Index B | C | D | F | G | H | I | L | M | N | P | R | S | T | U | V 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 IDENTITY_MEAN (spora_io.datasets.he.HEImagingDataset attribute) (spora_io.datasets.ihc.SingleIHCImagingDataset attribute) IDENTITY_STD (spora_io.datasets.he.HEImagingDataset attribute) (spora_io.datasets.ihc.SingleIHCImagingDataset attribute) 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)