfig attribute) FeatureStandardScaler (class in morphoclass.transforms) (class in morphoclass.transforms.scalers) (class in morphoclass.transforms.scalers.standard_scaler) filename_exclusion_filter() (in module morphoclass.data.filters) filename_inclusion_filter() (in module morphoclass.data.filters) find_point_on_branch() (in module morphoclass.utils) fit() (morphoclass.transforms.AbstractFeatureScaler method) (morphoclass.transforms.augmentors.equalize_node_counts.EqualizeNodeCounts method) (morphoclass.transforms.augmentors.EqualizeNodeCounts method) (morphoclass.transforms.EqualizeNodeCounts method) (morphoclass.transforms.scalers.abstract_scaler.AbstractFeatureScaler method) (morphoclass.transforms.scalers.AbstractFeatureScaler method) fit_3d_ray() (in module morphoclass.orientation) fit_tree_pca() (in module morphoclass.orientation) fit_tree_ray() (in module morphoclass.orientation) flat_labels() (morphoclass.model_utils.HierarchicalLabels method) flat_to_hierarchical_oh() (morphoclass.model_utils.HierarchicalLabels method) forward() (morphoclass.layers.attention_global_pool.AttentionGlobalPool method) (morphoclass.layers.AttentionGlobalPool method) (morphoclass.layers.bidirectional_block.BidirectionalBlock method) (morphoclass.layers.bidirectional_res_block.BidirectionalResBlock method) (morphoclass.layers.BidirectionalBlock method) (morphoclass.layers.BidirectionalResBlock method) (morphoclass.layers.Cat method) (morphoclass.layers.cat.Cat method) (morphoclass.layers.cheb_conv.ChebConv method) (morphoclass.layers.cheb_conv_separable.ChebConvSeparable method) (morphoclass.layers.ChebConv method) (morphoclass.layers.ChebConvSeparable method) (morphoclass.layers.GaussianPointTransformer method) (morphoclass.layers.PersLay method) (morphoclass.layers.perslay.GaussianPointTransformer method) (morphoclass.layers.perslay.PersLay method) (morphoclass.layers.perslay.PointTransformer method) (morphoclass.layers.perslay.PointwisePointTransformer method) (morphoclass.layers.PointwisePointTransformer method) (morphoclass.layers.tree_lstm_pool.TreeLSTMCell method) (morphoclass.layers.tree_lstm_pool.TreeLSTMPool method) (morphoclass.layers.TreeLSTMPool method) (morphoclass.models.bidirectional_net.BidirectionalNet method) (morphoclass.models.BidirectionalNet method) (morphoclass.models.CNNEmbedder method) (morphoclass.models.CNNet method) (morphoclass.models.cnnet.CNNEmbedder method) (morphoclass.models.cnnet.CNNet method) (morphoclass.models.ConcateCNNet method) (morphoclass.models.concatecnnet.ConcateCNNet method) (morphoclass.models.ConcateNet method) (morphoclass.models.concatenet.ConcateNet method) (morphoclass.models.coriander_net.CorianderNet method) (morphoclass.models.CorianderNet method) (morphoclass.models.HBNet method) (morphoclass.models.hbnet.HBNet method) (morphoclass.models.man_net.ManEmbedder method) (morphoclass.models.man_net.ManNet method) (morphoclass.models.man_net.ManNetR method) (morphoclass.models.man_res_nets.ManResNet1 method) (morphoclass.models.man_res_nets.ManResNet2 method) (morphoclass.models.man_res_nets.ManResNet3 method) (morphoclass.models.ManEmbedder method) (morphoclass.models.ManNet method) (morphoclass.models.ManNetR method) (morphoclass.models.ManResNet1 method) (morphoclass.models.ManResNet2 method) (morphoclass.models.ManResNet3 method) (morphoclass.models.multi_adj_net.MultiAdjNet method) (morphoclass.models.MultiAdjNet method)

fowlkes_mallows_score() (in module morphoclass.metrics) from_adjacency_matrix() (morphoclass.model_utils.HierarchicalLabels class method) from_csv() (morphoclass.data.morphology_dataset.MorphologyDataset class method) (morphoclass.data.MorphologyDataset class method) from_dict() (morphoclass.training.training_config.TrainingConfig class method) (morphoclass.training.training_log.TrainingLog class method) from_features() (morphoclass.data.morphology_dataset.MorphologyDataset class method) (morphoclass.data.MorphologyDataset class method) from_file() (morphoclass.training.training_config.TrainingConfig class method) from_flat_labels() (morphoclass.model_utils.HierarchicalLabels class method) from_morphio() (in module morphoclass.utils) from_morphio_to_tmd() (in module morphoclass.utils) from_paths() (morphoclass.data.morphology_dataset.MorphologyDataset class method) (morphoclass.data.MorphologyDataset class method) from_separate_configs() (morphoclass.training.training_config.TrainingConfig class method) from_structured_dir() (morphoclass.data.morphology_dataset.MorphologyDataset class method) (morphoclass.data.MorphologyDataset class method) from_tmd_to_morphio() (in module morphoclass.utils) frozen_backbone (morphoclass.training.training_config.TrainingConfig attribute)

G

GaussianPointTransformer (class in morphoclass.layers) (class in morphoclass.layers.perslay) gen_class_masks() (morphoclass.model_utils.HierarchicalLabels method) gen_hierarchical_probabilities() (morphoclass.models.HBNet method) (morphoclass.models.hbnet.HBNet method) generate_empty_image() (in module morphoclass.xai.embedding_visualization) generate_image() (in module morphoclass.xai.embedding_visualization) generate_tns_distributions() (in module morphoclass.data.tns_dataset) get() (morphoclass.data.morphology_dataset.MorphologyDataset method) (morphoclass.data.MorphologyDataset method) (morphoclass.data.tns_dataset.TNSDataset method) get_angle_deg() (in module morphoclass.orientation) get_angle_rad() (in module morphoclass.orientation) get_cam() (morphoclass.xai.grad_cam_explainer.GradCAMExplainer method) (morphoclass.xai.GradCAMExplainer method) get_class_segmentation_mask() (morphoclass.model_utils.HierarchicalLabels method) get_color_map() (in module morphoclass.vis) get_config() (morphoclass.transforms.AbstractFeatureScaler method) (morphoclass.transforms.FeatureManualScaler method) (morphoclass.transforms.FeatureMinMaxScaler method) (morphoclass.transforms.FeatureRobustScaler method) (morphoclass.transforms.FeatureStandardScaler method) (morphoclass.transforms.scalers.abstract_scaler.AbstractFeatureScaler method) (morphoclass.transforms.scalers.AbstractFeatureScaler method) (morphoclass.transforms.scalers.FeatureManualScaler method) (morphoclass.transforms.scalers.FeatureMinMaxScaler method) (morphoclass.transforms.scalers.FeatureRobustScaler method) (morphoclass.transforms.scalers.FeatureStandardScaler method) (morphoclass.transforms.scalers.manual_scaler.FeatureManualScaler method) (morphoclass.transforms.scalers.min_max_scaler.FeatureMinMaxScaler method) (morphoclass.transforms.scalers.robust_scaler.FeatureRobustScaler method) (morphoclass.transforms.scalers.standard_scaler.FeatureStandardScaler method) get_datasets() (in module morphoclass.console.cmd_xai) get_deepwalk_diagrams() (in module morphoclass.features.non_graph) get_distances() (morphoclass.transforms.ExtractDistances method) (morphoclass.transforms.ExtractPathDistances method) (morphoclass.transforms.ExtractRadialDistances method) (morphoclass.transforms.ExtractVerticalDistances method) (morphoclass.transforms.node_features.extract_distances.ExtractDistances method) (morphoclass.transforms.node_features.extract_path_distances.ExtractPathDistances method) (morphoclass.transforms.node_features.extract_radial_distances.ExtractRadialDistances method) (morphoclass.transforms.node_features.extract_vertical_distances.ExtractVerticalDistances method) (morphoclass.transforms.node_features.ExtractDistances method) (morphoclass.transforms.node_features.ExtractPathDistances method) (morphoclass.transforms.node_features.ExtractRadialDistances method) (morphoclass.transforms.node_features.ExtractVerticalDistances method)

get_edges_colors_based_on_barcode_colors() (in module morphoclass.xai.grad_cam_on_models) (in module morphoclass.xai.model_attributions) get_embedding() (in module morphoclass.deepwalk) get_embeddings_figure() (in module morphoclass.xai.embedding_visualization) get_env_metadata() (morphoclass.training.training_log.TrainingLog static method) get_images() (in module morphoclass.xai.embedding_visualization) get_latent_features() (morphoclass.training.trainers.Trainer method) get_loader() (in module morphoclass.report.plumbing) (in module morphoclass.utils) get_mask() (morphoclass.model_utils.HierarchicalLabelsDeprecated method) get_model() (in module morphoclass.training.cli) get_mse_loss() (in module morphoclass.training.training_loop_regression) get_outlier_detection_app() (in module morphoclass.xai) (in module morphoclass.xai.embedding_visualization) get_sample_by_morph_name() (morphoclass.data.morphology_dataset.MorphologyDataset method) (morphoclass.data.MorphologyDataset method) get_stratified_split() (in module morphoclass.utils) get_tmd_diagrams() (in module morphoclass.features.non_graph) get_tree_origin() (in module morphoclass.orientation) get_tree_pca() (in module morphoclass.orientation) GlobalFeatureToLabel (class in morphoclass.transforms) (class in morphoclass.transforms.global_feature_to_label) gnn_model_attributions() (in module morphoclass.xai) (in module morphoclass.xai.model_attributions) grad_cam_cnn_model() (in module morphoclass.xai) (in module morphoclass.xai.grad_cam_on_models) grad_cam_gnn_model() (in module morphoclass.xai) (in module morphoclass.xai.grad_cam_on_models) grad_cam_perslay_model() (in module morphoclass.xai) (in module morphoclass.xai.grad_cam_on_models) GradCAMExplainer (class in morphoclass.xai) (class in morphoclass.xai.grad_cam_explainer) guess_layer() (morphoclass.data.morphology_dataset.MorphologyDataset method) (morphoclass.data.MorphologyDataset method)

H

has_apicals_filter() (in module morphoclass.data.filters) HBNet (class in morphoclass.models) (class in morphoclass.models.hbnet) hierarchical_accuracies() (morphoclass.models.HBNet method) (morphoclass.models.hbnet.HBNet method)

HierarchicalLabels (class in morphoclass.model_utils) HierarchicalLabelsDeprecated (class in morphoclass.model_utils) how_to_install_msg() (in module morphoclass.cleanlab) (in module morphoclass.deepwalk)

I

import_obj() (morphoclass.training.training_config.TrainingConfig static method) inclusion_filter() (in module morphoclass.data.filters) input_csv (morphoclass.training.training_config.TrainingConfig attribute)

inter_rater_score() (in module morphoclass.metrics) interneurons (morphoclass.constants.DatasetType attribute) is_tree() (morphoclass.model_utils.HierarchicalLabelsDeprecated static method)

L

labels() (morphoclass.data.morphology_dataset.MorphologyDataset property) (morphoclass.data.MorphologyDataset property) (morphoclass.model_utils.HierarchicalLabels property) len() (morphoclass.data.morphology_dataset.MorphologyDataset method) (morphoclass.data.MorphologyDataset method) (morphoclass.data.tns_dataset.TNSDataset method) list_templates() (in module morphoclass.report.plumbing) load() (morphoclass.data.morphology_data.MorphologyData class method) (morphoclass.training.training_log.TrainingLog class method) load_apical_persistence_diagrams() (in module morphoclass.data) load_neuron() (morphoclass.console.stats_plotter.DatasetStatsPlotter static method) load_template() (in module morphoclass.report.plumbing) load_var() (in module morphoclass.utils) loss() (morphoclass.models.HBNet method) (morphoclass.models.hbnet.HBNet method)

loss_acc() (morphoclass.models.bidirectional_net.BidirectionalNet method) (morphoclass.models.BidirectionalNet method) (morphoclass.models.CNNet method) (morphoclass.models.cnnet.CNNet method) (morphoclass.models.coriander_net.CorianderNet method) (morphoclass.models.CorianderNet method) (morphoclass.models.man_net.ManNet method) (morphoclass.models.man_res_nets.ManResNet1 method) (morphoclass.models.man_res_nets.ManResNet2 method) (morphoclass.models.man_res_nets.ManResNet3 method) (morphoclass.models.ManNet method) (morphoclass.models.ManResNet1 method) (morphoclass.models.ManResNet2 method) (morphoclass.models.ManResNet3 method) (morphoclass.models.multi_adj_net.MultiAdjNet method) (morphoclass.models.MultiAdjNet method)

M

make_data_count_plots() (morphoclass.console.stats_plotter.DatasetStatsPlotter method) make_neuron_preview_plots() (morphoclass.console.stats_plotter.DatasetStatsPlotter method) make_node_count_plots() (morphoclass.console.stats_plotter.DatasetStatsPlotter method) make_performance_table() (in module morphoclass.console.performance_table) make_report_row() (in module morphoclass.console.performance_table) make_silhouette_plot() (in module morphoclass.unsupervised) (in module morphoclass.unsupervised.plotting) make_torch_deterministic() (in module morphoclass.utils) make_transform() (in module morphoclass.training) (in module morphoclass.training.rd_dataset_prep) MakeCopy (class in morphoclass.transforms) (class in morphoclass.transforms.make_copy) ManEmbedder (class in morphoclass.models) (class in morphoclass.models.man_net) ManNet (class in morphoclass.models) (class in morphoclass.models.man_net) ManNetR (class in morphoclass.models) (class in morphoclass.models.man_net) ManResNet1 (class in morphoclass.models) (class in morphoclass.models.man_res_nets) ManResNet2 (class in morphoclass.models) (class in morphoclass.models.man_res_nets) ManResNet3 (class in morphoclass.models) (class in morphoclass.models.man_res_nets) message() (morphoclass.layers.cheb_conv.ChebConv method) (morphoclass.layers.cheb_conv_separable.ChebConvSeparable method) (morphoclass.layers.ChebConv method) (morphoclass.layers.ChebConvSeparable method) model_class (morphoclass.training.training_config.TrainingConfig attribute) model_cls() (morphoclass.training.training_config.TrainingConfig property) model_params (morphoclass.training.training_config.TrainingConfig attribute) module morphoclass morphoclass.cleanlab morphoclass.console morphoclass.console.cmd_evaluate morphoclass.console.cmd_extract_features morphoclass.console.cmd_morphometrics morphoclass.console.cmd_organise_dataset morphoclass.console.cmd_performance_table morphoclass.console.cmd_plot_dataset_stats morphoclass.console.cmd_preprocess_dataset morphoclass.console.cmd_train morphoclass.console.cmd_xai morphoclass.console.dataset_preprocessor morphoclass.console.evaluate morphoclass.console.helpers morphoclass.console.main morphoclass.console.outlier_detection morphoclass.console.performance_table morphoclass.console.stats_plotter morphoclass.console.transfer_learning morphoclass.constants morphoclass.data morphoclass.data.filters morphoclass.data.morphology_data morphoclass.data.morphology_data_loader morphoclass.data.morphology_dataset morphoclass.data.tns_dataset morphoclass.deepwalk morphoclass.features morphoclass.features.non_graph morphoclass.layers morphoclass.layers.attention_global_pool morphoclass.layers.bidirectional_block morphoclass.layers.bidirectional_res_block morphoclass.layers.cat morphoclass.layers.cheb_conv morphoclass.layers.cheb_conv_separable morphoclass.layers.perslay morphoclass.layers.running_std morphoclass.layers.tree_lstm_pool morphoclass.metrics morphoclass.model_utils morphoclass.models morphoclass.models.bidirectional_net morphoclass.models.cnnet morphoclass.models.concatecnnet morphoclass.models.concatenet morphoclass.models.coriander_net morphoclass.models.hbnet morphoclass.models.man_net morphoclass.models.man_res_nets morphoclass.models.multi_adj_net morphoclass.morphometrics morphoclass.morphometrics.cli morphoclass.orientation morphoclass.report morphoclass.report.plumbing morphoclass.report.xai morphoclass.training morphoclass.training.cli morphoclass.training.rd_dataset_prep morphoclass.training.reports morphoclass.training.reports.transfer_learning_report morphoclass.training.tns_utils morphoclass.training.trainers morphoclass.training.training_config morphoclass.training.training_log morphoclass.training.training_loop_cv morphoclass.training.training_loop_loo morphoclass.training.training_loop_regression morphoclass.training.training_loop_simple morphoclass.training.transfer_learning morphoclass.transforms morphoclass.transforms.add_one_hot_labels morphoclass.transforms.augmentors morphoclass.transforms.augmentors.add_nodes_at_intervals morphoclass.transforms.augmentors.add_random_points_to_reduction_mask morphoclass.transforms.augmentors.add_section_middle_points morphoclass.transforms.augmentors.apply_node_reduction_masks morphoclass.transforms.augmentors.branching_only_neurites morphoclass.transforms.augmentors.branching_only_neuron morphoclass.transforms.augmentors.equalize_node_counts morphoclass.transforms.augmentors.extract_branching_node_reduction_masks morphoclass.transforms.augmentors.orient_apicals morphoclass.transforms.augmentors.orient_neuron morphoclass.transforms.augmentors.random_jitter morphoclass.transforms.augmentors.random_rotation morphoclass.transforms.augmentors.random_stretching morphoclass.transforms.compose morphoclass.transforms.edge_features morphoclass.transforms.edge_features.extract_distance_weights morphoclass.transforms.edge_features.extract_edge_features morphoclass.transforms.edge_features.extract_edge_index morphoclass.transforms.extract_tmd_neurites morphoclass.transforms.extract_tmd_neuron morphoclass.transforms.global_feature_to_label morphoclass.transforms.global_features morphoclass.transforms.global_features.abstract_global_feature_extractor morphoclass.transforms.global_features.average_branch_order morphoclass.transforms.global_features.average_radius morphoclass.transforms.global_features.extract_maximal_apical_path_length morphoclass.transforms.global_features.extract_number_branch_points morphoclass.transforms.global_features.extract_number_leaves morphoclass.transforms.global_features.total_path_length morphoclass.transforms.helper morphoclass.transforms.make_copy morphoclass.transforms.node_features morphoclass.transforms.node_features.extract_branching_angles morphoclass.transforms.node_features.extract_const_feature morphoclass.transforms.node_features.extract_coordinates morphoclass.transforms.node_features.extract_diameters morphoclass.transforms.node_features.extract_distances morphoclass.transforms.node_features.extract_node_features morphoclass.transforms.node_features.extract_node_onehot_properties morphoclass.transforms.node_features.extract_path_distances morphoclass.transforms.node_features.extract_radial_distances morphoclass.transforms.node_features.extract_vertical_distances morphoclass.transforms.scalers morphoclass.transforms.scalers.abstract_scaler morphoclass.transforms.scalers.manual_scaler morphoclass.transforms.scalers.min_max_scaler morphoclass.transforms.scalers.robust_scaler morphoclass.transforms.scalers.standard_scaler morphoclass.transforms.zero_out_features morphoclass.types morphoclass.unsupervised morphoclass.unsupervised.plotting morphoclass.utils morphoclass.vis morphoclass.xai morphoclass.xai.embedding_extractor morphoclass.xai.embedding_visualization morphoclass.xai.grad_cam_explainer morphoclass.xai.grad_cam_on_models morphoclass.xai.model_attributions morphoclass.xai.node_saliency morphio_root_section_to_tmd_tree() (in module morphoclass.utils) morphio_types (morphoclass.transforms.extract_tmd_neurites.ExtractTMDNeurites attribute) (morphoclass.transforms.ExtractTMDNeurites attribute) morphoclass module morphoclass.cleanlab module morphoclass.console module morphoclass.console.cmd_evaluate module morphoclass.console.cmd_extract_features module morphoclass.console.cmd_morphometrics module morphoclass.console.cmd_organise_dataset module morphoclass.console.cmd_performance_table module morphoclass.console.cmd_plot_dataset_stats module morphoclass.console.cmd_preprocess_dataset module morphoclass.console.cmd_train module morphoclass.console.cmd_xai module morphoclass.console.dataset_preprocessor module morphoclass.console.evaluate module morphoclass.console.helpers module morphoclass.console.main module morphoclass.console.outlier_detection module morphoclass.console.performance_table module morphoclass.console.stats_plotter module morphoclass.console.transfer_learning module morphoclass.constants module morphoclass.data module morphoclass.data.filters module morphoclass.data.morphology_data module morphoclass.data.morphology_data_loader module morphoclass.data.morphology_dataset module morphoclass.data.tns_dataset module

morphoclass.deepwalk module morphoclass.features module morphoclass.features.non_graph module morphoclass.layers module morphoclass.layers.attention_global_pool module morphoclass.layers.bidirectional_block module morphoclass.layers.bidirectional_res_block module morphoclass.layers.cat module morphoclass.layers.cheb_conv module morphoclass.layers.cheb_conv_separable module morphoclass.layers.perslay module morphoclass.layers.running_std module morphoclass.layers.tree_lstm_pool module morphoclass.metrics module morphoclass.model_utils module morphoclass.models module morphoclass.models.bidirectional_net module morphoclass.models.cnnet module morphoclass.models.concatecnnet module morphoclass.models.concatenet module morphoclass.models.coriander_net module morphoclass.models.hbnet module morphoclass.models.man_net module morphoclass.models.man_res_nets module morphoclass.models.multi_adj_net module morphoclass.morphometrics module morphoclass.morphometrics.cli module morphoclass.orientation module morphoclass.report module morphoclass.report.plumbing module morphoclass.report.xai module morphoclass.training module morphoclass.training.cli module morphoclass.training.rd_dataset_prep module morphoclass.training.reports module morphoclass.training.reports.transfer_learning_report module morphoclass.training.tns_utils module morphoclass.training.trainers module morphoclass.training.training_config module morphoclass.training.training_log module morphoclass.training.training_loop_cv module morphoclass.training.training_loop_loo module morphoclass.training.training_loop_regression module morphoclass.training.training_loop_simple module morphoclass.training.transfer_learning module morphoclass.transforms module morphoclass.transforms.add_one_hot_labels module morphoclass.transforms.augmentors module morphoclass.transforms.augmentors.add_nodes_at_intervals module morphoclass.transforms.augmentors.add_random_points_to_reduction_mask module morphoclass.transforms.augmentors.add_section_middle_points module morphoclass.transforms.augmentors.apply_node_reduction_masks module morphoclass.transforms.augmentors.branching_only_neurites module morphoclass.transforms.augmentors.branching_only_neuron module morphoclass.transforms.augmentors.equalize_node_counts module morphoclass.transforms.augmentors.extract_branching_node_reduction_masks module morphoclass.transforms.augmentors.orient_apicals module morphoclass.transforms.augmentors.orient_neuron module morphoclass.transforms.augmentors.random_jitter module morphoclass.transforms.augmentors.random_rotation module morphoclass.transforms.augmentors.random_stretching module morphoclass.transforms.compose module morphoclass.transforms.edge_features module morphoclass.transforms.edge_features.extract_distance_weights module morphoclass.transforms.edge_features.extract_edge_features module morphoclass.transforms.edge_features.extract_edge_index module morphoclass.transforms.extract_tmd_neurites module morphoclass.transforms.extract_tmd_neuron module morphoclass.transforms.global_feature_to_label module morphoclass.transforms.global_features module morphoclass.transforms.global_features.abstract_global_feature_extractor module morphoclass.transforms.global_features.average_branch_order module morphoclass.transforms.global_features.average_radius module morphoclass.transforms.global_features.extract_maximal_apical_path_length module morphoclass.transforms.global_features.extract_number_branch_points module morphoclass.transforms.global_features.extract_number_leaves module morphoclass.transforms.global_features.total_path_length module morphoclass.transforms.helper module morphoclass.transforms.make_copy module morphoclass.transforms.node_features module morphoclass.transforms.node_features.extract_branching_angles module morphoclass.transforms.node_features.extract_const_feature module morphoclass.transforms.node_features.extract_coordinates module morphoclass.transforms.node_features.extract_diameters module morphoclass.transforms.node_features.extract_distances module morphoclass.transforms.node_features.extract_node_features module morphoclass.transforms.node_features.extract_node_onehot_properties module morphoclass.transforms.node_features.extract_path_distances module morphoclass.transforms.node_features.extract_radial_distances module morphoclass.transforms.node_features.extract_vertical_distances module morphoclass.transforms.scalers module morphoclass.transforms.scalers.abstract_scaler module morphoclass.transforms.scalers.manual_scaler module morphoclass.transforms.scalers.min_max_scaler module morphoclass.transforms.scalers.robust_scaler module morphoclass.transforms.scalers.standard_scaler module morphoclass.transforms.zero_out_features module morphoclass.types module morphoclass.unsupervised module morphoclass.unsupervised.plotting module morphoclass.utils module morphoclass.vis module morphoclass.xai module morphoclass.xai.embedding_extractor module morphoclass.xai.embedding_visualization module morphoclass.xai.grad_cam_explainer module morphoclass.xai.grad_cam_on_models module morphoclass.xai.model_attributions module morphoclass.xai.node_saliency module MorphologyData (class in morphoclass.data.morphology_data) MorphologyDataLoader (class in morphoclass.data) (class in morphoclass.data.morphology_data_loader) MorphologyDataset (class in morphoclass.data) (class in morphoclass.data.morphology_dataset) mtype_exclusion_filter() (in module morphoclass.data.filters) MultiAdjNet (class in morphoclass.models) (class in morphoclass.models.multi_adj_net)

N

n_epochs (morphoclass.training.training_config.TrainingConfig attribute) n_leafs() (morphoclass.model_utils.HierarchicalLabels method) neurite_type (morphoclass.training.training_config.TrainingConfig attribute) neurons() (morphoclass.console.stats_plotter.DatasetStatsPlotter property) no_print() (in module morphoclass.utils) norm() (morphoclass.layers.cheb_conv.ChebConv static method) (morphoclass.layers.cheb_conv_separable.ChebConvSeparable static method) (morphoclass.layers.ChebConv static method) (morphoclass.layers.ChebConvSeparable static method)

normalize_features() (in module morphoclass.utils) np_temp_seed() (in module morphoclass.utils) num_workers (morphoclass.data.morphology_data_loader.MorphologyDataLoader attribute) (morphoclass.data.MorphologyDataLoader attribute)

O

optimizer_class (morphoclass.training.training_config.TrainingConfig attribute) optimizer_cls() (morphoclass.training.training_config.TrainingConfig property) optimizer_params (morphoclass.training.training_config.TrainingConfig attribute) orient_dataset() (in module morphoclass.orientation) orient_neuron() (in module morphoclass.orientation) OrientApicals (class in morphoclass.transforms) (class in morphoclass.transforms.augmentors) (class in morphoclass.transforms.augmentors.orient_apicals)

OrientNeuron (class in morphoclass.transforms) (class in morphoclass.transforms.augmentors) (class in morphoclass.transforms.augmentors.orient_neuron) oversample() (in module morphoclass.training.cli) oversampling (morphoclass.training.training_config.TrainingConfig attribute)

P

params2dict() (in module morphoclass.console.helpers) params_dict() (in module morphoclass.console.helpers) persistence_diagrams_to_persistence_images() (in module morphoclass.data) PersLay (class in morphoclass.layers) (class in morphoclass.layers.perslay) perslay_collate_fn() (morphoclass.training.trainers.ConcateNetTrainer static method) perslay_model_attributions() (in module morphoclass.xai) (in module morphoclass.xai.model_attributions) pickle_data() (in module morphoclass.data) pin_memory (morphoclass.data.morphology_data_loader.MorphologyDataLoader attribute) (morphoclass.data.MorphologyDataLoader attribute) plot_acc_cv() (in module morphoclass.vis) plot_accuracies() (in module morphoclass.vis) plot_barcode_enhanced() (in module morphoclass.vis) plot_confusion_matrices() (in module morphoclass.training.cli) plot_confusion_matrix() (in module morphoclass.vis) plot_counts_per_layer() (in module morphoclass.vis) plot_counts_per_subclass() (in module morphoclass.vis) plot_diagram_enhanced() (in module morphoclass.vis) plot_embedding_pca() (in module morphoclass.unsupervised) (in module morphoclass.unsupervised.plotting) plot_histogram() (in module morphoclass.vis) plot_histogram_panel() (in module morphoclass.vis) plot_learning_acc() (in module morphoclass.vis) plot_learning_curves() (in module morphoclass.vis) plot_mean_ci() (in module morphoclass.vis) plot_morphology_images() (in module morphoclass.vis) plot_neurite() (in module morphoclass.vis) plot_node_saliency() (in module morphoclass.xai) (in module morphoclass.xai.node_saliency) plot_number_of_nodes() (in module morphoclass.vis) plot_number_of_nodes_per_layer() (in module morphoclass.vis)

plot_persistence_diagram() (in module morphoclass.vis) plot_persistence_image() (in module morphoclass.vis) plot_tree() (in module morphoclass.vis) point_transformer (morphoclass.layers.perslay.PersLay attribute) PointTransformer (class in morphoclass.layers.perslay) PointwisePointTransformer (class in morphoclass.layers) (class in morphoclass.layers.perslay) populate_report() (in module morphoclass.report.xai) precision_recall_f1() (morphoclass.models.HBNet method) (morphoclass.models.hbnet.HBNet method) predict() (morphoclass.models.HBNet method) (morphoclass.models.hbnet.HBNet method) (morphoclass.training.trainers.Trainer method) predict_probabilities() (morphoclass.models.HBNet method) (morphoclass.models.hbnet.HBNet method) prefetch_factor (morphoclass.data.morphology_data_loader.MorphologyDataLoader attribute) (morphoclass.data.MorphologyDataLoader attribute) prepare_rd_split() (in module morphoclass.training) (in module morphoclass.training.rd_dataset_prep) prepare_rd_transforms() (in module morphoclass.training) (in module morphoclass.training.rd_dataset_prep) prepare_smart_split() (in module morphoclass.training) (in module morphoclass.training.rd_dataset_prep) Preprocessor (class in morphoclass.console.dataset_preprocessor) pretraining_log() (morphoclass.training.training_log.TrainingLog property) print_error() (in module morphoclass.utils) print_message_to_stderr() (in module morphoclass.utils) print_warning() (in module morphoclass.utils) process() (morphoclass.data.tns_dataset.TNSDataset method) processed_file_names() (morphoclass.data.tns_dataset.TNSDataset property) prune_one_member_classes() (in module morphoclass.training.cli) pyramidal (morphoclass.constants.DatasetType attribute)

R

raise_no_attribute() (in module morphoclass.transforms.helper) RandomJitter (class in morphoclass.transforms) (class in morphoclass.transforms.augmentors) (class in morphoclass.transforms.augmentors.random_jitter) RandomRotation (class in morphoclass.transforms) (class in morphoclass.transforms.augmentors) (class in morphoclass.transforms.augmentors.random_rotation) RandomStretching (class in morphoclass.transforms) (class in morphoclass.transforms.augmentors) (class in morphoclass.transforms.augmentors.random_stretching) raw_file_names() (morphoclass.data.tns_dataset.TNSDataset property) read_apical_from_file() (in module morphoclass.utils) read_layer_neurons_from_dir() (in module morphoclass.utils) read_tns_parameters() (in module morphoclass.training.tns_utils) reconstruct() (morphoclass.transforms.AbstractFeatureScaler method) (morphoclass.transforms.FeatureManualScaler method) (morphoclass.transforms.FeatureMinMaxScaler method) (morphoclass.transforms.FeatureRobustScaler method) (morphoclass.transforms.FeatureStandardScaler method) (morphoclass.transforms.scalers.abstract_scaler.AbstractFeatureScaler method) (morphoclass.transforms.scalers.AbstractFeatureScaler method) (morphoclass.transforms.scalers.FeatureManualScaler method) (morphoclass.transforms.scalers.FeatureMinMaxScaler method) (morphoclass.transforms.scalers.FeatureRobustScaler method) (morphoclass.transforms.scalers.FeatureStandardScaler method) (morphoclass.transforms.scalers.manual_scaler.FeatureManualScaler method) (morphoclass.transforms.scalers.min_max_scaler.FeatureMinMaxScaler method) (morphoclass.transforms.scalers.robust_scaler.FeatureRobustScaler method) (morphoclass.transforms.scalers.standard_scaler.FeatureStandardScaler method)

reduce_tree_to_branching() (in module morphoclass.data) reduction (morphoclass.layers.perslay.PersLay attribute) render() (in module morphoclass.report.plumbing) require_field() (in module morphoclass.transforms.helper) reset_parameters() (morphoclass.layers.cheb_conv.ChebConv method) (morphoclass.layers.cheb_conv_separable.ChebConvSeparable method) (morphoclass.layers.ChebConv method) (morphoclass.layers.ChebConvSeparable method) (morphoclass.layers.GaussianPointTransformer method) (morphoclass.layers.PersLay method) (morphoclass.layers.perslay.GaussianPointTransformer method) (morphoclass.layers.perslay.PersLay method) (morphoclass.layers.tree_lstm_pool.TreeLSTMCell method) reset_seeds() (in module morphoclass.training) resolve_paths() (morphoclass.training.training_config.TrainingConfig method) roots() (morphoclass.model_utils.HierarchicalLabels property) run() (morphoclass.console.dataset_preprocessor.Preprocessor method) (morphoclass.console.stats_plotter.DatasetStatsPlotter method) run_training() (in module morphoclass.morphometrics.cli) (in module morphoclass.training.cli) RunningStd (class in morphoclass.layers) (class in morphoclass.layers.running_std)

S

sample_inverse_sigmas (morphoclass.layers.GaussianPointTransformer attribute) (morphoclass.layers.perslay.GaussianPointTransformer attribute) sample_points (morphoclass.layers.GaussianPointTransformer attribute) (morphoclass.layers.perslay.GaussianPointTransformer attribute) sampler (morphoclass.data.morphology_data_loader.MorphologyDataLoader attribute) (morphoclass.data.MorphologyDataLoader attribute) save() (morphoclass.data.morphology_data.MorphologyData method) (morphoclass.training.training_log.TrainingLog method) save_data() (morphoclass.data.morphology_dataset.MorphologyDataset method) (morphoclass.data.MorphologyDataset method) save_dataset_csv() (morphoclass.console.dataset_preprocessor.Preprocessor method) save_report() (morphoclass.console.dataset_preprocessor.Preprocessor method) (morphoclass.console.stats_plotter.DatasetStatsPlotter method) save_var() (in module morphoclass.utils) savefig() (morphoclass.console.stats_plotter.DatasetStatsPlotter method) scaler_from_config() (in module morphoclass.transforms) (in module morphoclass.transforms.scalers)

seed (morphoclass.training.training_config.TrainingConfig attribute) set_all_history() (morphoclass.training.training_log.TrainingLog method) set_cleanlab_stats() (morphoclass.training.training_log.TrainingLog method) set_metrics() (morphoclass.training.training_log.TrainingLog method) set_y() (morphoclass.training.training_log.TrainingLog method) sklearn_model_attributions_shap() (in module morphoclass.xai) (in module morphoclass.xai.model_attributions) sklearn_model_attributions_tree() (in module morphoclass.xai) (in module morphoclass.xai.model_attributions) split_metrics() (in module morphoclass.training.cli) splitter_class (morphoclass.training.training_config.TrainingConfig attribute) splitter_cls() (morphoclass.training.training_config.TrainingConfig property) splitter_params (morphoclass.training.training_config.TrainingConfig attribute) str_time_delta() (in module morphoclass.utils) suppress_print() (in module morphoclass.utils) synthesize_samples() (morphoclass.data.tns_dataset.TNSDataset method)

T

template_variables() (in module morphoclass.report.plumbing) timeout (morphoclass.data.morphology_data_loader.MorphologyDataLoader attribute) (morphoclass.data.MorphologyDataLoader attribute) tmd_types (morphoclass.transforms.extract_tmd_neurites.ExtractTMDNeurites attribute) (morphoclass.transforms.ExtractTMDNeurites attribute) tns_distributions_from_dataset() (in module morphoclass.training.tns_utils) TNSDataset (class in morphoclass.data.tns_dataset) to_csv() (morphoclass.data.morphology_dataset.MorphologyDataset method) (morphoclass.data.MorphologyDataset method) to_dict() (morphoclass.data.morphology_data.MorphologyData method) (morphoclass.training.training_log.TrainingLog method) to_labels() (morphoclass.data.morphology_dataset.MorphologyDataset method) (morphoclass.data.MorphologyDataset method) to_one_hot() (morphoclass.model_utils.HierarchicalLabelsDeprecated method) to_persistence_dataset() (in module morphoclass.console.cmd_xai) topologically_sorted() (morphoclass.layers.tree_lstm_pool.TreeLSTMPool static method) (morphoclass.layers.TreeLSTMPool static method) TotalPathLength (class in morphoclass.transforms) (class in morphoclass.transforms.global_features) (class in morphoclass.transforms.global_features.total_path_length) train() (morphoclass.training.trainers.Trainer method) train_all_samples (morphoclass.training.training_config.TrainingConfig attribute) train_dm_model() (in module morphoclass.training.cli) train_ml_model() (in module morphoclass.morphometrics.cli) (in module morphoclass.training.cli) train_model() (in module morphoclass.training) (in module morphoclass.training.cli) (in module morphoclass.training.training_loop_simple) train_model_cv() (in module morphoclass.training) (in module morphoclass.training.training_loop_cv) train_model_loo() (in module morphoclass.training) (in module morphoclass.training.training_loop_loo) train_regression_model() (in module morphoclass.training) (in module morphoclass.training.training_loop_regression) train_split() (morphoclass.training.trainers.ConcateCNNetTrainer method) (morphoclass.training.trainers.ConcateNetTrainer method) Trainer (class in morphoclass.training.trainers) training (morphoclass.layers.attention_global_pool.AttentionGlobalPool attribute) (morphoclass.layers.AttentionGlobalPool attribute) (morphoclass.layers.bidirectional_block.BidirectionalBlock attribute) (morphoclass.layers.bidirectional_res_block.BidirectionalResBlock attribute) (morphoclass.layers.BidirectionalBlock attribute) (morphoclass.layers.BidirectionalResBlock attribute) (morphoclass.layers.Cat attribute) (morphoclass.layers.cat.Cat attribute) (morphoclass.layers.GaussianPointTransformer attribute) (morphoclass.layers.PersLay attribute) (morphoclass.layers.perslay.GaussianPointTransformer attribute) (morphoclass.layers.perslay.PersLay attribute) (morphoclass.layers.perslay.PointTransformer attribute) (morphoclass.layers.perslay.PointwisePointTransformer attribute) (morphoclass.layers.PointwisePointTransformer attribute) (morphoclass.layers.running_std.RunningStd attribute) (morphoclass.layers.RunningStd attribute) (morphoclass.layers.tree_lstm_pool.TreeLSTMCell attribute) (morphoclass.layers.tree_lstm_pool.TreeLSTMPool attribute) (morphoclass.layers.TreeLSTMPool attribute) (morphoclass.models.bidirectional_net.BidirectionalNet attribute) (morphoclass.models.BidirectionalNet attribute) (morphoclass.models.CNNEmbedder attribute) (morphoclass.models.CNNet attribute) (morphoclass.models.cnnet.CNNEmbedder attribute) (morphoclass.models.cnnet.CNNet attribute) (morphoclass.models.ConcateCNNet attribute) (morphoclass.models.concatecnnet.ConcateCNNet attribute) (morphoclass.models.ConcateNet attribute) (morphoclass.models.concatenet.ConcateNet attribute) (morphoclass.models.coriander_net.CorianderNet attribute) (morphoclass.models.CorianderNet attribute) (morphoclass.models.HBNet attribute) (morphoclass.models.hbnet.HBNet attribute) (morphoclass.models.man_net.ManEmbedder attribute) (morphoclass.models.man_net.ManNet attribute) (morphoclass.models.man_net.ManNetR attribute) (morphoclass.models.man_res_nets.ManResNet1 attribute) (morphoclass.models.man_res_nets.ManResNet2 attribute) (morphoclass.models.man_res_nets.ManResNet3 attribute) (morphoclass.models.ManEmbedder attribute) (morphoclass.models.ManNet attribute) (morphoclass.models.ManNetR attribute) (morphoclass.models.ManResNet1 attribute) (morphoclass.models.ManResNet2 attribute) (morphoclass.models.ManResNet3 attribute) (morphoclass.models.multi_adj_net.MultiAdjNet attribute) (morphoclass.models.MultiAdjNet attribute)

TrainingConfig (class in morphoclass.training.training_config) TrainingLog (class in morphoclass.training.training_log) transfer_learning_curves() (in module morphoclass.training) (in module morphoclass.training.transfer_learning) transfer_learning_report() (in module morphoclass.training) (in module morphoclass.training.reports.transfer_learning_report) tree_to_graph() (in module morphoclass.utils) TreeLSTMCell (class in morphoclass.layers.tree_lstm_pool) TreeLSTMPool (class in morphoclass.layers) (class in morphoclass.layers.tree_lstm_pool)

V

validate_params() (in module morphoclass.console.helpers) visualize_cleanlab_outliers() (in module morphoclass.console.evaluate)

visualize_latent_features() (in module morphoclass.console.evaluate) visualize_model_performance() (in module morphoclass.console.evaluate)

W

warn_if_nondeterministic() (in module morphoclass.utils) warn_if_not_installed() (in module morphoclass.cleanlab) (in module morphoclass.deepwalk)

write() (morphoclass.report.xai.XAIReport method)

X

XAIReport (class in morphoclass.report.xai)

Y

ys() (morphoclass.data.morphology_dataset.MorphologyDataset property) (morphoclass.data.MorphologyDataset property)

Z

ZeroOutFeatures (class in morphoclass.transforms) (class in morphoclass.transforms.zero_out_features)