Index

_

_instantiate_logger() (loki2.inference.inference_disk.CellViTInference method) _load_inference_transforms() (loki2.inference.inference_disk.CellViTInference method)

_load_model() (loki2.inference.inference_disk.CellViTInference method) _setup_worker() (loki2.inference.inference_disk.CellViTInference method)

A

act (loki2.models.base.vision_transformer.Mlp attribute) (loki2.models.utils.sam_utils.MLPBlock attribute) activation (loki2.models.classifier.linear_classifier.LinearClassifier attribute) adata_sc (in module loki2.retrieve_from_sc) add_decomposed_rel_pos() (in module loki2.models.utils.sam_utils) all_patch_metadata (loki2.data.dataclass.wsi.WSI attribute) apply_softmax_reorder() (loki2.inference.inference_disk.CellViTInference method) assign_df (in module loki2.retrieve_from_sc) assign_path (in module loki2.retrieve_from_sc)

Attention (class in loki2.models.base.vision_transformer) (class in loki2.models.utils.sam_utils) ATTENTION_BRANCHES (loki2.mil.models.src.model.GatedAttentionMIL attribute), [1] attention_U (loki2.mil.models.src.model.GatedAttentionMIL attribute), [1] attention_V (loki2.mil.models.src.model.GatedAttentionMIL attribute), [1] attention_w (loki2.mil.models.src.model.GatedAttentionMIL attribute), [1] attn (loki2.models.base.vision_transformer.Block attribute) (loki2.models.utils.sam_utils.Block attribute) attn_drop (loki2.models.base.vision_transformer.Attention attribute) attn_drop_rate (loki2.models.cell_segmentation.cellvit.CellViT attribute)

B

bag_size (loki2.mil.models.src.dataset.PatientTileBagDataset_v2 attribute), [1] (loki2.mil.models.src.dataset.PatientTileBagDatasetForAttention_V7 attribute), [1] batch_size (loki2.inference.inference_disk.CellViTInference attribute), [1] (loki2.models.cell_segmentation.cellvit.DataclassHVStorage attribute) BatchPoolingActor (class in loki2.inference.postprocessing_cupy) bias (loki2.models.utils.sam_utils.LayerNorm2d attribute) binary (loki2.inference.inference_disk.CellViTInference attribute), [1] (loki2.inference.postprocessing_cupy.DetectionCellPostProcessorCupy attribute) Block (class in loki2.models.base.vision_transformer) (class in loki2.models.utils.sam_utils)

block (loki2.models.utils.blocks.Conv2DBlock attribute) (loki2.models.utils.blocks.Deconv2DBlock attribute) blocks (loki2.models.base.vision_transformer.VisionTransformer attribute) (loki2.models.utils.sam_utils.ImageEncoderViT attribute) bounds (in module loki2.plot) branches_output (loki2.models.cell_segmentation.cellvit.CellViT attribute) build_dataset_for_patches() (in module loki2.immstain) build_enrichment_features() (in module loki2.immstain) build_parser() (in module loki2.encode_trans) build_samples() (in module loki2.cl.prepare_training)

C

calculate_instance_map() (loki2.models.cell_segmentation.cellvit.CellViT method) calculate_metrics() (in module loki2.mil.models.src.utils) calculate_protein_expression_single_channel() (in module loki2.immstain) cell_df (loki2.inference.overlap_cell_cleaner.OverlapCellCleaner attribute) cell_df_margin (loki2.inference.overlap_cell_cleaner.OverlapCellCleaner attribute) cell_id_to_index() (in module loki2.cl.prepare_training) cell_ids_pool (in module loki2.retrieve_from_sc) CellGraphDataWSI (class in loki2.data.dataclass.cell_graph) CellViT (class in loki2.models.cell_segmentation.cellvit) CellViTInference (class in loki2.inference.inference_disk) CellViTInferenceMemory (class in loki2.inference.inference_memory) CellViTSAM (class in loki2.models.cell_segmentation.loki2_sam) check_network_output() (loki2.inference.postprocessing_cupy.DetectionCellPostProcessorCupy method) (loki2.models.cell_segmentation.postprocessing.DetectionCellPostProcessor method) classifier (loki2.inference.inference_disk.CellViTInference attribute), [1] (loki2.inference.postprocessing_cupy.DetectionCellPostProcessorCupy attribute) (loki2.mil.models.src.model.GatedAttentionMIL attribute) classifier_head (loki2.models.cell_segmentation.loki2_sam.CellViTSAM attribute) clean_detected_cells() (loki2.inference.overlap_cell_cleaner.OverlapCellCleaner method) clean_geojson() (in module loki2.inference.inference_memory) cls_token (loki2.models.base.vision_transformer.VisionTransformer attribute) collate_batch() (in module loki2.cl.train_projection_wds) (loki2.data.dataclass.wsi.PatchedWSIInference static method) COLOR_CODES_LOGGING (in module loki2.config.config) COLOR_DICT (in module loki2.plot) COLOR_DICT_CELLS (in module loki2.config.config) COLOR_DICT_FLOAT (in module loki2.plot) COLOR_DICT_NORM (in module loki2.plot) color_list (in module loki2.plot)

ColoredFormatter (class in loki2.utils.logger) combined_df (in module loki2.mil.prampt_generate.blca_metastasis_prampt) comment (loki2.utils.logger.Logger attribute), [1] compare_labelings() (in module loki2.retrieve) compression (loki2.inference.inference_disk.CellViTInference attribute), [1] compute_and_plot_overall_metrics() (in module loki2.mil.models.src.utils) compute_level_scale() (in module loki2.immstain) compute_neighbor_statistics() (in module loki2.immstain) compute_regression_metrics() (in module loki2.immstain) compute_ssim_1d() (in module loki2.immstain) Conv2DBlock (class in loki2.models.utils.blocks) convert_batch_to_graph_nodes() (loki2.inference.postprocessing_cupy.BatchPoolingActor method) convert_coordinates() (in module loki2.inference.overlap_cell_cleaner) convert_coordinates_vectorized() (loki2.inference.overlap_cell_cleaner.OverlapCellCleaner method) convert_patch_to_graph_nodes() (loki2.inference.postprocessing_cupy.BatchPoolingActor method) count_shards() (in module loki2.cl.train_projection_wds) create_bagging_dataframe_All_v7() (in module loki2.mil.models.src.dataset) create_bagging_dataframe_noreplacement_V12() (in module loki2.mil.models.src.dataset) create_balanced_fold_assignments() (in module loki2.mil.models.src.dataset) create_balanced_train_val_split() (in module loki2.mil.models.src.dataset) create_handler() (loki2.utils.logger.Logger method) create_loader() (in module loki2.cl.train_projection_wds) create_logger() (loki2.utils.logger.Logger method), [1] create_upsampling_branch() (loki2.models.cell_segmentation.cellvit.CellViT method) cross_modal_retrieve() (in module loki2.retrieve) current_dir (in module loki2.detect_cells) (in module loki2.inference.inference_disk) current_logit_scale() (loki2.cl.model_cl.ProjectionCL method) custom_collate_fn() (in module loki2.mil.models.src.dataset)

D

data (loki2.mil.models.src.dataset.PatientTileBagDataset_v2 attribute), [1] (loki2.mil.models.src.dataset.PatientTileBagDatasetForAttention_V7 attribute), [1] data_morph (in module loki2.retrieve_from_sc) DataclassHVStorage (class in loki2.models.cell_segmentation.cellvit) decode_sample() (in module loki2.cl.train_projection_wds) decoder0 (loki2.models.cell_segmentation.cellvit.CellViT attribute) decoder1 (loki2.models.cell_segmentation.cellvit.CellViT attribute) decoder2 (loki2.models.cell_segmentation.cellvit.CellViT attribute) decoder3 (loki2.models.cell_segmentation.cellvit.CellViT attribute) Deconv2DBlock (class in loki2.models.utils.blocks) depth (loki2.models.cell_segmentation.cellvit.CellViT attribute) detection_cell_postprocessor (loki2.inference.postprocessing_cupy.BatchPoolingActor attribute) DetectionCellPostProcessor (class in loki2.models.cell_segmentation.postprocessing) DetectionCellPostProcessorCupy (class in loki2.inference.postprocessing_cupy) device (loki2.inference.inference_disk.CellViTInference attribute), [1]

directory_path (in module loki2.mil.prampt_generate.blca_metastasis_prampt) (in module loki2.mil.prampt_generate.blca_stage_prampt) downsample_by_group() (in module loki2.mil.prampt_downsample) downsample_data() (in module loki2.mil.models.src.utils) dpr (loki2.models.base.vision_transformer.VisionTransformer attribute) drop (loki2.models.base.vision_transformer.Mlp attribute) drop_path (loki2.models.base.vision_transformer.Block attribute) drop_path() (in module loki2.models.base.vision_transformer) drop_path_rate (loki2.models.cell_segmentation.cellvit.CellViT attribute) drop_prob (loki2.models.base.vision_transformer.DropPath attribute) drop_rate (loki2.models.cell_segmentation.cellvit.CellViT attribute) dropout (loki2.models.classifier.linear_classifier.LinearClassifier attribute) DropPath (class in loki2.models.base.vision_transformer) DTYPE_MAP (in module loki2.cl.prepare_training) dynamic_multiplication_factor() (in module loki2.mil.models.src.dataset)

E

embed_dim (loki2.models.cell_segmentation.cellvit.CellViT attribute) embedding_name (loki2.data.dataclass.wsi.WSI attribute) embedding_pool (in module loki2.retrieve_from_sc) embeddings_to_hex() (in module loki2.plot) encode_a() (loki2.cl.model_cl.ProjectionCL method) encode_b() (loki2.cl.model_cl.ProjectionCL method) encode_texts() (in module loki2.encode_trans) encode_transcriptomics() (in module loki2.encode_trans)

encoder (loki2.models.cell_segmentation.cellvit.CellViT attribute) (loki2.models.cell_segmentation.loki2_sam.CellViTSAM attribute) epoch (in module loki2.retrieve_from_sc) eps (loki2.models.utils.sam_utils.LayerNorm2d attribute) evaluate_model() (in module loki2.mil.models.src.utils) expand_nuclei_watershed_multichannel() (in module loki2.immstain) extract_layers (loki2.models.cell_segmentation.backbones.ViTCellViT attribute) (loki2.models.cell_segmentation.backbones.ViTCellViTDeit attribute) (loki2.models.cell_segmentation.cellvit.CellViT attribute)

F

fc1 (loki2.models.base.vision_transformer.Mlp attribute) (loki2.models.classifier.linear_classifier.LinearClassifier attribute) fc2 (loki2.models.base.vision_transformer.Mlp attribute) (loki2.models.classifier.linear_classifier.LinearClassifier attribute) feature_extractor (loki2.mil.models.src.model.GatedAttentionMIL attribute), [1] file_level (loki2.utils.logger.Logger attribute) format() (loki2.utils.logger.ColoredFormatter method), [1] formatter (loki2.utils.logger.Logger attribute) forward() (loki2.cl.model_cl.ProjectionCL method) (loki2.mil.models.src.model.GatedAttentionMIL method) (loki2.models.base.vision_transformer.Attention method) (loki2.models.base.vision_transformer.Block method) (loki2.models.base.vision_transformer.DropPath method) (loki2.models.base.vision_transformer.Mlp method) (loki2.models.base.vision_transformer.PatchEmbed method) (loki2.models.base.vision_transformer.VisionTransformer method) (loki2.models.cell_segmentation.backbones.ViTCellViT method) (loki2.models.cell_segmentation.backbones.ViTCellViTDeit method) (loki2.models.cell_segmentation.cellvit.CellViT method) (loki2.models.cell_segmentation.loki2_sam.CellViTSAM method) (loki2.models.classifier.linear_classifier.LinearClassifier method) (loki2.models.utils.blocks.Conv2DBlock method) (loki2.models.utils.blocks.Deconv2DBlock method) (loki2.models.utils.sam_utils.Attention method) (loki2.models.utils.sam_utils.Block method) (loki2.models.utils.sam_utils.ImageEncoderViT method) (loki2.models.utils.sam_utils.LayerNorm2d method) (loki2.models.utils.sam_utils.MLPBlock method) (loki2.models.utils.sam_utils.PatchEmbed method)

freeze_encoder() (loki2.models.cell_segmentation.cellvit.CellViT method)

G

GatedAttentionMIL (class in loki2.mil.models.src.model) generate_epoch_attention_analysis() (in module loki2.mil.models.src.utils) generate_gene_df() (in module loki2.encode_trans) generate_heatmaps() (in module loki2.mil.models.src.utils) generate_instance_nuclei_map() (loki2.models.cell_segmentation.cellvit.CellViT method) generate_patch_json_and_embeddings() (in module loki2.immstain) geojson (loki2.inference.inference_disk.CellViTInference attribute), [1] geojson_gz (loki2.inference.inference_memory.CellViTInferenceMemory attribute) get_balanced_sample_names() (in module loki2.mil.prampt_generate.blca_stage_prampt) get_bounding_box() (in module loki2.utils.tools) get_cell_position() (in module loki2.inference.postprocessing_cupy) get_cell_position_marging() (in module loki2.inference.postprocessing_cupy) get_dict() (loki2.models.cell_segmentation.cellvit.DataclassHVStorage method) get_edge_patch() (in module loki2.inference.postprocessing_cupy) get_intermediate_layers() (loki2.models.base.vision_transformer.VisionTransformer method) get_kmeans() (in module loki2.psdtime)

get_last_selfattention() (loki2.models.base.vision_transformer.VisionTransformer method) get_number_patches() (loki2.data.dataclass.wsi.WSI method) get_patches() (loki2.data.dataclass.wsi.WSI method) get_pca() (in module loki2.psdtime) get_rel_pos() (in module loki2.models.utils.sam_utils) get_template_point() (in module loki2.config.templates) get_template_segmentation() (in module loki2.config.templates) get_umap() (in module loki2.psdtime) global_embedding_pt (loki2.immstain.TutorialConfig attribute), [1] global_nuclei_json (loki2.immstain.TutorialConfig attribute), [1] graph (loki2.inference.inference_disk.CellViTInference attribute), [1] group (loki2.inference.cli.InferenceWSIParser attribute) group_classifier (loki2.inference.cli.InferenceWSIParser attribute) group_cols (loki2.mil.models.src.dataset.PatientTileBagDatasetForAttention_V7 attribute), [1] gt (loki2.inference.postprocessing_cupy.DetectionCellPostProcessorCupy attribute) (loki2.models.cell_segmentation.postprocessing.DetectionCellPostProcessor attribute)

H

h (loki2.models.cell_segmentation.cellvit.DataclassHVStorage attribute) he_ome_path (loki2.immstain.TutorialConfig attribute), [1] head (loki2.models.base.vision_transformer.VisionTransformer attribute) head_dim (loki2.models.base.vision_transformer.Attention attribute) (loki2.models.utils.sam_utils.Attention attribute)

hidden_dim (loki2.cl.model_cl.ProjectionCL attribute) hidden_features (loki2.models.base.vision_transformer.Mlp attribute) hv_map (loki2.models.cell_segmentation.cellvit.DataclassHVStorage attribute) hv_map_decoder (loki2.models.cell_segmentation.cellvit.CellViT attribute)

I

if_patch_dir (loki2.immstain.TutorialConfig attribute), [1] if_patch_pattern (loki2.immstain.TutorialConfig attribute), [1] ImageEncoderViT (class in loki2.models.utils.sam_utils) img_size (loki2.models.base.vision_transformer.PatchEmbed attribute) (loki2.models.utils.sam_utils.ImageEncoderViT attribute) indices (loki2.retrieve.RetrievalResult attribute) (loki2.retrieve_from_sc.RetrievalResult attribute) infer_pseudotime_palantir() (in module loki2.psdtime) inference_transforms (loki2.inference.inference_disk.CellViTInference attribute), [1] InferenceWSIParser (class in loki2.inference.cli)

init_value (loki2.cl.model_cl.ProjectionCL attribute) init_vit_b() (loki2.models.cell_segmentation.loki2_sam.CellViTSAM method) init_vit_h() (loki2.models.cell_segmentation.loki2_sam.CellViTSAM method) init_vit_l() (loki2.models.cell_segmentation.loki2_sam.CellViTSAM method) input_channels (loki2.models.cell_segmentation.cellvit.CellViT attribute) (loki2.models.cell_segmentation.loki2_sam.CellViTSAM attribute) instance_map (loki2.models.cell_segmentation.cellvit.DataclassHVStorage attribute) instance_types (loki2.models.cell_segmentation.cellvit.DataclassHVStorage attribute) instance_types_nuclei (loki2.models.cell_segmentation.cellvit.DataclassHVStorage attribute) interpolate_pos_encoding() (loki2.models.base.vision_transformer.VisionTransformer method)

K

keys (loki2.mil.models.src.dataset.PatientTileBagDatasetForAttention_V7 attribute), [1]

knn_majority_vote() (in module loki2.retrieve) knn_numeric_pool() (in module loki2.retrieve)

L

L (loki2.mil.models.src.model.GatedAttentionMIL attribute), [1] l2_normalize_embeddings() (in module loki2.immstain) label (loki2.data.dataclass.wsi.WSI attribute) label_map (loki2.inference.inference_disk.CellViTInference attribute), [1] labels_to_hex() (in module loki2.plot) (in module loki2.retrieve) LayerNorm2d (class in loki2.models.utils.sam_utils) layers (loki2.mil.models.src.model.GatedAttentionMIL attribute) level (loki2.utils.logger.Logger attribute), [1] level0_idx (loki2.immstain.TutorialConfig attribute), [1] level1_idx (loki2.immstain.TutorialConfig attribute), [1] lin1 (loki2.models.utils.sam_utils.MLPBlock attribute) lin2 (loki2.models.utils.sam_utils.MLPBlock attribute) LinearClassifier (class in loki2.models.classifier.linear_classifier) list_available_patches() (in module loki2.immstain) load() (loki2.retrieve.RetrievalResult class method) (loki2.retrieve_from_sc.RetrievalResult class method) load_and_print_tensor() (in module loki2.cl.utils) (in module loki2.preprocess) load_attention_df() (in module loki2.plot) load_embedding() (loki2.data.dataclass.wsi.WSI method) load_global_embeddings() (in module loki2.immstain) load_keys() (in module loki2.cl.train_projection_wds) load_model() (in module loki2.cl.project_raw_embeddings) (in module loki2.encode_trans) load_morph_embeddings() (in module loki2.cl.project_raw_embeddings) load_patch_if_image() (in module loki2.immstain) load_patch_json_and_embeddings() (in module loki2.immstain) load_patch_metadata() (loki2.data.dataclass.wsi.WSI method) load_predictions_for_patch() (in module loki2.immstain) load_pretrained_encoder() (loki2.models.cell_segmentation.loki2_sam.CellViTSAM method) load_prompts_csv() (in module loki2.encode_trans) load_sample() (in module loki2.preprocess) load_stage_data() (in module loki2.mil.prampt_generate.blca_stage_prampt) load_tensor() (in module loki2.mil.prampt_generate.blca_metastasis_prampt) (in module loki2.mil.prampt_generate.blca_stage_prampt) load_trans_embeddings() (in module loki2.cl.project_raw_embeddings) load_txt() (in module loki2.psdtime) load_wsi_meta() (in module loki2.inference.wsi_meta) log_parent_dir (loki2.utils.logger.Logger attribute), [1] Logger (class in loki2.utils.logger) logger (loki2.data.dataclass.wsi.WSI attribute) (loki2.inference.inference_disk.CellViTInference attribute), [1] (loki2.inference.overlap_cell_cleaner.OverlapCellCleaner attribute) LOGGER_NAME (in module loki2.cl.train_projection_wds) logit_scale (loki2.cl.model_cl.ProjectionCL attribute) loki2 module loki2.cl module loki2.cl.model_cl module loki2.cl.prepare_training module loki2.cl.project_raw_embeddings module loki2.cl.train_projection_wds module loki2.cl.utils module loki2.config module loki2.config.config module loki2.config.templates module loki2.data module loki2.data.dataclass module loki2.data.dataclass.cell_graph module loki2.data.dataclass.wsi module loki2.detect_cells module loki2.encode_trans module loki2.immstain module loki2.inference module

loki2.inference.cli module loki2.inference.inference_disk module loki2.inference.inference_memory module loki2.inference.overlap_cell_cleaner module loki2.inference.postprocessing_cupy module loki2.inference.wsi_meta module loki2.mil module loki2.mil.models module loki2.mil.models.src module loki2.mil.models.src.dataset module loki2.mil.models.src.model module loki2.mil.models.src.train module loki2.mil.models.src.utils module loki2.mil.models.TCGA-Loki2_MILCell_blca_metastasis_5fold module loki2.mil.models.TCGA-Loki2_MILCell_blca_stage_5fold module loki2.mil.prampt_downsample module loki2.mil.prampt_generate module loki2.mil.prampt_generate.blca_metastasis_prampt module loki2.mil.prampt_generate.blca_stage_prampt module loki2.models module loki2.models.base module loki2.models.base.vision_transformer module loki2.models.cell_segmentation module loki2.models.cell_segmentation.backbones module loki2.models.cell_segmentation.cellvit module loki2.models.cell_segmentation.loki2_sam module loki2.models.cell_segmentation.postprocessing module loki2.models.classifier module loki2.models.classifier.linear_classifier module loki2.models.utils module loki2.models.utils.blocks module loki2.models.utils.sam_utils module loki2.plot module loki2.preprocess module loki2.psdtime module loki2.retrieve module loki2.retrieve_from_sc module loki2.utils module loki2.utils.logger module loki2.utils.tools module LOKI2_CMAP (in module loki2.plot)

M

M (loki2.mil.models.src.model.GatedAttentionMIL attribute), [1] magnification (loki2.models.cell_segmentation.postprocessing.DetectionCellPostProcessor attribute) main() (in module loki2.cl.prepare_training) (in module loki2.cl.project_raw_embeddings) (in module loki2.cl.train_projection_wds) (in module loki2.detect_cells) (in module loki2.encode_trans) (in module loki2.mil.models.TCGA-Loki2_MILCell_blca_metastasis_5fold) (in module loki2.mil.models.TCGA-Loki2_MILCell_blca_stage_5fold) majority_vote() (loki2.retrieve.RetrievalResult method) (loki2.retrieve_from_sc.RetrievalResult method) make_slide_thumbnail() (in module loki2.plot) max_code (in module loki2.plot) merged_df (in module loki2.mil.prampt_generate.blca_metastasis_prampt) (in module loki2.mil.prampt_generate.blca_stage_prampt) meta_df (in module loki2.mil.prampt_generate.blca_metastasis_prampt) meta_path (in module loki2.mil.prampt_generate.blca_metastasis_prampt) metadata (loki2.data.dataclass.cell_graph.CellGraphDataWSI attribute) (loki2.data.dataclass.wsi.WSI attribute) (loki2.data.dataclass.wsi.WSIMetadata attribute) mid_cells (loki2.inference.overlap_cell_cleaner.OverlapCellCleaner attribute) mixed_precision (loki2.inference.inference_disk.CellViTInference attribute), [1] Mlp (class in loki2.models.base.vision_transformer) mlp (loki2.models.base.vision_transformer.Block attribute) (loki2.models.utils.sam_utils.Block attribute) mlp_hidden_dim (loki2.models.base.vision_transformer.Block attribute) mlp_ratio (loki2.models.cell_segmentation.cellvit.CellViT attribute) (loki2.models.cell_segmentation.loki2_sam.CellViTSAM attribute) MLPBlock (class in loki2.models.utils.sam_utils) model (loki2.inference.inference_disk.CellViTInference attribute), [1] model_arch (loki2.inference.inference_disk.CellViTInference attribute), [1] model_path (loki2.inference.inference_disk.CellViTInference attribute), [1] (loki2.models.cell_segmentation.loki2_sam.CellViTSAM attribute) module loki2 loki2.cl loki2.cl.model_cl loki2.cl.prepare_training loki2.cl.project_raw_embeddings loki2.cl.train_projection_wds loki2.cl.utils loki2.config loki2.config.config loki2.config.templates loki2.data loki2.data.dataclass loki2.data.dataclass.cell_graph loki2.data.dataclass.wsi loki2.detect_cells loki2.encode_trans loki2.immstain loki2.inference loki2.inference.cli loki2.inference.inference_disk loki2.inference.inference_memory loki2.inference.overlap_cell_cleaner loki2.inference.postprocessing_cupy loki2.inference.wsi_meta loki2.mil loki2.mil.models loki2.mil.models.src loki2.mil.models.src.dataset loki2.mil.models.src.model loki2.mil.models.src.train loki2.mil.models.src.utils loki2.mil.models.TCGA-Loki2_MILCell_blca_metastasis_5fold loki2.mil.models.TCGA-Loki2_MILCell_blca_stage_5fold loki2.mil.prampt_downsample loki2.mil.prampt_generate loki2.mil.prampt_generate.blca_metastasis_prampt loki2.mil.prampt_generate.blca_stage_prampt loki2.models loki2.models.base loki2.models.base.vision_transformer loki2.models.cell_segmentation loki2.models.cell_segmentation.backbones loki2.models.cell_segmentation.cellvit loki2.models.cell_segmentation.loki2_sam loki2.models.cell_segmentation.postprocessing loki2.models.classifier loki2.models.classifier.linear_classifier loki2.models.utils loki2.models.utils.blocks loki2.models.utils.sam_utils loki2.plot loki2.preprocess loki2.psdtime loki2.retrieve loki2.retrieve_from_sc loki2.utils loki2.utils.logger loki2.utils.tools

N

name (loki2.data.dataclass.wsi.WSI attribute) (loki2.data.dataclass.wsi.WSIMetadata attribute) neck (loki2.models.utils.sam_utils.ImageEncoderViT attribute) None (loki2.utils.logger.ColoredFormatter attribute) norm (in module loki2.plot) (loki2.models.base.vision_transformer.VisionTransformer attribute) norm1 (loki2.models.base.vision_transformer.Block attribute) (loki2.models.utils.sam_utils.Block attribute) norm2 (loki2.models.base.vision_transformer.Block attribute) (loki2.models.utils.sam_utils.Block attribute) norm_type (loki2.mil.models.src.model.GatedAttentionMIL attribute), [1] normalize() (in module loki2.plot) normalize_patch_name() (in module loki2.immstain) NormalizeT (in module loki2.retrieve_from_sc) nr_types (loki2.inference.postprocessing_cupy.DetectionCellPostProcessorCupy attribute) (loki2.models.cell_segmentation.postprocessing.DetectionCellPostProcessor attribute) nuclei_binary_map (loki2.models.cell_segmentation.cellvit.DataclassHVStorage attribute)

nuclei_binary_map_decoder (loki2.models.cell_segmentation.cellvit.CellViT attribute) nuclei_type_map (loki2.models.cell_segmentation.cellvit.DataclassHVStorage attribute) nuclei_type_maps_decoder (loki2.models.cell_segmentation.cellvit.CellViT attribute) num_heads (loki2.models.base.vision_transformer.Attention attribute) (loki2.models.cell_segmentation.cellvit.CellViT attribute) (loki2.models.utils.sam_utils.Attention attribute) num_nuclei_classes (loki2.models.cell_segmentation.cellvit.CellViT attribute) (loki2.models.cell_segmentation.cellvit.DataclassHVStorage attribute) (loki2.models.cell_segmentation.loki2_sam.CellViTSAM attribute) num_patches (loki2.models.base.vision_transformer.PatchEmbed attribute) (loki2.models.base.vision_transformer.VisionTransformer attribute) num_tissue_classes (loki2.models.cell_segmentation.cellvit.CellViT attribute) (loki2.models.cell_segmentation.cellvit.DataclassHVStorage attribute) num_workers (loki2.inference.inference_disk.CellViTInference attribute), [1], [2] numeric_pool() (loki2.retrieve.RetrievalResult method) (loki2.retrieve_from_sc.RetrievalResult method) NumericReductionT (in module loki2.retrieve_from_sc)

O

offset_branches (loki2.models.cell_segmentation.cellvit.CellViT attribute) open_level_chw() (in module loki2.immstain) out_features (loki2.models.base.vision_transformer.Mlp attribute) outdir (loki2.inference.inference_memory.CellViTInferenceMemory attribute)

output_dir (in module loki2.retrieve_from_sc), [1] output_type (loki2.mil.models.src.model.GatedAttentionMIL attribute), [1] overlap (loki2.inference.inference_disk.CellViTInference attribute), [1] OverlapCellCleaner (class in loki2.inference.overlap_cell_cleaner)

P

parse_args() (in module loki2.cl.prepare_training) (in module loki2.cl.project_raw_embeddings) (in module loki2.cl.train_projection_wds) parse_arguments() (loki2.inference.cli.InferenceWSIParser method) parse_patch_index() (in module loki2.immstain) parse_wsi_properties() (in module loki2.inference.cli) parser (in module loki2.mil.models.TCGA-Loki2_MILCell_blca_metastasis_5fold) (in module loki2.mil.models.TCGA-Loki2_MILCell_blca_stage_5fold) (in module loki2.mil.prampt_downsample) (loki2.inference.cli.InferenceWSIParser attribute) patch_emb_dir (loki2.immstain.TutorialConfig attribute), [1] patch_embed (loki2.models.base.vision_transformer.VisionTransformer attribute) (loki2.models.utils.sam_utils.ImageEncoderViT attribute) patch_json_dir (loki2.immstain.TutorialConfig attribute), [1] patch_size (loki2.immstain.TutorialConfig attribute), [1] (loki2.inference.inference_disk.CellViTInference attribute), [1] (loki2.models.base.vision_transformer.PatchEmbed attribute) (loki2.models.cell_segmentation.cellvit.CellViT attribute) patch_transform (loki2.data.dataclass.wsi.WSI attribute) patched_slide_path (loki2.data.dataclass.wsi.WSI attribute) PatchedWSIInference (class in loki2.data.dataclass.wsi) PatchEmbed (class in loki2.models.base.vision_transformer) (class in loki2.models.utils.sam_utils) patches_list (loki2.data.dataclass.wsi.WSI attribute) patient (loki2.data.dataclass.wsi.WSI attribute) patient_embeddings (in module loki2.mil.prampt_generate.blca_metastasis_prampt) patient_groups (loki2.mil.models.src.dataset.PatientTileBagDataset_v2 attribute), [1] (loki2.mil.models.src.dataset.PatientTileBagDatasetForAttention_V7 attribute), [1] patient_id (in module loki2.mil.prampt_generate.blca_metastasis_prampt) patient_ids (loki2.mil.models.src.dataset.PatientTileBagDataset_v2 attribute), [1] PatientTileBagDataset_v2 (class in loki2.mil.models.src.dataset) PatientTileBagDatasetForAttention_V7 (class in loki2.mil.models.src.dataset) plot_attention_on_slide() (in module loki2.plot) plot_cell_types() (in module loki2.plot) plot_gene() (in module loki2.plot)

plot_indices_on_patch() (in module loki2.plot) plot_pred_vs_true() (in module loki2.immstain) plot_residual_hist() (in module loki2.immstain) plot_training_curves() (in module loki2.mil.models.src.utils) plot_type_legend() (in module loki2.plot) pool_labels (in module loki2.retrieve_from_sc) pop_tensor() (in module loki2.cl.train_projection_wds) pos_drop (loki2.models.base.vision_transformer.VisionTransformer attribute) pos_embed (loki2.models.base.vision_transformer.VisionTransformer attribute) (loki2.models.utils.sam_utils.ImageEncoderViT attribute) positions (loki2.data.dataclass.cell_graph.CellGraphDataWSI attribute) post_process_batch() (loki2.inference.postprocessing_cupy.DetectionCellPostProcessorCupy method) (loki2.models.cell_segmentation.postprocessing.DetectionCellPostProcessor method) post_process_single_image() (loki2.inference.postprocessing_cupy.DetectionCellPostProcessorCupy method) (loki2.models.cell_segmentation.postprocessing.DetectionCellPostProcessor method) pred_scores_np (in module loki2.retrieve_from_sc) predict_with_model() (in module loki2.immstain) prepare_data_for_attention_dataset() (in module loki2.mil.models.src.dataset) prepare_tokens() (loki2.models.base.vision_transformer.VisionTransformer method) process_patch_image() (loki2.data.dataclass.wsi.WSI method) process_stage_samples() (in module loki2.mil.prampt_generate.blca_stage_prampt) process_wsi() (loki2.inference.inference_disk.CellViTInference method) (loki2.inference.inference_memory.CellViTInferenceMemory method) proj (loki2.models.base.vision_transformer.Attention attribute) (loki2.models.base.vision_transformer.PatchEmbed attribute) (loki2.models.utils.sam_utils.Attention attribute) (loki2.models.utils.sam_utils.PatchEmbed attribute) proj_a (loki2.cl.model_cl.ProjectionCL attribute) proj_b (loki2.cl.model_cl.ProjectionCL attribute) proj_drop (loki2.models.base.vision_transformer.Attention attribute) proj_path (in module loki2.retrieve_from_sc) project_batches() (in module loki2.cl.project_raw_embeddings) project_root (in module loki2.detect_cells) (in module loki2.inference.inference_disk), [1] ProjectionCL (class in loki2.cl.model_cl) prompt_embed_dim (loki2.models.cell_segmentation.loki2_sam.CellViTSAM attribute)

Q

qkv (loki2.models.base.vision_transformer.Attention attribute) (loki2.models.utils.sam_utils.Attention attribute)

qkv_bias (loki2.models.cell_segmentation.cellvit.CellViT attribute) (loki2.models.cell_segmentation.loki2_sam.CellViTSAM attribute) query_embedding (in module loki2.retrieve_from_sc)

R

ray_actors (loki2.inference.inference_disk.CellViTInference attribute), [1] records (in module loki2.mil.prampt_generate.blca_metastasis_prampt) (in module loki2.mil.prampt_generate.blca_stage_prampt) regression_loss (loki2.models.cell_segmentation.cellvit.CellViT attribute) (loki2.models.cell_segmentation.cellvit.DataclassHVStorage attribute) regression_map (loki2.models.cell_segmentation.cellvit.DataclassHVStorage attribute) remap_label() (in module loki2.utils.tools) remove_small_objects() (in module loki2.utils.tools) remove_small_objects_cp() (in module loki2.utils.tools) requiredNamed (loki2.inference.cli.InferenceWSIParser attribute)

resolution (loki2.inference.postprocessing_cupy.DetectionCellPostProcessorCupy attribute) resolve_num_workers() (in module loki2.cl.train_projection_wds) retrieval_path (in module loki2.retrieve_from_sc) RetrievalResult (class in loki2.retrieve) (class in loki2.retrieve_from_sc) retrieve_with_celltype_filter() (in module loki2.retrieve) (in module loki2.retrieve_from_sc) rng (loki2.mil.models.src.dataset.PatientTileBagDataset_v2 attribute), [1] (loki2.mil.models.src.dataset.PatientTileBagDatasetForAttention_V7 attribute), [1] run_conf (loki2.inference.inference_disk.CellViTInference attribute), [1] (loki2.inference.postprocessing_cupy.BatchPoolingActor attribute)

S

sam (in module loki2.retrieve_from_sc) sample (in module loki2.retrieve_from_sc) sample_ratio (in module loki2.mil.prampt_generate.blca_metastasis_prampt) (in module loki2.mil.prampt_generate.blca_stage_prampt) save() (loki2.retrieve.RetrievalResult method) (loki2.retrieve_from_sc.RetrievalResult method) save_output() (in module loki2.cl.project_raw_embeddings) save_prediction_json() (in module loki2.immstain) SC_COLOR_DICT (in module loki2.plot) sc_data_trans (in module loki2.retrieve_from_sc) sc_meta_path (in module loki2.retrieve_from_sc) sc_proj_path (in module loki2.retrieve_from_sc) scale (loki2.models.base.vision_transformer.Attention attribute) (loki2.models.utils.sam_utils.Attention attribute) scatter_plot() (in module loki2.plot) scores (loki2.retrieve.RetrievalResult attribute) (loki2.retrieve_from_sc.RetrievalResult attribute)

select_keys() (in module loki2.cl.train_projection_wds) set_patch_transform() (loki2.data.dataclass.wsi.WSI method) setup_dummy_cellvit_modules() (in module loki2.immstain) setup_dummy_modules() (in module loki2.cl.utils) (in module loki2.mil.prampt_generate.blca_metastasis_prampt) (in module loki2.mil.prampt_generate.blca_stage_prampt) (in module loki2.preprocess) setup_logging() (in module loki2.cl.train_projection_wds) slide_path (loki2.data.dataclass.wsi.WSI attribute) (loki2.data.dataclass.wsi.WSIMetadata attribute) stack_pred_maps() (in module loki2.models.cell_segmentation.postprocessing) stage_df (in module loki2.mil.prampt_generate.blca_stage_prampt) subdir_name (loki2.inference.inference_disk.CellViTInference attribute), [1] subparser_dataset (loki2.inference.cli.InferenceWSIParser attribute) subparser_wsi (loki2.inference.cli.InferenceWSIParser attribute) subparsers (loki2.inference.cli.InferenceWSIParser attribute) successful_stage_0 (in module loki2.mil.prampt_generate.blca_stage_prampt) successful_stage_1 (in module loki2.mil.prampt_generate.blca_stage_prampt)

T

target_samples_per_stage (in module loki2.mil.prampt_generate.blca_stage_prampt) tensor_to_bytes() (in module loki2.cl.prepare_training) timed_section() (in module loki2.immstain) tissue_types (loki2.models.cell_segmentation.cellvit.DataclassHVStorage attribute) to_tuple() (loki2.retrieve.RetrievalResult method) (loki2.retrieve_from_sc.RetrievalResult method) train() (in module loki2.cl.train_projection_wds)

train_lightgbm_regressor() (in module loki2.immstain) train_single_fold() (in module loki2.mil.models.src.train) transform (loki2.data.dataclass.wsi.PatchedWSIInference attribute) trunc_normal_() (in module loki2.models.base.vision_transformer) TutorialConfig (class in loki2.immstain) TYPE_MAP_JSON (in module loki2.plot) TYPE_NUCLEI_DICT_UNISEG (in module loki2.config.config)

U

UMAP (in module loki2.plot) unflatten_dict() (in module loki2.utils.tools) unfreeze_encoder() (loki2.models.cell_segmentation.cellvit.CellViT method)

usage() (in module loki2.retrieve_from_sc) use_rel_pos (loki2.models.utils.sam_utils.Attention attribute) use_timestamp (loki2.utils.logger.Logger attribute), [1]

V

VisionTransformer (class in loki2.models.base.vision_transformer) visualize_patch_prediction() (in module loki2.immstain)

ViTCellViT (class in loki2.models.cell_segmentation.backbones) ViTCellViTDeit (class in loki2.models.cell_segmentation.backbones)

W

w (loki2.models.cell_segmentation.cellvit.DataclassHVStorage attribute) weight (loki2.models.utils.sam_utils.LayerNorm2d attribute) window_partition() (in module loki2.models.utils.sam_utils) window_size (loki2.models.utils.sam_utils.Block attribute) window_unpartition() (in module loki2.models.utils.sam_utils)

write_shard() (in module loki2.cl.prepare_training) write_txt() (in module loki2.psdtime) WSI (class in loki2.data.dataclass.wsi) wsi (loki2.inference.postprocessing_cupy.DetectionCellPostProcessorCupy attribute) wsi_object (loki2.data.dataclass.wsi.PatchedWSIInference attribute) WSIMetadata (class in loki2.data.dataclass.wsi)

X

x (loki2.data.dataclass.cell_graph.CellGraphDataWSI attribute)