Index

_

__init__() (trident.AnyToTiffConverter method) (trident.CuCIMWSI method) (trident.CZIWSI method) (trident.ImageWSI method) (trident.OMEZarrWSI method) (trident.OpenSlideWSI method) (trident.patch_encoder_models.Conchv15InferenceEncoder method) (trident.patch_encoder_models.Conchv1InferenceEncoder method) (trident.patch_encoder_models.CTransPathInferenceEncoder method) (trident.patch_encoder_models.CustomInferenceEncoder method) (trident.patch_encoder_models.GenBioPathFMInferenceEncoder method) (trident.patch_encoder_models.GigaPathInferenceEncoder method) (trident.patch_encoder_models.GPFMInferenceEncoder method) (trident.patch_encoder_models.H0MiniInferenceEncoder method) (trident.patch_encoder_models.HibouLInferenceEncoder method) (trident.patch_encoder_models.HOptimus0InferenceEncoder method) (trident.patch_encoder_models.HOptimus1InferenceEncoder method) (trident.patch_encoder_models.KaikoB16InferenceEncoder method) (trident.patch_encoder_models.KaikoB8InferenceEncoder method) (trident.patch_encoder_models.KaikoL14InferenceEncoder method) (trident.patch_encoder_models.KaikoS16InferenceEncoder method) (trident.patch_encoder_models.KaikoS8InferenceEncoder method) (trident.patch_encoder_models.KeepInferenceEncoder method) (trident.patch_encoder_models.LunitS8InferenceEncoder method) (trident.patch_encoder_models.Midnight12kInferenceEncoder method) (trident.patch_encoder_models.MuskInferenceEncoder method) (trident.patch_encoder_models.OpenMidnightInferenceEncoder method) (trident.patch_encoder_models.PhikonInferenceEncoder method) (trident.patch_encoder_models.Phikonv2InferenceEncoder method) (trident.patch_encoder_models.ResNet50InferenceEncoder method) (trident.patch_encoder_models.UNIInferenceEncoder method) (trident.patch_encoder_models.UNIv2InferenceEncoder method) (trident.patch_encoder_models.Virchow2InferenceEncoder method) (trident.patch_encoder_models.VirchowInferenceEncoder method) (trident.Processor method) (trident.SDPCWSI method) (trident.segmentation_models.GrandQCArtifactSegmenter method) (trident.segmentation_models.GrandQCSegmenter method) (trident.segmentation_models.HESTSegmenter method) (trident.slide_encoder_models.ABMILSlideEncoder method) (trident.slide_encoder_models.CHIEFSlideEncoder method) (trident.slide_encoder_models.FeatherSlideEncoder method) (trident.slide_encoder_models.FeatherUni2SlideEncoder method) (trident.slide_encoder_models.GigaPathSlideEncoder method) (trident.slide_encoder_models.MadeleineSlideEncoder method) (trident.slide_encoder_models.MeanSlideEncoder method) (trident.slide_encoder_models.PRISMSlideEncoder method) (trident.slide_encoder_models.ThreadsSlideEncoder method) (trident.slide_encoder_models.TitanSlideEncoder method) (trident.WSIPatcher method)

A

ABMILSlideEncoder (class in trident.slide_encoder_models)

AnyToTiffConverter (class in trident) apply_otsu_thresholding() (in module trident.segmentation_models)

B

bigtiff (trident.AnyToTiffConverter attribute)

C

CHIEFSlideEncoder (class in trident.slide_encoder_models) close() (trident.CuCIMWSI method) (trident.ImageWSI method) Conchv15InferenceEncoder (class in trident.patch_encoder_models) Conchv1InferenceEncoder (class in trident.patch_encoder_models) coords_only (trident.WSIPatcher attribute) create_patcher() (trident.CuCIMWSI method) (trident.CZIWSI method) (trident.ImageWSI method) (trident.OMEZarrWSI method) (trident.OpenSlideWSI method) (trident.SDPCWSI method)

CTransPathInferenceEncoder (class in trident.patch_encoder_models) CuCIMWSI (class in trident) CustomInferenceEncoder (class in trident.patch_encoder_models) CZIWSI (class in trident)

D

deprecated() (in module trident) dump_patches() (trident.CuCIMWSI method) (trident.CZIWSI method) (trident.ImageWSI method) (trident.OMEZarrWSI method) (trident.OpenSlideWSI method) (trident.SDPCWSI method)

E

enc_name (trident.patch_encoder_models.Gemma426BInferenceEncoder attribute) (trident.patch_encoder_models.Gemma4E4BInferenceEncoder attribute) encoder_factory() (in module trident.patch_encoder_models) (in module trident.slide_encoder_models) eval_transforms (trident.patch_encoder_models.Gemma426BInferenceEncoder attribute) (trident.patch_encoder_models.Gemma4E4BInferenceEncoder attribute) (trident.segmentation_models.OtsuSegmenter attribute) extract_patch_features() (trident.CuCIMWSI method) (trident.CZIWSI method) (trident.ImageWSI method) (trident.OMEZarrWSI method) (trident.OpenSlideWSI method) (trident.SDPCWSI method)

extract_slide_features() (trident.CuCIMWSI method) (trident.CZIWSI method) (trident.ImageWSI method) (trident.OMEZarrWSI method) (trident.OpenSlideWSI method) (trident.SDPCWSI method) extract_tissue_coords() (trident.CuCIMWSI method) (trident.CZIWSI method) (trident.ImageWSI method) (trident.OMEZarrWSI method) (trident.OpenSlideWSI method) (trident.SDPCWSI method)

F

FeatherSlideEncoder (class in trident.slide_encoder_models) FeatherUni2SlideEncoder (class in trident.slide_encoder_models) forward() (trident.patch_encoder_models.Conchv1InferenceEncoder method) (trident.patch_encoder_models.GenBioPathFMInferenceEncoder method) (trident.patch_encoder_models.H0MiniInferenceEncoder method) (trident.patch_encoder_models.HibouLInferenceEncoder method) (trident.patch_encoder_models.KeepInferenceEncoder method) (trident.patch_encoder_models.Midnight12kInferenceEncoder method) (trident.patch_encoder_models.MuskInferenceEncoder method) (trident.patch_encoder_models.OpenMidnightInferenceEncoder method) (trident.patch_encoder_models.PhikonInferenceEncoder method) (trident.patch_encoder_models.Phikonv2InferenceEncoder method) (trident.patch_encoder_models.ResNet50InferenceEncoder method) (trident.patch_encoder_models.Virchow2InferenceEncoder method) (trident.patch_encoder_models.VirchowInferenceEncoder method) (trident.segmentation_models.GrandQCArtifactSegmenter method) (trident.segmentation_models.GrandQCSegmenter method) (trident.segmentation_models.HESTSegmenter method) (trident.segmentation_models.OtsuSegmenter method) (trident.slide_encoder_models.ABMILSlideEncoder method) (trident.slide_encoder_models.CHIEFSlideEncoder method) (trident.slide_encoder_models.FeatherSlideEncoder method) (trident.slide_encoder_models.FeatherUni2SlideEncoder method) (trident.slide_encoder_models.GigaPathSlideEncoder method) (trident.slide_encoder_models.MadeleineSlideEncoder method) (trident.slide_encoder_models.MeanSlideEncoder method) (trident.slide_encoder_models.PRISMSlideEncoder method) (trident.slide_encoder_models.ThreadsSlideEncoder method) (trident.slide_encoder_models.TitanSlideEncoder method)

forward_features() (trident.patch_encoder_models.HibouLInferenceEncoder method) (trident.patch_encoder_models.PhikonInferenceEncoder method) (trident.patch_encoder_models.ResNet50InferenceEncoder method) from_legacy_coords() (trident.OpenSlideWSIPatcher class method) (trident.WSIPatcher class method) from_legacy_coords_file() (trident.OpenSlideWSIPatcher class method) (trident.WSIPatcher class method)

G

Gemma426BInferenceEncoder (class in trident.patch_encoder_models) Gemma4E4BInferenceEncoder (class in trident.patch_encoder_models) GenBioPathFMInferenceEncoder (class in trident.patch_encoder_models) get_best_level_and_custom_downsample() (trident.CuCIMWSI method) (trident.CZIWSI method) (trident.ImageWSI method) (trident.OMEZarrWSI method) (trident.OpenSlideWSI method) (trident.SDPCWSI method) get_cols_rows() (trident.OpenSlideWSIPatcher method) (trident.WSIPatcher method) get_dimensions() (trident.CuCIMWSI method) (trident.CZIWSI method) (trident.ImageWSI method) (trident.OMEZarrWSI method) (trident.OpenSlideWSI method) (trident.SDPCWSI method)

get_thumbnail() (trident.CuCIMWSI method) (trident.CZIWSI method) (trident.ImageWSI method) (trident.OMEZarrWSI method) (trident.OpenSlideWSI method) (trident.SDPCWSI method) get_tile() (trident.OpenSlideWSIPatcher method) (trident.WSIPatcher method) get_tile_xy() (trident.OpenSlideWSIPatcher method) (trident.WSIPatcher method) GigaPathInferenceEncoder (class in trident.patch_encoder_models) GigaPathSlideEncoder (class in trident.slide_encoder_models) GPFMInferenceEncoder (class in trident.patch_encoder_models) GrandQCArtifactSegmenter (class in trident.segmentation_models) GrandQCSegmenter (class in trident.segmentation_models)

H

H0MiniInferenceEncoder (class in trident.patch_encoder_models) height (trident.WSIPatcher attribute) HESTSegmenter (class in trident.segmentation_models) HF_HUB_ID (trident.patch_encoder_models.KaikoB16InferenceEncoder attribute) (trident.patch_encoder_models.KaikoB8InferenceEncoder attribute) (trident.patch_encoder_models.KaikoL14InferenceEncoder attribute) (trident.patch_encoder_models.KaikoS16InferenceEncoder attribute) (trident.patch_encoder_models.KaikoS8InferenceEncoder attribute)

HF_REPO (trident.patch_encoder_models.Gemma426BInferenceEncoder attribute) (trident.patch_encoder_models.Gemma4E4BInferenceEncoder attribute) HibouLInferenceEncoder (class in trident.patch_encoder_models) HOptimus0InferenceEncoder (class in trident.patch_encoder_models) HOptimus1InferenceEncoder (class in trident.patch_encoder_models)

I

ImageWSI (class in trident) IMG_SIZE (trident.patch_encoder_models.KaikoB16InferenceEncoder attribute) (trident.patch_encoder_models.KaikoB8InferenceEncoder attribute) (trident.patch_encoder_models.KaikoL14InferenceEncoder attribute) (trident.patch_encoder_models.KaikoS16InferenceEncoder attribute) (trident.patch_encoder_models.KaikoS8InferenceEncoder attribute)

J

job_dir (trident.AnyToTiffConverter attribute)

K

KaikoB16InferenceEncoder (class in trident.patch_encoder_models) KaikoB8InferenceEncoder (class in trident.patch_encoder_models) KaikoL14InferenceEncoder (class in trident.patch_encoder_models)

KaikoS16InferenceEncoder (class in trident.patch_encoder_models) KaikoS8InferenceEncoder (class in trident.patch_encoder_models) KeepInferenceEncoder (class in trident.patch_encoder_models)

L

load_wsi() (in module trident)

LunitS8InferenceEncoder (class in trident.patch_encoder_models)

M

MadeleineSlideEncoder (class in trident.slide_encoder_models) mask (trident.WSIPatcher attribute) mask_rgb() (in module trident.segmentation_models) MeanSlideEncoder (class in trident.slide_encoder_models) Midnight12kInferenceEncoder (class in trident.patch_encoder_models) model (trident.patch_encoder_models.Gemma426BInferenceEncoder attribute) (trident.patch_encoder_models.Gemma4E4BInferenceEncoder attribute) (trident.segmentation_models.OtsuSegmenter attribute) MODEL_NAME (trident.patch_encoder_models.KaikoB16InferenceEncoder attribute) (trident.patch_encoder_models.KaikoB8InferenceEncoder attribute) (trident.patch_encoder_models.KaikoL14InferenceEncoder attribute) (trident.patch_encoder_models.KaikoS16InferenceEncoder attribute) (trident.patch_encoder_models.KaikoS8InferenceEncoder attribute)

module trident trident.patch_encoder_models trident.segmentation_models trident.slide_encoder_models MuskInferenceEncoder (class in trident.patch_encoder_models)

O

OMEZarrWSI (class in trident) OpenMidnightInferenceEncoder (class in trident.patch_encoder_models) OpenSlideWSI (class in trident)

OpenSlideWSIPatcher (class in trident) OtsuSegmenter (class in trident.segmentation_models) overlap (trident.WSIPatcher attribute)

P

patch_size_target (trident.WSIPatcher attribute) PhikonInferenceEncoder (class in trident.patch_encoder_models) Phikonv2InferenceEncoder (class in trident.patch_encoder_models) pil (trident.WSIPatcher attribute) precision (trident.patch_encoder_models.Gemma426BInferenceEncoder attribute) (trident.patch_encoder_models.Gemma4E4BInferenceEncoder attribute)

PRISMSlideEncoder (class in trident.slide_encoder_models) process_all() (trident.AnyToTiffConverter method) process_file() (trident.AnyToTiffConverter method) Processor (class in trident)

R

read_region() (trident.CuCIMWSI method) (trident.CZIWSI method) (trident.ImageWSI method) (trident.OMEZarrWSI method) (trident.OpenSlideWSI method) (trident.SDPCWSI method) release() (trident.CuCIMWSI method) (trident.CZIWSI method) (trident.ImageWSI method) (trident.OMEZarrWSI method) (trident.OpenSlideWSI method) (trident.Processor method) (trident.SDPCWSI method)

ResNet50InferenceEncoder (class in trident.patch_encoder_models) run_feature_extraction_job() (trident.Processor method) run_patch_feature_extraction_job() (trident.Processor method) run_patching_job() (trident.Processor method) run_segmentation_job() (trident.Processor method) run_slide_feature_extraction_job() (trident.Processor method)

S

save_config() (trident.Processor method) SDPCWSI (class in trident) segment_semantic() (trident.CuCIMWSI method) (trident.CZIWSI method) (trident.ImageWSI method) (trident.OMEZarrWSI method) (trident.OpenSlideWSI method) (trident.SDPCWSI method)

segment_tissue() (trident.CuCIMWSI method) (trident.CZIWSI method) (trident.ImageWSI method) (trident.OMEZarrWSI method) (trident.OpenSlideWSI method) (trident.SDPCWSI method) segmentation_model_factory() (in module trident.segmentation_models)

T

ThreadsSlideEncoder (class in trident.slide_encoder_models) timm (trident.patch_encoder_models.Virchow2InferenceEncoder attribute) (trident.patch_encoder_models.VirchowInferenceEncoder attribute) TitanSlideEncoder (class in trident.slide_encoder_models) trident module

trident.patch_encoder_models module trident.segmentation_models module trident.slide_encoder_models module

U

UNIInferenceEncoder (class in trident.patch_encoder_models)

UNIv2InferenceEncoder (class in trident.patch_encoder_models)

V

VARIANT (trident.patch_encoder_models.Gemma426BInferenceEncoder attribute) (trident.patch_encoder_models.Gemma4E4BInferenceEncoder attribute) Virchow2InferenceEncoder (class in trident.patch_encoder_models) VirchowInferenceEncoder (class in trident.patch_encoder_models) visualize() (trident.OpenSlideWSIPatcher method) (trident.WSIPatcher method)

visualize_coords() (trident.CuCIMWSI method) (trident.CZIWSI method) (trident.ImageWSI method) (trident.OMEZarrWSI method) (trident.OpenSlideWSI method) (trident.SDPCWSI method) visualize_heatmap() (in module trident)

W

weights_path (trident.patch_encoder_models.Gemma426BInferenceEncoder attribute) (trident.patch_encoder_models.Gemma4E4BInferenceEncoder attribute) width (trident.WSIPatcher attribute)

wsi (trident.WSIPatcher attribute) WSIPatcher (class in trident) WSIPatcherDataset (class in trident)