Index _ | A | B | C | D | E | F | G | H | I | J | L | M | N | O | P | R | S | T | W _ __call__() (AlbuStrongAugment method) (ApplyEach method) (BinarizeTransform method) (CellposeTransform method) (ContourTransform method) (DistTransform method) (EdgeWeightTransform method) (HoverNetTransform method) (OmniposeTransform method) (SmoothDistTransform method) (StardistTransform method) __getitem__() (FolderDatasetInfer method) (HDF5DatasetInfer method) (SpotCoordinates method) (TileCoordinates method) (TrainDatasetFolder method) (TrainDatasetH5 method) (WSIDatasetInfer method) __iter__() (SpotCoordinates method) (TileCoordinates method) __len__() (FolderDatasetInfer method) (HDF5DatasetInfer method) (SpotCoordinates method) (TileCoordinates method) (TrainDatasetFolder method) (TrainDatasetH5 method) (WSIDatasetInfer method) A accuracy() (in module cellseg_models_pytorch.metrics) accuracy_multiclass() (in module cellseg_models_pytorch.metrics) aggregated_jaccard_index() (in module cellseg_models_pytorch.metrics) AlbuStrongAugment (class in cellseg_models_pytorch.transforms.albu_transforms) ApplyEach (class in cellseg_models_pytorch.transforms.albu_transforms) average_precision() (in module cellseg_models_pytorch.metrics) B backend_name (SlideReader property) BCELoss (class in cellseg_models_pytorch.losses) BinarizeTransform (class in cellseg_models_pytorch.transforms.albu_transforms) C CellPose (class in cellseg_models_pytorch.models.cellpose) cellpose_nuclei() (in module cellseg_models_pytorch.models.cellpose.cellpose_unet) CellposeTransform (class in cellseg_models_pytorch.transforms.albu_transforms) CellPoseUnet (class in cellseg_models_pytorch.models.cellpose.cellpose_unet) CellVit (class in cellseg_models_pytorch.models.cellvit) cellvit_nuclei() (in module cellseg_models_pytorch.models.cellvit.cellvit_unet) CellVitSamUnet (class in cellseg_models_pytorch.models.cellvit.cellvit_unet) CELoss (class in cellseg_models_pytorch.losses) ContourTransform (class in cellseg_models_pytorch.transforms.albu_transforms) coordinates (cellseg_models_pytorch.wsi.data.SpotCoordinates attribute) (cellseg_models_pytorch.wsi.data.TileCoordinates attribute) D data_bounds (SlideReader property) device (cellseg_models_pytorch.models.cellpose.CellPose attribute) (cellseg_models_pytorch.models.cellvit.CellVit attribute) (cellseg_models_pytorch.models.hovernet.HoverNet attribute) (cellseg_models_pytorch.models.instanseg.InstanSeg attribute) (cellseg_models_pytorch.models.stardist.StarDist attribute) dice2() (in module cellseg_models_pytorch.metrics) dice_coef() (in module cellseg_models_pytorch.metrics) dice_multiclass() (in module cellseg_models_pytorch.metrics) DiceLoss (class in cellseg_models_pytorch.losses) dimensions (SlideReader property) DistTransform (class in cellseg_models_pytorch.transforms.albu_transforms) E EdgeWeightTransform (class in cellseg_models_pytorch.transforms.albu_transforms) enc_name (cellseg_models_pytorch.models.cellpose.cellpose_unet.CellPoseUnet attribute) (cellseg_models_pytorch.models.cellvit.cellvit_unet.CellVitSamUnet attribute) (cellseg_models_pytorch.models.hovernet.hovernet_unet.HoverNetUnet attribute) (cellseg_models_pytorch.models.instanseg.InstanSegUnet attribute) (cellseg_models_pytorch.models.stardist.stardist_unet.StarDistUnet attribute) export_cellpose_onnx() (in module cellseg_models_pytorch.models.cellpose) export_cellvit_onnx() (in module cellseg_models_pytorch.models.cellvit) export_hovernet_onnx() (in module cellseg_models_pytorch.models.hovernet) export_instanseg_onnx() (in module cellseg_models_pytorch.models.instanseg) export_onnx() (CellPose method) (CellVit method) (HoverNet method) (InstanSeg method) (StarDist method) export_stardist_onnx() (in module cellseg_models_pytorch.models.stardist) F f1score() (in module cellseg_models_pytorch.metrics) f1score_multiclass() (in module cellseg_models_pytorch.metrics) FileHandler (class in cellseg_models_pytorch.utils) filter_nuclei() (in module cellseg_models_pytorch.wsi.inst_merger) float2ubyte() (in module cellseg_models_pytorch.transforms) FocalLoss (class in cellseg_models_pytorch.losses) FolderDatasetInfer (class in cellseg_models_pytorch.torch_datasets) forward() (BCELoss method) (CellPoseUnet method) (CellVitSamUnet method) (CELoss method) (DiceLoss method) (FocalLoss method) (HoverNetUnet method) (InstanSegCriterion method) (InstanSegUnet method) (IoULoss method) (JointLoss method) (Loss method) (MAE method) (MSE method) (MSSSIM method) (MultiTaskLoss method) (SCELoss method) (SSIM method) (StarDistUnet method) (TverskyLoss method) from_pretrained() (CellPose class method) (CellVit class method) (HoverNet class method) (InstanSeg class method) (StarDist class method) G gdf_to_file() (FileHandler static method) gen_contour_maps() (in module cellseg_models_pytorch.transforms) gen_dist_maps() (in module cellseg_models_pytorch.transforms) gen_flow_maps() (in module cellseg_models_pytorch.transforms) gen_hv_maps() (in module cellseg_models_pytorch.transforms) gen_omni_flow_maps() (in module cellseg_models_pytorch.transforms) gen_stardist_maps() (in module cellseg_models_pytorch.transforms) gen_weight_maps() (in module cellseg_models_pytorch.transforms) get_annotated_thumbnail() (SlideReader method) get_properties() (TileCoordinates method) get_spot_coordinates() (SlideReader method) get_stats() (in module cellseg_models_pytorch.metrics) get_tile_coordinates() (SlideReader method) get_tissue_mask() (SlideReader method) H HDF5DatasetInfer (class in cellseg_models_pytorch.torch_datasets.hdf5_dataset_infer) height (cellseg_models_pytorch.wsi.data.TileCoordinates attribute) HoverNet (class in cellseg_models_pytorch.models.hovernet) hovernet_nuclei() (in module cellseg_models_pytorch.models.hovernet.hovernet_unet) HoverNetTransform (class in cellseg_models_pytorch.transforms.albu_transforms) HoverNetUnet (class in cellseg_models_pytorch.models.hovernet.hovernet_unet) I inference_mode (cellseg_models_pytorch.models.cellpose.CellPose attribute) (cellseg_models_pytorch.models.cellvit.CellVit attribute) (cellseg_models_pytorch.models.hovernet.HoverNet attribute) (cellseg_models_pytorch.models.instanseg.InstanSeg attribute) (cellseg_models_pytorch.models.stardist.StarDist attribute) InstanSeg (class in cellseg_models_pytorch.models.instanseg) instanseg_nuclei() (in module cellseg_models_pytorch.models.instanseg) InstanSegCriterion (class in cellseg_models_pytorch.losses.criterions.instanseg) InstanSegUnet (class in cellseg_models_pytorch.models.instanseg) InstMerger (class in cellseg_models_pytorch.wsi.inst_merger) iou_multiclass() (in module cellseg_models_pytorch.metrics) iou_score() (in module cellseg_models_pytorch.metrics) IoULoss (class in cellseg_models_pytorch.losses) J JointLoss (class in cellseg_models_pytorch.losses) L level_count (SlideReader property) level_dimensions (SlideReader property) level_downsamples (SlideReader property) level_from_dimensions() (SlideReader method) level_from_max_dimension() (SlideReader method) Loss (class in cellseg_models_pytorch.losses) M MAE (class in cellseg_models_pytorch.losses) max_background (cellseg_models_pytorch.wsi.data.TileCoordinates attribute) merge() (InstMerger method) merge_instances() (WsiSegmenter method) minmax_normalize() (in module cellseg_models_pytorch.transforms) MinMaxNormalization (class in cellseg_models_pytorch.transforms.albu_transforms) model (cellseg_models_pytorch.models.cellpose.CellPose attribute) (cellseg_models_pytorch.models.cellvit.CellVit attribute) (cellseg_models_pytorch.models.hovernet.HoverNet attribute) (cellseg_models_pytorch.models.instanseg.InstanSeg attribute) (cellseg_models_pytorch.models.stardist.StarDist attribute) MSE (class in cellseg_models_pytorch.losses) MSSSIM (class in cellseg_models_pytorch.losses) MultiTaskLoss (class in cellseg_models_pytorch.losses) N name (BinarizeTransform attribute) (CellposeTransform attribute) (ContourTransform attribute) (DistTransform attribute) (EdgeWeightTransform attribute) (HoverNetTransform attribute) (OmniposeTransform attribute) (SlideReader property) (SmoothDistTransform attribute) (StardistTransform attribute) names (ApplyEach attribute) Normalization (class in cellseg_models_pytorch.transforms.albu_transforms) normalize() (in module cellseg_models_pytorch.transforms) O omnipose_nuclei() (in module cellseg_models_pytorch.models.cellpose.cellpose_unet) OmniposeTransform (class in cellseg_models_pytorch.transforms.albu_transforms) out_channels (ApplyEach attribute) (BinarizeTransform attribute) (CellposeTransform attribute) (ContourTransform attribute) (DistTransform attribute) (EdgeWeightTransform attribute) (HoverNetTransform attribute) (OmniposeTransform attribute) (SmoothDistTransform attribute) (StardistTransform attribute) overlap (cellseg_models_pytorch.wsi.data.TileCoordinates attribute) P pairwise_object_stats() (in module cellseg_models_pytorch.metrics) pairwise_pixel_stats() (in module cellseg_models_pytorch.metrics) panoptic_quality() (in module cellseg_models_pytorch.metrics) path (SlideReader property) percentile_normalize() (in module cellseg_models_pytorch.transforms) percentile_normalize99() (in module cellseg_models_pytorch.transforms) PercentileNormalization (class in cellseg_models_pytorch.transforms.albu_transforms) pixel_size (SlideReader property) post_process() (CellPose method) (CellVit method) (HoverNet method) (InstanSeg method) (StarDist method) post_processor (cellseg_models_pytorch.models.cellpose.CellPose attribute) (cellseg_models_pytorch.models.cellvit.CellVit attribute) (cellseg_models_pytorch.models.hovernet.HoverNet attribute) (cellseg_models_pytorch.models.instanseg.InstanSeg attribute) (cellseg_models_pytorch.models.stardist.StarDist attribute) postproc_inst() (PostProcessor method) postproc_parallel() (PostProcessor method) postproc_parallel_async() (PostProcessor method) postproc_serial() (PostProcessor method) postproc_tissuemap() (PostProcessor method) PostProcessor (class in cellseg_models_pytorch.inference.post_processor) predict() (CellPose method) (CellVit method) (HoverNet method) (InstanSeg method) (Predictor method) (StarDist method) predict_sliding_win() (Predictor method) Predictor (class in cellseg_models_pytorch.inference.predictor) R read_h5() (FileHandler static method) read_img() (FileHandler static method) read_level() (SlideReader method) read_mat() (FileHandler static method) read_region() (SlideReader method) S SCELoss (class in cellseg_models_pytorch.losses.criterions.sce) segment() (WsiSegmenter method) sensitivity_multiclass() (in module cellseg_models_pytorch.metrics) set_inference_mode() (CellPose method) (CellVit method) (HoverNet method) (InstanSeg method) (StarDist method) SlideReader (class in cellseg_models_pytorch.wsi) smooth_distance() (in module cellseg_models_pytorch.transforms.functional) SmoothDistTransform (class in cellseg_models_pytorch.transforms.albu_transforms) SoftInstanceOutput (class in cellseg_models_pytorch.decoders.multitask_decoder) SoftSemanticOutput (class in cellseg_models_pytorch.decoders.multitask_decoder) specificity_multiclass() (in module cellseg_models_pytorch.metrics) spot_names (cellseg_models_pytorch.wsi.data.SpotCoordinates attribute) SpotCoordinates (class in cellseg_models_pytorch.wsi.data) SSIM (class in cellseg_models_pytorch.losses) StarDist (class in cellseg_models_pytorch.models.stardist) stardist_nuclei() (in module cellseg_models_pytorch.models.stardist.stardist_unet) StardistTransform (class in cellseg_models_pytorch.transforms.albu_transforms) StarDistUnet (class in cellseg_models_pytorch.models.stardist.stardist_unet) suffix (SlideReader property) T TileCoordinates (class in cellseg_models_pytorch.wsi.data) tissue_mask (cellseg_models_pytorch.wsi.data.SpotCoordinates attribute) (cellseg_models_pytorch.wsi.data.TileCoordinates attribute) to_mat() (FileHandler static method) TrainDatasetFolder (class in cellseg_models_pytorch.torch_datasets) TrainDatasetH5 (class in cellseg_models_pytorch.torch_datasets) TverskyLoss (class in cellseg_models_pytorch.losses) W width (cellseg_models_pytorch.wsi.data.TileCoordinates attribute) write_img() (FileHandler static method) WSIDatasetInfer (class in cellseg_models_pytorch.torch_datasets) WsiSegmenter (class in cellseg_models_pytorch.inference.wsi_segmenter)
