Index

_

__enter__() (glasscut.Slide method) (glasscut.slides.backends.base.SlideBackend method) (glasscut.slides.backends.SlideBackend method) (glasscut.slides.Slide method) (glasscut.slides.slide.Slide method) __exit__() (glasscut.Slide method) (glasscut.slides.backends.base.SlideBackend method) (glasscut.slides.backends.SlideBackend method) (glasscut.slides.Slide method) (glasscut.slides.slide.Slide method) __getitem__() (glasscut.dataset.live.LiveSlideDataset method) (glasscut.dataset.LiveSlideDataset method) (glasscut.LiveSlideDataset method) __init__() (glasscut.data.fetcher.DataFetcher method) (glasscut.data.fetcher.PoochProtocol method) (glasscut.dataset.DatasetGenerator method) (glasscut.dataset.generator.DatasetGenerator method) (glasscut.dataset.live.LiveSlideDataset method) (glasscut.dataset.live.LiveSlideSample method) (glasscut.dataset.LiveSlideDataset method) (glasscut.dataset.LiveSlideSample method) (glasscut.DatasetGenerator method) (glasscut.GridTiler method) (glasscut.LiveSlideDataset method) (glasscut.LiveSlideSample method) (glasscut.MacenkoStainNormalizer method) (glasscut.ReinhardtStainNormalizer method) (glasscut.Slide method) (glasscut.slides.backends.cucim_backend.CuCimBackend method) (glasscut.slides.backends.cucim_backend.CuImageProtocol method) (glasscut.slides.backends.cucim_backend.CuPyArrayProtocol method) (glasscut.slides.backends.CuCimBackend method) (glasscut.slides.backends.openslide_backend.OpenSlideBackend method) (glasscut.slides.backends.OpenSlideBackend method) (glasscut.slides.Slide method) (glasscut.slides.slide.Slide method) (glasscut.stain_normalizers.macenko.MacenkoStainNormalizer method) (glasscut.stain_normalizers.MacenkoStainNormalizer method) (glasscut.stain_normalizers.reinhardt.ReinhardtStainNormalizer method) (glasscut.stain_normalizers.ReinhardtStainNormalizer method) (glasscut.storage.DatasetMetadata method) (glasscut.storage.manager.StorageOrganizer method) (glasscut.storage.SlideMetadata method) (glasscut.storage.StorageOrganizer method) (glasscut.storage.structures.DatasetMetadata method) (glasscut.storage.structures.SlideMetadata method) (glasscut.storage.structures.TileMetadata method) (glasscut.storage.TileMetadata method) (glasscut.Tile method) (glasscut.tile.Tile method) (glasscut.tiler.grid.GridTiler method) (glasscut.tiler.GridTiler method) (glasscut.utils.Profiler method)

__len__() (glasscut.dataset.live.LiveSlideDataset method) (glasscut.dataset.LiveSlideDataset method) (glasscut.LiveSlideDataset method)

A

aorta_tissue() (in module glasscut.data)

available_magnifications (glasscut.storage.SlideMetadata attribute) (glasscut.storage.structures.SlideMetadata attribute)

B

BackendError base_magnification (glasscut.slides.backends.base.SlideBackend property) (glasscut.slides.backends.cucim_backend.CuCimBackend property) (glasscut.slides.backends.CuCimBackend property) (glasscut.slides.backends.openslide_backend.OpenSlideBackend property) (glasscut.slides.backends.OpenSlideBackend property) (glasscut.slides.backends.SlideBackend property)

breast_tissue() (in module glasscut.data) breast_tissue_diagnostic_black_pen() (in module glasscut.data) breast_tissue_diagnostic_green_pen() (in module glasscut.data) breast_tissue_diagnostic_red_pen() (in module glasscut.data) build_magnification_mapping() (in module glasscut.slides.utils)

C

close() (glasscut.Slide method) (glasscut.slides.backends.base.SlideBackend method) (glasscut.slides.backends.cucim_backend.CuCimBackend method) (glasscut.slides.backends.CuCimBackend method) (glasscut.slides.backends.openslide_backend.OpenSlideBackend method) (glasscut.slides.backends.OpenSlideBackend method) (glasscut.slides.backends.SlideBackend method) (glasscut.slides.Slide method) (glasscut.slides.slide.Slide method)

cmu_small_region() (in module glasscut.data) config (glasscut.storage.DatasetMetadata attribute) (glasscut.storage.structures.DatasetMetadata attribute) created_at (glasscut.storage.DatasetMetadata attribute) (glasscut.storage.structures.DatasetMetadata attribute) CuCimBackend (class in glasscut.slides.backends) (class in glasscut.slides.backends.cucim_backend) CuImageProtocol (class in glasscut.slides.backends.cucim_backend) CuPyArrayProtocol (class in glasscut.slides.backends.cucim_backend)

D

dataclass_to_dict() (in module glasscut.storage) (in module glasscut.storage.structures) DataFetcher (class in glasscut.data.fetcher) dataset_id (glasscut.storage.DatasetMetadata attribute) (glasscut.storage.structures.DatasetMetadata attribute) DatasetGenerator (class in glasscut) (class in glasscut.dataset) (class in glasscut.dataset.generator) DatasetMetadata (class in glasscut.storage) (class in glasscut.storage.structures) detect() (glasscut.OtsuTissueDetector method) (glasscut.tissue_detectors.base.TissueDetector method) (glasscut.tissue_detectors.otsu.OtsuTissueDetector method) (glasscut.tissue_detectors.OtsuTissueDetector method) (glasscut.tissue_detectors.TissueDetector method)

dimensions (glasscut.dataset.live.LiveSlideSample attribute), [1] (glasscut.dataset.LiveSlideSample attribute), [1] (glasscut.LiveSlideSample attribute), [1] (glasscut.Slide property) (glasscut.slides.backends.base.SlideBackend property) (glasscut.slides.backends.cucim_backend.CuCimBackend property) (glasscut.slides.backends.CuCimBackend property) (glasscut.slides.backends.openslide_backend.OpenSlideBackend property) (glasscut.slides.backends.OpenSlideBackend property) (glasscut.slides.backends.SlideBackend property) (glasscut.slides.Slide property) (glasscut.slides.slide.Slide property) (glasscut.storage.SlideMetadata attribute) (glasscut.storage.structures.SlideMetadata attribute)

E

enabled (glasscut.utils.Profiler attribute) extract() (glasscut.GridTiler method) (glasscut.Tiler method) (glasscut.tiler.base.Tiler method) (glasscut.tiler.grid.GridTiler method) (glasscut.tiler.GridTiler method) (glasscut.tiler.Tiler method)

extract_tile() (glasscut.Slide method) (glasscut.slides.Slide method) (glasscut.slides.slide.Slide method)

F

fetch() (glasscut.data.fetcher.PoochProtocol method) file_path (glasscut.storage.structures.TileMetadata attribute) (glasscut.storage.TileMetadata attribute) FilterCompositionError fit() (glasscut.ReinhardtStainNormalizer method) (glasscut.stain_normalizers.base.StainNormalizer method) (glasscut.stain_normalizers.base.TransformerStainMatrixMixin method) (glasscut.stain_normalizers.reinhardt.ReinhardtStainNormalizer method) (glasscut.stain_normalizers.ReinhardtStainNormalizer method) (glasscut.stain_normalizers.StainNormalizer method) (glasscut.stain_normalizers.TransformerStainMatrixMixin method)

G

get() (glasscut.slides.backends.cucim_backend.CuPyArrayProtocol method) get_file() (glasscut.data.fetcher.DataFetcher method) get_thumbnail() (glasscut.slides.backends.base.SlideBackend method) (glasscut.slides.backends.cucim_backend.CuCimBackend method) (glasscut.slides.backends.CuCimBackend method) (glasscut.slides.backends.openslide_backend.OpenSlideBackend method) (glasscut.slides.backends.OpenSlideBackend method) (glasscut.slides.backends.SlideBackend method) get_tile_boxes() (glasscut.GridTiler method) (glasscut.Tiler method) (glasscut.tiler.base.Tiler method) (glasscut.tiler.grid.GridTiler method) (glasscut.tiler.GridTiler method) (glasscut.tiler.Tiler method) get_tile_candidates() (glasscut.GridTiler method) (glasscut.tiler.grid.GridTiler method) (glasscut.tiler.GridTiler method) glasscut module, [1] glasscut.data module glasscut.data.fetcher module glasscut.data.registry module glasscut.dataset module glasscut.dataset.generator module glasscut.dataset.live module glasscut.exceptions module glasscut.slides module glasscut.slides.backends module glasscut.slides.backends.base module glasscut.slides.backends.cucim_backend module

glasscut.slides.backends.openslide_backend module glasscut.slides.slide module glasscut.slides.utils module glasscut.stain_normalizers module glasscut.stain_normalizers.base module glasscut.stain_normalizers.macenko module glasscut.stain_normalizers.reinhardt module glasscut.storage module glasscut.storage.manager module glasscut.storage.structures module glasscut.tile module glasscut.tiler module glasscut.tiler.base module glasscut.tiler.grid module glasscut.tissue_detectors module glasscut.tissue_detectors.base module glasscut.tissue_detectors.otsu module glasscut.utils module GlassCutException GridTiler (class in glasscut) (class in glasscut.tiler) (class in glasscut.tiler.grid)

H

has_enough_tissue() (glasscut.Tile method) (glasscut.tile.Tile method)

heart_tissue() (in module glasscut.data) height (glasscut.storage.structures.TileMetadata attribute) (glasscut.storage.TileMetadata attribute)

I

ihc_breast() (in module glasscut.data) ihc_kidney() (in module glasscut.data) init_dataset() (glasscut.storage.manager.StorageOrganizer method) (glasscut.storage.StorageOrganizer method)

init_slide() (glasscut.storage.manager.StorageOrganizer method) (glasscut.storage.StorageOrganizer method)

L

lab_to_rgb() (glasscut.ReinhardtStainNormalizer static method) (glasscut.stain_normalizers.reinhardt.ReinhardtStainNormalizer static method) (glasscut.stain_normalizers.ReinhardtStainNormalizer static method) lazyproperty() (in module glasscut.utils) level (glasscut.storage.structures.TileMetadata attribute) (glasscut.storage.TileMetadata attribute) LiveSlideDataset (class in glasscut) (class in glasscut.dataset) (class in glasscut.dataset.live)

LiveSlideSample (class in glasscut) (class in glasscut.dataset) (class in glasscut.dataset.live) load_processed_json() (glasscut.storage.manager.StorageOrganizer method) (glasscut.storage.StorageOrganizer method) load_slide() (glasscut.data.fetcher.DataFetcher method) load_slide_metadata() (glasscut.storage.manager.StorageOrganizer method) (glasscut.storage.StorageOrganizer method)

M

MacenkoStainNormalizer (class in glasscut) (class in glasscut.stain_normalizers) (class in glasscut.stain_normalizers.macenko) magnification (glasscut.storage.structures.TileMetadata attribute) (glasscut.storage.TileMetadata attribute) magnification_to_level() (in module glasscut.slides.utils) MagnificationError magnifications (glasscut.dataset.live.LiveSlideSample attribute), [1] (glasscut.dataset.LiveSlideSample attribute), [1] (glasscut.LiveSlideSample attribute), [1] (glasscut.Slide property) (glasscut.slides.Slide property) (glasscut.slides.slide.Slide property) module glasscut, [1] glasscut.data glasscut.data.fetcher glasscut.data.registry glasscut.dataset glasscut.dataset.generator glasscut.dataset.live glasscut.exceptions glasscut.slides glasscut.slides.backends glasscut.slides.backends.base glasscut.slides.backends.cucim_backend glasscut.slides.backends.openslide_backend glasscut.slides.slide glasscut.slides.utils glasscut.stain_normalizers glasscut.stain_normalizers.base glasscut.stain_normalizers.macenko glasscut.stain_normalizers.reinhardt glasscut.storage glasscut.storage.manager glasscut.storage.structures glasscut.tile glasscut.tiler glasscut.tiler.base glasscut.tiler.grid glasscut.tissue_detectors glasscut.tissue_detectors.base glasscut.tissue_detectors.otsu glasscut.utils

mpp (glasscut.dataset.live.LiveSlideSample attribute), [1] (glasscut.dataset.LiveSlideSample attribute), [1] (glasscut.LiveSlideSample attribute), [1] (glasscut.Slide property) (glasscut.slides.backends.base.SlideBackend property) (glasscut.slides.backends.cucim_backend.CuCimBackend property) (glasscut.slides.backends.CuCimBackend property) (glasscut.slides.backends.openslide_backend.OpenSlideBackend property) (glasscut.slides.backends.OpenSlideBackend property) (glasscut.slides.backends.SlideBackend property) (glasscut.slides.Slide property) (glasscut.slides.slide.Slide property) (glasscut.storage.SlideMetadata attribute) (glasscut.storage.structures.SlideMetadata attribute)

N

name (glasscut.Slide property) (glasscut.slides.Slide property) (glasscut.slides.slide.Slide property) np_to_pil() (in module glasscut.utils) num_levels (glasscut.slides.backends.base.SlideBackend property) (glasscut.slides.backends.cucim_backend.CuCimBackend property) (glasscut.slides.backends.CuCimBackend property) (glasscut.slides.backends.openslide_backend.OpenSlideBackend property) (glasscut.slides.backends.OpenSlideBackend property) (glasscut.slides.backends.SlideBackend property)

O

open() (glasscut.slides.backends.base.SlideBackend method) (glasscut.slides.backends.cucim_backend.CuCimBackend method) (glasscut.slides.backends.CuCimBackend method) (glasscut.slides.backends.openslide_backend.OpenSlideBackend method) (glasscut.slides.backends.OpenSlideBackend method) (glasscut.slides.backends.SlideBackend method)

OpenSlideBackend (class in glasscut.slides.backends) (class in glasscut.slides.backends.openslide_backend) OtsuTissueDetector (class in glasscut) (class in glasscut.tissue_detectors) (class in glasscut.tissue_detectors.otsu) ovarian_tissue() (in module glasscut.data)

P

phase() (glasscut.utils.Profiler method) phases (glasscut.utils.Profiler property) PoochProtocol (class in glasscut.data.fetcher) print_profile() (glasscut.GridTiler method) (glasscut.tiler.grid.GridTiler method) (glasscut.tiler.GridTiler method) print_summary() (glasscut.utils.Profiler method) process_dataset() (glasscut.dataset.DatasetGenerator method) (glasscut.dataset.generator.DatasetGenerator method) (glasscut.DatasetGenerator method) Profiler (class in glasscut.utils)

properties (glasscut.Slide property) (glasscut.slides.backends.base.SlideBackend property) (glasscut.slides.backends.cucim_backend.CuCimBackend property) (glasscut.slides.backends.CuCimBackend property) (glasscut.slides.backends.openslide_backend.OpenSlideBackend property) (glasscut.slides.backends.OpenSlideBackend property) (glasscut.slides.backends.SlideBackend property) (glasscut.slides.Slide property) (glasscut.slides.slide.Slide property) prostate_tissue() (in module glasscut.data) pup (glasscut.data.fetcher.DataFetcher attribute)

R

read_region() (glasscut.slides.backends.base.SlideBackend method) (glasscut.slides.backends.cucim_backend.CuCimBackend method) (glasscut.slides.backends.cucim_backend.CuImageProtocol method) (glasscut.slides.backends.CuCimBackend method) (glasscut.slides.backends.openslide_backend.OpenSlideBackend method) (glasscut.slides.backends.OpenSlideBackend method) (glasscut.slides.backends.SlideBackend method)

record() (glasscut.utils.Profiler method) ReinhardtStainNormalizer (class in glasscut) (class in glasscut.stain_normalizers) (class in glasscut.stain_normalizers.reinhardt) reset() (glasscut.utils.Profiler method) rgb_to_lab() (glasscut.ReinhardtStainNormalizer static method) (glasscut.stain_normalizers.reinhardt.ReinhardtStainNormalizer static method) (glasscut.stain_normalizers.ReinhardtStainNormalizer static method)

S

save() (glasscut.Tile method) (glasscut.tile.Tile method) save_dataset_metadata() (glasscut.storage.manager.StorageOrganizer method) (glasscut.storage.StorageOrganizer method) save_processed_json() (glasscut.storage.manager.StorageOrganizer method) (glasscut.storage.StorageOrganizer method) save_slide_metadata() (glasscut.storage.manager.StorageOrganizer method) (glasscut.storage.StorageOrganizer method) set_precomputed_tissue_ratio() (glasscut.Tile method) (glasscut.tile.Tile method) shape (glasscut.slides.backends.cucim_backend.CuImageProtocol property) Slide (class in glasscut) (class in glasscut.slides) (class in glasscut.slides.slide) slide_id (glasscut.dataset.live.LiveSlideSample attribute), [1] (glasscut.dataset.LiveSlideSample attribute), [1] (glasscut.LiveSlideSample attribute), [1] (glasscut.storage.SlideMetadata attribute) (glasscut.storage.structures.SlideMetadata attribute) slide_name (glasscut.dataset.live.LiveSlideSample attribute), [1] (glasscut.dataset.LiveSlideSample attribute), [1] (glasscut.LiveSlideSample attribute), [1] (glasscut.storage.SlideMetadata attribute) (glasscut.storage.structures.SlideMetadata attribute)

slide_path (glasscut.dataset.live.LiveSlideSample attribute), [1] (glasscut.dataset.LiveSlideSample attribute), [1] (glasscut.LiveSlideSample attribute), [1] (glasscut.storage.SlideMetadata attribute) (glasscut.storage.structures.SlideMetadata attribute) SlideBackend (class in glasscut.slides.backends) (class in glasscut.slides.backends.base) SlideMetadata (class in glasscut.storage) (class in glasscut.storage.structures) SlidePropertyError slides (glasscut.storage.DatasetMetadata attribute) (glasscut.storage.structures.DatasetMetadata attribute) stain_color_map (glasscut.MacenkoStainNormalizer attribute), [1] (glasscut.stain_normalizers.macenko.MacenkoStainNormalizer attribute), [1] (glasscut.stain_normalizers.MacenkoStainNormalizer attribute), [1] stain_matrix() (glasscut.MacenkoStainNormalizer method) (glasscut.stain_normalizers.base.TransformerStainMatrixMixin method) (glasscut.stain_normalizers.macenko.MacenkoStainNormalizer method) (glasscut.stain_normalizers.MacenkoStainNormalizer method) (glasscut.stain_normalizers.TransformerStainMatrixMixin method) StainNormalizer (class in glasscut.stain_normalizers) (class in glasscut.stain_normalizers.base) StorageOrganizer (class in glasscut.storage) (class in glasscut.storage.manager) summary() (glasscut.utils.Profiler method)

T

target_means (glasscut.ReinhardtStainNormalizer attribute) (glasscut.stain_normalizers.reinhardt.ReinhardtStainNormalizer attribute) (glasscut.stain_normalizers.ReinhardtStainNormalizer attribute) target_stds (glasscut.ReinhardtStainNormalizer attribute) (glasscut.stain_normalizers.reinhardt.ReinhardtStainNormalizer attribute) (glasscut.stain_normalizers.ReinhardtStainNormalizer attribute) thumbnail (glasscut.Slide property) (glasscut.slides.Slide property) (glasscut.slides.slide.Slide property) Tile (class in glasscut) (class in glasscut.tile) tile_id (glasscut.storage.structures.TileMetadata attribute) (glasscut.storage.TileMetadata attribute) tile_size (glasscut.storage.SlideMetadata attribute) (glasscut.storage.structures.SlideMetadata attribute) TileMetadata (class in glasscut.storage) (class in glasscut.storage.structures) Tiler (class in glasscut) (class in glasscut.tiler) (class in glasscut.tiler.base) tiler_name (glasscut.storage.SlideMetadata attribute) (glasscut.storage.structures.SlideMetadata attribute) tiles (glasscut.dataset.live.LiveSlideSample attribute), [1] (glasscut.dataset.LiveSlideSample attribute), [1] (glasscut.LiveSlideSample attribute), [1] (glasscut.storage.SlideMetadata attribute) (glasscut.storage.structures.SlideMetadata attribute)

TileSizeOrCoordinatesError timestamp (glasscut.storage.SlideMetadata attribute) (glasscut.storage.structures.SlideMetadata attribute) tissue_mask (glasscut.Tile property) (glasscut.tile.Tile property) tissue_ratio (glasscut.storage.structures.TileMetadata attribute) (glasscut.storage.TileMetadata attribute) (glasscut.Tile property) (glasscut.tile.Tile property) TissueDetector (class in glasscut.tissue_detectors) (class in glasscut.tissue_detectors.base) total_slides (glasscut.storage.DatasetMetadata attribute) (glasscut.storage.structures.DatasetMetadata attribute) total_tiles (glasscut.storage.DatasetMetadata attribute) (glasscut.storage.SlideMetadata attribute) (glasscut.storage.structures.DatasetMetadata attribute) (glasscut.storage.structures.SlideMetadata attribute) transform() (glasscut.ReinhardtStainNormalizer method) (glasscut.stain_normalizers.base.StainNormalizer method) (glasscut.stain_normalizers.base.TransformerStainMatrixMixin method) (glasscut.stain_normalizers.reinhardt.ReinhardtStainNormalizer method) (glasscut.stain_normalizers.ReinhardtStainNormalizer method) (glasscut.stain_normalizers.StainNormalizer method) (glasscut.stain_normalizers.TransformerStainMatrixMixin method) TransformerStainMatrixMixin (class in glasscut.stain_normalizers) (class in glasscut.stain_normalizers.base)

V

visualize() (glasscut.Tiler method) (glasscut.tiler.base.Tiler method) (glasscut.tiler.Tiler method)

W

width (glasscut.storage.structures.TileMetadata attribute) (glasscut.storage.TileMetadata attribute)

X

x (glasscut.storage.structures.TileMetadata attribute) (glasscut.storage.TileMetadata attribute)

Y

y (glasscut.storage.structures.TileMetadata attribute) (glasscut.storage.TileMetadata attribute)