Index

A

AdaptiveHistogramEqualization (class in pathml.preprocessing) add() (pathml.core.Masks method) (pathml.core.Tiles method) add_mask() (pathml.core.h5managers.h5pathManager method) add_tile() (pathml.core.h5managers.h5pathManager method) apply() (pathml.preprocessing.AdaptiveHistogramEqualization method) (pathml.preprocessing.BinaryThreshold method) (pathml.preprocessing.BoxBlur method) (pathml.preprocessing.CollapseRunsCODEX method) (pathml.preprocessing.CollapseRunsVectra method) (pathml.preprocessing.ForegroundDetection method) (pathml.preprocessing.GaussianBlur method) (pathml.preprocessing.HistogramEqualization method) (pathml.preprocessing.LabelArtifactTileHE method) (pathml.preprocessing.LabelWhiteSpaceHE method) (pathml.preprocessing.MedianBlur method) (pathml.preprocessing.MorphClose method) (pathml.preprocessing.MorphOpen method) (pathml.preprocessing.NucleusDetectionHE method) (pathml.preprocessing.Pipeline method) (pathml.preprocessing.QuantifyMIF method) (pathml.preprocessing.RescaleIntensity method) (pathml.preprocessing.SegmentMIF method) (pathml.preprocessing.StainNormalizationHE method) (pathml.preprocessing.SuperpixelInterpolation method) (pathml.preprocessing.TissueDetectionHE method)

asdict() (pathml.core.SlideType method)

B

BinaryThreshold (class in pathml.preprocessing)

BioFormatsBackend (class in pathml.core) BoxBlur (class in pathml.preprocessing)

C

center_crop_im_batch() (in module pathml.ml.utils) CODEXSlide (class in pathml.core) CollapseRunsCODEX (class in pathml.preprocessing)

CollapseRunsVectra (class in pathml.preprocessing) compute_hv_map() (in module pathml.ml.hovernet) contour_centroid() (in module pathml.utils) counts (pathml.core.SlideData property)

D

DeepFocusDataModule (class in pathml.datasets) dice_loss() (in module pathml.ml.utils)

dice_score() (in module pathml.ml.utils) DICOMBackend (class in pathml.core) disable() (pathml.PathMLLogger static method)

E

enable() (pathml.PathMLLogger static method) extract_region() (pathml.core.BioFormatsBackend method) (pathml.core.DICOMBackend method) (pathml.core.OpenSlideBackend method) (pathml.core.SlideData method)

F

F() (pathml.preprocessing.AdaptiveHistogramEqualization method) (pathml.preprocessing.BinaryThreshold method) (pathml.preprocessing.BoxBlur method) (pathml.preprocessing.CollapseRunsCODEX method) (pathml.preprocessing.CollapseRunsVectra method) (pathml.preprocessing.ForegroundDetection method) (pathml.preprocessing.GaussianBlur method) (pathml.preprocessing.HistogramEqualization method) (pathml.preprocessing.LabelArtifactTileHE method) (pathml.preprocessing.LabelWhiteSpaceHE method) (pathml.preprocessing.MedianBlur method) (pathml.preprocessing.MorphClose method) (pathml.preprocessing.MorphOpen method) (pathml.preprocessing.NucleusDetectionHE method) (pathml.preprocessing.QuantifyMIF method) (pathml.preprocessing.RescaleIntensity method) (pathml.preprocessing.SegmentMIF method) (pathml.preprocessing.StainNormalizationHE method) (pathml.preprocessing.SuperpixelInterpolation method) (pathml.preprocessing.TissueDetectionHE method)

fit_to_reference() (pathml.preprocessing.StainNormalizationHE method) ForegroundDetection (class in pathml.preprocessing) forward() (pathml.ml.HoVerNet method)

G

GaussianBlur (class in pathml.preprocessing) generate_tiles() (pathml.core.BioFormatsBackend method) (pathml.core.DICOMBackend method) (pathml.core.OpenSlideBackend method) (pathml.core.SlideData method) get_bot() (pathml.core.DICOMBackend static method) get_image_shape() (pathml.core.BioFormatsBackend method) (pathml.core.DICOMBackend method) (pathml.core.OpenSlideBackend method)

get_mask() (pathml.core.h5managers.h5pathManager method) get_slidetype() (pathml.core.h5managers.h5pathManager method) get_sobel_kernels() (in module pathml.ml.utils) get_thumbnail() (pathml.core.BioFormatsBackend method) (pathml.core.DICOMBackend method) (pathml.core.OpenSlideBackend method) get_tile() (pathml.core.h5managers.h5pathManager method)

H

h5pathManager (class in pathml.core.h5managers) HESlide (class in pathml.core)

HistogramEqualization (class in pathml.preprocessing) HoVerNet (class in pathml.ml)

K

keys (pathml.core.Masks property) (pathml.core.Tiles property)

L

LabelArtifactTileHE (class in pathml.preprocessing)

LabelWhiteSpaceHE (class in pathml.preprocessing) loss_hovernet() (in module pathml.ml.hovernet)

M

Masks (class in pathml.core) MedianBlur (class in pathml.preprocessing)

MorphClose (class in pathml.preprocessing) MorphOpen (class in pathml.preprocessing) MultiparametricSlide (class in pathml.core)

N

normalize_matrix_cols() (in module pathml.utils)

normalize_matrix_rows() (in module pathml.utils) NucleusDetectionHE (class in pathml.preprocessing)

O

OpenSlideBackend (class in pathml.core)

P

pad_or_crop() (in module pathml.utils) pannuke_multiclass_mask_to_nucleus_mask() (in module pathml.datasets.utils) PanNukeDataModule (class in pathml.datasets) PathMLLogger (class in pathml) pil_to_rgb() (in module pathml.utils)

Pipeline (class in pathml.preprocessing) plot() (pathml.core.SlideData method) (pathml.core.Tile method) plot_mask() (in module pathml.utils) plot_segmentation() (in module pathml.utils) post_process_batch_hovernet() (in module pathml.ml.hovernet)

Q

QuantifyMIF (class in pathml.preprocessing)

R

readcounts() (in module pathml.core.utils) readtupleh5() (in module pathml.core.utils) remove() (pathml.core.Masks method) (pathml.core.Tiles method) remove_mask() (pathml.core.h5managers.h5pathManager method) remove_small_objs() (in module pathml.ml.hovernet) remove_tile() (pathml.core.h5managers.h5pathManager method)

RescaleIntensity (class in pathml.preprocessing) RGB_to_GREY() (in module pathml.utils) RGB_to_HSI() (in module pathml.utils) RGB_to_HSV() (in module pathml.utils) RGB_to_LAB() (in module pathml.utils) RGB_to_OD() (in module pathml.utils) run() (pathml.core.SlideData method) (pathml.core.SlideDataset method)

S

save() (pathml.preprocessing.Pipeline method) segmentation_lines() (in module pathml.utils) SegmentMIF (class in pathml.preprocessing) shape (pathml.core.SlideData property) (pathml.core.Tile property) slice() (pathml.core.Masks method)

slice_masks() (pathml.core.h5managers.h5pathManager method) SlideData (class in pathml.core) SlideDataset (class in pathml.core) SlideType (class in pathml.core) sort_points_clockwise() (in module pathml.utils) StainNormalizationHE (class in pathml.preprocessing) SuperpixelInterpolation (class in pathml.preprocessing)

T

test_dataloader (pathml.datasets.DeepFocusDataModule property) (pathml.datasets.PanNukeDataModule property) Tile (class in pathml.core) tile_shape (pathml.core.Tiles property)

TileDataset (class in pathml.ml) Tiles (class in pathml.core) TissueDetectionHE (class in pathml.preprocessing) train_dataloader (pathml.datasets.DeepFocusDataModule property) (pathml.datasets.PanNukeDataModule property)

U

update() (pathml.core.Tiles method)

update_mask() (pathml.core.h5managers.h5pathManager method) upsample_array() (in module pathml.utils)

V

valid_dataloader (pathml.datasets.DeepFocusDataModule property) (pathml.datasets.PanNukeDataModule property)

VectraSlide (class in pathml.core)

W

wrap_transform_multichannel() (in module pathml.ml.utils) write() (pathml.core.SlideData method) (pathml.core.SlideDataset method) writecounts() (in module pathml.core.utils)

writedataframeh5() (in module pathml.core.utils) writedicth5() (in module pathml.core.utils) writestringh5() (in module pathml.core.utils) writetupleh5() (in module pathml.core.utils)