Index

A

a_cls (dlup.annotations.AnnotationClass attribute) AbstractSlideBackend (class in dlup.backends.common) annotation_class (dlup.annotations.Point property) (dlup.annotations.Polygon property) (dlup.annotations.SingleAnnotationWrapper property) annotation_data (dlup.data.dataset.TileSampleWithAnnotationData attribute) AnnotationClass (class in dlup.annotations) AnnotationData (class in dlup.data.dataset) annotations (dlup.data.dataset.RegionFromWsiDatasetSample attribute) (dlup.data.dataset.TileSample attribute) AnnotationSorting (class in dlup.annotations)

AnnotationType (class in dlup.annotations) append() (dlup.annotations.SingleAnnotationWrapper method) ArrayEncoder (class in dlup.utils) as_geojson() (dlup.annotations.WsiAnnotations method) as_json() (dlup.annotations.SingleAnnotationWrapper method) as_list() (dlup.annotations.SingleAnnotationWrapper method) as_strtree() (dlup.annotations.SingleAnnotationWrapper method) aspect_ratio (dlup.SlideImage property) associated_images (dlup.experimental_backends.pyvips_backend.PyVipsSlide property) AUTODETECT() (dlup.experimental_backends.ImageBackend method) autodetect_backend() (in module dlup.experimental_backends)

B

BaseWsiDataset (class in dlup.data.dataset) BoundaryMode (class in dlup) bounding_box (dlup.annotations.WsiAnnotations property) bounding_boxes (dlup.annotations.SingleAnnotationWrapper property)

BOX (dlup.annotations.AnnotationType attribute) boxes (dlup.data.dataset.AnnotationData attribute) build_cli_logger() (in module dlup.logging) BY_AREA (dlup.annotations.AnnotationSorting attribute)

C

C (dlup.tiling.GridOrder attribute) CCITTFAX4 (dlup.writers.TiffCompression attribute) check_if_mpp_is_valid() (in module dlup.utils.image) close() (dlup.backends.common.AbstractSlideBackend method) (dlup.backends.tifffile_backend.TifffileSlide method) (dlup.experimental_backends.pyvips_backend.PyVipsSlide method) (dlup.SlideImage method) color_profile (dlup.backends.common.AbstractSlideBackend property) (dlup.experimental_backends.openslide_backend.OpenSlideSlide property) (dlup.experimental_backends.pyvips_backend.PyVipsSlide property) (dlup.SlideImage property) ConcatDataset (class in dlup.data.dataset)

ConcatSequences (class in dlup.tools) ContainsPolygonToLabel (class in dlup.data.transforms) convert_annotations() (in module dlup.data.transforms) ConvertAnnotationsToMask (class in dlup.data.transforms) coordinates (dlup.annotations.CoordinatesDict attribute) (dlup.data.dataset.RegionFromWsiDatasetSample attribute) (dlup.data.dataset.TileSample attribute) CoordinatesDict (class in dlup.annotations) copy() (dlup.annotations.WsiAnnotations method) crop (dlup.BoundaryMode attribute) (dlup.data.dataset.BaseWsiDataset property) cumsum() (dlup.data.dataset.ConcatDataset static method) cumulative_sizes (dlup.data.dataset.ConcatDataset attribute)

D

Dataset (class in dlup.data.dataset) dataset_to_polygon() (in module dlup.utils.mask) datasets (dlup.data.dataset.ConcatDataset attribute) default() (dlup.utils.ArrayEncoder method) DEFLATE (dlup.writers.TiffCompression attribute) dimensions (dlup.backends.common.AbstractSlideBackend property) dir_path() (in module dlup.cli) dlup module dlup.annotations module dlup.backends module dlup.backends.common module dlup.backends.tifffile_backend module dlup.background module dlup.cli module dlup.cli.mask module dlup.cli.wsi module dlup.data module dlup.data.dataset module dlup.data.transforms module

dlup.experimental_backends module dlup.experimental_backends.openslide_backend module dlup.experimental_backends.pyvips_backend module dlup.logging module dlup.tiling module dlup.tools module dlup.types module dlup.utils module dlup.utils.image module dlup.utils.imports module dlup.utils.mask module dlup.utils.pyvips_utils module dlup.utils.tifffile_utils module dlup.viz module dlup.viz.plotting module dlup.writers module

F

F (dlup.tiling.GridOrder attribute) features (dlup.annotations.GeoJsonDict attribute) file_path() (in module dlup.cli) filter() (dlup.annotations.WsiAnnotations method) from_asap_xml() (dlup.annotations.WsiAnnotations class method) from_darwin_json() (dlup.annotations.WsiAnnotations class method)

from_file_path() (dlup.SlideImage class method) from_geojson() (dlup.annotations.WsiAnnotations class method) from_halo_xml() (dlup.annotations.WsiAnnotations class method) from_pil() (dlup.writers.TifffileImageWriter method) from_standard_tiling() (dlup.data.dataset.TiledWsiDataset class method) from_tiles_iterator() (dlup.writers.TifffileImageWriter method) from_tiling() (dlup.tiling.Grid class method)

G

GeoJsonDict (class in dlup.annotations) get_best_level_for_downsample() (dlup.backends.common.AbstractSlideBackend method) get_closest_native_level() (dlup.SlideImage method) get_closest_native_mpp() (dlup.SlideImage method) get_mpp() (dlup.SlideImage method) get_scaled_size() (dlup.SlideImage method) get_scaled_slide_bounds() (dlup.SlideImage method) get_scaled_view() (dlup.SlideImage method) get_scaling() (dlup.SlideImage method)

get_thumbnail() (dlup.backends.common.AbstractSlideBackend method) (dlup.experimental_backends.openslide_backend.OpenSlideSlide method) (dlup.SlideImage method) get_tile() (in module dlup.utils.tifffile_utils) Grid (class in dlup.tiling) grid_index (dlup.data.dataset.RegionFromWsiDatasetSample attribute) grid_local_coordinates (dlup.data.dataset.RegionFromWsiDatasetSample attribute) GridOrder (class in dlup.tiling) grids (dlup.data.dataset.TiledWsiDataset property)

I

id (dlup.annotations.GeoJsonDict attribute) identifier (dlup.SlideImage property) image (dlup.data.dataset.RegionFromWsiDatasetSample attribute) (dlup.data.dataset.TileSample attribute) ImageBackend (class in dlup.experimental_backends)

ImageWriter (class in dlup.writers) index_to_dataset() (dlup.data.dataset.ConcatDataset method) indexed_ndmesh() (in module dlup.tiling) info() (in module dlup.cli.wsi) is_foreground() (in module dlup.background)

J

JP2K (dlup.writers.TiffCompression attribute)

JP2K_LOSSY (dlup.writers.TiffCompression attribute) JPEG (dlup.writers.TiffCompression attribute)

L

label (dlup.annotations.AnnotationClass attribute) (dlup.annotations.Point property) (dlup.annotations.Polygon property) (dlup.annotations.SingleAnnotationWrapper property) labels (dlup.data.dataset.RegionFromWsiDatasetSample attribute) (dlup.data.dataset.TileSample attribute)

level_count (dlup.backends.common.AbstractSlideBackend property) level_dimensions (dlup.backends.common.AbstractSlideBackend property) level_downsamples (dlup.backends.common.AbstractSlideBackend property) level_spacings (dlup.backends.common.AbstractSlideBackend property) LZW (dlup.writers.TiffCompression attribute)

M

magnification (dlup.backends.common.AbstractSlideBackend property) (dlup.backends.tifffile_backend.TifffileSlide property) (dlup.experimental_backends.openslide_backend.OpenSlideSlide property) (dlup.experimental_backends.pyvips_backend.PyVipsSlide property) (dlup.SlideImage property) main() (in module dlup.cli) MajorityClassToLabel (class in dlup.data.transforms) MapSequence (class in dlup.tools) mask (dlup.data.dataset.AnnotationData attribute) mask_to_polygon() (in module dlup.cli.mask) mask_to_polygons() (in module dlup.utils.mask) mode (dlup.backends.common.AbstractSlideBackend property) (dlup.experimental_backends.openslide_backend.OpenSlideSlide property) (dlup.experimental_backends.pyvips_backend.PyVipsSlide property) module dlup dlup.annotations dlup.backends dlup.backends.common dlup.backends.tifffile_backend dlup.background dlup.cli dlup.cli.mask dlup.cli.wsi dlup.data dlup.data.dataset dlup.data.transforms dlup.experimental_backends dlup.experimental_backends.openslide_backend dlup.experimental_backends.pyvips_backend dlup.logging dlup.tiling dlup.tools dlup.types dlup.utils dlup.utils.image dlup.utils.imports dlup.utils.mask dlup.utils.pyvips_utils dlup.utils.tifffile_utils dlup.viz dlup.viz.plotting dlup.writers

mpp (dlup.data.dataset.RegionFromWsiDatasetSample attribute) (dlup.data.dataset.TileSample attribute) (dlup.SlideImage property)

N

name (dlup.annotations.Point attribute) (dlup.annotations.Polygon attribute) NONE (dlup.annotations.AnnotationSorting attribute) (dlup.writers.TiffCompression attribute)

numpy_to_pil() (in module dlup.backends.common) numpy_to_vips() (in module dlup.utils.pyvips_utils)

O

offset_to_slide_bounds (dlup.annotations.WsiAnnotations property) open_slide() (in module dlup.backends.tifffile_backend) (in module dlup.experimental_backends.openslide_backend) (in module dlup.experimental_backends.pyvips_backend)

OPENSLIDE (dlup.experimental_backends.ImageBackend attribute) OpenSlideSlide (class in dlup.experimental_backends.openslide_backend) overflow (dlup.tiling.TilingMode attribute)

P

PACKBITS (dlup.writers.TiffCompression attribute) parse_rois() (in module dlup.data.dataset) path (dlup.data.dataset.BaseWsiDataset property) (dlup.data.dataset.RegionFromWsiDatasetSample attribute) (dlup.data.dataset.TileSample attribute) plot_2d() (in module dlup.viz.plotting) PNG (dlup.writers.TiffCompression attribute) Point (class in dlup.annotations) POINT (dlup.annotations.AnnotationType attribute)

points (dlup.data.dataset.AnnotationData attribute) Polygon (class in dlup.annotations) POLYGON (dlup.annotations.AnnotationType attribute) properties (dlup.backends.common.AbstractSlideBackend property) (dlup.backends.tifffile_backend.TifffileSlide property) (dlup.experimental_backends.pyvips_backend.PyVipsSlide property) (dlup.SlideImage property) PYVIPS (dlup.experimental_backends.ImageBackend attribute) PyVipsSlide (class in dlup.experimental_backends.pyvips_backend)

R

read_region() (dlup.annotations.WsiAnnotations method) (dlup.backends.common.AbstractSlideBackend method) (dlup.backends.tifffile_backend.TifffileSlide method) (dlup.experimental_backends.pyvips_backend.PyVipsSlide method) (dlup.RegionView method) (dlup.SlideImage method) region_index (dlup.data.dataset.RegionFromWsiDatasetSample attribute) (dlup.data.dataset.TileSample attribute) RegionFromWsiDatasetSample (class in dlup.data.dataset)

RegionView (class in dlup) register_parser() (in module dlup.cli.mask) (in module dlup.cli.wsi) relabel() (dlup.annotations.WsiAnnotations method) rename_labels() (in module dlup.data.transforms) RenameLabels (class in dlup.data.transforms) rescale_geometry() (in module dlup.annotations) REVERSE (dlup.annotations.AnnotationSorting attribute) roi (dlup.data.dataset.AnnotationData attribute)

S

set_cache() (dlup.backends.tifffile_backend.TifffileSlide method) (dlup.experimental_backends.pyvips_backend.PyVipsSlide method) setup_logging() (in module dlup.logging) shape() (in module dlup.annotations) simplify() (dlup.annotations.SingleAnnotationWrapper method) (dlup.annotations.WsiAnnotations method) SingleAnnotationWrapper (class in dlup.annotations) size (dlup.RegionView property) (dlup.SlideImage property) (dlup.tiling.Grid property)

skip (dlup.tiling.TilingMode attribute) slide_bounds (dlup.backends.common.AbstractSlideBackend property) (dlup.experimental_backends.openslide_backend.OpenSlideSlide property) (dlup.experimental_backends.pyvips_backend.PyVipsSlide property) (dlup.SlideImage property) slide_image (dlup.data.dataset.BaseWsiDataset property) SlideImage (class in dlup) spacing (dlup.backends.common.AbstractSlideBackend property) (dlup.experimental_backends.openslide_backend.OpenSlideSlide property) (dlup.experimental_backends.pyvips_backend.PyVipsSlide property)

T

thumbnail (dlup.SlideImage property) TiffCompression (class in dlup.writers) TIFFFILE (dlup.experimental_backends.ImageBackend attribute) TifffileImageWriter (class in dlup.writers) TifffileSlide (class in dlup.backends.tifffile_backend) TiledROIsSlideImageDataset (class in dlup.data.dataset) TiledWsiDataset (class in dlup.data.dataset) tiles_grid_coordinates() (in module dlup.tiling)

TileSample (class in dlup.data.dataset) TileSampleWithAnnotationData (class in dlup.data.dataset) TilingMode (class in dlup.tiling) type (dlup.annotations.CoordinatesDict attribute) (dlup.annotations.GeoJsonDict attribute) (dlup.annotations.Point property) (dlup.annotations.Polygon property) (dlup.annotations.SingleAnnotationWrapper property)

U

UnsupportedSlideError

V

vendor (dlup.backends.common.AbstractSlideBackend property) (dlup.backends.tifffile_backend.TifffileSlide property) (dlup.experimental_backends.openslide_backend.OpenSlideSlide property) (dlup.experimental_backends.pyvips_backend.PyVipsSlide property) (dlup.SlideImage property)

vips_to_numpy() (in module dlup.utils.pyvips_utils)

W

WEBP (dlup.writers.TiffCompression attribute)

wsi_indices (dlup.data.dataset.ConcatDataset attribute) WsiAnnotations (class in dlup.annotations)

Z

zero (dlup.BoundaryMode attribute)

ZSTD (dlup.writers.TiffCompression attribute)