Index

A

AggregationMethod (class in beast.utils) args (beast.file_readers.SlideReadException attribute) (beast.file_readers.TileReadException attribute) (beast.reinhard.ArrayTypeExcpeiton attribute)

ArrayTypeExcpeiton augment_colour() (beast.macenko.MacenkoStainAugmenter method) (beast.vahadane.VahadaneStainAugmenter method) augment_intensity() (beast.macenko.MacenkoStainAugmenter method) (beast.vahadane.VahadaneStainAugmenter method)

B

beast.file_readers module beast.file_writers module beast.macenko module beast.reinhard module

beast.tools module beast.utils module beast.vahadane module

C

convert_to_stain1() (beast.macenko.MacenkoTileNormaliser method) (beast.macenko.MacenkoWSINormaliser method) (beast.vahadane.VahadaneTileNormaliser method) (beast.vahadane.VahadaneWSINormaliser method) convert_to_stain2() (beast.macenko.MacenkoTileNormaliser method) (beast.macenko.MacenkoWSINormaliser method) (beast.vahadane.VahadaneTileNormaliser method) (beast.vahadane.VahadaneWSINormaliser method)

convert_to_stain_concentrations() (beast.macenko.MacenkoTileNormaliser method) (beast.macenko.MacenkoWSINormaliser method) (beast.vahadane.VahadaneTileNormaliser method) (beast.vahadane.VahadaneWSINormaliser method) count() (beast.utils.TileCoordinate method) (beast.utils.TileDimensions method)

E

estimate() (beast.tools.StainMetadataEstimator method)

F

fit() (beast.macenko.MacenkoStainAugmenter method) (beast.macenko.MacenkoTileNormaliser method) (beast.macenko.MacenkoWSINormaliser method) (beast.reinhard.ReinhardTileNormaliser method) (beast.reinhard.ReinhardWSINormaliser method) (beast.vahadane.VahadaneStainAugmenter method) (beast.vahadane.VahadaneTileNormaliser method) (beast.vahadane.VahadaneWSINormaliser method)

G

generate_tile_coordinates() (in module beast.utils) get_background_mask() (in module beast.utils)

get_mpp() (in module beast.file_writers) get_otsu_tissue_mask() (in module beast.utils) get_tissue_mask() (in module beast.utils)

I

index() (beast.utils.TileCoordinate method) (beast.utils.TileDimensions method)

IntensitySamplingMethod (class in beast.utils)

L

lab_luminosity_standardiser() (in module beast.utils) load_fit() (beast.macenko.MacenkoStainAugmenter method) (beast.macenko.MacenkoTileNormaliser method) (beast.macenko.MacenkoWSINormaliser method) (beast.reinhard.ReinhardTileNormaliser method) (beast.reinhard.ReinhardWSINormaliser method) (beast.tools.ParallelTileNormaliser method) (beast.tools.TesselatedWSINormaliser method) (beast.vahadane.VahadaneStainAugmenter method) (beast.vahadane.VahadaneTileNormaliser method) (beast.vahadane.VahadaneWSINormaliser method)

M

MacenkoStainAugmenter (class in beast.macenko) MacenkoTileNormaliser (class in beast.macenko) MacenkoWSINormaliser (class in beast.macenko) MAX (beast.utils.AggregationMethod attribute) (beast.utils.IntensitySamplingMethod attribute) MEAN (beast.utils.AggregationMethod attribute) (beast.utils.IntensitySamplingMethod attribute) MEDIAN (beast.utils.AggregationMethod attribute) (beast.utils.IntensitySamplingMethod attribute)

MIN (beast.utils.AggregationMethod attribute) (beast.utils.IntensitySamplingMethod attribute) module beast.file_readers beast.file_writers beast.macenko beast.reinhard beast.tools beast.utils beast.vahadane

N

normalise() (beast.macenko.MacenkoTileNormaliser method) (beast.macenko.MacenkoWSINormaliser method) (beast.reinhard.ReinhardTileNormaliser method) (beast.reinhard.ReinhardWSINormaliser method) (beast.tools.ParallelTileNormaliser method) (beast.tools.TesselatedWSINormaliser method) (beast.vahadane.VahadaneTileNormaliser method) (beast.vahadane.VahadaneWSINormaliser method)

P

ParallelTileNormaliser (class in beast.tools)

PERCENTILE (beast.utils.AggregationMethod attribute) (beast.utils.IntensitySamplingMethod attribute)

R

read_tile() (in module beast.file_readers) read_wsi() (in module beast.file_readers)

ReinhardTileNormaliser (class in beast.reinhard) ReinhardWSINormaliser (class in beast.reinhard) rgb_luminosity_standardiser() (in module beast.utils)

S

save_fit() (beast.macenko.MacenkoStainAugmenter method) (beast.macenko.MacenkoTileNormaliser method) (beast.macenko.MacenkoWSINormaliser method) (beast.reinhard.ReinhardTileNormaliser method) (beast.reinhard.ReinhardWSINormaliser method) (beast.tools.StainMetadataEstimator method) (beast.vahadane.VahadaneStainAugmenter method) (beast.vahadane.VahadaneTileNormaliser method) (beast.vahadane.VahadaneWSINormaliser method)

SlideReadException StainMetadataEstimator (class in beast.tools)

T

TesselatedWSINormaliser (class in beast.tools) TileCoordinate (class in beast.utils)

TileDimensions (class in beast.utils) TileReadException

V

VahadaneStainAugmenter (class in beast.vahadane)

VahadaneTileNormaliser (class in beast.vahadane) VahadaneWSINormaliser (class in beast.vahadane)

W

with_traceback() (beast.file_readers.SlideReadException method) (beast.file_readers.TileReadException method) (beast.reinhard.ArrayTypeExcpeiton method)

write_ome_tiff() (in module beast.file_writers) write_tile() (in module beast.file_writers)

X

x (beast.utils.TileDimensions attribute)

xend (beast.utils.TileCoordinate attribute) xstart (beast.utils.TileCoordinate attribute)

Y

y (beast.utils.TileDimensions attribute)

yend (beast.utils.TileCoordinate attribute) ystart (beast.utils.TileCoordinate attribute)