Index A | B | C | D | E | F | G | H | I | K | L | M | P | R | S | T | U | V | W A aggregate_metrics() (in module plismbench.utils.aggregate) B BasePlismMetric (class in plismbench.metrics.base) C choices() (plismbench.models.StringEnum class method) collate() (in module plismbench.engine.extract.extract_from_h5) (in module plismbench.engine.extract.extract_from_png) compute_metric() (plismbench.metrics.base.BasePlismMetric method) (plismbench.metrics.cosine_similarity.CosineSimilarity method) (plismbench.metrics.CosineSimilarity method) (plismbench.metrics.retrieval.TopkAccuracy method) (plismbench.metrics.TopkAccuracy method) CONCH (class in plismbench.models.mahmood_lab) (plismbench.models.FeatureExtractorsEnum attribute) CONCHv15 (class in plismbench.models.mahmood_lab) CONCHV15 (plismbench.models.FeatureExtractorsEnum attribute) CosineSimilarity (class in plismbench.metrics) (class in plismbench.metrics.cosine_similarity) D device (plismbench.metrics.base.BasePlismMetric attribute) (plismbench.models.extractor.Extractor attribute) DINOV2_VIT_GIANT_IMAGENET (plismbench.models.FeatureExtractorsEnum attribute) Dinov2ViTGiant (class in plismbench.models.meta) display_plism_metrics() (in module plismbench.utils.viz) download_state_dict() (in module plismbench.utils.core) E expand_columns() (in module plismbench.utils.viz) Extractor (class in plismbench.models.extractor) F feature_extractor (plismbench.models.extractor.Extractor property) FeatureExtractorsEnum (class in plismbench.models) format_results() (in module plismbench.utils.aggregate) (in module plismbench.utils.metrics) forward() (plismbench.models.utils.PrecisionModule method) G get_aggregated_results() (in module plismbench.utils.metrics) get_dataloader() (in module plismbench.engine.extract.extract_from_h5) get_extractor_results() (in module plismbench.utils.metrics) get_leaderboard_results() (in module plismbench.utils.metrics) get_results() (in module plismbench.utils.aggregate) (in module plismbench.utils.metrics) get_tiles_subset_idx() (in module plismbench.utils.evaluate) GPFM (class in plismbench.models.hkust) (plismbench.models.FeatureExtractorsEnum attribute) H H0_MINI (plismbench.models.FeatureExtractorsEnum attribute) H0Mini (class in plismbench.models.bioptimus) H5Dataset (class in plismbench.engine.extract.extract_from_h5) HIBOU_BASE (plismbench.models.FeatureExtractorsEnum attribute) HIBOU_LARGE (plismbench.models.FeatureExtractorsEnum attribute) HibouBase (class in plismbench.models.histai) HibouLarge (class in plismbench.models.histai) HOptimus0 (class in plismbench.models.bioptimus) HOPTIMUS0 (plismbench.models.FeatureExtractorsEnum attribute) HOptimus1 (class in plismbench.models.bioptimus) I init() (plismbench.models.FeatureExtractorsEnum method) iqr() (in module plismbench.utils.aggregate) K KAIKO_VIT_BASE (plismbench.models.FeatureExtractorsEnum attribute) KAIKO_VIT_LARGE (plismbench.models.FeatureExtractorsEnum attribute) KaikoViTBase (class in plismbench.models.kaiko_ai) KaikoViTLarge (class in plismbench.models.kaiko_ai) L load_features() (in module plismbench.utils.evaluate) load_pickle() (in module plismbench.utils.core) LUNIT_VIT_SMALL_8 (plismbench.models.FeatureExtractorsEnum attribute) LunitViTS8 (class in plismbench.models.lunit) M Midnight12k (class in plismbench.models.kaiko_ai) MIDNIGHT_12K (plismbench.models.FeatureExtractorsEnum attribute) module plismbench plismbench.engine plismbench.engine.extract plismbench.engine.extract.core plismbench.engine.extract.extract_from_h5 plismbench.engine.extract.extract_from_png plismbench.engine.extract.utils plismbench.metrics plismbench.metrics.base plismbench.metrics.cosine_similarity plismbench.metrics.retrieval plismbench.models plismbench.models.bioptimus plismbench.models.extractor plismbench.models.histai plismbench.models.hkust plismbench.models.kaiko_ai plismbench.models.lunit plismbench.models.mahmood_lab plismbench.models.meta plismbench.models.microsoft plismbench.models.owkin plismbench.models.paige_ai plismbench.models.standford plismbench.models.utils plismbench.utils plismbench.utils.aggregate plismbench.utils.core plismbench.utils.evaluate plismbench.utils.metrics plismbench.utils.viz P pad() (in module plismbench.utils.aggregate) Phikon (class in plismbench.models.owkin) PHIKON (plismbench.models.FeatureExtractorsEnum attribute) PhikonV2 (class in plismbench.models.owkin) PHIKONV2 (plismbench.models.FeatureExtractorsEnum attribute) PLIP (class in plismbench.models.standford) (plismbench.models.FeatureExtractorsEnum attribute) plismbench module plismbench.engine module plismbench.engine.extract module plismbench.engine.extract.core module plismbench.engine.extract.extract_from_h5 module plismbench.engine.extract.extract_from_png module plismbench.engine.extract.utils module plismbench.metrics module plismbench.metrics.base module plismbench.metrics.cosine_similarity module plismbench.metrics.retrieval module plismbench.models module plismbench.models.bioptimus module plismbench.models.extractor module plismbench.models.histai module plismbench.models.hkust module plismbench.models.kaiko_ai module plismbench.models.lunit module plismbench.models.mahmood_lab module plismbench.models.meta module plismbench.models.microsoft module plismbench.models.owkin module plismbench.models.paige_ai module plismbench.models.standford module plismbench.models.utils module plismbench.utils module plismbench.utils.aggregate module plismbench.utils.core module plismbench.utils.evaluate module plismbench.utils.metrics module plismbench.utils.viz module PrecisionModule (class in plismbench.models.utils) prepare_device() (in module plismbench.models.utils) prepare_features_dataframe() (in module plismbench.utils.evaluate) prepare_module() (in module plismbench.models.utils) prepare_pairs_dataframe() (in module plismbench.utils.evaluate) process() (plismbench.models.histai.HibouBase method) (plismbench.models.histai.HibouLarge method) (plismbench.models.mahmood_lab.CONCH method) (plismbench.models.owkin.Phikon method) (plismbench.models.owkin.PhikonV2 method) (plismbench.models.standford.PLIP method) process_imgs() (in module plismbench.engine.extract.utils) ProvGigaPath (class in plismbench.models.microsoft) PROVGIGAPATH (plismbench.models.FeatureExtractorsEnum attribute) R rank_results() (in module plismbench.utils.metrics) resume_streaming() (in module plismbench.engine.extract.extract_from_png) run_extract() (in module plismbench.engine.extract.core) run_extract_h5() (in module plismbench.engine.extract.extract_from_h5) run_extract_streaming() (in module plismbench.engine.extract.extract_from_png) S save_features() (in module plismbench.engine.extract.utils) sort_coords() (in module plismbench.engine.extract.utils) StringEnum (class in plismbench.models) T TopkAccuracy (class in plismbench.metrics) (class in plismbench.metrics.retrieval) transform (plismbench.models.bioptimus.H0Mini property) (plismbench.models.bioptimus.HOptimus0 property) (plismbench.models.bioptimus.HOptimus1 property) (plismbench.models.extractor.Extractor property) (plismbench.models.histai.HibouBase property) (plismbench.models.histai.HibouLarge property) (plismbench.models.hkust.GPFM property) (plismbench.models.kaiko_ai.KaikoViTBase property) (plismbench.models.kaiko_ai.KaikoViTLarge property) (plismbench.models.kaiko_ai.Midnight12k property) (plismbench.models.lunit.LunitViTS8 property) (plismbench.models.mahmood_lab.CONCH property) (plismbench.models.mahmood_lab.CONCHv15 property) (plismbench.models.mahmood_lab.UNI property) (plismbench.models.mahmood_lab.UNI2h property) (plismbench.models.meta.Dinov2ViTGiant property) (plismbench.models.microsoft.ProvGigaPath property) (plismbench.models.owkin.Phikon property) (plismbench.models.owkin.PhikonV2 property) (plismbench.models.paige_ai.Virchow property) (plismbench.models.paige_ai.Virchow2 property) (plismbench.models.standford.PLIP property) U UNI (class in plismbench.models.mahmood_lab) (plismbench.models.FeatureExtractorsEnum attribute) UNI2h (class in plismbench.models.mahmood_lab) UNI2H (plismbench.models.FeatureExtractorsEnum attribute) V Virchow (class in plismbench.models.paige_ai) VIRCHOW (plismbench.models.FeatureExtractorsEnum attribute) Virchow2 (class in plismbench.models.paige_ai) VIRCHOW2 (plismbench.models.FeatureExtractorsEnum attribute) W write_pickle() (in module plismbench.utils.core)
