Search.setIndex({"docnames": ["biscuit", "cellseg", "custom_extractors", "custom_loops", "dataloaders", "dataset", "dataset_features", "datasets_and_val", "evaluation", "features", "gan", "grad", "heatmap", "index", "installation", "io", "io_tensorflow", "io_torch", "mil", "mil_module", "model", "model_params", "model_tensorflow", "model_torch", "mosaic", "norm", "overview", "plugins", "posthoc", "project", "project_setup", "quickstart", "saliency", "segmentation", "simclr", "slide", "slide_processing", "slide_qc", "slideflow", "slideflow_cellseg", "slidemap", "ssl", "stats", "studio", "studio_module", "stylegan", "tfrecords", "tile_labels", "training", "troubleshooting", "tutorial1", "tutorial2", "tutorial3", "tutorial4", "tutorial5", "tutorial6", "tutorial7", "tutorial8", "uq", "util"], "filenames": ["biscuit.rst", "cellseg.rst", "custom_extractors.rst", "custom_loops.rst", "dataloaders.rst", "dataset.rst", "dataset_features.rst", "datasets_and_val.rst", "evaluation.rst", "features.rst", "gan.rst", "grad.rst", "heatmap.rst", "index.rst", "installation.rst", "io.rst", "io_tensorflow.rst", "io_torch.rst", "mil.rst", "mil_module.rst", "model.rst", "model_params.rst", "model_tensorflow.rst", "model_torch.rst", "mosaic.rst", "norm.rst", "overview.rst", "plugins.rst", "posthoc.rst", "project.rst", "project_setup.rst", "quickstart.rst", "saliency.rst", "segmentation.rst", "simclr.rst", "slide.rst", "slide_processing.rst", "slide_qc.rst", "slideflow.rst", "slideflow_cellseg.rst", "slidemap.rst", "ssl.rst", "stats.rst", "studio.rst", "studio_module.rst", "stylegan.rst", "tfrecords.rst", "tile_labels.rst", "training.rst", "troubleshooting.rst", "tutorial1.rst", "tutorial2.rst", "tutorial3.rst", "tutorial4.rst", "tutorial5.rst", "tutorial6.rst", "tutorial7.rst", "tutorial8.rst", "uq.rst", "util.rst"], "titles": ["slideflow.biscuit", "Cell Segmentation", "Custom Feature Extractors", "Custom Training Loops", "Dataloaders: Sampling and Augmentation", "slideflow.Dataset", "slideflow.DatasetFeatures", "Datasets", "Evaluation", "Generating Features", "slideflow.gan", "slideflow.grad", "slideflow.Heatmap", "Slideflow Documentation", "Installation", "slideflow.io", "slideflow.io.tensorflow", "slideflow.io.torch", "Multiple-Instance Learning (MIL)", "slideflow.mil", "slideflow.model", "slideflow.ModelParams", "slideflow.model.tensorflow", "slideflow.model.torch", "slideflow.Mosaic", "slideflow.norm", "Overview", "Creating a Slideflow Plugin", "Layer Activations", "slideflow.Project", "Setting up a Project", "Quickstart", "Saliency Maps", "Tissue Segmentation", "slideflow.simclr", "slideflow.slide", "Slide Processing", "slideflow.slide.qc", "slideflow", "slideflow.cellseg", "slideflow.SlideMap", "Self-Supervised Learning (SSL)", "slideflow.stats", "Slideflow Studio: Live Visualization", "slideflow.studio", "Generative Networks (GANs)", "TFRecords: Reading and Writing", "Strong Supervision with Tile Labels", "Training", "Troubleshooting", 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"training-with-a-project"]], "Using a Trainer": [[48, "using-a-trainer"]], "Multiple outcomes": [[48, "multiple-outcomes"]], "Time-to-event / survival outcomes": [[48, "time-to-event-survival-outcomes"]], "Multimodal models": [[48, "multimodal-models"]], "Hyperparameter optimization": [[48, "hyperparameter-optimization"]], "Testing multiple combinations": [[48, "testing-multiple-combinations"]], "Grid-search sweep": [[48, "grid-search-sweep"]], "Bayesian optimization": [[48, "bayesian-optimization"]], "Customizing model or loss": [[48, "customizing-model-or-loss"]], "Using multiple GPUs": [[48, "using-multiple-gpus"]], "Training without TFRecords": [[48, "training-without-tfrecords"]], "Monitoring performance": [[48, "monitoring-performance"]], "Tensorboard": [[48, "tensorboard"]], "Neptune.ai": [[48, "neptune-ai"]], "Troubleshooting": [[49, "troubleshooting"]], "Testing": [[49, "testing"]], "Issue Reporting": [[49, "issue-reporting"]], "Tutorial 1: Model training (simple)": [[50, "tutorial-1-model-training-simple"]], "Create a Project": [[50, "create-a-project"]], "Setting up annotations": [[50, "setting-up-annotations"]], "Monitoring with Tensorboard": [[50, "monitoring-with-tensorboard"]], "Tutorial 2: Model training (advanced)": [[51, "tutorial-2-model-training-advanced"]], "Project Setup": [[51, "project-setup"]], "Creating a Dataset": [[51, "creating-a-dataset"]], "Tutorial 3: Using a custom architecture": [[52, "tutorial-3-using-a-custom-architecture"]], "Custom Tensorflow model": [[52, "custom-tensorflow-model"]], "Custom PyTorch model": [[52, "custom-pytorch-model"]], "Tutorial 4: Model evaluation & heatmaps": [[53, "tutorial-4-model-evaluation-heatmaps"]], "Locate a saved model": [[53, "locate-a-saved-model"], [54, "locate-a-saved-model"]], "From a dataset": [[53, "from-a-dataset"]], "Tutorial 5: Creating a mosaic map": [[54, "tutorial-5-creating-a-mosaic-map"]], "Train a model": [[54, "train-a-model"]], "Generate layer activations": [[54, "generate-layer-activations"]], "Create the mosaic map": [[54, "create-the-mosaic-map"]], "Save corresponding UMAPs": [[54, "save-corresponding-umaps"]], "Tutorial 6: Custom slide filtering": [[55, "tutorial-6-custom-slide-filtering"]], "Tutorial 7: Training with custom augmentations": [[56, "tutorial-7-training-with-custom-augmentations"]], "Tutorial 8: Multiple-Instance Learning": [[57, "tutorial-8-multiple-instance-learning"]], "Uncertainty Quantification": [[58, "uncertainty-quantification"]], "Training with UQ": [[58, "training-with-uq"]], "Evaluating with UQ": [[58, "evaluating-with-uq"]], "Uncertainty heatmaps": [[58, "uncertainty-heatmaps"]], "Uncertainty thresholding": [[58, "uncertainty-thresholding"]], "Prepare an Experiment": [[58, "prepare-an-experiment"]], "Train with cross-validation": [[58, "train-with-cross-validation"]], "Train inner cross-validation": [[58, "train-inner-cross-validation"]], "Apply thresholds to test set": [[58, "apply-thresholds-to-test-set"]], 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"slideflow.biscuit.utils.read_group_predictions"]], "results() (in module slideflow.biscuit.experiment)": [[0, "slideflow.biscuit.Experiment.results"]], "thresholds_from_nested_cv() (in module slideflow.biscuit.experiment)": [[0, "slideflow.biscuit.Experiment.thresholds_from_nested_cv"]], "train() (in module slideflow.biscuit.experiment)": [[0, "slideflow.biscuit.Experiment.train"]], "train_nested_cv() (in module slideflow.biscuit.experiment)": [[0, "slideflow.biscuit.Experiment.train_nested_cv"]], "truncate_colormap() (in module slideflow.biscuit.utils)": [[0, "slideflow.biscuit.utils.truncate_colormap"]], "dataset (class in slideflow)": [[5, "slideflow.Dataset"]], "balance() (in module slideflow.dataset)": [[5, "slideflow.Dataset.balance"]], "build_index() (in module slideflow.dataset)": [[5, "slideflow.Dataset.build_index"]], "cell_segmentation() (in module slideflow.dataset)": [[5, "slideflow.Dataset.cell_segmentation"]], "check_duplicates() (in module slideflow.dataset)": [[5, "slideflow.Dataset.check_duplicates"]], "clear_filters() (in module slideflow.dataset)": [[5, "slideflow.Dataset.clear_filters"]], "clip() (in module slideflow.dataset)": [[5, "slideflow.Dataset.clip"]], "convert_xml_rois() (in module slideflow.dataset)": [[5, "slideflow.Dataset.convert_xml_rois"]], "extract_cells() (in module slideflow.dataset)": [[5, "slideflow.Dataset.extract_cells"]], "extract_tiles() (in module slideflow.dataset)": [[5, "slideflow.Dataset.extract_tiles"]], "extract_tiles_from_tfrecords() (in module slideflow.dataset)": [[5, "slideflow.Dataset.extract_tiles_from_tfrecords"]], "filter() (in module slideflow.dataset)": [[5, "slideflow.Dataset.filter"]], "find_slide() (in module slideflow.dataset)": [[5, "slideflow.Dataset.find_slide"]], "find_tfrecord() (in module slideflow.dataset)": [[5, "slideflow.Dataset.find_tfrecord"]], "generate_feature_bags() (in module slideflow.dataset)": [[5, "slideflow.Dataset.generate_feature_bags"]], "get_bags() (in module 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"slideflow.Dataset.torch"]], "transform_tfrecords() (in module slideflow.dataset)": [[5, "slideflow.Dataset.transform_tfrecords"]], "unclip() (in module slideflow.dataset)": [[5, "slideflow.Dataset.unclip"]], "update_annotations_with_slidenames() (in module slideflow.dataset)": [[5, "slideflow.Dataset.update_annotations_with_slidenames"]], "update_manifest() (in module slideflow.dataset)": [[5, "slideflow.Dataset.update_manifest"]], "verify_annotations_slides() (in module slideflow.dataset)": [[5, "slideflow.Dataset.verify_annotations_slides"]], "verify_img_format() (in module slideflow.dataset)": [[5, "slideflow.Dataset.verify_img_format"]], "verify_slide_names() (in module slideflow.dataset)": [[5, "slideflow.Dataset.verify_slide_names"]], "datasetfeatures (class in slideflow)": [[6, "slideflow.DatasetFeatures"]], "activations_by_category() (in module slideflow.datasetfeatures)": [[6, "slideflow.DatasetFeatures.activations_by_category"]], "box_plots() (in module slideflow.datasetfeatures)": [[6, "slideflow.DatasetFeatures.box_plots"]], "concat() (in module slideflow.datasetfeatures)": [[6, "slideflow.DatasetFeatures.concat"]], "from_df() (in module slideflow.datasetfeatures)": [[6, "slideflow.DatasetFeatures.from_df"]], "load_cache() (in module slideflow.datasetfeatures)": [[6, "slideflow.DatasetFeatures.load_cache"]], "map_activations() (in module slideflow.datasetfeatures)": [[6, "slideflow.DatasetFeatures.map_activations"]], "map_predictions() (in module slideflow.datasetfeatures)": [[6, "slideflow.DatasetFeatures.map_predictions"]], "merge() (in module slideflow.datasetfeatures)": [[6, "slideflow.DatasetFeatures.merge"]], "remove_slide() (in module slideflow.datasetfeatures)": [[6, "slideflow.DatasetFeatures.remove_slide"]], "save_cache() (in module slideflow.datasetfeatures)": [[6, "slideflow.DatasetFeatures.save_cache"]], "save_example_tiles() (in module slideflow.datasetfeatures)": [[6, "slideflow.DatasetFeatures.save_example_tiles"]], "softmax_mean() (in module slideflow.datasetfeatures)": [[6, "slideflow.DatasetFeatures.softmax_mean"]], "softmax_percent() (in module slideflow.datasetfeatures)": [[6, "slideflow.DatasetFeatures.softmax_percent"]], "softmax_predict() (in module slideflow.datasetfeatures)": [[6, "slideflow.DatasetFeatures.softmax_predict"]], "stats() (in module slideflow.datasetfeatures)": [[6, "slideflow.DatasetFeatures.stats"]], "to_csv() (in module slideflow.datasetfeatures)": [[6, "slideflow.DatasetFeatures.to_csv"]], "to_df() (in module slideflow.datasetfeatures)": [[6, "slideflow.DatasetFeatures.to_df"]], "to_torch() (in module slideflow.datasetfeatures)": [[6, "slideflow.DatasetFeatures.to_torch"]], "stylegan2interpolator (class in slideflow.gan)": [[10, "slideflow.gan.StyleGAN2Interpolator"]], "__init__() (stylegan2interpolator method)": [[10, "slideflow.gan.StyleGAN2Interpolator.__init__"]], "class_interpolate() (stylegan2interpolator method)": [[10, "slideflow.gan.StyleGAN2Interpolator.class_interpolate"]], "crop() (in module slideflow.gan.utils)": [[10, "slideflow.gan.utils.crop"]], "generate() (stylegan2interpolator method)": [[10, "slideflow.gan.StyleGAN2Interpolator.generate"]], "generate_end() (stylegan2interpolator method)": [[10, "slideflow.gan.StyleGAN2Interpolator.generate_end"]], "generate_np_end() (stylegan2interpolator method)": [[10, "slideflow.gan.StyleGAN2Interpolator.generate_np_end"]], "generate_np_from_embedding() (stylegan2interpolator method)": [[10, "slideflow.gan.StyleGAN2Interpolator.generate_np_from_embedding"]], "generate_np_start() (stylegan2interpolator method)": [[10, "slideflow.gan.StyleGAN2Interpolator.generate_np_start"]], "generate_start() (stylegan2interpolator method)": [[10, "slideflow.gan.StyleGAN2Interpolator.generate_start"]], "generate_tf_end() (stylegan2interpolator method)": [[10, "slideflow.gan.StyleGAN2Interpolator.generate_tf_end"]], "generate_tf_from_embedding() (stylegan2interpolator method)": [[10, "slideflow.gan.StyleGAN2Interpolator.generate_tf_from_embedding"]], "generate_tf_start() (stylegan2interpolator method)": [[10, "slideflow.gan.StyleGAN2Interpolator.generate_tf_start"]], "interpolate_and_predict() (stylegan2interpolator method)": [[10, "slideflow.gan.StyleGAN2Interpolator.interpolate_and_predict"]], "linear_interpolate() (stylegan2interpolator method)": [[10, "slideflow.gan.StyleGAN2Interpolator.linear_interpolate"]], "module": [[10, "module-slideflow.gan"], [10, "module-slideflow.gan.utils"], [11, "module-slideflow.grad"], [16, "module-slideflow.io.tensorflow"], [17, "module-slideflow.io.torch"], [44, "module-slideflow.studio"], [59, "module-slideflow.util"]], "noise_tensor() (in module slideflow.gan.utils)": [[10, "slideflow.gan.utils.noise_tensor"]], "plot_comparison() (stylegan2interpolator method)": [[10, "slideflow.gan.StyleGAN2Interpolator.plot_comparison"]], "seed_search() (stylegan2interpolator method)": [[10, "slideflow.gan.StyleGAN2Interpolator.seed_search"]], "set_classifier() (stylegan2interpolator method)": [[10, "slideflow.gan.StyleGAN2Interpolator.set_classifier"]], "slideflow.gan": [[10, "module-slideflow.gan"]], "slideflow.gan.utils": [[10, "module-slideflow.gan.utils"]], "z() (stylegan2interpolator method)": [[10, "slideflow.gan.StyleGAN2Interpolator.z"]], "saliencymap (class in slideflow.grad)": [[11, "slideflow.grad.SaliencyMap"]], "__init__() (saliencymap method)": [[11, "slideflow.grad.SaliencyMap.__init__"]], "all() (saliencymap method)": [[11, "slideflow.grad.SaliencyMap.all"]], "blur_integrated_gradients() (saliencymap method)": [[11, "slideflow.grad.SaliencyMap.blur_integrated_gradients"]], "comparison_plot() (in module slideflow.grad)": [[11, "slideflow.grad.comparison_plot"]], "gradcam() (saliencymap method)": [[11, "slideflow.grad.SaliencyMap.gradcam"]], "grayscale() (in module slideflow.grad)": [[11, "slideflow.grad.grayscale"]], "guided_integrated_gradients() (saliencymap method)": [[11, "slideflow.grad.SaliencyMap.guided_integrated_gradients"]], "inferno() (in module slideflow.grad)": [[11, "slideflow.grad.inferno"]], "integrated_gradients() (saliencymap method)": [[11, "slideflow.grad.SaliencyMap.integrated_gradients"]], "multi_plot() (in module slideflow.grad)": [[11, "slideflow.grad.multi_plot"]], "oranges() (in module slideflow.grad)": [[11, "slideflow.grad.oranges"]], "overlay() (in module slideflow.grad)": [[11, "slideflow.grad.overlay"]], "saliency_map_comparison() (in module slideflow.grad)": [[11, "slideflow.grad.saliency_map_comparison"]], "slideflow.grad": [[11, "module-slideflow.grad"]], "vanilla() (saliencymap method)": [[11, "slideflow.grad.SaliencyMap.vanilla"]], "xrai() (saliencymap method)": [[11, "slideflow.grad.SaliencyMap.xrai"]], "xrai_fast() (saliencymap method)": [[11, "slideflow.grad.SaliencyMap.xrai_fast"]], "heatmap (class in slideflow)": [[12, "slideflow.Heatmap"]], "add_inset() (in module slideflow.heatmap)": [[12, "slideflow.Heatmap.add_inset"]], "clear_insets() (in module slideflow.heatmap)": [[12, "slideflow.Heatmap.clear_insets"]], "generate() (in module slideflow.heatmap)": [[12, "slideflow.Heatmap.generate"]], "load() (in module slideflow.heatmap)": [[12, "slideflow.Heatmap.load"]], "load_npz() (in module slideflow.heatmap)": [[12, "slideflow.Heatmap.load_npz"]], "plot() (in module slideflow.heatmap)": [[12, "slideflow.Heatmap.plot"]], "plot_thumbnail() (in module slideflow.heatmap)": [[12, "slideflow.Heatmap.plot_thumbnail"]], "plot_uncertainty() (in module slideflow.heatmap)": [[12, "slideflow.Heatmap.plot_uncertainty"]], "plot_with_logit_cmap() (in module slideflow.heatmap)": [[12, "slideflow.Heatmap.plot_with_logit_cmap"]], "save() (in module slideflow.heatmap)": [[12, "slideflow.Heatmap.save"]], "save_npz() (in module slideflow.heatmap)": [[12, "slideflow.Heatmap.save_npz"]], "view() (in module slideflow.heatmap)": [[12, "slideflow.Heatmap.view"]], "convert_dtype() (in module slideflow.io)": [[15, "slideflow.io.convert_dtype"]], "detect_tfrecord_format() (in module slideflow.io)": [[15, "slideflow.io.detect_tfrecord_format"]], "extract_tiles() (in module slideflow.io)": [[15, "slideflow.io.extract_tiles"]], "generate_crossfolds() (in module slideflow.io.preservedsite)": [[15, "slideflow.io.preservedsite.generate_crossfolds"]], "get_locations_from_tfrecord() (in module slideflow.io)": [[15, "slideflow.io.get_locations_from_tfrecord"]], "get_tfrecord_by_index() (in module slideflow.io)": [[15, "slideflow.io.get_tfrecord_by_index"]], "get_tfrecord_by_location() (in module slideflow.io)": [[15, "slideflow.io.get_tfrecord_by_location"]], "get_tfrecord_length() (in module slideflow.io)": [[15, "slideflow.io.get_tfrecord_length"]], "get_tfrecord_parser() (in module slideflow.io)": [[15, "slideflow.io.get_tfrecord_parser"]], "read_and_return_record() (in module slideflow.io)": [[15, "slideflow.io.read_and_return_record"]], "serialized_record() (in module slideflow.io)": [[15, "slideflow.io.serialized_record"]], "tfrecord_has_locations() (in module slideflow.io)": [[15, "slideflow.io.tfrecord_has_locations"]], "update_manifest_at_dir() (in module slideflow.io)": [[15, "slideflow.io.update_manifest_at_dir"]], "write_tfrecords_merge() (in module slideflow.io)": [[15, "slideflow.io.write_tfrecords_merge"]], "write_tfrecords_multi() (in module slideflow.io)": [[15, "slideflow.io.write_tfrecords_multi"]], "write_tfrecords_single() (in module slideflow.io)": [[15, "slideflow.io.write_tfrecords_single"]], "checkpoint_to_tf_model() (in module slideflow.io.tensorflow)": [[16, "slideflow.io.tensorflow.checkpoint_to_tf_model"]], "decode_image() (in module slideflow.io.tensorflow)": [[16, "slideflow.io.tensorflow.decode_image"]], "get_tfrecord_parser() (in module slideflow.io.tensorflow)": [[16, "slideflow.io.tensorflow.get_tfrecord_parser"]], "interleave() (in module slideflow.io.tensorflow)": [[16, "slideflow.io.tensorflow.interleave"]], "join_tfrecord() (in module slideflow.io.tensorflow)": [[16, "slideflow.io.tensorflow.join_tfrecord"]], "multi_image_example() (in module slideflow.io.tensorflow)": [[16, "slideflow.io.tensorflow.multi_image_example"]], "parser_from_labels() (in module slideflow.io.tensorflow)": [[16, "slideflow.io.tensorflow.parser_from_labels"]], "preprocess_uint8() (in module slideflow.io.tensorflow)": [[16, "slideflow.io.tensorflow.preprocess_uint8"]], "print_tfrecord() (in module slideflow.io.tensorflow)": [[16, "slideflow.io.tensorflow.print_tfrecord"]], "process_image() (in module slideflow.io.tensorflow)": [[16, "slideflow.io.tensorflow.process_image"]], "read_and_return_record() (in module slideflow.io.tensorflow)": [[16, "slideflow.io.tensorflow.read_and_return_record"]], "serialized_record() (in module slideflow.io.tensorflow)": [[16, "slideflow.io.tensorflow.serialized_record"]], "shuffle_tfrecord() (in module slideflow.io.tensorflow)": [[16, "slideflow.io.tensorflow.shuffle_tfrecord"]], "shuffle_tfrecords_by_dir() (in module slideflow.io.tensorflow)": [[16, "slideflow.io.tensorflow.shuffle_tfrecords_by_dir"]], "slideflow.io.tensorflow": [[16, "module-slideflow.io.tensorflow"]], "split_tfrecord() (in module slideflow.io.tensorflow)": [[16, "slideflow.io.tensorflow.split_tfrecord"]], "tfrecord_example() (in module slideflow.io.tensorflow)": [[16, "slideflow.io.tensorflow.tfrecord_example"]], "transform_tfrecord() (in module slideflow.io.tensorflow)": [[16, "slideflow.io.tensorflow.transform_tfrecord"]], "indexedinterleaver (class in slideflow.io.torch)": [[17, "slideflow.io.torch.IndexedInterleaver"]], "interleaveiterator (class in slideflow.io.torch)": [[17, "slideflow.io.torch.InterleaveIterator"]], "slideflow.io.torch": [[17, "module-slideflow.io.torch"]], "clammodelconfig (class in slideflow.clam)": [[19, "slideflow.clam.CLAMModelConfig"]], "milmodelconfig (class in slideflow.mil)": [[19, "slideflow.mil.MILModelConfig"]], "trainerconfig (class in slideflow.mil)": [[19, "slideflow.mil.TrainerConfig"]], "batched_predict() (in module slideflow.mil.milmodelconfig)": [[19, "slideflow.mil.MILModelConfig.batched_predict"]], "batched_predict() (in module slideflow.mil.trainerconfig)": [[19, "slideflow.mil.TrainerConfig.batched_predict"]], "build_fastai_learner() (in module slideflow.mil)": [[19, "slideflow.mil.build_fastai_learner"]], "build_model() (in module slideflow.mil.milmodelconfig)": [[19, "slideflow.mil.MILModelConfig.build_model"]], "build_model() (in module slideflow.mil.trainerconfig)": [[19, "slideflow.mil.TrainerConfig.build_model"]], "build_multimodal_learner() (in module slideflow.mil)": [[19, "slideflow.mil.build_multimodal_learner"]], "build_train_dataloader() (in module slideflow.mil.trainerconfig)": [[19, "slideflow.mil.TrainerConfig.build_train_dataloader"]], "build_val_dataloader() (in module slideflow.mil.trainerconfig)": [[19, "slideflow.mil.TrainerConfig.build_val_dataloader"]], "eval() (in module slideflow.mil.trainerconfig)": [[19, "slideflow.mil.TrainerConfig.eval"]], "eval_mil() (in module slideflow.mil)": [[19, "slideflow.mil.eval_mil"]], "generate_attention_heatmaps() (in module slideflow.mil)": [[19, "slideflow.mil.generate_attention_heatmaps"]], "generate_mil_features() (in module slideflow.mil)": [[19, "slideflow.mil.generate_mil_features"]], "get_metrics() (in module slideflow.mil.trainerconfig)": [[19, "slideflow.mil.TrainerConfig.get_metrics"]], "get_mil_tile_predictions() (in module slideflow.mil)": [[19, "slideflow.mil.get_mil_tile_predictions"]], "inspect_batch() (in module slideflow.mil.milmodelconfig)": [[19, "slideflow.mil.MILModelConfig.inspect_batch"]], "inspect_batch() (in module slideflow.mil.trainerconfig)": [[19, "slideflow.mil.TrainerConfig.inspect_batch"]], "is_classification() (in module slideflow.mil.milmodelconfig)": [[19, "slideflow.mil.MILModelConfig.is_classification"]], "is_classification() (in module slideflow.mil.trainerconfig)": [[19, "slideflow.mil.TrainerConfig.is_classification"]], "json_dump() (in module slideflow.mil.trainerconfig)": [[19, "slideflow.mil.TrainerConfig.json_dump"]], "mil_config() (in module slideflow.mil)": [[19, "slideflow.mil.mil_config"]], "predict() (in module slideflow.mil.milmodelconfig)": [[19, "slideflow.mil.MILModelConfig.predict"]], "predict() (in module slideflow.mil.trainerconfig)": [[19, "slideflow.mil.TrainerConfig.predict"]], "predict_from_bags() (in module slideflow.mil)": [[19, "slideflow.mil.predict_from_bags"]], "predict_from_multimodal_bags() (in module slideflow.mil)": [[19, "slideflow.mil.predict_from_multimodal_bags"]], "predict_mil() (in module slideflow.mil)": [[19, "slideflow.mil.predict_mil"]], "predict_multimodal_mil() (in module slideflow.mil)": [[19, "slideflow.mil.predict_multimodal_mil"]], "predict_slide() (in module slideflow.mil)": [[19, "slideflow.mil.predict_slide"]], "prepare_training() (in module slideflow.mil.trainerconfig)": [[19, "slideflow.mil.TrainerConfig.prepare_training"]], "run_metrics() (in module slideflow.mil.milmodelconfig)": [[19, "slideflow.mil.MILModelConfig.run_metrics"]], "run_metrics() (in module slideflow.mil.trainerconfig)": [[19, "slideflow.mil.TrainerConfig.run_metrics"]], "to_dict() (in module slideflow.mil.milmodelconfig)": [[19, "slideflow.mil.MILModelConfig.to_dict"]], "to_dict() (in module slideflow.mil.trainerconfig)": [[19, "slideflow.mil.TrainerConfig.to_dict"]], "train() (in module slideflow.mil.trainerconfig)": [[19, "slideflow.mil.TrainerConfig.train"]], "train_mil() (in module slideflow.mil)": [[19, "slideflow.mil.train_mil"]], "features (class in slideflow.model)": [[20, "slideflow.model.Features"]], "regressiontrainer (class in slideflow.model)": [[20, "slideflow.model.RegressionTrainer"]], "survivaltrainer (class in slideflow.model)": [[20, "slideflow.model.SurvivalTrainer"]], "trainer (class in slideflow.model)": [[20, "slideflow.model.Trainer"]], "__call__() (in module slideflow.model.features)": [[20, "slideflow.model.Features.__call__"]], "build_feature_extractor() (in module slideflow.model)": [[20, "slideflow.model.build_feature_extractor"]], "build_trainer() (in module slideflow.model)": [[20, "slideflow.model.build_trainer"]], "evaluate() (in module slideflow.model.trainer)": [[20, "slideflow.model.Trainer.evaluate"]], "from_model() (in module slideflow.model.features)": [[20, "slideflow.model.Features.from_model"]], "is_tensorflow_model() (in module slideflow.model)": [[20, "slideflow.model.is_tensorflow_model"]], "is_tensorflow_tensor() (in module slideflow.model)": [[20, "slideflow.model.is_tensorflow_tensor"]], "is_torch_model() (in module slideflow.model)": [[20, "slideflow.model.is_torch_model"]], "is_torch_tensor() (in module slideflow.model)": [[20, "slideflow.model.is_torch_tensor"]], "list_extractors() (in module slideflow.model)": [[20, "slideflow.model.list_extractors"]], "load() (in module slideflow.model)": [[20, "slideflow.model.load"]], "load() (in module slideflow.model.trainer)": [[20, "slideflow.model.Trainer.load"]], "predict() (in module slideflow.model.trainer)": [[20, "slideflow.model.Trainer.predict"]], "read_hp_sweep() (in module slideflow.model)": [[20, "slideflow.model.read_hp_sweep"]], "rebuild_extractor() (in module slideflow.model)": [[20, "slideflow.model.rebuild_extractor"]], "train() (in module slideflow.model.trainer)": [[20, "slideflow.model.Trainer.train"]], "modelparams (class in slideflow)": [[21, "slideflow.ModelParams"]], "get_normalizer() (in module slideflow.modelparams)": [[21, "slideflow.ModelParams.get_normalizer"]], "model_type() (in module slideflow.modelparams)": [[21, "slideflow.ModelParams.model_type"]], "to_dict() (in module slideflow.modelparams)": [[21, "slideflow.ModelParams.to_dict"]], "validate() (in module slideflow.modelparams)": [[21, "slideflow.ModelParams.validate"]], "flatten() (in module slideflow.model.tensorflow)": [[22, "slideflow.model.tensorflow.flatten"]], "load() (in module slideflow.model.tensorflow)": [[22, "slideflow.model.tensorflow.load"]], "log_manifest() (in module slideflow.model.tensorflow)": [[22, "slideflow.model.tensorflow.log_manifest"]], "unwrap() (in module slideflow.model.tensorflow)": [[22, "slideflow.model.tensorflow.unwrap"]], "lazy_load_pretrained() (in module slideflow.model.torch)": [[23, "slideflow.model.torch.lazy_load_pretrained"]], "load() (in module slideflow.model.torch)": [[23, "slideflow.model.torch.load"]], "log_manifest() (in module slideflow.model.torch)": [[23, "slideflow.model.torch.log_manifest"]], "mosaic (class in slideflow)": [[24, "slideflow.Mosaic"]], "generate_grid() (in module slideflow.mosaic)": [[24, "slideflow.Mosaic.generate_grid"]], "plot() (in module slideflow.mosaic)": [[24, "slideflow.Mosaic.plot"]], "points_at_grid_index() (in module slideflow.mosaic)": [[24, "slideflow.Mosaic.points_at_grid_index"]], "save() (in module slideflow.mosaic)": [[24, "slideflow.Mosaic.save"]], "save_report() (in module slideflow.mosaic)": [[24, "slideflow.Mosaic.save_report"]], "view() (in module slideflow.mosaic)": [[24, "slideflow.Mosaic.view"]], "stainnormalizer (class in slideflow.norm)": [[25, "slideflow.norm.StainNormalizer"]], "augment() (in module slideflow.norm.stainnormalizer)": [[25, "slideflow.norm.StainNormalizer.augment"]], "fit() (in module slideflow.norm.stainnormalizer)": [[25, "slideflow.norm.StainNormalizer.fit"]], "get_fit() (in module slideflow.norm.stainnormalizer)": [[25, "slideflow.norm.StainNormalizer.get_fit"]], "jpeg_to_jpeg() (in module slideflow.norm.stainnormalizer)": [[25, "slideflow.norm.StainNormalizer.jpeg_to_jpeg"]], "jpeg_to_rgb() (in module slideflow.norm.stainnormalizer)": [[25, "slideflow.norm.StainNormalizer.jpeg_to_rgb"]], "png_to_png() (in module slideflow.norm.stainnormalizer)": [[25, "slideflow.norm.StainNormalizer.png_to_png"]], "png_to_rgb() (in module slideflow.norm.stainnormalizer)": [[25, "slideflow.norm.StainNormalizer.png_to_rgb"]], "rgb_to_rgb() (in module slideflow.norm.stainnormalizer)": [[25, "slideflow.norm.StainNormalizer.rgb_to_rgb"]], "set_fit() (in module slideflow.norm.stainnormalizer)": [[25, "slideflow.norm.StainNormalizer.set_fit"]], "tf_to_rgb() (in module slideflow.norm.stainnormalizer)": [[25, "slideflow.norm.StainNormalizer.tf_to_rgb"]], "tf_to_tf() (in module slideflow.norm.stainnormalizer)": [[25, "slideflow.norm.StainNormalizer.tf_to_tf"]], "torch_to_torch() (in module slideflow.norm.stainnormalizer)": [[25, "slideflow.norm.StainNormalizer.torch_to_torch"]], "transform() (in module slideflow.norm.stainnormalizer)": [[25, "slideflow.norm.StainNormalizer.transform"]], "project (class in slideflow)": [[29, "slideflow.Project"]], "add_source() (in module slideflow.project)": [[29, "slideflow.Project.add_source"]], "associate_slide_names() (in module slideflow.project)": [[29, "slideflow.Project.associate_slide_names"]], "cell_segmentation() (in module slideflow.project)": [[29, "slideflow.Project.cell_segmentation"]], "create_blank_annotations() (in module slideflow.project)": [[29, "slideflow.Project.create_blank_annotations"]], "create_hp_sweep() (in module slideflow.project)": [[29, "slideflow.Project.create_hp_sweep"]], "dataset() (in module slideflow.project)": [[29, "slideflow.Project.dataset"]], "evaluate() (in module slideflow.project)": [[29, "slideflow.Project.evaluate"]], "evaluate_mil() (in module slideflow.project)": [[29, "slideflow.Project.evaluate_mil"]], "extract_cells() (in module slideflow.project)": [[29, "slideflow.Project.extract_cells"]], "extract_tiles() (in module slideflow.project)": [[29, "slideflow.Project.extract_tiles"]], "gan_generate() (in module slideflow.project)": [[29, "slideflow.Project.gan_generate"]], "gan_train() (in module slideflow.project)": [[29, "slideflow.Project.gan_train"]], "generate_feature_bags() (in module slideflow.project)": [[29, "slideflow.Project.generate_feature_bags"]], "generate_features() (in module slideflow.project)": [[29, "slideflow.Project.generate_features"]], "generate_heatmaps() (in module slideflow.project)": [[29, "slideflow.Project.generate_heatmaps"]], "generate_mosaic() (in module slideflow.project)": [[29, "slideflow.Project.generate_mosaic"]], "generate_mosaic_from_annotations() (in module slideflow.project)": [[29, "slideflow.Project.generate_mosaic_from_annotations"]], "generate_tfrecord_heatmap() (in module slideflow.project)": [[29, "slideflow.Project.generate_tfrecord_heatmap"]], "predict() (in module slideflow.project)": [[29, "slideflow.Project.predict"]], "predict_ensemble() (in module slideflow.project)": [[29, "slideflow.Project.predict_ensemble"]], "predict_wsi() (in module slideflow.project)": [[29, "slideflow.Project.predict_wsi"]], "save() (in module slideflow.project)": [[29, "slideflow.Project.save"]], "smac_search() (in module slideflow.project)": [[29, "slideflow.Project.smac_search"]], "train() (in module slideflow.project)": [[29, "slideflow.Project.train"]], "train_ensemble() (in module slideflow.project)": [[29, "slideflow.Project.train_ensemble"]], "train_mil() (in module slideflow.project)": [[29, "slideflow.Project.train_mil"]], "train_simclr() (in module slideflow.project)": [[29, "slideflow.Project.train_simclr"]], "datasetbuilder (class in slideflow.simclr)": [[34, "slideflow.simclr.DatasetBuilder"]], "simclr (class in slideflow.simclr)": [[34, "slideflow.simclr.SimCLR"]], "simclr_args (class in slideflow.simclr)": [[34, "slideflow.simclr.SimCLR_Args"]], "get_args() (in module slideflow.simclr)": [[34, "slideflow.simclr.get_args"]], "load() (in module slideflow.simclr)": [[34, "slideflow.simclr.load"]], "load_model_args() (in module slideflow.simclr)": [[34, "slideflow.simclr.load_model_args"]], "run_simclr() (in module slideflow.simclr)": [[34, "slideflow.simclr.run_simclr"]], "wsi (class in slideflow.slide)": [[35, "slideflow.slide.WSI"]], "align_tiles_to() (in module slideflow.wsi)": [[35, "slideflow.WSI.align_tiles_to"]], "align_to() (in module slideflow.wsi)": [[35, "slideflow.WSI.align_to"]], "apply_qc_mask() (in module slideflow.wsi)": [[35, "slideflow.WSI.apply_qc_mask"]], "apply_segmentation() (in module slideflow.wsi)": [[35, "slideflow.WSI.apply_segmentation"]], "area() (in module slideflow.wsi)": [[35, "slideflow.WSI.area"]], "build_generator() (in module slideflow.wsi)": [[35, "slideflow.WSI.build_generator"]], "dim_to_mpp() (in module slideflow.wsi)": [[35, "slideflow.WSI.dim_to_mpp"]], "export_rois() (in module slideflow.wsi)": [[35, "slideflow.WSI.export_rois"]], "extract_cells() (in module slideflow.wsi)": [[35, "slideflow.WSI.extract_cells"]], "extract_tiles() (in module slideflow.wsi)": [[35, "slideflow.WSI.extract_tiles"]], "get_tile_dataframe() (in module slideflow.wsi)": [[35, "slideflow.WSI.get_tile_dataframe"]], "get_tile_mask() (in module slideflow.wsi)": [[35, "slideflow.WSI.get_tile_mask"]], "has_rois() (in module slideflow.wsi)": [[35, "slideflow.WSI.has_rois"]], "load_csv_roi() (in module slideflow.wsi)": [[35, "slideflow.WSI.load_csv_roi"]], "load_json_roi() (in module slideflow.wsi)": [[35, "slideflow.WSI.load_json_roi"]], "load_roi_array() (in module slideflow.wsi)": [[35, "slideflow.WSI.load_roi_array"]], "mpp_to_dim() (in module slideflow.wsi)": [[35, "slideflow.WSI.mpp_to_dim"]], "predict() (in module slideflow.wsi)": [[35, "slideflow.WSI.predict"]], "predict() (in module slideflow.slide)": [[35, "slideflow.slide.predict"]], "preview() (in module slideflow.wsi)": [[35, "slideflow.WSI.preview"]], "process_rois() (in module slideflow.wsi)": [[35, "slideflow.WSI.process_rois"]], "qc() (in module slideflow.wsi)": [[35, "slideflow.WSI.qc"]], "remove_qc() (in module slideflow.wsi)": [[35, "slideflow.WSI.remove_qc"]], "remove_roi() (in module slideflow.wsi)": [[35, "slideflow.WSI.remove_roi"]], "show_alignment() (in module slideflow.wsi)": [[35, "slideflow.WSI.show_alignment"]], "square_thumb() (in module slideflow.wsi)": [[35, "slideflow.WSI.square_thumb"]], "tensorflow() (in module slideflow.wsi)": [[35, "slideflow.WSI.tensorflow"]], "thumb() (in module slideflow.wsi)": [[35, "slideflow.WSI.thumb"]], "torch() (in module slideflow.wsi)": [[35, "slideflow.WSI.torch"]], "verify_alignment() (in module slideflow.wsi)": [[35, "slideflow.WSI.verify_alignment"]], "view() (in module slideflow.wsi)": [[35, "slideflow.WSI.view"]], "gaussian (class in slideflow.slide.qc)": [[37, "slideflow.slide.qc.Gaussian"]], "load (class in slideflow.slide.qc)": [[37, "slideflow.slide.qc.Load"]], "otsu (class in slideflow.slide.qc)": [[37, "slideflow.slide.qc.Otsu"]], "save (class in slideflow.slide.qc)": [[37, "slideflow.slide.qc.Save"]], "strideddl (class in slideflow.slide.qc)": [[37, "slideflow.slide.qc.StridedDL"]], "about() (in module slideflow)": [[38, "slideflow.about"]], "build_feature_extractor() (in module slideflow)": [[38, "slideflow.build_feature_extractor"]], "create_project() (in module slideflow)": [[38, "slideflow.create_project"]], "getlogginglevel() (in module slideflow)": [[38, "slideflow.getLoggingLevel"]], "load_project() (in module slideflow)": [[38, "slideflow.load_project"]], "setlogginglevel() (in module slideflow)": [[38, "slideflow.setLoggingLevel"]], "segmentation (class in slideflow.cellseg)": [[39, "slideflow.cellseg.Segmentation"]], "apply_rois() (in module slideflow.cellseg.segmentation)": [[39, "slideflow.cellseg.Segmentation.apply_rois"]], "calculate_centroids() (in module slideflow.cellseg.segmentation)": [[39, "slideflow.cellseg.Segmentation.calculate_centroids"]], "calculate_outlines() (in module slideflow.cellseg.segmentation)": [[39, "slideflow.cellseg.Segmentation.calculate_outlines"]], "centroid_to_image() (in module slideflow.cellseg.segmentation)": [[39, "slideflow.cellseg.Segmentation.centroid_to_image"]], "centroids() (in module slideflow.cellseg.segmentation)": [[39, "slideflow.cellseg.Segmentation.centroids"]], "extract_centroids() (in module slideflow.cellseg.segmentation)": [[39, "slideflow.cellseg.Segmentation.extract_centroids"]], "mask_to_image() (in module slideflow.cellseg.segmentation)": [[39, "slideflow.cellseg.Segmentation.mask_to_image"]], "outline_to_image() (in module slideflow.cellseg.segmentation)": [[39, "slideflow.cellseg.Segmentation.outline_to_image"]], "save() (in module slideflow.cellseg.segmentation)": [[39, "slideflow.cellseg.Segmentation.save"]], "segment_slide() (in module slideflow.cellseg)": [[39, "slideflow.cellseg.segment_slide"]], "slidemap (class in slideflow)": [[40, "slideflow.SlideMap"]], "activations() (in module slideflow.slidemap)": [[40, "slideflow.SlideMap.activations"]], "build_mosaic() (in module slideflow.slidemap)": [[40, "slideflow.SlideMap.build_mosaic"]], "cluster() (in module slideflow.slidemap)": [[40, "slideflow.SlideMap.cluster"]], "filter() (in module slideflow.slidemap)": [[40, "slideflow.SlideMap.filter"]], "label() (in module slideflow.slidemap)": [[40, "slideflow.SlideMap.label"]], "label_by_preds() (in module slideflow.slidemap)": [[40, "slideflow.SlideMap.label_by_preds"]], "label_by_slide() (in module slideflow.slidemap)": [[40, "slideflow.SlideMap.label_by_slide"]], "label_by_uncertainty() (in module slideflow.slidemap)": [[40, "slideflow.SlideMap.label_by_uncertainty"]], "load() (in module slideflow.slidemap)": [[40, "slideflow.SlideMap.load"]], "load_coordinates() (in module slideflow.slidemap)": [[40, "slideflow.SlideMap.load_coordinates"]], "load_umap() (in module slideflow.slidemap)": [[40, "slideflow.SlideMap.load_umap"]], "neighbors() (in module slideflow.slidemap)": [[40, "slideflow.SlideMap.neighbors"]], "plot() (in module slideflow.slidemap)": [[40, "slideflow.SlideMap.plot"]], "plot_3d() (in module slideflow.slidemap)": [[40, "slideflow.SlideMap.plot_3d"]], "save() (in module slideflow.slidemap)": [[40, "slideflow.SlideMap.save"]], "save_3d() (in module slideflow.slidemap)": [[40, "slideflow.SlideMap.save_3d"]], "save_coordinates() (in module slideflow.slidemap)": [[40, "slideflow.SlideMap.save_coordinates"]], "save_encoder() (in module slideflow.slidemap)": [[40, "slideflow.SlideMap.save_encoder"]], "save_plot() (in module slideflow.slidemap)": [[40, "slideflow.SlideMap.save_plot"]], "save_umap() (in module slideflow.slidemap)": [[40, "slideflow.SlideMap.save_umap"]], "umap_transform() (in module slideflow.slidemap)": [[40, "slideflow.SlideMap.umap_transform"]], "calculate_centroid() (in module slideflow.stats)": [[42, "slideflow.stats.calculate_centroid"]], "df_from_pred() (in module slideflow.stats)": [[42, "slideflow.stats.df_from_pred"]], "eval_dataset() (in module slideflow.stats)": [[42, "slideflow.stats.eval_dataset"]], "get_centroid_index() (in module slideflow.stats)": [[42, "slideflow.stats.get_centroid_index"]], "group_reduce() (in module slideflow.stats)": [[42, "slideflow.stats.group_reduce"]], "metrics_from_dataset() (in module slideflow.stats)": [[42, "slideflow.stats.metrics_from_dataset"]], "name_columns() (in module slideflow.stats)": [[42, "slideflow.stats.name_columns"]], "predict_dataset() (in module slideflow.stats)": [[42, "slideflow.stats.predict_dataset"]], "p (studio property)": [[44, "slideflow.studio.Studio.P"]], "sidebar (class in slideflow.studio)": [[44, "slideflow.studio.Sidebar"]], "studio (class in slideflow.studio)": [[44, "slideflow.studio.Studio"]], "__init__() (sidebar method)": [[44, "slideflow.studio.Sidebar.__init__"]], "__init__() (studio method)": [[44, "slideflow.studio.Studio.__init__"]], "add_to_render_pipeline() (studio method)": [[44, "slideflow.studio.Studio.add_to_render_pipeline"]], "add_widgets() (sidebar method)": [[44, "slideflow.studio.Sidebar.add_widgets"]], "add_widgets() (studio method)": [[44, "slideflow.studio.Studio.add_widgets"]], "ask_load_heatmap() (studio method)": [[44, "slideflow.studio.Studio.ask_load_heatmap"]], "ask_load_model() (studio method)": [[44, "slideflow.studio.Studio.ask_load_model"]], "ask_load_project() (studio method)": [[44, "slideflow.studio.Studio.ask_load_project"]], "ask_load_slide() (studio method)": [[44, "slideflow.studio.Studio.ask_load_slide"]], "ask_zoom_to_mpp() (studio method)": [[44, "slideflow.studio.Studio.ask_zoom_to_mpp"]], "autoload() (studio method)": [[44, "slideflow.studio.Studio.autoload"]], "center_next_window() (studio method)": [[44, "slideflow.studio.Studio.center_next_window"]], "clear_message() (studio method)": [[44, "slideflow.studio.Studio.clear_message"]], "clear_model_results() (studio method)": [[44, "slideflow.studio.Studio.clear_model_results"]], "clear_overlay() (studio method)": [[44, "slideflow.studio.Studio.clear_overlay"]], "clear_result() (studio method)": [[44, "slideflow.studio.Studio.clear_result"]], "clear_status_message() (studio method)": [[44, "slideflow.studio.Studio.clear_status_message"]], "close() (studio method)": [[44, "slideflow.studio.Studio.close"]], "close_model() (studio method)": [[44, "slideflow.studio.Studio.close_model"]], "close_slide() (studio method)": [[44, "slideflow.studio.Studio.close_slide"]], "collapsing_header() (studio method)": [[44, "slideflow.studio.Studio.collapsing_header"]], "collapsing_header2() (studio method)": [[44, "slideflow.studio.Studio.collapsing_header2"]], "content_width (sidebar property)": [[44, "slideflow.studio.Sidebar.content_width"]], "decrease_tile_zoom() (studio method)": [[44, "slideflow.studio.Studio.decrease_tile_zoom"]], "defer_rendering() (studio method)": [[44, "slideflow.studio.Studio.defer_rendering"]], "dim_text() (studio method)": [[44, "slideflow.studio.Studio.dim_text"]], "draw() (sidebar method)": [[44, "slideflow.studio.Sidebar.draw"]], "draw_frame() (studio method)": [[44, "slideflow.studio.Studio.draw_frame"]], "full_button() (sidebar method)": [[44, "slideflow.studio.Sidebar.full_button"]], "full_button2() (sidebar method)": [[44, "slideflow.studio.Sidebar.full_button2"]], "full_width (sidebar property)": [[44, "slideflow.studio.Sidebar.full_width"]], "get_default_widgets() (studio static method)": [[44, "slideflow.studio.Studio.get_default_widgets"]], "get_extension() (studio method)": [[44, "slideflow.studio.Studio.get_extension"]], "get_renderer() (studio method)": [[44, "slideflow.studio.Studio.get_renderer"]], "get_widget() (studio method)": [[44, "slideflow.studio.Studio.get_widget"]], "has_live_viewer() (studio method)": [[44, "slideflow.studio.Studio.has_live_viewer"]], "has_uq() (studio method)": [[44, "slideflow.studio.Studio.has_uq"]], "header() (studio method)": [[44, "slideflow.studio.Studio.header"]], "header_with_buttons() (studio method)": [[44, "slideflow.studio.Studio.header_with_buttons"]], "highlighted() (studio method)": [[44, "slideflow.studio.Studio.highlighted"]], "increase_tile_zoom() (studio method)": [[44, "slideflow.studio.Studio.increase_tile_zoom"]], "is_mouse_down() (studio method)": [[44, "slideflow.studio.Studio.is_mouse_down"]], "is_mouse_released() (studio method)": [[44, "slideflow.studio.Studio.is_mouse_released"]], "large_image_button() (sidebar method)": [[44, "slideflow.studio.Sidebar.large_image_button"]], "load_heatmap() (studio method)": [[44, "slideflow.studio.Studio.load_heatmap"]], "load_model() (studio method)": [[44, "slideflow.studio.Studio.load_model"]], "load_project() (studio method)": [[44, "slideflow.studio.Studio.load_project"]], "load_slide() (studio method)": [[44, "slideflow.studio.Studio.load_slide"]], "model (studio property)": [[44, "slideflow.studio.Studio.model"]], "mouse_input_is_suspended() (studio method)": [[44, "slideflow.studio.Studio.mouse_input_is_suspended"]], "mouse_is_over_viewer (studio property)": [[44, "slideflow.studio.Studio.mouse_is_over_viewer"]], "offset_x (studio property)": [[44, "slideflow.studio.Studio.offset_x"]], "offset_x_pixels (studio property)": [[44, "slideflow.studio.Studio.offset_x_pixels"]], "offset_y (studio property)": [[44, "slideflow.studio.Studio.offset_y"]], "offset_y_pixels (studio property)": [[44, "slideflow.studio.Studio.offset_y_pixels"]], "print_error() (studio method)": [[44, "slideflow.studio.Studio.print_error"]], "reload_model() (studio method)": [[44, "slideflow.studio.Studio.reload_model"]], "reload_viewer() (studio method)": [[44, "slideflow.studio.Studio.reload_viewer"]], "reload_wsi() (studio method)": [[44, "slideflow.studio.Studio.reload_wsi"]], "remove_from_render_pipeline() (studio method)": [[44, "slideflow.studio.Studio.remove_from_render_pipeline"]], "remove_widget() (sidebar method)": [[44, "slideflow.studio.Sidebar.remove_widget"]], "remove_widget() (studio method)": [[44, "slideflow.studio.Studio.remove_widget"]], "reset_background() (studio method)": [[44, "slideflow.studio.Studio.reset_background"]], "reset_tile_zoom() (studio method)": [[44, "slideflow.studio.Studio.reset_tile_zoom"]], "resume_keyboard_input() (studio method)": [[44, "slideflow.studio.Studio.resume_keyboard_input"]], "resume_mouse_input_handling() (studio method)": [[44, "slideflow.studio.Studio.resume_mouse_input_handling"]], "set_grid_overlay() (studio method)": [[44, "slideflow.studio.Studio.set_grid_overlay"]], "set_message() (studio method)": [[44, "slideflow.studio.Studio.set_message"]], "set_overlay() (studio method)": [[44, "slideflow.studio.Studio.set_overlay"]], "set_prediction_message() (studio method)": [[44, "slideflow.studio.Studio.set_prediction_message"]], "set_status_message() (studio method)": [[44, "slideflow.studio.Studio.set_status_message"]], "set_viewer() (studio method)": [[44, "slideflow.studio.Studio.set_viewer"]], "show_overlay (studio property)": [[44, "slideflow.studio.Studio.show_overlay"]], "slideflow.studio": [[44, "module-slideflow.studio"]], "small_button() (sidebar method)": [[44, "slideflow.studio.Sidebar.small_button"]], "suspend_keyboard_input() (studio method)": [[44, "slideflow.studio.Studio.suspend_keyboard_input"]], "suspend_mouse_input_handling() (studio method)": [[44, "slideflow.studio.Studio.suspend_mouse_input_handling"]], "theme (sidebar property)": [[44, "slideflow.studio.Sidebar.theme"]], "tile_preview_enabled (studio property)": [[44, "slideflow.studio.Studio.tile_preview_enabled"]], "easydict (class in slideflow.util)": [[59, "slideflow.util.EasyDict"]], "featureextractionprogress (class in slideflow.util)": [[59, "slideflow.util.FeatureExtractionProgress"]], "imgbatchspeedcolumn (class in slideflow.util)": [[59, "slideflow.util.ImgBatchSpeedColumn"]], "labeledmofncompletecolumn (class in slideflow.util)": [[59, "slideflow.util.LabeledMofNCompleteColumn"]], "multiprocessprogress (class in slideflow.util)": [[59, "slideflow.util.MultiprocessProgress"]], "multiprocessprogresstracker (class in slideflow.util)": [[59, "slideflow.util.MultiprocessProgressTracker"]], "tileextractionprogress (class in slideflow.util)": [[59, "slideflow.util.TileExtractionProgress"]], "tileextractionspeedcolumn (class in slideflow.util)": [[59, "slideflow.util.TileExtractionSpeedColumn"]], "validjsonencoder (class in slideflow.util)": [[59, "slideflow.util.ValidJSONEncoder"]], "__init__() (imgbatchspeedcolumn method)": [[59, "slideflow.util.ImgBatchSpeedColumn.__init__"]], "__init__() (labeledmofncompletecolumn method)": [[59, "slideflow.util.LabeledMofNCompleteColumn.__init__"]], "__init__() (multiprocessprogress method)": [[59, "slideflow.util.MultiprocessProgress.__init__"]], "__init__() (multiprocessprogresstracker method)": [[59, "slideflow.util.MultiprocessProgressTracker.__init__"]], "about() (in module slideflow.util)": [[59, "slideflow.util.about"]], "batch() (in module slideflow.util)": [[59, "slideflow.util.batch"]], "batch_generator() (in module slideflow.util)": [[59, "slideflow.util.batch_generator"]], "bin_values_to_slide_grid() (in module slideflow.util)": [[59, "slideflow.util.bin_values_to_slide_grid"]], "choice_input() (in module slideflow.util)": [[59, "slideflow.util.choice_input"]], "create_triangles() (in module slideflow.util)": [[59, "slideflow.util.create_triangles"]], "default() (validjsonencoder method)": [[59, "slideflow.util.ValidJSONEncoder.default"]], "download_from_tcga() (in module slideflow.util)": [[59, "slideflow.util.download_from_tcga"]], "getlogginglevel() (in module slideflow.util)": [[59, "slideflow.util.getLoggingLevel"]], "get_ensemble_model_config() (in module slideflow.util)": [[59, "slideflow.util.get_ensemble_model_config"]], "get_gan_config() (in module slideflow.util)": [[59, "slideflow.util.get_gan_config"]], "get_model_config() (in module slideflow.util)": [[59, "slideflow.util.get_model_config"]], "get_model_normalizer() (in module slideflow.util)": [[59, "slideflow.util.get_model_normalizer"]], "get_preprocess_fn() (in module slideflow.util)": [[59, "slideflow.util.get_preprocess_fn"]], "get_relative_tfrecord_paths() (in module slideflow.util)": [[59, "slideflow.util.get_relative_tfrecord_paths"]], "get_renderables() (featureextractionprogress method)": [[59, "slideflow.util.FeatureExtractionProgress.get_renderables"]], "get_renderables() (tileextractionprogress method)": [[59, "slideflow.util.TileExtractionProgress.get_renderables"]], "get_slide_paths() (in module slideflow.util)": [[59, "slideflow.util.get_slide_paths"]], "get_slides_from_model_manifest() (in module slideflow.util)": [[59, "slideflow.util.get_slides_from_model_manifest"]], "get_valid_model_dir() (in module slideflow.util)": [[59, "slideflow.util.get_valid_model_dir"]], "global_path() (in module slideflow.util)": [[59, "slideflow.util.global_path"]], "infer_stride() (in module slideflow.util)": [[59, "slideflow.util.infer_stride"]], "is_model() (in module slideflow.util)": [[59, "slideflow.util.is_model"]], "is_project() (in module slideflow.util)": [[59, "slideflow.util.is_project"]], "is_simclr_model_path() (in module slideflow.util)": [[59, "slideflow.util.is_simclr_model_path"]], "is_slide() (in module slideflow.util)": [[59, "slideflow.util.is_slide"]], "is_tensorflow_model_path() (in module slideflow.util)": [[59, "slideflow.util.is_tensorflow_model_path"]], "is_tile_size_compatible() (in module slideflow.util)": [[59, "slideflow.util.is_tile_size_compatible"]], "is_torch_model_path() (in module slideflow.util)": [[59, "slideflow.util.is_torch_model_path"]], "is_uq_model() (in module slideflow.util)": [[59, "slideflow.util.is_uq_model"]], "isnumeric() (in module slideflow.util)": [[59, "slideflow.util.isnumeric"]], "load_json() (in module slideflow.util)": [[59, "slideflow.util.load_json"]], "load_predictions() (in module slideflow.util)": [[59, "slideflow.util.load_predictions"]], "location_heatmap() (in module slideflow.util)": [[59, "slideflow.util.location_heatmap"]], "log_manifest() (in module slideflow.util)": [[59, "slideflow.util.log_manifest"]], "make_dir() (in module slideflow.util)": [[59, "slideflow.util.make_dir"]], "map_values_to_slide_grid() (in module slideflow.util)": [[59, "slideflow.util.map_values_to_slide_grid"]], "md5() (in module slideflow.util)": [[59, "slideflow.util.md5"]], "multi_warn() (in module slideflow.util)": [[59, "slideflow.util.multi_warn"]], "path_input() (in module slideflow.util)": [[59, "slideflow.util.path_input"]], "path_to_ext() (in module slideflow.util)": [[59, "slideflow.util.path_to_ext"]], "path_to_name() (in module slideflow.util)": [[59, "slideflow.util.path_to_name"]], "read_annotations() (in module slideflow.util)": [[59, "slideflow.util.read_annotations"]], "relative_path() (in module slideflow.util)": [[59, "slideflow.util.relative_path"]], "render() (imgbatchspeedcolumn method)": [[59, "slideflow.util.ImgBatchSpeedColumn.render"]], "render() (labeledmofncompletecolumn method)": [[59, "slideflow.util.LabeledMofNCompleteColumn.render"]], "render() (tileextractionspeedcolumn method)": [[59, "slideflow.util.TileExtractionSpeedColumn.render"]], "setlogginglevel() (in module slideflow.util)": [[59, "slideflow.util.setLoggingLevel"]], "set_ignore_sigint() (in module slideflow.util)": [[59, "slideflow.util.set_ignore_sigint"]], "slideflow.util": [[59, "module-slideflow.util"]], "split_list() (in module slideflow.util)": [[59, "slideflow.util.split_list"]], "tfrecord_heatmap() (in module slideflow.util)": [[59, "slideflow.util.tfrecord_heatmap"]], "tile_size_label() (in module slideflow.util)": [[59, "slideflow.util.tile_size_label"]], "to_onehot() (in module slideflow.util)": [[59, "slideflow.util.to_onehot"]], "update_results_log() (in module slideflow.util)": [[59, "slideflow.util.update_results_log"]], "write_json() (in module slideflow.util)": [[59, "slideflow.util.write_json"]], "yes_no_input() (in module slideflow.util)": [[59, "slideflow.util.yes_no_input"]]}})