Index

B

BaseImagingDataset (class in spora_io.datasets.base)

best_mask_tiling_try_to_stop() (in module spora_io.utils.helpers.tile)

C

CellMask (class in spora_io.datasets._types)

ComposedImagingDataset (class in spora_io.datasets.compose) ComposedTissue (class in spora_io.datasets._types)

D

disable_quantile_mask (spora_io.datasets.multiplex.MultiplexImagingDataset attribute)

F

filter_list (spora_io.datasets.multiplex.MultiplexImagingDataset attribute)

FilterFactory (class in spora_io.utils.dataset.transforms)

G

get_available_modalities() (spora_io.datasets.compose.ComposedImagingDataset method) get_cell_instance_mask() (spora_io.datasets.base.BaseImagingDataset method) get_cell_task_mask() (spora_io.datasets.base.BaseImagingDataset method) get_cell_task_mask_types() (spora_io.datasets.base.BaseImagingDataset method) get_channel_names() (spora_io.datasets.multiplex.MultiplexImagingDataset method) get_composed_tile() (spora_io.datasets.compose.ComposedImagingDataset method) get_composed_tissue() (spora_io.datasets.compose.ComposedImagingDataset method) get_composed_tissue_by_patient() (spora_io.datasets.compose.ComposedImagingDataset method) get_dataset() (spora_io.datasets.compose.ComposedImagingDataset method) get_datasets_dir() (in module spora_io._config) get_grid_tile() (in module spora_io.utils.helpers.tile) get_modalities_of_dataset() (in module spora_io.utils.utils) get_modalities_of_tissue() (spora_io.datasets.compose.ComposedImagingDataset method) get_tile() (spora_io.datasets.base.BaseImagingDataset method) (spora_io.datasets.he.HEImagingDataset method) (spora_io.datasets.ihc.SingleIHCImagingDataset method) (spora_io.datasets.multiplex.MultiplexImagingDataset method)

get_tile_by_coordinates() (spora_io.datasets.base.BaseImagingDataset method) (spora_io.datasets.he.HEImagingDataset method) (spora_io.datasets.ihc.SingleIHCImagingDataset method) (spora_io.datasets.multiplex.MultiplexImagingDataset method) get_tissue() (spora_io.datasets.base.BaseImagingDataset method) (spora_io.datasets.he.HEImagingDataset method) (spora_io.datasets.ihc.SingleIHCImagingDataset method) (spora_io.datasets.multiplex.MultiplexImagingDataset method) get_tissue_by_patient() (spora_io.datasets.base.BaseImagingDataset method) get_tissue_ids() (spora_io.datasets.base.BaseImagingDataset method) (spora_io.datasets.compose.ComposedImagingDataset method) get_tissue_mask() (spora_io.datasets.base.BaseImagingDataset method) get_unimodal_tile() (spora_io.datasets.compose.ComposedImagingDataset method) get_unimodal_tissue() (spora_io.datasets.compose.ComposedImagingDataset method) get_unimodal_tissue_mask() (spora_io.datasets.compose.ComposedImagingDataset method) get_unimodal_tissue_size() (spora_io.datasets.compose.ComposedImagingDataset method) get_uniprot_ids() (spora_io.datasets.multiplex.MultiplexImagingDataset method)

H

HEImagingDataset (class in spora_io.datasets.he) HETissue (class in spora_io.datasets._types) HIBOU_MEAN (spora_io.datasets.he.HEImagingDataset attribute) (spora_io.datasets.ihc.SingleIHCImagingDataset attribute)

HIBOU_STD (spora_io.datasets.he.HEImagingDataset attribute) (spora_io.datasets.ihc.SingleIHCImagingDataset attribute)

I

IHCTissue (class in spora_io.datasets._types) IMAGENET_MEAN (spora_io.datasets.he.HEImagingDataset attribute) (spora_io.datasets.ihc.SingleIHCImagingDataset attribute)

IMAGENET_STD (spora_io.datasets.he.HEImagingDataset attribute) (spora_io.datasets.ihc.SingleIHCImagingDataset attribute)

L

label (spora_io.datasets.base.BaseImagingDataset attribute) label_modifying_fn (spora_io.datasets.base.BaseImagingDataset attribute)

label_type (spora_io.datasets.base.BaseImagingDataset attribute) labels_to_keep (spora_io.datasets.base.BaseImagingDataset attribute)

M

mean_std_type (spora_io.datasets.he.HEImagingDataset attribute) (spora_io.datasets.ihc.SingleIHCImagingDataset attribute)

modality (spora_io.datasets.base.BaseImagingDataset attribute) MultiplexImagingDataset (class in spora_io.datasets.multiplex) MultiplexTissue (class in spora_io.datasets._types)

N

name (spora_io.datasets.base.BaseImagingDataset attribute)

P

path (spora_io.datasets.base.BaseImagingDataset attribute)

R

replace_nuclear_uniprot_ids (spora_io.datasets.multiplex.MultiplexImagingDataset attribute)

resolution (spora_io.datasets.base.BaseImagingDataset attribute) return_uniprot_ids (spora_io.datasets.multiplex.MultiplexImagingDataset attribute)

S

SingleIHCImagingDataset (class in spora_io.datasets.ihc)

SporaDataset (class in spora_io.datasets.spora) standardization (spora_io.datasets.multiplex.MultiplexImagingDataset attribute)

T

Tile (class in spora_io.utils.helpers.tile) tile_size (spora_io.datasets.base.BaseImagingDataset attribute)

tile_strategy (spora_io.datasets.base.BaseImagingDataset attribute) TissueMask (class in spora_io.datasets._types)

U

use_mean_std (spora_io.datasets.multiplex.MultiplexImagingDataset attribute)

V

VALID_MODALITIES (spora_io.datasets.multiplex.MultiplexImagingDataset attribute)