Index

Symbols

--channels_out dacapo-segment-blockwise command line option --context dacapo-segment-blockwise command line option --criterion dacapo-apply command line option --input_container dacapo-apply command line option dacapo-predict command line option dacapo-run-blockwise command line option dacapo-segment-blockwise command line option --input_dataset dacapo-apply command line option dacapo-predict command line option dacapo-run-blockwise command line option dacapo-segment-blockwise command line option --iteration dacapo-apply command line option dacapo-predict command line option dacapo-validate command line option --log-level dacapo command line option --max_retries dacapo-run-blockwise command line option dacapo-segment-blockwise command line option --no-validation dacapo-train command line option --num_workers dacapo-apply command line option dacapo-predict command line option dacapo-run-blockwise command line option dacapo-segment-blockwise command line option dacapo-validate command line option --output_container dacapo-run-blockwise command line option dacapo-segment-blockwise command line option --output_dataset dacapo-run-blockwise command line option dacapo-segment-blockwise command line option --output_dtype dacapo-apply command line option dacapo-predict command line option dacapo-run-blockwise command line option dacapo-validate command line option --output_path dacapo-apply command line option dacapo-predict command line option --output_roi dacapo-predict command line option --overwrite dacapo-apply command line option dacapo-predict command line option dacapo-run-blockwise command line option dacapo-segment-blockwise command line option dacapo-validate command line option --parameters dacapo-apply command line option --read_roi_size dacapo-run-blockwise command line option dacapo-segment-blockwise command line option --roi dacapo-apply command line option --run-name dacapo-apply command line option dacapo-predict command line option dacapo-train command line option dacapo-validate command line option --segment_function_file dacapo-segment-blockwise command line option --timeout dacapo-run-blockwise command line option dacapo-segment-blockwise command line option --total_roi dacapo-run-blockwise command line option dacapo-segment-blockwise command line option --validation_dataset dacapo-apply command line option --worker_file dacapo-run-blockwise command line option --write_roi_size dacapo-run-blockwise command line option dacapo-segment-blockwise command line option

-c dacapo-apply command line option dacapo-segment-blockwise command line option -channels_out dacapo-run-blockwise command line option -co dacapo-run-blockwise command line option dacapo-segment-blockwise command line option -dt dacapo-apply command line option dacapo-predict command line option dacapo-run-blockwise command line option dacapo-validate command line option -i dacapo-apply command line option dacapo-predict command line option dacapo-validate command line option -ic dacapo-apply command line option dacapo-predict command line option dacapo-run-blockwise command line option dacapo-segment-blockwise command line option -id dacapo-apply command line option dacapo-predict command line option dacapo-run-blockwise command line option dacapo-segment-blockwise command line option -mr dacapo-run-blockwise command line option dacapo-segment-blockwise command line option -nw dacapo-run-blockwise command line option dacapo-segment-blockwise command line option -oc dacapo-run-blockwise command line option dacapo-segment-blockwise command line option -od dacapo-run-blockwise command line option dacapo-segment-blockwise command line option -op dacapo-apply command line option dacapo-predict command line option -ow dacapo-apply command line option dacapo-predict command line option dacapo-run-blockwise command line option dacapo-segment-blockwise command line option dacapo-validate command line option -p dacapo-apply command line option -r dacapo-apply command line option dacapo-predict command line option dacapo-train command line option dacapo-validate command line option -roi dacapo-apply command line option dacapo-predict command line option -rr dacapo-run-blockwise command line option dacapo-segment-blockwise command line option -sf dacapo-segment-blockwise command line option -t dacapo-run-blockwise command line option dacapo-segment-blockwise command line option -tr dacapo-run-blockwise command line option dacapo-segment-blockwise command line option -vd dacapo-apply command line option -w dacapo-apply command line option dacapo-predict command line option dacapo-run-blockwise command line option dacapo-validate command line option -wr dacapo-run-blockwise command line option dacapo-segment-blockwise command line option

_

__attrs_post_init__() (dacapo.experiments.arraytypes.intensities.IntensitiesArray method) (dacapo.experiments.arraytypes.IntensitiesArray method) (dacapo.experiments.datasplits.datasets.arrays.concat_array_config.ConcatArrayConfig method) (dacapo.experiments.datasplits.datasets.arrays.ConcatArrayConfig method) __augment() (dacapo.gp.gamma_noise.GammaAugment method) (dacapo.gp.GammaAugment method) __enter__() (dacapo.experiments.trainers.dummy_trainer.DummyTrainer method) (dacapo.experiments.trainers.DummyTrainer method) (dacapo.experiments.trainers.gunpowder_trainer.GunpowderTrainer method) (dacapo.experiments.trainers.GunpowderTrainer method) __eq__() (dacapo.experiments.datasplits.datasets.Dataset method) (dacapo.experiments.datasplits.datasets.dataset.Dataset method) __exception (dacapo.ext.NoSuchModule attribute) __exit__() (dacapo.experiments.trainers.dummy_trainer.DummyTrainer method) (dacapo.experiments.trainers.DummyTrainer method) (dacapo.experiments.trainers.gunpowder_trainer.GunpowderTrainer method) (dacapo.experiments.trainers.GunpowderTrainer method) __find_boundaries() (dacapo.experiments.tasks.predictors.inner_distance_predictor.InnerDistancePredictor method) (dacapo.experiments.tasks.predictors.InnerDistancePredictor method) __generate_semantic_seg_dataset_crop() (dacapo.experiments.datasplits.datasplit_generator.DataSplitGenerator method) (dacapo.experiments.datasplits.DataSplitGenerator method) __generate_semantic_seg_datasplit() (dacapo.experiments.datasplits.datasplit_generator.DataSplitGenerator method) (dacapo.experiments.datasplits.DataSplitGenerator method) __getattr__() (dacapo.ext.NoSuchModule method) __getitem__() (dacapo.experiments.datasplits.datasplit_generator.CustomEnumMeta method) __hash__() (dacapo.experiments.datasplits.datasets.Dataset method) (dacapo.experiments.datasplits.datasets.dataset.Dataset method) __init__() (dacapo.blockwise.blockwise_task.DaCapoBlockwiseTask method) (dacapo.blockwise.DaCapoBlockwiseTask method) (dacapo.experiments.datasplits.datasets.dummy_dataset.DummyDataset method) (dacapo.experiments.datasplits.datasets.DummyDataset method) (dacapo.experiments.datasplits.datasets.raw_gt_dataset.RawGTDataset method) (dacapo.experiments.datasplits.datasets.RawGTDataset method) (dacapo.experiments.datasplits.DatasetSpec method) (dacapo.experiments.datasplits.DataSplit method) (dacapo.experiments.datasplits.datasplit.DataSplit method) (dacapo.experiments.datasplits.datasplit_generator.DatasetSpec method) (dacapo.experiments.datasplits.datasplit_generator.DataSplitGenerator method) (dacapo.experiments.datasplits.DataSplitGenerator method) (dacapo.experiments.datasplits.dummy_datasplit.DummyDataSplit method) (dacapo.experiments.datasplits.DummyDataSplit method) (dacapo.experiments.datasplits.train_validate_datasplit.TrainValidateDataSplit method) (dacapo.experiments.datasplits.train_validate_datasplit_config.TrainValidateDataSplitConfig method) (dacapo.experiments.datasplits.TrainValidateDataSplit method) (dacapo.experiments.datasplits.TrainValidateDataSplitConfig method) (dacapo.experiments.starts.cosem_start.CosemStart method) (dacapo.experiments.starts.cosem_start_config.CosemStartConfig method) (dacapo.experiments.starts.CosemStart method) (dacapo.experiments.starts.CosemStartConfig method) (dacapo.experiments.starts.Start method) (dacapo.experiments.starts.start.Start method) (dacapo.experiments.starts.start_config.StartConfig method) (dacapo.experiments.starts.StartConfig method) (dacapo.experiments.tasks.affinities_task.AffinitiesTask method) (dacapo.experiments.tasks.AffinitiesTask method) (dacapo.experiments.tasks.distance_task.DistanceTask method) (dacapo.experiments.tasks.DistanceTask method) (dacapo.experiments.tasks.dummy_task.DummyTask method) (dacapo.experiments.tasks.DummyTask method) (dacapo.experiments.tasks.hot_distance_task.HotDistanceTask method) (dacapo.experiments.tasks.HotDistanceTask method) (dacapo.experiments.tasks.inner_distance_task.InnerDistanceTask method) (dacapo.experiments.tasks.InnerDistanceTask method) (dacapo.experiments.trainers.dummy_trainer.DummyTrainer method) (dacapo.experiments.trainers.DummyTrainer method) (dacapo.store.weights_store.Weights method)

__init_db() (dacapo.store.mongo_config_store.MongoConfigStore method) __iter__() (dacapo.experiments.trainers.gunpowder_trainer.GunpowderTrainer method) (dacapo.experiments.trainers.GunpowderTrainer method) __load() (dacapo.store.file_config_store.FileConfigStore method) __name (dacapo.ext.NoSuchModule attribute) __normalize() (dacapo.experiments.tasks.predictors.inner_distance_predictor.InnerDistancePredictor method) (dacapo.experiments.tasks.predictors.InnerDistancePredictor method) __open_collections() (dacapo.store.mongo_config_store.MongoConfigStore method) __parse_options() (dacapo.Options method) (dacapo.options.Options method) __parse_options_from_file() (dacapo.Options method) (dacapo.options.Options method) __repr__() (dacapo.experiments.datasplits.datasets.Dataset method) (dacapo.experiments.datasplits.datasets.dataset.Dataset method) __same_doc() (dacapo.store.mongo_config_store.MongoConfigStore method) __save_insert() (dacapo.store.file_config_store.FileConfigStore method) (dacapo.store.mongo_config_store.MongoConfigStore method) __str__ (dacapo.experiments.datasplits.datasplit_generator.CustomEnum attribute) __str__() (dacapo.experiments.datasplits.datasets.Dataset method) (dacapo.experiments.datasplits.datasets.dataset.Dataset method) (dacapo.experiments.datasplits.DatasetSpec method) (dacapo.experiments.datasplits.datasplit_generator.CustomEnum method) (dacapo.experiments.datasplits.datasplit_generator.DatasetSpec method) (dacapo.experiments.datasplits.datasplit_generator.DatasetType method) (dacapo.experiments.datasplits.datasplit_generator.DataSplitGenerator method) (dacapo.experiments.datasplits.datasplit_generator.SegmentationType method) (dacapo.experiments.datasplits.DataSplitGenerator method) (dacapo.experiments.datasplits.keys.ArrayKey method) (dacapo.experiments.datasplits.keys.DataKey method) (dacapo.experiments.datasplits.keys.GraphKey method) (dacapo.experiments.datasplits.keys.keys.ArrayKey method) (dacapo.experiments.datasplits.keys.keys.DataKey method) (dacapo.experiments.datasplits.keys.keys.GraphKey method) (dacapo.store.config_store.DuplicateNameError method) __traceback_str (dacapo.ext.NoSuchModule attribute) __typed_structure() (dacapo.store.converter.TypedConverter method) __typed_unstructure() (dacapo.store.converter.TypedConverter method) _axes (dacapo.experiments.datasplits.datasets.arrays.zarr_array_config.ZarrArrayConfig attribute) (dacapo.experiments.datasplits.datasets.arrays.ZarrArrayConfig attribute) _device (dacapo.compute_context.local_torch.LocalTorch attribute) (dacapo.compute_context.LocalTorch attribute) _eval_shape_increase (dacapo.experiments.architectures.cnnectome_unet_config.CNNectomeUNetConfig attribute) (dacapo.experiments.architectures.CNNectomeUNetConfig attribute) _grow_boundaries() (dacapo.experiments.tasks.predictors.affinities_predictor.AffinitiesPredictor method) (dacapo.experiments.tasks.predictors.AffinitiesPredictor method) _gt_key (dacapo.experiments.trainers.AugmentConfig attribute) (dacapo.experiments.trainers.gp_augments.augment_config.AugmentConfig attribute) (dacapo.experiments.trainers.gp_augments.AugmentConfig attribute) _mask_key (dacapo.experiments.trainers.AugmentConfig attribute) (dacapo.experiments.trainers.gp_augments.augment_config.AugmentConfig attribute) (dacapo.experiments.trainers.gp_augments.AugmentConfig attribute) _member_names_ (dacapo.experiments.datasplits.datasplit_generator.CustomEnumMeta attribute) _neuroglancer_layers() (dacapo.experiments.datasplits.datasets.Dataset method) (dacapo.experiments.datasplits.datasets.dataset.Dataset method) _raw_key (dacapo.experiments.trainers.AugmentConfig attribute) (dacapo.experiments.trainers.gp_augments.augment_config.AugmentConfig attribute) (dacapo.experiments.trainers.gp_augments.AugmentConfig attribute) _spec (dacapo.utils.pipeline.ZerosSource attribute) _wrap_command() (dacapo.compute_context.Bsub method) (dacapo.compute_context.bsub.Bsub method) (dacapo.compute_context.compute_context.ComputeContext method) (dacapo.compute_context.ComputeContext method) (dacapo.compute_context.local_torch.LocalTorch method) (dacapo.compute_context.LocalTorch method)

A

activation (dacapo.experiments.architectures.cnnectome_unet.CNNectomeUNet attribute) (dacapo.experiments.architectures.CNNectomeUNet attribute) activation_on_upsample (dacapo.experiments.architectures.cnnectome_unet.CNNectomeUNet attribute) (dacapo.experiments.architectures.cnnectome_unet.CNNectomeUNetModule attribute) (dacapo.experiments.architectures.CNNectomeUNet attribute) add_iteration_scores() (dacapo.experiments.validation_scores.ValidationScores method), [1] (dacapo.experiments.ValidationScores method), [1] add_iteration_stats() (dacapo.experiments.training_stats.TrainingStats method) (dacapo.experiments.TrainingStats method) add_scalar_layer() (in module dacapo.utils.view) add_seg_layer() (in module dacapo.utils.view) AffinitiesLoss (class in dacapo.experiments.tasks.losses) (class in dacapo.experiments.tasks.losses.affinities_loss) AffinitiesPredictor (class in dacapo.experiments.tasks.predictors) (class in dacapo.experiments.tasks.predictors.affinities_predictor) AffinitiesTask (class in dacapo.experiments.tasks) (class in dacapo.experiments.tasks.affinities_task) AffinitiesTaskConfig (class in dacapo.experiments.tasks) (class in dacapo.experiments.tasks.affinities_task_config) affs_weight_clipmax (dacapo.experiments.tasks.affinities_task_config.AffinitiesTaskConfig attribute), [1] (dacapo.experiments.tasks.AffinitiesTaskConfig attribute), [1] (dacapo.experiments.tasks.predictors.affinities_predictor.AffinitiesPredictor attribute), [1] (dacapo.experiments.tasks.predictors.AffinitiesPredictor attribute), [1] affs_weight_clipmin (dacapo.experiments.tasks.affinities_task_config.AffinitiesTaskConfig attribute), [1] (dacapo.experiments.tasks.AffinitiesTaskConfig attribute), [1] (dacapo.experiments.tasks.predictors.affinities_predictor.AffinitiesPredictor attribute), [1] (dacapo.experiments.tasks.predictors.AffinitiesPredictor attribute), [1] AnnotationArray (class in dacapo.experiments.arraytypes) (class in dacapo.experiments.arraytypes.annotations) apply() (in module dacapo) (in module dacapo.apply) apply_run() (in module dacapo.apply) Architecture (class in dacapo.experiments.architectures) (class in dacapo.experiments.architectures.architecture) architecture (dacapo.experiments.Model attribute), [1] (dacapo.experiments.model.Model attribute), [1] (dacapo.experiments.run.Run attribute), [1] architecture_config (dacapo.experiments.run_config.RunConfig attribute) (dacapo.experiments.RunConfig attribute) architecture_type (dacapo.experiments.architectures.cnnectome_unet_config.CNNectomeUNetConfig attribute) (dacapo.experiments.architectures.CNNectomeUNetConfig attribute) (dacapo.experiments.architectures.dummy_architecture_config.DummyArchitectureConfig attribute), [1] (dacapo.experiments.architectures.DummyArchitectureConfig attribute), [1] architecture_type() (dacapo.experiments.architectures.cnnectome_unet_config.CNNectomeUNetConfig method) (dacapo.experiments.architectures.CNNectomeUNetConfig method) ArchitectureConfig (class in dacapo.experiments.architectures) (class in dacapo.experiments.architectures.architecture_config) architectures (dacapo.store.config_store.ConfigStore attribute), [1] (dacapo.store.file_config_store.FileConfigStore property) (dacapo.store.mongo_config_store.MongoConfigStore attribute) ArgmaxPostProcessor (class in dacapo.experiments.tasks.post_processors) (class in dacapo.experiments.tasks.post_processors.argmax_post_processor) ArgmaxPostProcessorParameters (class in dacapo.experiments.tasks.post_processors) (class in dacapo.experiments.tasks.post_processors.argmax_post_processor_parameters) array() (dacapo.experiments.datasplits.datasets.arrays.array_config.ArrayConfig method) (dacapo.experiments.datasplits.datasets.arrays.ArrayConfig method) (dacapo.experiments.datasplits.datasets.arrays.binarize_array_config.BinarizeArrayConfig method) (dacapo.experiments.datasplits.datasets.arrays.BinarizeArrayConfig method) (dacapo.experiments.datasplits.datasets.arrays.concat_array_config.ConcatArrayConfig method) (dacapo.experiments.datasplits.datasets.arrays.ConcatArrayConfig method) (dacapo.experiments.datasplits.datasets.arrays.constant_array_config.ConstantArrayConfig method) (dacapo.experiments.datasplits.datasets.arrays.ConstantArrayConfig method) (dacapo.experiments.datasplits.datasets.arrays.crop_array_config.CropArrayConfig method) (dacapo.experiments.datasplits.datasets.arrays.CropArrayConfig method) (dacapo.experiments.datasplits.datasets.arrays.dummy_array_config.DummyArrayConfig method) (dacapo.experiments.datasplits.datasets.arrays.DummyArrayConfig method) (dacapo.experiments.datasplits.datasets.arrays.dvid_array_config.DVIDArrayConfig method) (dacapo.experiments.datasplits.datasets.arrays.DVIDArrayConfig method) (dacapo.experiments.datasplits.datasets.arrays.IntensitiesArrayConfig method) (dacapo.experiments.datasplits.datasets.arrays.intensity_array_config.IntensitiesArrayConfig method) (dacapo.experiments.datasplits.datasets.arrays.logical_or_array_config.LogicalOrArrayConfig method) (dacapo.experiments.datasplits.datasets.arrays.LogicalOrArrayConfig method) (dacapo.experiments.datasplits.datasets.arrays.merge_instances_array_config.MergeInstancesArrayConfig method) (dacapo.experiments.datasplits.datasets.arrays.MergeInstancesArrayConfig method) (dacapo.experiments.datasplits.datasets.arrays.missing_annotations_mask_config.MissingAnnotationsMaskConfig method) (dacapo.experiments.datasplits.datasets.arrays.MissingAnnotationsMaskConfig method) (dacapo.experiments.datasplits.datasets.arrays.ones_array_config.OnesArrayConfig method) (dacapo.experiments.datasplits.datasets.arrays.OnesArrayConfig method) (dacapo.experiments.datasplits.datasets.arrays.resampled_array_config.ResampledArrayConfig method) (dacapo.experiments.datasplits.datasets.arrays.ResampledArrayConfig method) (dacapo.experiments.datasplits.datasets.arrays.sum_array_config.SumArrayConfig method) (dacapo.experiments.datasplits.datasets.arrays.SumArrayConfig method) (dacapo.experiments.datasplits.datasets.arrays.tiff_array_config.TiffArrayConfig method) (dacapo.experiments.datasplits.datasets.arrays.zarr_array_config.ZarrArrayConfig method) (dacapo.experiments.datasplits.datasets.arrays.ZarrArrayConfig method)

array_identifier() (dacapo.store.array_store.LocalContainerIdentifier method) array_key (dacapo.gp.copy.CopyMask attribute), [1] (dacapo.gp.CopyMask attribute), [1] array_store (dacapo.utils.view.BestScore attribute), [1] (dacapo.utils.view.NeuroglancerRunViewer attribute) ArrayConfig (class in dacapo.experiments.datasplits.datasets.arrays) (class in dacapo.experiments.datasplits.datasets.arrays.array_config) ArrayEvaluator (class in dacapo.experiments.tasks.evaluators.binary_segmentation_evaluator) ArrayKey (class in dacapo.experiments.datasplits.keys) (class in dacapo.experiments.datasplits.keys.keys) arrays (dacapo.gp.gamma_noise.GammaAugment attribute), [1] (dacapo.gp.GammaAugment attribute), [1] (dacapo.store.config_store.ConfigStore attribute), [1] (dacapo.store.file_config_store.FileConfigStore property) (dacapo.store.mongo_config_store.MongoConfigStore attribute) ArrayStore (class in dacapo.store.array_store) ArrayType (class in dacapo.experiments.arraytypes.arraytype) attention (dacapo.experiments.architectures.cnnectome_unet.CNNectomeUNetModule attribute) AttentionBlockModule (class in dacapo.experiments.architectures.cnnectome_unet) augmentation_probability (dacapo.experiments.trainers.gp_augments.elastic_config.ElasticAugmentConfig attribute) (dacapo.experiments.trainers.gp_augments.ElasticAugmentConfig attribute) (dacapo.experiments.trainers.gp_augments.intensity_config.IntensityAugmentConfig attribute) (dacapo.experiments.trainers.gp_augments.IntensityAugmentConfig attribute) (dacapo.experiments.trainers.gp_augments.simple_config.SimpleAugmentConfig attribute) (dacapo.experiments.trainers.gp_augments.SimpleAugmentConfig attribute) (dacapo.gp.elastic_augment_fuse.ElasticAugment attribute) (dacapo.gp.ElasticAugment attribute) AugmentConfig (class in dacapo.experiments.trainers) (class in dacapo.experiments.trainers.gp_augments) (class in dacapo.experiments.trainers.gp_augments.augment_config) augments (dacapo.experiments.trainers.gunpowder_trainer.GunpowderTrainer attribute), [1] (dacapo.experiments.trainers.gunpowder_trainer_config.GunpowderTrainerConfig attribute), [1] (dacapo.experiments.trainers.GunpowderTrainer attribute), [1] (dacapo.experiments.trainers.GunpowderTrainerConfig attribute), [1] axis_names (dacapo.experiments.datasplits.datasets.arrays.tiff_array_config.TiffArrayConfig attribute), [1]

B

background (dacapo.experiments.datasplits.datasets.arrays.binarize_array_config.BinarizeArrayConfig attribute), [1] (dacapo.experiments.datasplits.datasets.arrays.BinarizeArrayConfig attribute), [1] (dacapo.gp.reject_if_empty.RejectIfEmpty attribute) (dacapo.gp.RejectIfEmpty attribute) (dacapo.utils.pipeline.ExpandLabels attribute), [1] background_as_object (dacapo.experiments.tasks.affinities_task_config.AffinitiesTaskConfig attribute), [1] (dacapo.experiments.tasks.AffinitiesTaskConfig attribute), [1] (dacapo.experiments.tasks.predictors.affinities_predictor.AffinitiesPredictor attribute), [1] (dacapo.experiments.tasks.predictors.AffinitiesPredictor attribute), [1] balance_weights() (in module dacapo.utils.balance_weights) basedir (dacapo.store.local_array_store.LocalArrayStore attribute), [1] (dacapo.store.local_weights_store.LocalWeightsStore attribute), [1] batch_norm (dacapo.experiments.architectures.cnnectome_unet.AttentionBlockModule attribute) (dacapo.experiments.architectures.cnnectome_unet.CNNectomeUNet attribute) (dacapo.experiments.architectures.cnnectome_unet.CNNectomeUNetModule attribute) (dacapo.experiments.architectures.cnnectome_unet_config.CNNectomeUNetConfig attribute) (dacapo.experiments.architectures.CNNectomeUNet attribute) (dacapo.experiments.architectures.CNNectomeUNetConfig attribute) batch_size (dacapo.experiments.trainers.dummy_trainer.DummyTrainer attribute), [1] (dacapo.experiments.trainers.DummyTrainer attribute), [1] (dacapo.experiments.trainers.gunpowder_trainer.GunpowderTrainer attribute), [1] (dacapo.experiments.trainers.GunpowderTrainer attribute), [1] (dacapo.experiments.trainers.Trainer attribute), [1] (dacapo.experiments.trainers.trainer.Trainer attribute), [1] (dacapo.experiments.trainers.trainer_config.TrainerConfig attribute), [1] (dacapo.experiments.trainers.TrainerConfig attribute), [1] best_score (dacapo.utils.view.NeuroglancerRunViewer attribute), [1] best_scores (dacapo.experiments.tasks.evaluators.Evaluator attribute) (dacapo.experiments.tasks.evaluators.Evaluator property) (dacapo.experiments.tasks.evaluators.evaluator.Evaluator attribute) (dacapo.experiments.tasks.evaluators.evaluator.Evaluator property) best_validation_array() (dacapo.store.local_array_store.LocalArrayStore method), [1] BestScore (class in dacapo.utils.view) (in module dacapo.experiments.tasks.evaluators.evaluator) BG (in module dacapo.experiments.tasks.evaluators.binary_segmentation_evaluator) bias (dacapo.experiments.tasks.post_processors.watershed_post_processor_parameters.WatershedPostProcessorParameters attribute), [1] (dacapo.experiments.tasks.post_processors.WatershedPostProcessorParameters attribute), [1] billing (dacapo.compute_context.Bsub attribute), [1] (dacapo.compute_context.bsub.Bsub attribute), [1]

binarize_gt (dacapo.experiments.datasplits.datasplit_generator.DataSplitGenerator attribute) (dacapo.experiments.datasplits.DataSplitGenerator attribute) BinarizeArrayConfig (class in dacapo.experiments.datasplits.datasets.arrays) (class in dacapo.experiments.datasplits.datasets.arrays.binarize_array_config) BinaryArray (class in dacapo.experiments.arraytypes.binary) BinarySegmentationEvaluationScores (class in dacapo.experiments.tasks.evaluators) (class in dacapo.experiments.tasks.evaluators.binary_segmentation_evaluation_scores) BinarySegmentationEvaluator (class in dacapo.experiments.tasks.evaluators) (class in dacapo.experiments.tasks.evaluators.binary_segmentation_evaluator) blipp_score (dacapo.experiments.tasks.evaluators.dummy_evaluation_scores.DummyEvaluationScores attribute), [1] (dacapo.experiments.tasks.evaluators.DummyEvaluationScores attribute), [1] bokeh_plot_runs() (in module dacapo.plot) bounds() (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluation_scores.BinarySegmentationEvaluationScores static method) (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluation_scores.MultiChannelBinarySegmentationEvaluationScores static method) (dacapo.experiments.tasks.evaluators.BinarySegmentationEvaluationScores static method) (dacapo.experiments.tasks.evaluators.dummy_evaluation_scores.DummyEvaluationScores method) (dacapo.experiments.tasks.evaluators.dummy_evaluation_scores.DummyEvaluationScores static method) (dacapo.experiments.tasks.evaluators.DummyEvaluationScores method) (dacapo.experiments.tasks.evaluators.DummyEvaluationScores static method) (dacapo.experiments.tasks.evaluators.evaluation_scores.EvaluationScores method) (dacapo.experiments.tasks.evaluators.evaluation_scores.EvaluationScores static method) (dacapo.experiments.tasks.evaluators.EvaluationScores method) (dacapo.experiments.tasks.evaluators.EvaluationScores static method) (dacapo.experiments.tasks.evaluators.Evaluator method), [1] (dacapo.experiments.tasks.evaluators.evaluator.Evaluator method), [1] (dacapo.experiments.tasks.evaluators.instance_evaluation_scores.InstanceEvaluationScores method) (dacapo.experiments.tasks.evaluators.instance_evaluation_scores.InstanceEvaluationScores static method) (dacapo.experiments.tasks.evaluators.InstanceEvaluationScores method) (dacapo.experiments.tasks.evaluators.InstanceEvaluationScores static method) (dacapo.experiments.tasks.evaluators.MultiChannelBinarySegmentationEvaluationScores static method) Bsub (class in dacapo.compute_context) (class in dacapo.compute_context.bsub) build_batch_provider() (dacapo.experiments.trainers.dummy_trainer.DummyTrainer method), [1] (dacapo.experiments.trainers.DummyTrainer method), [1] (dacapo.experiments.trainers.gunpowder_trainer.GunpowderTrainer method) (dacapo.experiments.trainers.GunpowderTrainer method) (dacapo.experiments.trainers.Trainer method) (dacapo.experiments.trainers.trainer.Trainer method)

C

calculate_and_apply_padding() (dacapo.experiments.architectures.cnnectome_unet.AttentionBlockModule method) can_train() (dacapo.experiments.trainers.dummy_trainer.DummyTrainer method), [1] (dacapo.experiments.trainers.DummyTrainer method), [1] (dacapo.experiments.trainers.gunpowder_trainer.GunpowderTrainer method) (dacapo.experiments.trainers.GunpowderTrainer method) (dacapo.experiments.trainers.Trainer method) (dacapo.experiments.trainers.trainer.Trainer method) chain (dacapo.experiments.Model attribute), [1] (dacapo.experiments.model.Model attribute), [1] channel_names (dacapo.experiments.arraytypes.arraytype.ArrayType attribute) channel_scores (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluation_scores.MultiChannelBinarySegmentationEvaluationScores attribute), [1] (dacapo.experiments.tasks.evaluators.MultiChannelBinarySegmentationEvaluationScores attribute), [1] channels (dacapo.experiments.arraytypes.binary.BinaryArray attribute), [1] (dacapo.experiments.arraytypes.intensities.IntensitiesArray attribute), [1] (dacapo.experiments.arraytypes.IntensitiesArray attribute), [1] (dacapo.experiments.datasplits.datasets.arrays.concat_array_config.ConcatArrayConfig attribute), [1] (dacapo.experiments.datasplits.datasets.arrays.ConcatArrayConfig attribute), [1] (dacapo.experiments.starts.cosem_start.CosemStart attribute), [1] (dacapo.experiments.starts.CosemStart attribute), [1] (dacapo.experiments.starts.Start attribute), [1] (dacapo.experiments.starts.start.Start attribute), [1] (dacapo.experiments.tasks.distance_task_config.DistanceTaskConfig attribute), [1] (dacapo.experiments.tasks.DistanceTaskConfig attribute), [1] (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluator.BinarySegmentationEvaluator attribute), [1] (dacapo.experiments.tasks.evaluators.BinarySegmentationEvaluator attribute), [1] (dacapo.experiments.tasks.hot_distance_task_config.HotDistanceTaskConfig attribute), [1] (dacapo.experiments.tasks.HotDistanceTaskConfig attribute), [1] (dacapo.experiments.tasks.inner_distance_task_config.InnerDistanceTaskConfig attribute), [1] (dacapo.experiments.tasks.InnerDistanceTaskConfig attribute), [1] (dacapo.experiments.tasks.predictors.distance_predictor.DistancePredictor attribute), [1] (dacapo.experiments.tasks.predictors.DistancePredictor attribute), [1] (dacapo.experiments.tasks.predictors.hot_distance_predictor.HotDistancePredictor attribute), [1] (dacapo.experiments.tasks.predictors.HotDistancePredictor attribute), [1] (dacapo.experiments.tasks.predictors.inner_distance_predictor.InnerDistancePredictor attribute), [1] (dacapo.experiments.tasks.predictors.InnerDistancePredictor attribute), [1] channels_in (dacapo.experiments.architectures.dummy_architecture.DummyArchitecture attribute), [1] (dacapo.experiments.architectures.DummyArchitecture attribute), [1] channels_out (dacapo.experiments.architectures.dummy_architecture.DummyArchitecture attribute), [1] (dacapo.experiments.architectures.DummyArchitecture attribute), [1] check() (dacapo.experiments.starts.cosem_start.CosemStart method), [1] (dacapo.experiments.starts.CosemStart method), [1] check_class_name() (dacapo.experiments.datasplits.datasplit_generator.DataSplitGenerator method), [1] (dacapo.experiments.datasplits.DataSplitGenerator method), [1] class_name (dacapo.experiments.datasplits.datasplit_generator.DataSplitGenerator property) (dacapo.experiments.datasplits.DataSplitGenerator property) class_name() (dacapo.experiments.datasplits.datasplit_generator.DataSplitGenerator method) (dacapo.experiments.datasplits.DataSplitGenerator method) classes (dacapo.experiments.arraytypes.AnnotationArray attribute), [1] (dacapo.experiments.arraytypes.annotations.AnnotationArray attribute), [1] (dacapo.experiments.arraytypes.DistanceArray attribute), [1] (dacapo.experiments.arraytypes.distances.DistanceArray attribute), [1] (dacapo.experiments.arraytypes.probabilities.ProbabilityArray attribute), [1] (dacapo.experiments.arraytypes.ProbabilityArray attribute), [1] (dacapo.experiments.tasks.one_hot_task_config.OneHotTaskConfig attribute), [1] (dacapo.experiments.tasks.OneHotTaskConfig attribute), [1] (dacapo.experiments.tasks.predictors.hot_distance_predictor.HotDistancePredictor property) (dacapo.experiments.tasks.predictors.HotDistancePredictor property) (dacapo.experiments.tasks.predictors.one_hot_predictor.OneHotPredictor attribute), [1] (dacapo.experiments.tasks.predictors.OneHotPredictor attribute), [1] classes_separator_character (dacapo.experiments.datasplits.datasplit_generator.DataSplitGenerator attribute), [1] (dacapo.experiments.datasplits.DataSplitGenerator attribute), [1] cli() (in module dacapo.blockwise.argmax_worker) (in module dacapo.blockwise.predict_worker) (in module dacapo.blockwise.relabel_worker) (in module dacapo.blockwise.segment_worker) (in module dacapo.blockwise.threshold_worker) client (dacapo.store.mongo_config_store.MongoConfigStore attribute), [1] (dacapo.store.mongo_stats_store.MongoStatsStore attribute), [1] clip (dacapo.experiments.trainers.gp_augments.intensity_config.IntensityAugmentConfig attribute), [1] (dacapo.experiments.trainers.gp_augments.IntensityAugmentConfig attribute), [1] clip_distance (dacapo.experiments.tasks.distance_task_config.DistanceTaskConfig attribute), [1] (dacapo.experiments.tasks.DistanceTaskConfig attribute), [1] (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluator.BinarySegmentationEvaluator attribute), [1] (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluator.CremiEvaluator attribute), [1] (dacapo.experiments.tasks.evaluators.BinarySegmentationEvaluator attribute), [1] (dacapo.experiments.tasks.hot_distance_task_config.HotDistanceTaskConfig attribute), [1] (dacapo.experiments.tasks.HotDistanceTaskConfig attribute), [1] (dacapo.experiments.tasks.inner_distance_task_config.InnerDistanceTaskConfig attribute), [1] (dacapo.experiments.tasks.InnerDistanceTaskConfig attribute), [1] clip_raw (dacapo.experiments.trainers.gunpowder_trainer.GunpowderTrainer attribute), [1] (dacapo.experiments.trainers.gunpowder_trainer_config.GunpowderTrainerConfig attribute), [1] (dacapo.experiments.trainers.GunpowderTrainer attribute), [1] (dacapo.experiments.trainers.GunpowderTrainerConfig attribute), [1] clipmax (dacapo.experiments.tasks.distance_task_config.DistanceTaskConfig attribute), [1] (dacapo.experiments.tasks.DistanceTaskConfig attribute), [1] (dacapo.experiments.tasks.predictors.distance_predictor.DistancePredictor attribute), [1] (dacapo.experiments.tasks.predictors.DistancePredictor attribute), [1] clipmin (dacapo.experiments.tasks.distance_task_config.DistanceTaskConfig attribute), [1] (dacapo.experiments.tasks.DistanceTaskConfig attribute), [1] (dacapo.experiments.tasks.predictors.distance_predictor.DistancePredictor attribute), [1] (dacapo.experiments.tasks.predictors.DistancePredictor attribute), [1] cls_fun() (in module dacapo.store.conversion_hooks) CNNectomeUNet (class in dacapo.experiments.architectures) (class in dacapo.experiments.architectures.cnnectome_unet) CNNectomeUNetConfig (class in dacapo.experiments.architectures) (class in dacapo.experiments.architectures.cnnectome_unet_config) CNNectomeUNetModule (class in dacapo.experiments.architectures.cnnectome_unet) compare() (dacapo.experiments.tasks.evaluators.Evaluator method), [1] (dacapo.experiments.tasks.evaluators.evaluator.Evaluator method), [1] (dacapo.experiments.validation_scores.ValidationScores method), [1] (dacapo.experiments.ValidationScores method), [1] compute() (dacapo.experiments.datasplits.datasplit_generator.DataSplitGenerator method), [1] (dacapo.experiments.datasplits.DataSplitGenerator method), [1] (dacapo.experiments.tasks.losses.affinities_loss.AffinitiesLoss method), [1] (dacapo.experiments.tasks.losses.AffinitiesLoss method), [1] (dacapo.experiments.tasks.losses.dummy_loss.DummyLoss method), [1] (dacapo.experiments.tasks.losses.DummyLoss method), [1] (dacapo.experiments.tasks.losses.hot_distance_loss.HotDistanceLoss method), [1] (dacapo.experiments.tasks.losses.HotDistanceLoss method), [1] (dacapo.experiments.tasks.losses.Loss method), [1] (dacapo.experiments.tasks.losses.loss.Loss method), [1] (dacapo.experiments.tasks.losses.mse_loss.MSELoss method), [1] (dacapo.experiments.tasks.losses.MSELoss method), [1] compute_context (dacapo.options.DaCapoConfig attribute), [1] compute_output_shape() (dacapo.experiments.Model method) (dacapo.experiments.model.Model method) ComputeContext (class in dacapo.compute_context) (class in dacapo.compute_context.compute_context) ConcatArrayConfig (class in dacapo.experiments.datasplits.datasets.arrays) (class in dacapo.experiments.datasplits.datasets.arrays.concat_array_config) config_file() (dacapo.Options class method) (dacapo.Options method) (dacapo.options.Options class method) (dacapo.options.Options method) ConfigStore (class in dacapo.store.config_store) connectivity (dacapo.utils.pipeline.Relabel attribute) constant (dacapo.experiments.datasplits.datasets.arrays.constant_array_config.ConstantArrayConfig attribute) (dacapo.experiments.datasplits.datasets.arrays.ConstantArrayConfig attribute) constant_upsample (dacapo.experiments.architectures.cnnectome_unet.CNNectomeUNet attribute), [1] (dacapo.experiments.architectures.cnnectome_unet.CNNectomeUNetModule attribute) (dacapo.experiments.architectures.cnnectome_unet_config.CNNectomeUNetConfig attribute), [1] (dacapo.experiments.architectures.CNNectomeUNet attribute), [1] (dacapo.experiments.architectures.CNNectomeUNetConfig attribute), [1] ConstantArrayConfig (class in dacapo.experiments.datasplits.datasets.arrays) (class in dacapo.experiments.datasplits.datasets.arrays.constant_array_config) container (dacapo.store.array_store.ArrayStore attribute) (dacapo.store.array_store.LocalArrayIdentifier attribute), [1] (dacapo.store.array_store.LocalContainerIdentifier attribute), [1] context (dacapo.experiments.tasks.post_processors.watershed_post_processor_parameters.WatershedPostProcessorParameters attribute), [1] (dacapo.experiments.tasks.post_processors.WatershedPostProcessorParameters attribute), [1]

contingency_table() (in module dacapo.utils.voi) control_point_displacement_sigma (dacapo.experiments.trainers.gp_augments.elastic_config.ElasticAugmentConfig attribute), [1] (dacapo.experiments.trainers.gp_augments.ElasticAugmentConfig attribute), [1] (dacapo.gp.elastic_augment_fuse.ElasticAugment attribute) (dacapo.gp.ElasticAugment attribute) control_point_spacing (dacapo.experiments.trainers.gp_augments.elastic_config.ElasticAugmentConfig attribute), [1] (dacapo.experiments.trainers.gp_augments.ElasticAugmentConfig attribute), [1] (dacapo.gp.elastic_augment_fuse.ElasticAugment attribute) (dacapo.gp.ElasticAugment attribute) conv (dacapo.experiments.architectures.dummy_architecture.DummyArchitecture attribute), [1] (dacapo.experiments.architectures.DummyArchitecture attribute), [1] conv_pass (dacapo.experiments.architectures.cnnectome_unet.ConvPass attribute), [1] converter (in module dacapo.store.converter) ConvPass (class in dacapo.experiments.architectures.cnnectome_unet) copy_key (dacapo.gp.copy.CopyMask attribute), [1] (dacapo.gp.CopyMask attribute), [1] CopyMask (class in dacapo.gp) (class in dacapo.gp.copy) CosemStart (class in dacapo.experiments.starts) (class in dacapo.experiments.starts.cosem_start) CosemStartConfig (class in dacapo.experiments.starts) (class in dacapo.experiments.starts.cosem_start_config) create_array() (dacapo.experiments.datasplits.datasets.arrays.constant_array_config.ConstantArrayConfig method) (dacapo.experiments.datasplits.datasets.arrays.ConstantArrayConfig method) (dacapo.experiments.datasplits.datasets.arrays.crop_array_config.CropArrayConfig method) (dacapo.experiments.datasplits.datasets.arrays.CropArrayConfig method) (dacapo.experiments.datasplits.datasets.arrays.merge_instances_array_config.MergeInstancesArrayConfig method) (dacapo.experiments.datasplits.datasets.arrays.MergeInstancesArrayConfig method) (dacapo.experiments.datasplits.datasets.arrays.ones_array_config.OnesArrayConfig method) (dacapo.experiments.datasplits.datasets.arrays.OnesArrayConfig method) (dacapo.experiments.datasplits.datasets.arrays.resampled_array_config.ResampledArrayConfig method) (dacapo.experiments.datasplits.datasets.arrays.ResampledArrayConfig method) create_array_store() (in module dacapo.store.create_store) create_compute_context() (in module dacapo.compute_context) (in module dacapo.compute_context.compute_context) create_config_store() (in module dacapo.store.create_store) create_distance_mask() (dacapo.experiments.tasks.predictors.distance_predictor.DistancePredictor method), [1] (dacapo.experiments.tasks.predictors.DistancePredictor method), [1] (dacapo.experiments.tasks.predictors.hot_distance_predictor.HotDistancePredictor method), [1] (dacapo.experiments.tasks.predictors.HotDistancePredictor method), [1] create_from_identifier() (in module dacapo.tmp) create_model() (dacapo.experiments.tasks.one_hot_task.OneHotTask method) (dacapo.experiments.tasks.OneHotTask method) (dacapo.experiments.tasks.predictors.affinities_predictor.AffinitiesPredictor method), [1] (dacapo.experiments.tasks.predictors.AffinitiesPredictor method), [1] (dacapo.experiments.tasks.predictors.distance_predictor.DistancePredictor method), [1] (dacapo.experiments.tasks.predictors.DistancePredictor method), [1] (dacapo.experiments.tasks.predictors.dummy_predictor.DummyPredictor method), [1] (dacapo.experiments.tasks.predictors.DummyPredictor method), [1] (dacapo.experiments.tasks.predictors.hot_distance_predictor.HotDistancePredictor method), [1] (dacapo.experiments.tasks.predictors.HotDistancePredictor method), [1] (dacapo.experiments.tasks.predictors.inner_distance_predictor.InnerDistancePredictor method), [1] (dacapo.experiments.tasks.predictors.InnerDistancePredictor method), [1] (dacapo.experiments.tasks.predictors.one_hot_predictor.OneHotPredictor method), [1] (dacapo.experiments.tasks.predictors.OneHotPredictor method), [1] (dacapo.experiments.tasks.predictors.Predictor method) (dacapo.experiments.tasks.predictors.predictor.Predictor method) (dacapo.experiments.tasks.pretrained_task.PretrainedTask method), [1] (dacapo.experiments.tasks.PretrainedTask method), [1] (dacapo.experiments.tasks.Task method) (dacapo.experiments.tasks.task.Task method) create_optimizer() (dacapo.experiments.trainers.dummy_trainer.DummyTrainer method), [1] (dacapo.experiments.trainers.DummyTrainer method), [1] (dacapo.experiments.trainers.gunpowder_trainer.GunpowderTrainer method) (dacapo.experiments.trainers.GunpowderTrainer method) (dacapo.experiments.trainers.Trainer method) (dacapo.experiments.trainers.trainer.Trainer method) create_stats_store() (in module dacapo.store.create_store) create_target() (dacapo.experiments.tasks.predictors.affinities_predictor.AffinitiesPredictor method), [1] (dacapo.experiments.tasks.predictors.AffinitiesPredictor method), [1] (dacapo.experiments.tasks.predictors.distance_predictor.DistancePredictor method), [1] (dacapo.experiments.tasks.predictors.DistancePredictor method), [1] (dacapo.experiments.tasks.predictors.dummy_predictor.DummyPredictor method), [1] (dacapo.experiments.tasks.predictors.DummyPredictor method), [1] (dacapo.experiments.tasks.predictors.hot_distance_predictor.HotDistancePredictor method), [1] (dacapo.experiments.tasks.predictors.HotDistancePredictor method), [1] (dacapo.experiments.tasks.predictors.inner_distance_predictor.InnerDistancePredictor method), [1] (dacapo.experiments.tasks.predictors.InnerDistancePredictor method), [1] (dacapo.experiments.tasks.predictors.one_hot_predictor.OneHotPredictor method), [1] (dacapo.experiments.tasks.predictors.OneHotPredictor method), [1] (dacapo.experiments.tasks.predictors.Predictor method) (dacapo.experiments.tasks.predictors.predictor.Predictor method) create_weight() (dacapo.experiments.tasks.predictors.affinities_predictor.AffinitiesPredictor method), [1] (dacapo.experiments.tasks.predictors.AffinitiesPredictor method), [1] (dacapo.experiments.tasks.predictors.distance_predictor.DistancePredictor method), [1] (dacapo.experiments.tasks.predictors.DistancePredictor method), [1] (dacapo.experiments.tasks.predictors.dummy_predictor.DummyPredictor method), [1] (dacapo.experiments.tasks.predictors.DummyPredictor method), [1] (dacapo.experiments.tasks.predictors.hot_distance_predictor.HotDistancePredictor method), [1] (dacapo.experiments.tasks.predictors.HotDistancePredictor method), [1] (dacapo.experiments.tasks.predictors.inner_distance_predictor.InnerDistancePredictor method), [1] (dacapo.experiments.tasks.predictors.InnerDistancePredictor method), [1] (dacapo.experiments.tasks.predictors.one_hot_predictor.OneHotPredictor method), [1] (dacapo.experiments.tasks.predictors.OneHotPredictor method), [1] (dacapo.experiments.tasks.predictors.Predictor method) (dacapo.experiments.tasks.predictors.predictor.Predictor method) create_weights_store() (in module dacapo.store.create_store) CreatePoints (class in dacapo.utils.pipeline) cremieval (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluator.ArrayEvaluator attribute), [1] CremiEvaluator (class in dacapo.experiments.tasks.evaluators.binary_segmentation_evaluator) criteria (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluation_scores.BinarySegmentationEvaluationScores attribute) (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluation_scores.MultiChannelBinarySegmentationEvaluationScores property) (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluator.BinarySegmentationEvaluator attribute), [1] (dacapo.experiments.tasks.evaluators.BinarySegmentationEvaluationScores attribute) (dacapo.experiments.tasks.evaluators.BinarySegmentationEvaluator attribute), [1] (dacapo.experiments.tasks.evaluators.dummy_evaluation_scores.DummyEvaluationScores attribute) (dacapo.experiments.tasks.evaluators.dummy_evaluator.DummyEvaluator attribute), [1] (dacapo.experiments.tasks.evaluators.DummyEvaluationScores attribute) (dacapo.experiments.tasks.evaluators.DummyEvaluator attribute), [1] (dacapo.experiments.tasks.evaluators.evaluation_scores.EvaluationScores attribute) (dacapo.experiments.tasks.evaluators.evaluation_scores.EvaluationScores property) (dacapo.experiments.tasks.evaluators.EvaluationScores attribute) (dacapo.experiments.tasks.evaluators.EvaluationScores property) (dacapo.experiments.tasks.evaluators.Evaluator property) (dacapo.experiments.tasks.evaluators.evaluator.Evaluator property) (dacapo.experiments.tasks.evaluators.instance_evaluation_scores.InstanceEvaluationScores attribute) (dacapo.experiments.tasks.evaluators.instance_evaluator.InstanceEvaluator attribute), [1] (dacapo.experiments.tasks.evaluators.InstanceEvaluationScores attribute) (dacapo.experiments.tasks.evaluators.InstanceEvaluator attribute), [1] (dacapo.experiments.tasks.evaluators.MultiChannelBinarySegmentationEvaluationScores property) (dacapo.experiments.validation_scores.ValidationScores property) (dacapo.experiments.ValidationScores property) criteria() (dacapo.experiments.validation_scores.ValidationScores method) (dacapo.experiments.ValidationScores method) criterion (dacapo.experiments.starts.cosem_start.CosemStart attribute), [1] (dacapo.experiments.starts.cosem_start_config.CosemStartConfig attribute) (dacapo.experiments.starts.CosemStart attribute), [1] (dacapo.experiments.starts.CosemStartConfig attribute) (dacapo.experiments.starts.Start attribute) (dacapo.experiments.starts.start.Start attribute) (dacapo.experiments.starts.start_config.StartConfig attribute), [1] (dacapo.experiments.starts.StartConfig attribute), [1] crop() (dacapo.experiments.architectures.cnnectome_unet.Upsample method), [1] crop_factor (dacapo.experiments.architectures.cnnectome_unet.Upsample attribute), [1] crop_to_factor() (dacapo.experiments.architectures.cnnectome_unet.Upsample method), [1] CropArrayConfig (class in dacapo.experiments.datasplits.datasets.arrays) (class in dacapo.experiments.datasplits.datasets.arrays.crop_array_config) CustomEnum (class in dacapo.experiments.datasplits.datasplit_generator) CustomEnumMeta (class in dacapo.experiments.datasplits.datasplit_generator)

D

dacapo module, [1], [2], [3] dacapo command line option --log-level dacapo-apply command line option --criterion --input_container --input_dataset --iteration --num_workers --output_dtype --output_path --overwrite --parameters --roi --run-name --validation_dataset -c -dt -i -ic -id -op -ow -p -r -roi -vd -w dacapo-predict command line option --input_container --input_dataset --iteration --num_workers --output_dtype --output_path --output_roi --overwrite --run-name -dt -i -ic -id -op -ow -r -roi -w dacapo-run-blockwise command line option --input_container --input_dataset --max_retries --num_workers --output_container --output_dataset --output_dtype --overwrite --read_roi_size --timeout --total_roi --worker_file --write_roi_size -channels_out -co -dt -ic -id -mr -nw -oc -od -ow -rr -t -tr -w -wr dacapo-segment-blockwise command line option --channels_out --context --input_container --input_dataset --max_retries --num_workers --output_container --output_dataset --overwrite --read_roi_size --segment_function_file --timeout --total_roi --write_roi_size -c -co -ic -id -mr -nw -oc -od -ow -rr -sf -t -tr -wr dacapo-train command line option --no-validation --run-name -r dacapo-validate command line option --iteration --num_workers --output_dtype --overwrite --run-name -dt -i -ow -r -w dacapo.apply module dacapo.blockwise module dacapo.blockwise.argmax_worker module dacapo.blockwise.blockwise_task module dacapo.blockwise.empanada_function module dacapo.blockwise.predict_worker module dacapo.blockwise.relabel_worker module dacapo.blockwise.scheduler module dacapo.blockwise.segment_worker module dacapo.blockwise.threshold_worker module dacapo.blockwise.watershed_function module dacapo.compute_context module dacapo.compute_context.bsub module dacapo.compute_context.compute_context module dacapo.compute_context.local_torch module dacapo.experiments module dacapo.experiments.architectures module dacapo.experiments.architectures.architecture module dacapo.experiments.architectures.architecture_config module dacapo.experiments.architectures.cnnectome_unet module dacapo.experiments.architectures.cnnectome_unet_config module dacapo.experiments.architectures.dummy_architecture module dacapo.experiments.architectures.dummy_architecture_config module dacapo.experiments.arraytypes module dacapo.experiments.arraytypes.annotations module dacapo.experiments.arraytypes.arraytype module dacapo.experiments.arraytypes.binary module dacapo.experiments.arraytypes.distances module dacapo.experiments.arraytypes.embedding module dacapo.experiments.arraytypes.intensities module dacapo.experiments.arraytypes.mask module dacapo.experiments.arraytypes.probabilities module dacapo.experiments.datasplits module dacapo.experiments.datasplits.datasets module dacapo.experiments.datasplits.datasets.arrays module dacapo.experiments.datasplits.datasets.arrays.array_config module dacapo.experiments.datasplits.datasets.arrays.binarize_array_config module dacapo.experiments.datasplits.datasets.arrays.concat_array_config module dacapo.experiments.datasplits.datasets.arrays.constant_array_config module dacapo.experiments.datasplits.datasets.arrays.crop_array_config module dacapo.experiments.datasplits.datasets.arrays.dummy_array_config module dacapo.experiments.datasplits.datasets.arrays.dvid_array_config module dacapo.experiments.datasplits.datasets.arrays.intensity_array_config module dacapo.experiments.datasplits.datasets.arrays.logical_or_array_config module dacapo.experiments.datasplits.datasets.arrays.merge_instances_array_config module dacapo.experiments.datasplits.datasets.arrays.missing_annotations_mask_config module dacapo.experiments.datasplits.datasets.arrays.ones_array_config module dacapo.experiments.datasplits.datasets.arrays.resampled_array_config module dacapo.experiments.datasplits.datasets.arrays.sum_array_config module dacapo.experiments.datasplits.datasets.arrays.tiff_array_config module dacapo.experiments.datasplits.datasets.arrays.zarr_array_config module dacapo.experiments.datasplits.datasets.dataset module dacapo.experiments.datasplits.datasets.dataset_config module dacapo.experiments.datasplits.datasets.dummy_dataset module dacapo.experiments.datasplits.datasets.dummy_dataset_config module dacapo.experiments.datasplits.datasets.graphstores module dacapo.experiments.datasplits.datasets.graphstores.graph_source_config module dacapo.experiments.datasplits.datasets.raw_gt_dataset module dacapo.experiments.datasplits.datasets.raw_gt_dataset_config module dacapo.experiments.datasplits.datasets.simple module dacapo.experiments.datasplits.datasplit module dacapo.experiments.datasplits.datasplit_config module dacapo.experiments.datasplits.datasplit_generator module dacapo.experiments.datasplits.dummy_datasplit module dacapo.experiments.datasplits.dummy_datasplit_config module dacapo.experiments.datasplits.keys module dacapo.experiments.datasplits.keys.keys module dacapo.experiments.datasplits.simple_config module dacapo.experiments.datasplits.train_validate_datasplit module dacapo.experiments.datasplits.train_validate_datasplit_config module dacapo.experiments.model module dacapo.experiments.run module dacapo.experiments.run_config module dacapo.experiments.starts module dacapo.experiments.starts.cosem_start module dacapo.experiments.starts.cosem_start_config module dacapo.experiments.starts.start module dacapo.experiments.starts.start_config module dacapo.experiments.tasks module dacapo.experiments.tasks.affinities_task module dacapo.experiments.tasks.affinities_task_config module dacapo.experiments.tasks.distance_task module dacapo.experiments.tasks.distance_task_config module dacapo.experiments.tasks.dummy_task module dacapo.experiments.tasks.dummy_task_config module dacapo.experiments.tasks.evaluators module dacapo.experiments.tasks.evaluators.binary_segmentation_evaluation_scores module dacapo.experiments.tasks.evaluators.binary_segmentation_evaluator module dacapo.experiments.tasks.evaluators.dummy_evaluation_scores module dacapo.experiments.tasks.evaluators.dummy_evaluator module dacapo.experiments.tasks.evaluators.evaluation_scores module dacapo.experiments.tasks.evaluators.evaluator module dacapo.experiments.tasks.evaluators.instance_evaluation_scores module dacapo.experiments.tasks.evaluators.instance_evaluator module dacapo.experiments.tasks.hot_distance_task module dacapo.experiments.tasks.hot_distance_task_config module dacapo.experiments.tasks.inner_distance_task module dacapo.experiments.tasks.inner_distance_task_config module dacapo.experiments.tasks.losses module dacapo.experiments.tasks.losses.affinities_loss module dacapo.experiments.tasks.losses.dummy_loss module dacapo.experiments.tasks.losses.hot_distance_loss module dacapo.experiments.tasks.losses.loss module dacapo.experiments.tasks.losses.mse_loss module dacapo.experiments.tasks.one_hot_task module dacapo.experiments.tasks.one_hot_task_config module dacapo.experiments.tasks.post_processors module dacapo.experiments.tasks.post_processors.argmax_post_processor module dacapo.experiments.tasks.post_processors.argmax_post_processor_parameters module dacapo.experiments.tasks.post_processors.dummy_post_processor module dacapo.experiments.tasks.post_processors.dummy_post_processor_parameters module dacapo.experiments.tasks.post_processors.post_processor module

dacapo.experiments.tasks.post_processors.post_processor_parameters module dacapo.experiments.tasks.post_processors.threshold_post_processor module dacapo.experiments.tasks.post_processors.threshold_post_processor_parameters module dacapo.experiments.tasks.post_processors.watershed_post_processor module dacapo.experiments.tasks.post_processors.watershed_post_processor_parameters module dacapo.experiments.tasks.predictors module dacapo.experiments.tasks.predictors.affinities_predictor module dacapo.experiments.tasks.predictors.distance_predictor module dacapo.experiments.tasks.predictors.dummy_predictor module dacapo.experiments.tasks.predictors.hot_distance_predictor module dacapo.experiments.tasks.predictors.inner_distance_predictor module dacapo.experiments.tasks.predictors.one_hot_predictor module dacapo.experiments.tasks.predictors.predictor module dacapo.experiments.tasks.pretrained_task module dacapo.experiments.tasks.pretrained_task_config module dacapo.experiments.tasks.task module dacapo.experiments.tasks.task_config module dacapo.experiments.trainers module dacapo.experiments.trainers.dummy_trainer module dacapo.experiments.trainers.dummy_trainer_config module dacapo.experiments.trainers.gp_augments module dacapo.experiments.trainers.gp_augments.augment_config module dacapo.experiments.trainers.gp_augments.elastic_config module dacapo.experiments.trainers.gp_augments.gamma_config module dacapo.experiments.trainers.gp_augments.intensity_config module dacapo.experiments.trainers.gp_augments.intensity_scale_shift_config module dacapo.experiments.trainers.gp_augments.simple_config module dacapo.experiments.trainers.gunpowder_trainer module dacapo.experiments.trainers.gunpowder_trainer_config module dacapo.experiments.trainers.optimizers module dacapo.experiments.trainers.trainer module dacapo.experiments.trainers.trainer_config module dacapo.experiments.training_iteration_stats module dacapo.experiments.training_stats module dacapo.experiments.validation_iteration_scores module dacapo.experiments.validation_scores module dacapo.ext module dacapo.gp module dacapo.gp.copy module dacapo.gp.dacapo_create_target module dacapo.gp.dacapo_points_source module dacapo.gp.elastic_augment_fuse module dacapo.gp.gamma_noise module dacapo.gp.product module dacapo.gp.reject_if_empty module dacapo.options module dacapo.plot module dacapo.predict module dacapo.predict_local module dacapo.store module dacapo.store.array_store module dacapo.store.config_store module dacapo.store.conversion_hooks module dacapo.store.converter module dacapo.store.create_store module dacapo.store.file_config_store module dacapo.store.file_stats_store module dacapo.store.local_array_store module dacapo.store.local_weights_store module dacapo.store.mongo_config_store module dacapo.store.mongo_stats_store module dacapo.store.stats_store module dacapo.store.weights_store module dacapo.tmp module dacapo.train module dacapo.utils module dacapo.utils.affinities module dacapo.utils.array_utils module dacapo.utils.balance_weights module dacapo.utils.pipeline module dacapo.utils.view module dacapo.utils.voi module dacapo.validate module DaCapoBlockwiseTask (class in dacapo.blockwise) (class in dacapo.blockwise.blockwise_task) DaCapoConfig (class in dacapo.options) DaCapoTargetFilter (class in dacapo.gp) (class in dacapo.gp.dacapo_create_target) database (dacapo.store.mongo_config_store.MongoConfigStore attribute), [1] (dacapo.store.mongo_stats_store.MongoStatsStore attribute), [1] DataKey (class in dacapo.experiments.datasplits.keys) (class in dacapo.experiments.datasplits.keys.keys) Dataset (class in dacapo.experiments.datasplits.datasets) (class in dacapo.experiments.datasplits.datasets.dataset) dataset (dacapo.experiments.datasplits.datasets.arrays.zarr_array_config.ZarrArrayConfig attribute), [1] (dacapo.experiments.datasplits.datasets.arrays.ZarrArrayConfig attribute), [1] (dacapo.store.array_store.ArrayStore attribute) (dacapo.store.array_store.LocalArrayIdentifier attribute), [1] dataset_type (dacapo.experiments.datasplits.datasets.dummy_dataset_config.DummyDatasetConfig attribute), [1] (dacapo.experiments.datasplits.datasets.DummyDatasetConfig attribute), [1] (dacapo.experiments.datasplits.datasets.raw_gt_dataset_config.RawGTDatasetConfig attribute), [1] (dacapo.experiments.datasplits.datasets.RawGTDatasetConfig attribute), [1] (dacapo.experiments.datasplits.DatasetSpec attribute), [1] (dacapo.experiments.datasplits.datasplit_generator.DatasetSpec attribute), [1] dataset_type() (dacapo.experiments.datasplits.datasets.simple.SimpleDataset static method) (dacapo.experiments.datasplits.datasets.SimpleDataset static method) DatasetConfig (class in dacapo.experiments.datasplits.datasets) (class in dacapo.experiments.datasplits.datasets.dataset_config) datasets (dacapo.experiments.datasplits.datasplit_generator.DataSplitGenerator attribute), [1] (dacapo.experiments.datasplits.DataSplitGenerator attribute), [1] (dacapo.experiments.validation_scores.ValidationScores attribute), [1] (dacapo.experiments.ValidationScores attribute), [1] (dacapo.store.config_store.ConfigStore attribute), [1] (dacapo.store.file_config_store.FileConfigStore property) (dacapo.store.mongo_config_store.MongoConfigStore attribute) DatasetSpec (class in dacapo.experiments.datasplits) (class in dacapo.experiments.datasplits.datasplit_generator) DatasetType (class in dacapo.experiments.datasplits.datasplit_generator) DataSplit (class in dacapo.experiments.datasplits) (class in dacapo.experiments.datasplits.datasplit) datasplit (dacapo.experiments.run.Run attribute) (dacapo.experiments.run.Run property) datasplit_config (dacapo.experiments.run_config.RunConfig attribute) (dacapo.experiments.RunConfig attribute) datasplit_type (dacapo.experiments.datasplits.dummy_datasplit_config.DummyDataSplitConfig attribute), [1] (dacapo.experiments.datasplits.DummyDataSplitConfig attribute), [1] (dacapo.experiments.datasplits.train_validate_datasplit_config.TrainValidateDataSplitConfig attribute) (dacapo.experiments.datasplits.TrainValidateDataSplitConfig attribute) datasplit_type() (dacapo.experiments.datasplits.simple_config.SimpleDataSplitConfig static method) (dacapo.experiments.datasplits.SimpleDataSplitConfig static method) DataSplitConfig (class in dacapo.experiments.datasplits) (class in dacapo.experiments.datasplits.datasplit_config) DataSplitGenerator (class in dacapo.experiments.datasplits) (class in dacapo.experiments.datasplits.datasplit_generator) datasplits (dacapo.store.config_store.ConfigStore attribute), [1] (dacapo.store.file_config_store.FileConfigStore property) (dacapo.store.mongo_config_store.MongoConfigStore attribute) db_host (dacapo.store.mongo_config_store.MongoConfigStore attribute), [1] (dacapo.store.mongo_stats_store.MongoStatsStore attribute), [1] db_name (dacapo.store.mongo_config_store.MongoConfigStore attribute), [1] (dacapo.store.mongo_stats_store.MongoStatsStore attribute), [1] default_config (dacapo.experiments.datasplits.datasets.arrays.concat_array_config.ConcatArrayConfig attribute), [1] (dacapo.experiments.datasplits.datasets.arrays.ConcatArrayConfig attribute), [1] default_parameters (in module dacapo.blockwise.empanada_function) delete_after() (dacapo.experiments.training_stats.TrainingStats method) (dacapo.experiments.TrainingStats method) (dacapo.experiments.validation_scores.ValidationScores method), [1] (dacapo.experiments.ValidationScores method), [1] delete_architecture_config() (dacapo.store.config_store.ConfigStore method), [1] delete_array_config() (dacapo.store.config_store.ConfigStore method), [1] delete_config() (dacapo.store.config_store.ConfigStore method), [1] (dacapo.store.file_config_store.FileConfigStore method) (dacapo.store.mongo_config_store.MongoConfigStore method) delete_datasplit_config() (dacapo.store.config_store.ConfigStore method), [1] delete_run_config() (dacapo.store.config_store.ConfigStore method), [1] (dacapo.store.mongo_config_store.MongoConfigStore method), [1] delete_task_config() (dacapo.store.config_store.ConfigStore method), [1] delete_trainer_config() (dacapo.store.config_store.ConfigStore method), [1] delete_training_stats() (dacapo.store.file_stats_store.FileStatsStore method) (dacapo.store.mongo_stats_store.MongoStatsStore method), [1] (dacapo.store.stats_store.StatsStore method), [1] delete_validation_scores() (dacapo.store.mongo_stats_store.MongoStatsStore method) deprecated_start_neuroglancer() (dacapo.utils.view.NeuroglancerRunViewer method), [1] detection_threshold (dacapo.experiments.tasks.dummy_task_config.DummyTaskConfig attribute), [1] (dacapo.experiments.tasks.DummyTaskConfig attribute), [1] (dacapo.experiments.tasks.post_processors.dummy_post_processor.DummyPostProcessor attribute), [1] (dacapo.experiments.tasks.post_processors.DummyPostProcessor attribute), [1] device (dacapo.compute_context.Bsub property) (dacapo.compute_context.bsub.Bsub property) (dacapo.compute_context.compute_context.ComputeContext attribute) (dacapo.compute_context.compute_context.ComputeContext property) (dacapo.compute_context.ComputeContext attribute) (dacapo.compute_context.ComputeContext property) (dacapo.compute_context.local_torch.LocalTorch attribute) (dacapo.compute_context.local_torch.LocalTorch property) (dacapo.compute_context.LocalTorch attribute) (dacapo.compute_context.LocalTorch property) device() (dacapo.compute_context.Bsub method) (dacapo.compute_context.bsub.Bsub method) (dacapo.compute_context.local_torch.LocalTorch method) (dacapo.compute_context.LocalTorch method) dice (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluation_scores.BinarySegmentationEvaluationScores attribute), [1] (dacapo.experiments.tasks.evaluators.BinarySegmentationEvaluationScores attribute), [1] dice() (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluator.ArrayEvaluator method), [1] DilatePoints (class in dacapo.utils.pipeline) dilations (dacapo.utils.pipeline.DilatePoints attribute), [1] (dacapo.utils.pipeline.RandomDilateLabels attribute), [1] dims (dacapo.experiments.architectures.Architecture property) (dacapo.experiments.architectures.architecture.Architecture property) (dacapo.experiments.architectures.cnnectome_unet.AttentionBlockModule attribute) (dacapo.experiments.architectures.cnnectome_unet.CNNectomeUNetModule attribute), [1] (dacapo.experiments.architectures.cnnectome_unet.ConvPass attribute) (dacapo.experiments.architectures.cnnectome_unet.Downsample attribute), [1] (dacapo.experiments.architectures.cnnectome_unet.Upsample attribute), [1] (dacapo.experiments.tasks.predictors.affinities_predictor.AffinitiesPredictor property) (dacapo.experiments.tasks.predictors.AffinitiesPredictor property) dims() (dacapo.experiments.architectures.Architecture method) (dacapo.experiments.architectures.architecture.Architecture method) (dacapo.experiments.tasks.predictors.affinities_predictor.AffinitiesPredictor method) (dacapo.experiments.tasks.predictors.AffinitiesPredictor method) distance_loss (dacapo.experiments.tasks.losses.hot_distance_loss.HotDistanceLoss attribute) (dacapo.experiments.tasks.losses.HotDistanceLoss attribute) distance_loss() (dacapo.experiments.tasks.losses.hot_distance_loss.HotDistanceLoss method) (dacapo.experiments.tasks.losses.HotDistanceLoss method) DistanceArray (class in dacapo.experiments.arraytypes) (class in dacapo.experiments.arraytypes.distances) DistancePredictor (class in dacapo.experiments.tasks.predictors) (class in dacapo.experiments.tasks.predictors.distance_predictor) DistanceTask (class in dacapo.experiments.tasks) (class in dacapo.experiments.tasks.distance_task) DistanceTaskConfig (class in dacapo.experiments.tasks) (class in dacapo.experiments.tasks.distance_task_config) distribute_workers (dacapo.compute_context.Bsub attribute) (dacapo.compute_context.bsub.Bsub attribute) (dacapo.compute_context.compute_context.ComputeContext attribute) (dacapo.compute_context.ComputeContext attribute) (dacapo.compute_context.local_torch.LocalTorch attribute) (dacapo.compute_context.LocalTorch attribute) divide_columns() (in module dacapo.utils.voi) divide_rows() (in module dacapo.utils.voi) do_augment (dacapo.gp.elastic_augment_fuse.ElasticAugment attribute) (dacapo.gp.ElasticAugment attribute) does_new_best_exist() (dacapo.utils.view.BestScore method), [1] down (dacapo.experiments.architectures.cnnectome_unet.Downsample attribute), [1] Downsample (class in dacapo.experiments.architectures.cnnectome_unet) downsample (dacapo.experiments.datasplits.datasets.arrays.resampled_array_config.ResampledArrayConfig attribute), [1] (dacapo.experiments.datasplits.datasets.arrays.ResampledArrayConfig attribute), [1] downsample_factor (dacapo.experiments.architectures.cnnectome_unet.Downsample attribute), [1] downsample_factors (dacapo.experiments.architectures.cnnectome_unet.CNNectomeUNet attribute), [1] (dacapo.experiments.architectures.cnnectome_unet.CNNectomeUNetModule attribute) (dacapo.experiments.architectures.cnnectome_unet_config.CNNectomeUNetConfig attribute), [1] (dacapo.experiments.architectures.CNNectomeUNet attribute), [1] (dacapo.experiments.architectures.CNNectomeUNetConfig attribute), [1] downsample_lsds (dacapo.experiments.tasks.affinities_task_config.AffinitiesTaskConfig attribute), [1] (dacapo.experiments.tasks.AffinitiesTaskConfig attribute), [1] (dacapo.experiments.tasks.predictors.affinities_predictor.AffinitiesPredictor attribute) (dacapo.experiments.tasks.predictors.AffinitiesPredictor attribute) drop_channels (dacapo.gp.copy.CopyMask attribute), [1] (dacapo.gp.CopyMask attribute), [1] ds (dacapo.utils.view.BestScore attribute) dt_scale_factor (dacapo.experiments.tasks.predictors.distance_predictor.DistancePredictor attribute) (dacapo.experiments.tasks.predictors.DistancePredictor attribute) (dacapo.experiments.tasks.predictors.hot_distance_predictor.HotDistancePredictor attribute), [1] (dacapo.experiments.tasks.predictors.HotDistancePredictor attribute), [1] (dacapo.experiments.tasks.predictors.inner_distance_predictor.InnerDistancePredictor attribute) (dacapo.experiments.tasks.predictors.InnerDistancePredictor attribute) DummyArchitecture (class in dacapo.experiments.architectures) (class in dacapo.experiments.architectures.dummy_architecture) DummyArchitectureConfig (class in dacapo.experiments.architectures) (class in dacapo.experiments.architectures.dummy_architecture_config) DummyArrayConfig (class in dacapo.experiments.datasplits.datasets.arrays) (class in dacapo.experiments.datasplits.datasets.arrays.dummy_array_config) DummyDataset (class in dacapo.experiments.datasplits.datasets) (class in dacapo.experiments.datasplits.datasets.dummy_dataset) DummyDatasetConfig (class in dacapo.experiments.datasplits.datasets) (class in dacapo.experiments.datasplits.datasets.dummy_dataset_config) DummyDataSplit (class in dacapo.experiments.datasplits) (class in dacapo.experiments.datasplits.dummy_datasplit) DummyDataSplitConfig (class in dacapo.experiments.datasplits) (class in dacapo.experiments.datasplits.dummy_datasplit_config) DummyEvaluationScores (class in dacapo.experiments.tasks.evaluators) (class in dacapo.experiments.tasks.evaluators.dummy_evaluation_scores) DummyEvaluator (class in dacapo.experiments.tasks.evaluators) (class in dacapo.experiments.tasks.evaluators.dummy_evaluator) DummyLoss (class in dacapo.experiments.tasks.losses) (class in dacapo.experiments.tasks.losses.dummy_loss) DummyPostProcessor (class in dacapo.experiments.tasks.post_processors) (class in dacapo.experiments.tasks.post_processors.dummy_post_processor) DummyPostProcessorParameters (class in dacapo.experiments.tasks.post_processors) (class in dacapo.experiments.tasks.post_processors.dummy_post_processor_parameters) DummyPredictor (class in dacapo.experiments.tasks.predictors) (class in dacapo.experiments.tasks.predictors.dummy_predictor) DummyTask (class in dacapo.experiments.tasks) (class in dacapo.experiments.tasks.dummy_task) DummyTaskConfig (class in dacapo.experiments.tasks) (class in dacapo.experiments.tasks.dummy_task_config) DummyTrainer (class in dacapo.experiments.trainers) (class in dacapo.experiments.trainers.dummy_trainer) DummyTrainerConfig (class in dacapo.experiments.trainers) (class in dacapo.experiments.trainers.dummy_trainer_config) DuplicateNameError DVIDArrayConfig (class in dacapo.experiments.datasplits.datasets.arrays) (class in dacapo.experiments.datasplits.datasets.arrays.dvid_array_config)

E

ElasticAugment (class in dacapo.gp) (class in dacapo.gp.elastic_augment_fuse) ElasticAugmentConfig (class in dacapo.experiments.trainers.gp_augments) (class in dacapo.experiments.trainers.gp_augments.elastic_config) embedded (dacapo.utils.view.NeuroglancerRunViewer attribute), [1] embedding_dims (dacapo.experiments.arraytypes.embedding.EmbeddingArray attribute), [1] (dacapo.experiments.arraytypes.EmbeddingArray attribute), [1] (dacapo.experiments.tasks.dummy_task_config.DummyTaskConfig attribute), [1] (dacapo.experiments.tasks.DummyTaskConfig attribute), [1] (dacapo.experiments.tasks.predictors.distance_predictor.DistancePredictor property) (dacapo.experiments.tasks.predictors.DistancePredictor property) (dacapo.experiments.tasks.predictors.dummy_predictor.DummyPredictor attribute), [1] (dacapo.experiments.tasks.predictors.DummyPredictor attribute), [1] (dacapo.experiments.tasks.predictors.hot_distance_predictor.HotDistancePredictor property) (dacapo.experiments.tasks.predictors.HotDistancePredictor property) (dacapo.experiments.tasks.predictors.inner_distance_predictor.InnerDistancePredictor property) (dacapo.experiments.tasks.predictors.InnerDistancePredictor property) (dacapo.experiments.tasks.predictors.one_hot_predictor.OneHotPredictor property) (dacapo.experiments.tasks.predictors.OneHotPredictor property) EmbeddingArray (class in dacapo.experiments.arraytypes) (class in dacapo.experiments.arraytypes.embedding) empanada_segmenter() (in module dacapo.blockwise.empanada_function) enumerate_parameters() (dacapo.experiments.tasks.post_processors.argmax_post_processor.ArgmaxPostProcessor method), [1] (dacapo.experiments.tasks.post_processors.ArgmaxPostProcessor method), [1] (dacapo.experiments.tasks.post_processors.dummy_post_processor.DummyPostProcessor method), [1] (dacapo.experiments.tasks.post_processors.DummyPostProcessor method), [1] (dacapo.experiments.tasks.post_processors.post_processor.PostProcessor method), [1] (dacapo.experiments.tasks.post_processors.PostProcessor method), [1] (dacapo.experiments.tasks.post_processors.threshold_post_processor.ThresholdPostProcessor method), [1] (dacapo.experiments.tasks.post_processors.ThresholdPostProcessor method), [1] (dacapo.experiments.tasks.post_processors.watershed_post_processor.WatershedPostProcessor method), [1] (dacapo.experiments.tasks.post_processors.WatershedPostProcessor method), [1] epsilon (dacapo.experiments.tasks.predictors.distance_predictor.DistancePredictor attribute) (dacapo.experiments.tasks.predictors.DistancePredictor attribute) (dacapo.experiments.tasks.predictors.hot_distance_predictor.HotDistancePredictor attribute), [1] (dacapo.experiments.tasks.predictors.HotDistancePredictor attribute), [1] (dacapo.experiments.tasks.predictors.inner_distance_predictor.InnerDistancePredictor attribute) (dacapo.experiments.tasks.predictors.InnerDistancePredictor attribute) eval_activation (dacapo.experiments.Model attribute), [1] (dacapo.experiments.model.Model attribute), [1] eval_input_shape (dacapo.experiments.Model attribute), [1] (dacapo.experiments.model.Model attribute), [1] eval_shape_increase (dacapo.experiments.architectures.Architecture attribute) (dacapo.experiments.architectures.Architecture property) (dacapo.experiments.architectures.architecture.Architecture attribute) (dacapo.experiments.architectures.architecture.Architecture property) (dacapo.experiments.architectures.cnnectome_unet.CNNectomeUNet property) (dacapo.experiments.architectures.CNNectomeUNet property)

evaluate() (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluator.BinarySegmentationEvaluator method), [1] (dacapo.experiments.tasks.evaluators.BinarySegmentationEvaluator method), [1] (dacapo.experiments.tasks.evaluators.dummy_evaluator.DummyEvaluator method), [1] (dacapo.experiments.tasks.evaluators.DummyEvaluator method), [1] (dacapo.experiments.tasks.evaluators.Evaluator method), [1] (dacapo.experiments.tasks.evaluators.evaluator.Evaluator method), [1] (dacapo.experiments.tasks.evaluators.instance_evaluator.InstanceEvaluator method), [1] (dacapo.experiments.tasks.evaluators.InstanceEvaluator method), [1] evaluation_scores (dacapo.experiments.tasks.Task property) (dacapo.experiments.tasks.task.Task property) (dacapo.experiments.validation_scores.ValidationScores attribute), [1] (dacapo.experiments.ValidationScores attribute), [1] EvaluationScores (class in dacapo.experiments.tasks.evaluators) (class in dacapo.experiments.tasks.evaluators.evaluation_scores) Evaluator (class in dacapo.experiments.tasks.evaluators) (class in dacapo.experiments.tasks.evaluators.evaluator) evaluator (dacapo.experiments.tasks.affinities_task.AffinitiesTask attribute), [1] (dacapo.experiments.tasks.AffinitiesTask attribute), [1] (dacapo.experiments.tasks.distance_task.DistanceTask attribute), [1] (dacapo.experiments.tasks.DistanceTask attribute), [1] (dacapo.experiments.tasks.dummy_task.DummyTask attribute), [1] (dacapo.experiments.tasks.DummyTask attribute), [1] (dacapo.experiments.tasks.hot_distance_task.HotDistanceTask attribute), [1] (dacapo.experiments.tasks.HotDistanceTask attribute), [1] (dacapo.experiments.tasks.inner_distance_task.InnerDistanceTask attribute), [1] (dacapo.experiments.tasks.InnerDistanceTask attribute), [1] (dacapo.experiments.tasks.one_hot_task.OneHotTask attribute) (dacapo.experiments.tasks.OneHotTask attribute) (dacapo.experiments.tasks.pretrained_task.PretrainedTask attribute) (dacapo.experiments.tasks.PretrainedTask attribute) (dacapo.experiments.tasks.Task attribute) (dacapo.experiments.tasks.task.Task attribute) execute() (dacapo.compute_context.compute_context.ComputeContext method), [1] (dacapo.compute_context.ComputeContext method), [1] (dacapo.compute_context.local_torch.LocalTorch method) (dacapo.compute_context.LocalTorch method) ExpandLabels (class in dacapo.utils.pipeline) extractor() (dacapo.experiments.tasks.predictors.affinities_predictor.AffinitiesPredictor method), [1] (dacapo.experiments.tasks.predictors.AffinitiesPredictor method), [1]

F

f1_score (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluation_scores.BinarySegmentationEvaluationScores attribute), [1] (dacapo.experiments.tasks.evaluators.BinarySegmentationEvaluationScores attribute), [1] f1_score() (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluator.ArrayEvaluator method), [1] f1_score_with_tolerance (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluation_scores.BinarySegmentationEvaluationScores attribute), [1] (dacapo.experiments.tasks.evaluators.BinarySegmentationEvaluationScores attribute), [1] f1_score_with_tolerance() (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluator.ArrayEvaluator method), [1] (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluator.CremiEvaluator method), [1] false_discovery_rate (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluation_scores.BinarySegmentationEvaluationScores attribute), [1] (dacapo.experiments.tasks.evaluators.BinarySegmentationEvaluationScores attribute), [1] false_discovery_rate() (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluator.ArrayEvaluator method), [1] false_negative_distances() (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluator.CremiEvaluator method), [1] false_negative_rate (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluation_scores.BinarySegmentationEvaluationScores attribute), [1] (dacapo.experiments.tasks.evaluators.BinarySegmentationEvaluationScores attribute), [1] false_negative_rate() (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluator.ArrayEvaluator method), [1] false_negative_rate_with_tolerance (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluation_scores.BinarySegmentationEvaluationScores attribute), [1] (dacapo.experiments.tasks.evaluators.BinarySegmentationEvaluationScores attribute), [1] false_negative_rate_with_tolerance() (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluator.ArrayEvaluator method), [1] (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluator.CremiEvaluator method), [1] false_negatives_with_tolerance() (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluator.CremiEvaluator method), [1] false_positive_distances() (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluator.CremiEvaluator method), [1] false_positive_rate (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluation_scores.BinarySegmentationEvaluationScores attribute), [1] (dacapo.experiments.tasks.evaluators.BinarySegmentationEvaluationScores attribute), [1] false_positive_rate() (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluator.ArrayEvaluator method), [1] false_positive_rate_with_tolerance (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluation_scores.BinarySegmentationEvaluationScores attribute), [1] (dacapo.experiments.tasks.evaluators.BinarySegmentationEvaluationScores attribute), [1] false_positive_rate_with_tolerance() (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluator.ArrayEvaluator method), [1] (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluator.CremiEvaluator method), [1] false_positives_with_tolerance() (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluator.CremiEvaluator method), [1] file_name (dacapo.experiments.datasplits.datasets.arrays.tiff_array_config.TiffArrayConfig attribute), [1] (dacapo.experiments.datasplits.datasets.arrays.zarr_array_config.ZarrArrayConfig attribute), [1] (dacapo.experiments.datasplits.datasets.arrays.ZarrArrayConfig attribute), [1] FileConfigStore (class in dacapo.store.file_config_store) FileStatsStore (class in dacapo.store.file_stats_store) find_components() (in module dacapo.blockwise.relabel_worker)

fit (in module dacapo.blockwise.argmax_worker) (in module dacapo.blockwise.predict_worker) (in module dacapo.blockwise.relabel_worker) (in module dacapo.blockwise.segment_worker) (in module dacapo.blockwise.threshold_worker) fmap_inc_factor (dacapo.experiments.architectures.cnnectome_unet.CNNectomeUNet attribute), [1] (dacapo.experiments.architectures.cnnectome_unet.CNNectomeUNetModule attribute) (dacapo.experiments.architectures.cnnectome_unet_config.CNNectomeUNetConfig attribute), [1] (dacapo.experiments.architectures.CNNectomeUNet attribute), [1] (dacapo.experiments.architectures.CNNectomeUNetConfig attribute), [1] fmaps_in (dacapo.experiments.architectures.cnnectome_unet.CNNectomeUNet attribute), [1] (dacapo.experiments.architectures.cnnectome_unet_config.CNNectomeUNetConfig attribute), [1] (dacapo.experiments.architectures.CNNectomeUNet attribute), [1] (dacapo.experiments.architectures.CNNectomeUNetConfig attribute), [1] fmaps_out (dacapo.experiments.architectures.cnnectome_unet.CNNectomeUNet attribute), [1] (dacapo.experiments.architectures.cnnectome_unet_config.CNNectomeUNetConfig attribute), [1] (dacapo.experiments.architectures.CNNectomeUNet attribute), [1] (dacapo.experiments.architectures.CNNectomeUNetConfig attribute), [1] format_class_name() (in module dacapo.experiments.datasplits.datasplit_generator) forward() (dacapo.experiments.architectures.cnnectome_unet.AttentionBlockModule method) (dacapo.experiments.architectures.cnnectome_unet.CNNectomeUNet method) (dacapo.experiments.architectures.cnnectome_unet.CNNectomeUNetModule method), [1] (dacapo.experiments.architectures.cnnectome_unet.ConvPass method), [1] (dacapo.experiments.architectures.cnnectome_unet.Downsample method), [1] (dacapo.experiments.architectures.cnnectome_unet.Upsample method), [1] (dacapo.experiments.architectures.CNNectomeUNet method) (dacapo.experiments.architectures.dummy_architecture.DummyArchitecture method), [1] (dacapo.experiments.architectures.DummyArchitecture method), [1] (dacapo.experiments.Model method) (dacapo.experiments.model.Model method) fov (dacapo.experiments.architectures.cnnectome_unet.CNNectomeUNet attribute) (dacapo.experiments.architectures.CNNectomeUNet attribute) frizz_level (dacapo.experiments.tasks.evaluators.dummy_evaluation_scores.DummyEvaluationScores attribute), [1] (dacapo.experiments.tasks.evaluators.DummyEvaluationScores attribute), [1]

G

gamma_max (dacapo.gp.gamma_noise.GammaAugment attribute), [1] (dacapo.gp.GammaAugment attribute), [1] gamma_min (dacapo.gp.gamma_noise.GammaAugment attribute), [1] (dacapo.gp.GammaAugment attribute), [1] gamma_range (dacapo.experiments.trainers.gp_augments.gamma_config.GammaAugmentConfig attribute), [1] (dacapo.experiments.trainers.gp_augments.GammaAugmentConfig attribute), [1] GammaAugment (class in dacapo.gp) (class in dacapo.gp.gamma_noise) GammaAugmentConfig (class in dacapo.experiments.trainers.gp_augments) (class in dacapo.experiments.trainers.gp_augments.gamma_config) gaussian_blur_args (dacapo.utils.pipeline.MakeRaw attribute) (dacapo.utils.pipeline.MakeRaw.Pipeline attribute) gaussian_noise_args (dacapo.utils.pipeline.MakeRaw attribute) (dacapo.utils.pipeline.MakeRaw.Pipeline attribute) gaussian_noise_lim (dacapo.utils.pipeline.MakeRaw attribute) (dacapo.utils.pipeline.MakeRaw.Pipeline attribute) generate_csv() (dacapo.experiments.datasplits.datasplit_generator.DataSplitGenerator method) (dacapo.experiments.datasplits.DataSplitGenerator method) generate_dataspec_from_csv() (in module dacapo.experiments.datasplits.datasplit_generator) generate_from_csv() (dacapo.experiments.datasplits.datasplit_generator.DataSplitGenerator method) (dacapo.experiments.datasplits.datasplit_generator.DataSplitGenerator static method) (dacapo.experiments.datasplits.DataSplitGenerator method) (dacapo.experiments.datasplits.DataSplitGenerator static method) get_best() (dacapo.experiments.validation_scores.ValidationScores method), [1] (dacapo.experiments.ValidationScores method), [1] get_datasets() (dacapo.utils.view.NeuroglancerRunViewer method), [1] get_ds() (dacapo.utils.view.BestScore method), [1] get_model_setup() (in module dacapo.experiments.starts.cosem_start) get_overall_best() (dacapo.experiments.tasks.evaluators.Evaluator method), [1] (dacapo.experiments.tasks.evaluators.evaluator.Evaluator method), [1] get_overall_best_parameters() (dacapo.experiments.tasks.evaluators.Evaluator method), [1] (dacapo.experiments.tasks.evaluators.evaluator.Evaluator method), [1] get_paths() (dacapo.experiments.datasplits.simple_config.SimpleDataSplitConfig method) (dacapo.experiments.datasplits.SimpleDataSplitConfig method) get_right_resolution_array_config() (in module dacapo.experiments.datasplits.datasplit_generator) get_runs_info() (in module dacapo.plot) get_validation_scores() (dacapo.experiments.run.Run method) (dacapo.experiments.run.Run static method) get_viewer() (in module dacapo.utils.view) gp_to_funlib_array() (in module dacapo.tmp) graph (dacapo.gp.dacapo_points_source.GraphSource attribute), [1] (dacapo.gp.GraphSource attribute), [1] GraphKey (class in dacapo.experiments.datasplits.keys) (class in dacapo.experiments.datasplits.keys.keys) GraphSource (class in dacapo.gp) (class in dacapo.gp.dacapo_points_source) GraphStoreConfig (class in dacapo.experiments.datasplits.datasets.graphstores) (class in dacapo.experiments.datasplits.datasets.graphstores.graph_source_config) groupings (dacapo.experiments.datasplits.datasets.arrays.binarize_array_config.BinarizeArrayConfig attribute), [1] (dacapo.experiments.datasplits.datasets.arrays.BinarizeArrayConfig attribute), [1] (dacapo.experiments.datasplits.datasets.arrays.missing_annotations_mask_config.MissingAnnotationsMaskConfig attribute), [1] (dacapo.experiments.datasplits.datasets.arrays.MissingAnnotationsMaskConfig attribute), [1]

grow_boundary_iterations (dacapo.experiments.tasks.predictors.affinities_predictor.AffinitiesPredictor attribute), [1] (dacapo.experiments.tasks.predictors.AffinitiesPredictor attribute), [1] gt (dacapo.experiments.datasplits.datasets.Dataset attribute), [1] (dacapo.experiments.datasplits.datasets.dataset.Dataset attribute), [1] (dacapo.experiments.datasplits.datasets.raw_gt_dataset.RawGTDataset attribute), [1] (dacapo.experiments.datasplits.datasets.RawGTDataset attribute), [1] (dacapo.experiments.datasplits.datasets.simple.SimpleDataset property) (dacapo.experiments.datasplits.datasets.SimpleDataset property) GT (dacapo.experiments.datasplits.keys.ArrayKey attribute), [1] (dacapo.experiments.datasplits.keys.DataKey attribute) (dacapo.experiments.datasplits.keys.keys.ArrayKey attribute), [1] (dacapo.experiments.datasplits.keys.keys.DataKey attribute) gt (dacapo.gp.dacapo_create_target.DaCapoTargetFilter attribute) (dacapo.gp.DaCapoTargetFilter attribute) (dacapo.gp.reject_if_empty.RejectIfEmpty attribute) (dacapo.gp.RejectIfEmpty attribute) (dacapo.utils.view.NeuroglancerRunViewer attribute) gt_config (dacapo.experiments.datasplits.datasets.raw_gt_dataset_config.RawGTDatasetConfig attribute), [1] (dacapo.experiments.datasplits.datasets.RawGTDatasetConfig attribute), [1] gt_container (dacapo.experiments.datasplits.DatasetSpec attribute), [1] (dacapo.experiments.datasplits.datasplit_generator.DatasetSpec attribute), [1] gt_dataset (dacapo.experiments.datasplits.DatasetSpec attribute), [1] (dacapo.experiments.datasplits.datasplit_generator.DatasetSpec attribute), [1] gt_key (dacapo.gp.dacapo_create_target.DaCapoTargetFilter attribute) (dacapo.gp.DaCapoTargetFilter attribute) gt_min_reject (dacapo.experiments.trainers.gunpowder_trainer.GunpowderTrainer attribute) (dacapo.experiments.trainers.gunpowder_trainer_config.GunpowderTrainerConfig attribute) (dacapo.experiments.trainers.GunpowderTrainer attribute) (dacapo.experiments.trainers.GunpowderTrainerConfig attribute) gt_name (dacapo.experiments.datasplits.datasets.simple.SimpleDataset attribute) (dacapo.experiments.datasplits.datasets.SimpleDataset attribute) (dacapo.experiments.datasplits.simple_config.SimpleDataSplitConfig attribute) (dacapo.experiments.datasplits.SimpleDataSplitConfig attribute) gt_region_for_roi() (dacapo.experiments.tasks.predictors.affinities_predictor.AffinitiesPredictor method), [1] (dacapo.experiments.tasks.predictors.AffinitiesPredictor method), [1] (dacapo.experiments.tasks.predictors.distance_predictor.DistancePredictor method), [1] (dacapo.experiments.tasks.predictors.DistancePredictor method), [1] (dacapo.experiments.tasks.predictors.hot_distance_predictor.HotDistancePredictor method), [1] (dacapo.experiments.tasks.predictors.HotDistancePredictor method), [1] (dacapo.experiments.tasks.predictors.inner_distance_predictor.InnerDistancePredictor method), [1] (dacapo.experiments.tasks.predictors.InnerDistancePredictor method), [1] (dacapo.experiments.tasks.predictors.Predictor method), [1] (dacapo.experiments.tasks.predictors.predictor.Predictor method), [1] GunpowderTrainer (class in dacapo.experiments.trainers) (class in dacapo.experiments.trainers.gunpowder_trainer) GunpowderTrainerConfig (class in dacapo.experiments.trainers) (class in dacapo.experiments.trainers.gunpowder_trainer_config)

H

hausdorff (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluation_scores.BinarySegmentationEvaluationScores attribute), [1] (dacapo.experiments.tasks.evaluators.BinarySegmentationEvaluationScores attribute), [1] hausdorff() (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluator.ArrayEvaluator method), [1] head_keys (in module dacapo.experiments.starts.start) higher_is_better() (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluation_scores.BinarySegmentationEvaluationScores static method) (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluation_scores.MultiChannelBinarySegmentationEvaluationScores static method) (dacapo.experiments.tasks.evaluators.BinarySegmentationEvaluationScores static method) (dacapo.experiments.tasks.evaluators.dummy_evaluation_scores.DummyEvaluationScores method) (dacapo.experiments.tasks.evaluators.dummy_evaluation_scores.DummyEvaluationScores static method) (dacapo.experiments.tasks.evaluators.DummyEvaluationScores method) (dacapo.experiments.tasks.evaluators.DummyEvaluationScores static method) (dacapo.experiments.tasks.evaluators.evaluation_scores.EvaluationScores method) (dacapo.experiments.tasks.evaluators.evaluation_scores.EvaluationScores static method) (dacapo.experiments.tasks.evaluators.EvaluationScores method) (dacapo.experiments.tasks.evaluators.EvaluationScores static method) (dacapo.experiments.tasks.evaluators.Evaluator method), [1] (dacapo.experiments.tasks.evaluators.evaluator.Evaluator method), [1] (dacapo.experiments.tasks.evaluators.instance_evaluation_scores.InstanceEvaluationScores method) (dacapo.experiments.tasks.evaluators.instance_evaluation_scores.InstanceEvaluationScores static method) (dacapo.experiments.tasks.evaluators.InstanceEvaluationScores method) (dacapo.experiments.tasks.evaluators.InstanceEvaluationScores static method) (dacapo.experiments.tasks.evaluators.MultiChannelBinarySegmentationEvaluationScores static method)

hooks (dacapo.store.converter.TypedConverter attribute) hot_loss (dacapo.experiments.tasks.losses.hot_distance_loss.HotDistanceLoss attribute) (dacapo.experiments.tasks.losses.HotDistanceLoss attribute) hot_loss() (dacapo.experiments.tasks.losses.hot_distance_loss.HotDistanceLoss method) (dacapo.experiments.tasks.losses.HotDistanceLoss method) HotDistanceLoss (class in dacapo.experiments.tasks.losses) (class in dacapo.experiments.tasks.losses.hot_distance_loss) HotDistancePredictor (class in dacapo.experiments.tasks.predictors) (class in dacapo.experiments.tasks.predictors.hot_distance_predictor) HotDistanceTask (class in dacapo.experiments.tasks) (class in dacapo.experiments.tasks.hot_distance_task) HotDistanceTaskConfig (class in dacapo.experiments.tasks) (class in dacapo.experiments.tasks.hot_distance_task_config)

I

id (dacapo.experiments.tasks.post_processors.post_processor_parameters.PostProcessorParameters attribute), [1] (dacapo.experiments.tasks.post_processors.PostProcessorParameters attribute), [1] in_channels (dacapo.experiments.architectures.cnnectome_unet.CNNectomeUNetModule attribute), [1] initialize_weights() (dacapo.experiments.starts.cosem_start.CosemStart method), [1] (dacapo.experiments.starts.CosemStart method), [1] (dacapo.experiments.starts.Start method), [1] (dacapo.experiments.starts.start.Start method), [1] InnerDistancePredictor (class in dacapo.experiments.tasks.predictors) (class in dacapo.experiments.tasks.predictors.inner_distance_predictor) InnerDistanceTask (class in dacapo.experiments.tasks) (class in dacapo.experiments.tasks.inner_distance_task) InnerDistanceTaskConfig (class in dacapo.experiments.tasks) (class in dacapo.experiments.tasks.inner_distance_task_config) input_resolution (dacapo.experiments.datasplits.datasplit_generator.DataSplitGenerator attribute), [1] (dacapo.experiments.datasplits.DataSplitGenerator attribute), [1] input_shape (dacapo.experiments.architectures.Architecture attribute) (dacapo.experiments.architectures.Architecture property) (dacapo.experiments.architectures.architecture.Architecture attribute) (dacapo.experiments.architectures.architecture.Architecture property) (dacapo.experiments.architectures.cnnectome_unet.CNNectomeUNet property) (dacapo.experiments.architectures.cnnectome_unet_config.CNNectomeUNetConfig attribute), [1] (dacapo.experiments.architectures.CNNectomeUNet property) (dacapo.experiments.architectures.CNNectomeUNetConfig attribute), [1] (dacapo.experiments.architectures.dummy_architecture.DummyArchitecture attribute) (dacapo.experiments.architectures.dummy_architecture.DummyArchitecture property) (dacapo.experiments.architectures.DummyArchitecture attribute) (dacapo.experiments.architectures.DummyArchitecture property) (dacapo.experiments.Model attribute), [1] (dacapo.experiments.model.Model attribute), [1] inside_value (dacapo.utils.pipeline.MakeRaw attribute) (dacapo.utils.pipeline.MakeRaw.Pipeline attribute) instance (dacapo.experiments.datasplits.datasplit_generator.SegmentationType attribute), [1] instance() (dacapo.Options class method) (dacapo.Options method) (dacapo.options.Options class method) (dacapo.options.Options method) InstanceEvaluationScores (class in dacapo.experiments.tasks.evaluators) (class in dacapo.experiments.tasks.evaluators.instance_evaluation_scores) InstanceEvaluator (class in dacapo.experiments.tasks.evaluators) (class in dacapo.experiments.tasks.evaluators.instance_evaluator) IntensitiesArray (class in dacapo.experiments.arraytypes) (class in dacapo.experiments.arraytypes.intensities) IntensitiesArrayConfig (class in dacapo.experiments.datasplits.datasets.arrays) (class in dacapo.experiments.datasplits.datasets.arrays.intensity_array_config) IntensityAugmentConfig (class in dacapo.experiments.trainers.gp_augments) (class in dacapo.experiments.trainers.gp_augments.intensity_config) IntensityScaleShiftAugmentConfig (class in dacapo.experiments.trainers.gp_augments) (class in dacapo.experiments.trainers.gp_augments.intensity_scale_shift_config) interp_order (dacapo.experiments.datasplits.datasets.arrays.resampled_array_config.ResampledArrayConfig attribute), [1] (dacapo.experiments.datasplits.datasets.arrays.ResampledArrayConfig attribute), [1]

interpolatable (dacapo.experiments.arraytypes.AnnotationArray property) (dacapo.experiments.arraytypes.annotations.AnnotationArray property) (dacapo.experiments.arraytypes.arraytype.ArrayType property) (dacapo.experiments.arraytypes.binary.BinaryArray property) (dacapo.experiments.arraytypes.DistanceArray property) (dacapo.experiments.arraytypes.distances.DistanceArray property) (dacapo.experiments.arraytypes.embedding.EmbeddingArray property) (dacapo.experiments.arraytypes.EmbeddingArray property) (dacapo.experiments.arraytypes.intensities.IntensitiesArray property) (dacapo.experiments.arraytypes.IntensitiesArray property) (dacapo.experiments.arraytypes.Mask property) (dacapo.experiments.arraytypes.mask.Mask property) (dacapo.experiments.arraytypes.probabilities.ProbabilityArray property) (dacapo.experiments.arraytypes.ProbabilityArray property) interpolatable() (dacapo.experiments.arraytypes.AnnotationArray method) (dacapo.experiments.arraytypes.annotations.AnnotationArray method) (dacapo.experiments.arraytypes.arraytype.ArrayType method) (dacapo.experiments.arraytypes.binary.BinaryArray method) (dacapo.experiments.arraytypes.DistanceArray method) (dacapo.experiments.arraytypes.distances.DistanceArray method) (dacapo.experiments.arraytypes.embedding.EmbeddingArray method) (dacapo.experiments.arraytypes.EmbeddingArray method) (dacapo.experiments.arraytypes.intensities.IntensitiesArray method) (dacapo.experiments.arraytypes.IntensitiesArray method) (dacapo.experiments.arraytypes.Mask method) (dacapo.experiments.arraytypes.mask.Mask method) is_best() (dacapo.experiments.tasks.evaluators.Evaluator method), [1] (dacapo.experiments.tasks.evaluators.evaluator.Evaluator method), [1] is_zarr_group() (in module dacapo.experiments.datasplits.datasplit_generator) iterate() (dacapo.experiments.trainers.dummy_trainer.DummyTrainer method) (dacapo.experiments.trainers.DummyTrainer method) (dacapo.experiments.trainers.gunpowder_trainer.GunpowderTrainer method) (dacapo.experiments.trainers.GunpowderTrainer method) (dacapo.experiments.trainers.Trainer method) (dacapo.experiments.trainers.trainer.Trainer method) iteration (dacapo.experiments.trainers.dummy_trainer.DummyTrainer attribute) (dacapo.experiments.trainers.DummyTrainer attribute) (dacapo.experiments.trainers.gunpowder_trainer.GunpowderTrainer attribute) (dacapo.experiments.trainers.GunpowderTrainer attribute) (dacapo.experiments.trainers.Trainer attribute), [1] (dacapo.experiments.trainers.trainer.Trainer attribute), [1] (dacapo.experiments.training_iteration_stats.TrainingIterationStats attribute), [1] (dacapo.experiments.TrainingIterationStats attribute), [1] (dacapo.experiments.validation_iteration_scores.ValidationIterationScores attribute), [1] (dacapo.experiments.ValidationIterationScores attribute), [1] (dacapo.utils.view.BestScore attribute), [1] Iteration (in module dacapo.experiments.tasks.evaluators.evaluator) iteration_stats (dacapo.experiments.training_stats.TrainingStats attribute), [1] (dacapo.experiments.TrainingStats attribute), [1]

J

jaccard (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluation_scores.BinarySegmentationEvaluationScores attribute), [1] (dacapo.experiments.tasks.evaluators.BinarySegmentationEvaluationScores attribute), [1]

jaccard() (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluator.ArrayEvaluator method), [1]

K

kernel_size (dacapo.experiments.tasks.hot_distance_task_config.HotDistanceTaskConfig attribute) (dacapo.experiments.tasks.HotDistanceTaskConfig attribute) (dacapo.experiments.tasks.one_hot_task_config.OneHotTaskConfig attribute) (dacapo.experiments.tasks.OneHotTaskConfig attribute) (dacapo.experiments.tasks.predictors.hot_distance_predictor.HotDistancePredictor attribute) (dacapo.experiments.tasks.predictors.HotDistancePredictor attribute) (dacapo.experiments.tasks.predictors.one_hot_predictor.OneHotPredictor attribute) (dacapo.experiments.tasks.predictors.OneHotPredictor attribute) kernel_size_down (dacapo.experiments.architectures.cnnectome_unet.CNNectomeUNet attribute), [1] (dacapo.experiments.architectures.cnnectome_unet.CNNectomeUNetModule attribute), [1] (dacapo.experiments.architectures.cnnectome_unet_config.CNNectomeUNetConfig attribute), [1] (dacapo.experiments.architectures.CNNectomeUNet attribute), [1] (dacapo.experiments.architectures.CNNectomeUNetConfig attribute), [1]

kernel_size_up (dacapo.experiments.architectures.cnnectome_unet.CNNectomeUNet attribute), [1] (dacapo.experiments.architectures.cnnectome_unet.CNNectomeUNetModule attribute), [1] (dacapo.experiments.architectures.cnnectome_unet_config.CNNectomeUNetConfig attribute), [1] (dacapo.experiments.architectures.CNNectomeUNet attribute), [1] (dacapo.experiments.architectures.CNNectomeUNetConfig attribute), [1] kernel_sizes (dacapo.experiments.architectures.cnnectome_unet.AttentionBlockModule attribute) key (dacapo.gp.dacapo_points_source.GraphSource attribute), [1] (dacapo.gp.GraphSource attribute), [1] (dacapo.utils.pipeline.ZerosSource attribute), [1]

L

l_conv (dacapo.experiments.architectures.cnnectome_unet.CNNectomeUNetModule attribute), [1] l_down (dacapo.experiments.architectures.cnnectome_unet.CNNectomeUNetModule attribute), [1] labels (dacapo.utils.pipeline.CreatePoints attribute), [1] (dacapo.utils.pipeline.DilatePoints attribute), [1] (dacapo.utils.pipeline.ExpandLabels attribute), [1] (dacapo.utils.pipeline.MakeRaw attribute) (dacapo.utils.pipeline.MakeRaw.Pipeline attribute) (dacapo.utils.pipeline.RandomDilateLabels attribute), [1] (dacapo.utils.pipeline.Relabel attribute) latest_iteration() (dacapo.store.local_weights_store.LocalWeightsStore method), [1] (dacapo.store.weights_store.WeightsStore method), [1] learning_rate (dacapo.experiments.trainers.dummy_trainer.DummyTrainer attribute), [1] (dacapo.experiments.trainers.DummyTrainer attribute), [1] (dacapo.experiments.trainers.gunpowder_trainer.GunpowderTrainer attribute), [1] (dacapo.experiments.trainers.GunpowderTrainer attribute), [1] (dacapo.experiments.trainers.Trainer attribute), [1] (dacapo.experiments.trainers.trainer.Trainer attribute), [1] (dacapo.experiments.trainers.trainer_config.TrainerConfig attribute), [1] (dacapo.experiments.trainers.TrainerConfig attribute), [1] limit_validation_crop_size() (in module dacapo.experiments.datasplits.datasplit_generator) load_best() (dacapo.store.weights_store.WeightsStore method), [1] load_weights() (dacapo.store.weights_store.WeightsStore method), [1] LocalArrayIdentifier (class in dacapo.store.array_store) LocalArrayStore (class in dacapo.store.local_array_store) LocalContainerIdentifier (class in dacapo.store.array_store) LocalTorch (class in dacapo.compute_context) (class in dacapo.compute_context.local_torch) LocalWeightsStore (class in dacapo.store.local_weights_store) logger (in module dacapo.apply) (in module dacapo.blockwise.argmax_worker) (in module dacapo.blockwise.empanada_function) (in module dacapo.blockwise.predict_worker) (in module dacapo.blockwise.scheduler) (in module dacapo.blockwise.segment_worker) (in module dacapo.blockwise.threshold_worker) (in module dacapo.experiments.datasplits.datasplit_generator) (in module dacapo.experiments.starts.cosem_start) (in module dacapo.experiments.starts.start) (in module dacapo.experiments.tasks.evaluators.binary_segmentation_evaluator) (in module dacapo.experiments.tasks.evaluators.instance_evaluator) (in module dacapo.experiments.tasks.post_processors.threshold_post_processor) (in module dacapo.experiments.tasks.predictors.distance_predictor) (in module dacapo.experiments.tasks.predictors.hot_distance_predictor) (in module dacapo.experiments.tasks.predictors.inner_distance_predictor) (in module dacapo.experiments.tasks.predictors.one_hot_predictor) (in module dacapo.experiments.trainers.gunpowder_trainer) (in module dacapo.experiments.training_stats) (in module dacapo.gp.elastic_augment_fuse) (in module dacapo.gp.gamma_noise) (in module dacapo.gp.reject_if_empty) (in module dacapo.options) (in module dacapo.predict) (in module dacapo.predict_local) (in module dacapo.store.file_config_store) (in module dacapo.store.file_stats_store) (in module dacapo.store.local_array_store) (in module dacapo.store.local_weights_store) (in module dacapo.store.mongo_config_store) (in module dacapo.store.mongo_stats_store) (in module dacapo.train) (in module dacapo.utils.affinities) (in module dacapo.validate)

LogicalOrArrayConfig (class in dacapo.experiments.datasplits.datasets.arrays) (class in dacapo.experiments.datasplits.datasets.arrays.logical_or_array_config) Loss (class in dacapo.experiments.tasks.losses) (class in dacapo.experiments.tasks.losses.loss) loss (dacapo.experiments.tasks.affinities_task.AffinitiesTask attribute), [1] (dacapo.experiments.tasks.AffinitiesTask attribute), [1] (dacapo.experiments.tasks.distance_task.DistanceTask attribute), [1] (dacapo.experiments.tasks.DistanceTask attribute), [1] (dacapo.experiments.tasks.dummy_task.DummyTask attribute), [1] (dacapo.experiments.tasks.DummyTask attribute), [1] (dacapo.experiments.tasks.hot_distance_task.HotDistanceTask attribute), [1] (dacapo.experiments.tasks.HotDistanceTask attribute), [1] (dacapo.experiments.tasks.inner_distance_task.InnerDistanceTask attribute), [1] (dacapo.experiments.tasks.InnerDistanceTask attribute), [1] (dacapo.experiments.tasks.one_hot_task.OneHotTask attribute) (dacapo.experiments.tasks.OneHotTask attribute) (dacapo.experiments.tasks.pretrained_task.PretrainedTask attribute) (dacapo.experiments.tasks.PretrainedTask attribute) (dacapo.experiments.tasks.Task attribute) (dacapo.experiments.tasks.task.Task attribute) (dacapo.experiments.training_iteration_stats.TrainingIterationStats attribute), [1] (dacapo.experiments.TrainingIterationStats attribute), [1] lsd_pad() (dacapo.experiments.tasks.predictors.affinities_predictor.AffinitiesPredictor method), [1] (dacapo.experiments.tasks.predictors.AffinitiesPredictor method), [1] lsd_weight_clipmax (dacapo.experiments.tasks.affinities_task_config.AffinitiesTaskConfig attribute), [1] (dacapo.experiments.tasks.AffinitiesTaskConfig attribute), [1] (dacapo.experiments.tasks.predictors.affinities_predictor.AffinitiesPredictor attribute), [1] (dacapo.experiments.tasks.predictors.AffinitiesPredictor attribute), [1] lsd_weight_clipmin (dacapo.experiments.tasks.affinities_task_config.AffinitiesTaskConfig attribute), [1] (dacapo.experiments.tasks.AffinitiesTaskConfig attribute), [1] (dacapo.experiments.tasks.predictors.affinities_predictor.AffinitiesPredictor attribute), [1] (dacapo.experiments.tasks.predictors.AffinitiesPredictor attribute), [1] lsds (dacapo.experiments.tasks.affinities_task_config.AffinitiesTaskConfig attribute), [1] (dacapo.experiments.tasks.AffinitiesTaskConfig attribute), [1] (dacapo.experiments.tasks.predictors.affinities_predictor.AffinitiesPredictor attribute), [1] (dacapo.experiments.tasks.predictors.AffinitiesPredictor attribute), [1] lsds_to_affs_weight_ratio (dacapo.experiments.tasks.affinities_task_config.AffinitiesTaskConfig attribute), [1] (dacapo.experiments.tasks.AffinitiesTaskConfig attribute), [1] (dacapo.experiments.tasks.losses.affinities_loss.AffinitiesLoss attribute), [1] (dacapo.experiments.tasks.losses.AffinitiesLoss attribute), [1]

M

MakeRaw (class in dacapo.utils.pipeline) MakeRaw.Pipeline (class in dacapo.utils.pipeline) Mask (class in dacapo.experiments.arraytypes) (class in dacapo.experiments.arraytypes.mask) mask (dacapo.experiments.datasplits.datasets.Dataset attribute), [1] (dacapo.experiments.datasplits.datasets.dataset.Dataset attribute), [1] (dacapo.experiments.datasplits.datasets.raw_gt_dataset.RawGTDataset attribute), [1] (dacapo.experiments.datasplits.datasets.RawGTDataset attribute), [1] (dacapo.experiments.datasplits.datasets.simple.SimpleDataset property) (dacapo.experiments.datasplits.datasets.SimpleDataset property) MASK (dacapo.experiments.datasplits.keys.ArrayKey attribute), [1] (dacapo.experiments.datasplits.keys.DataKey attribute) (dacapo.experiments.datasplits.keys.keys.ArrayKey attribute), [1] (dacapo.experiments.datasplits.keys.keys.DataKey attribute) mask_config (dacapo.experiments.datasplits.datasets.raw_gt_dataset_config.RawGTDatasetConfig attribute), [1] (dacapo.experiments.datasplits.datasets.RawGTDatasetConfig attribute), [1] mask_distances (dacapo.experiments.tasks.distance_task_config.DistanceTaskConfig attribute), [1] (dacapo.experiments.tasks.DistanceTaskConfig attribute), [1] (dacapo.experiments.tasks.hot_distance_task_config.HotDistanceTaskConfig attribute), [1] (dacapo.experiments.tasks.HotDistanceTaskConfig attribute), [1] (dacapo.experiments.tasks.predictors.distance_predictor.DistancePredictor attribute), [1] (dacapo.experiments.tasks.predictors.DistancePredictor attribute), [1] (dacapo.experiments.tasks.predictors.hot_distance_predictor.HotDistancePredictor attribute), [1] (dacapo.experiments.tasks.predictors.HotDistancePredictor attribute), [1] mask_integral_downsample_factor (dacapo.experiments.trainers.gunpowder_trainer.GunpowderTrainer attribute), [1] (dacapo.experiments.trainers.GunpowderTrainer attribute), [1] mask_key (dacapo.gp.dacapo_create_target.DaCapoTargetFilter attribute), [1] (dacapo.gp.DaCapoTargetFilter attribute), [1] mask_name (dacapo.experiments.datasplits.datasets.simple.SimpleDataset attribute) (dacapo.experiments.datasplits.datasets.SimpleDataset attribute) (dacapo.experiments.datasplits.simple_config.SimpleDataSplitConfig attribute) (dacapo.experiments.datasplits.SimpleDataSplitConfig attribute) match_heads() (in module dacapo.experiments.starts.start) max (dacapo.experiments.arraytypes.DistanceArray attribute) (dacapo.experiments.arraytypes.distances.DistanceArray attribute) (dacapo.experiments.arraytypes.intensities.IntensitiesArray attribute), [1] (dacapo.experiments.arraytypes.IntensitiesArray attribute), [1] (dacapo.experiments.datasplits.datasets.arrays.IntensitiesArrayConfig attribute), [1] (dacapo.experiments.datasplits.datasets.arrays.intensity_array_config.IntensitiesArrayConfig attribute), [1] max_distance (dacapo.experiments.tasks.predictors.distance_predictor.DistancePredictor attribute) (dacapo.experiments.tasks.predictors.DistancePredictor attribute) (dacapo.experiments.tasks.predictors.hot_distance_predictor.HotDistancePredictor attribute), [1] (dacapo.experiments.tasks.predictors.HotDistancePredictor attribute), [1] (dacapo.experiments.tasks.predictors.inner_distance_predictor.InnerDistancePredictor attribute) (dacapo.experiments.tasks.predictors.InnerDistancePredictor attribute) max_gt_downsample (dacapo.experiments.datasplits.datasplit_generator.DataSplitGenerator attribute), [1] (dacapo.experiments.datasplits.DataSplitGenerator attribute), [1] max_gt_upsample (dacapo.experiments.datasplits.datasplit_generator.DataSplitGenerator attribute), [1] (dacapo.experiments.datasplits.DataSplitGenerator attribute), [1] max_raw_training_downsample (dacapo.experiments.datasplits.datasplit_generator.DataSplitGenerator attribute), [1] (dacapo.experiments.datasplits.DataSplitGenerator attribute), [1] max_raw_training_upsample (dacapo.experiments.datasplits.datasplit_generator.DataSplitGenerator attribute), [1] (dacapo.experiments.datasplits.DataSplitGenerator attribute), [1] max_raw_validation_downsample (dacapo.experiments.datasplits.datasplit_generator.DataSplitGenerator attribute), [1] (dacapo.experiments.datasplits.DataSplitGenerator attribute), [1] max_raw_validation_upsample (dacapo.experiments.datasplits.datasplit_generator.DataSplitGenerator attribute), [1] (dacapo.experiments.datasplits.DataSplitGenerator attribute), [1] max_retries (dacapo.blockwise.blockwise_task.DaCapoBlockwiseTask attribute) (dacapo.blockwise.DaCapoBlockwiseTask attribute) max_validation_volume_size (dacapo.experiments.datasplits.datasplit_generator.DataSplitGenerator attribute), [1] (dacapo.experiments.datasplits.DataSplitGenerator attribute), [1] mean_false_distance (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluation_scores.BinarySegmentationEvaluationScores attribute), [1] (dacapo.experiments.tasks.evaluators.BinarySegmentationEvaluationScores attribute), [1] mean_false_distance() (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluator.ArrayEvaluator method), [1] (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluator.CremiEvaluator method), [1] mean_false_distance_clipped (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluation_scores.BinarySegmentationEvaluationScores attribute), [1] (dacapo.experiments.tasks.evaluators.BinarySegmentationEvaluationScores attribute), [1] mean_false_distance_clipped() (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluator.ArrayEvaluator method), [1] (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluator.CremiEvaluator method), [1] mean_false_negative_distance (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluation_scores.BinarySegmentationEvaluationScores attribute), [1] (dacapo.experiments.tasks.evaluators.BinarySegmentationEvaluationScores attribute), [1] mean_false_negative_distance() (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluator.ArrayEvaluator method), [1] (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluator.CremiEvaluator method), [1] mean_false_negative_distance_clipped (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluation_scores.BinarySegmentationEvaluationScores attribute), [1] (dacapo.experiments.tasks.evaluators.BinarySegmentationEvaluationScores attribute), [1] mean_false_negative_distance_clipped() (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluator.ArrayEvaluator method), [1] mean_false_negative_distances_clipped() (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluator.CremiEvaluator method), [1] mean_false_positive_distance (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluation_scores.BinarySegmentationEvaluationScores attribute), [1] (dacapo.experiments.tasks.evaluators.BinarySegmentationEvaluationScores attribute), [1] mean_false_positive_distance() (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluator.ArrayEvaluator method), [1] (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluator.CremiEvaluator method), [1] mean_false_positive_distance_clipped (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluation_scores.BinarySegmentationEvaluationScores attribute), [1] (dacapo.experiments.tasks.evaluators.BinarySegmentationEvaluationScores attribute), [1] mean_false_positive_distance_clipped() (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluator.ArrayEvaluator method), [1] mean_false_positive_distances_clipped() (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluator.CremiEvaluator method), [1] membrane_like (dacapo.utils.pipeline.MakeRaw attribute) (dacapo.utils.pipeline.MakeRaw.Pipeline attribute) membrane_size (dacapo.utils.pipeline.MakeRaw attribute) (dacapo.utils.pipeline.MakeRaw.Pipeline attribute) MergeInstancesArrayConfig (class in dacapo.experiments.datasplits.datasets.arrays) (class in dacapo.experiments.datasplits.datasets.arrays.merge_instances_array_config) message (dacapo.store.config_store.DuplicateNameError attribute) min (dacapo.experiments.arraytypes.intensities.IntensitiesArray attribute), [1] (dacapo.experiments.arraytypes.IntensitiesArray attribute), [1] (dacapo.experiments.datasplits.datasets.arrays.IntensitiesArrayConfig attribute), [1] (dacapo.experiments.datasplits.datasets.arrays.intensity_array_config.IntensitiesArrayConfig attribute), [1] min_masked (dacapo.experiments.trainers.gunpowder_trainer.GunpowderTrainer attribute), [1] (dacapo.experiments.trainers.gunpowder_trainer_config.GunpowderTrainerConfig attribute), [1] (dacapo.experiments.trainers.GunpowderTrainer attribute), [1] (dacapo.experiments.trainers.GunpowderTrainerConfig attribute), [1] min_size (dacapo.experiments.tasks.post_processors.dummy_post_processor_parameters.DummyPostProcessorParameters attribute), [1] (dacapo.experiments.tasks.post_processors.DummyPostProcessorParameters attribute), [1] (dacapo.experiments.tasks.post_processors.watershed_post_processor_parameters.WatershedPostProcessorParameters attribute) (dacapo.experiments.tasks.post_processors.WatershedPostProcessorParameters attribute) min_training_volume_size (dacapo.experiments.datasplits.datasplit_generator.DataSplitGenerator attribute), [1] (dacapo.experiments.datasplits.DataSplitGenerator attribute), [1] mirror_augment (dacapo.experiments.trainers.dummy_trainer.DummyTrainer attribute), [1] (dacapo.experiments.trainers.dummy_trainer_config.DummyTrainerConfig attribute), [1] (dacapo.experiments.trainers.DummyTrainer attribute), [1] (dacapo.experiments.trainers.DummyTrainerConfig attribute), [1] MissingAnnotationsMaskConfig (class in dacapo.experiments.datasplits.datasets.arrays) (class in dacapo.experiments.datasplits.datasets.arrays.missing_annotations_mask_config) mode (dacapo.experiments.datasplits.datasets.arrays.zarr_array_config.ZarrArrayConfig attribute) (dacapo.experiments.datasplits.datasets.arrays.ZarrArrayConfig attribute) Model (class in dacapo.experiments) (class in dacapo.experiments.model) model (dacapo.experiments.run.Run attribute), [1] (dacapo.store.weights_store.Weights attribute), [1] model_configs (in module dacapo.blockwise.empanada_function) module dacapo, [1], [2], [3] dacapo.apply dacapo.blockwise dacapo.blockwise.argmax_worker dacapo.blockwise.blockwise_task dacapo.blockwise.empanada_function dacapo.blockwise.predict_worker dacapo.blockwise.relabel_worker dacapo.blockwise.scheduler dacapo.blockwise.segment_worker dacapo.blockwise.threshold_worker dacapo.blockwise.watershed_function dacapo.compute_context dacapo.compute_context.bsub dacapo.compute_context.compute_context dacapo.compute_context.local_torch dacapo.experiments dacapo.experiments.architectures dacapo.experiments.architectures.architecture dacapo.experiments.architectures.architecture_config dacapo.experiments.architectures.cnnectome_unet dacapo.experiments.architectures.cnnectome_unet_config dacapo.experiments.architectures.dummy_architecture dacapo.experiments.architectures.dummy_architecture_config dacapo.experiments.arraytypes dacapo.experiments.arraytypes.annotations dacapo.experiments.arraytypes.arraytype dacapo.experiments.arraytypes.binary dacapo.experiments.arraytypes.distances dacapo.experiments.arraytypes.embedding dacapo.experiments.arraytypes.intensities dacapo.experiments.arraytypes.mask dacapo.experiments.arraytypes.probabilities dacapo.experiments.datasplits dacapo.experiments.datasplits.datasets dacapo.experiments.datasplits.datasets.arrays dacapo.experiments.datasplits.datasets.arrays.array_config dacapo.experiments.datasplits.datasets.arrays.binarize_array_config dacapo.experiments.datasplits.datasets.arrays.concat_array_config dacapo.experiments.datasplits.datasets.arrays.constant_array_config dacapo.experiments.datasplits.datasets.arrays.crop_array_config dacapo.experiments.datasplits.datasets.arrays.dummy_array_config dacapo.experiments.datasplits.datasets.arrays.dvid_array_config dacapo.experiments.datasplits.datasets.arrays.intensity_array_config dacapo.experiments.datasplits.datasets.arrays.logical_or_array_config dacapo.experiments.datasplits.datasets.arrays.merge_instances_array_config dacapo.experiments.datasplits.datasets.arrays.missing_annotations_mask_config dacapo.experiments.datasplits.datasets.arrays.ones_array_config dacapo.experiments.datasplits.datasets.arrays.resampled_array_config dacapo.experiments.datasplits.datasets.arrays.sum_array_config dacapo.experiments.datasplits.datasets.arrays.tiff_array_config dacapo.experiments.datasplits.datasets.arrays.zarr_array_config dacapo.experiments.datasplits.datasets.dataset dacapo.experiments.datasplits.datasets.dataset_config dacapo.experiments.datasplits.datasets.dummy_dataset dacapo.experiments.datasplits.datasets.dummy_dataset_config dacapo.experiments.datasplits.datasets.graphstores dacapo.experiments.datasplits.datasets.graphstores.graph_source_config dacapo.experiments.datasplits.datasets.raw_gt_dataset dacapo.experiments.datasplits.datasets.raw_gt_dataset_config dacapo.experiments.datasplits.datasets.simple dacapo.experiments.datasplits.datasplit dacapo.experiments.datasplits.datasplit_config dacapo.experiments.datasplits.datasplit_generator dacapo.experiments.datasplits.dummy_datasplit dacapo.experiments.datasplits.dummy_datasplit_config dacapo.experiments.datasplits.keys dacapo.experiments.datasplits.keys.keys dacapo.experiments.datasplits.simple_config dacapo.experiments.datasplits.train_validate_datasplit dacapo.experiments.datasplits.train_validate_datasplit_config dacapo.experiments.model dacapo.experiments.run dacapo.experiments.run_config dacapo.experiments.starts dacapo.experiments.starts.cosem_start dacapo.experiments.starts.cosem_start_config dacapo.experiments.starts.start dacapo.experiments.starts.start_config dacapo.experiments.tasks dacapo.experiments.tasks.affinities_task dacapo.experiments.tasks.affinities_task_config dacapo.experiments.tasks.distance_task dacapo.experiments.tasks.distance_task_config dacapo.experiments.tasks.dummy_task dacapo.experiments.tasks.dummy_task_config dacapo.experiments.tasks.evaluators dacapo.experiments.tasks.evaluators.binary_segmentation_evaluation_scores dacapo.experiments.tasks.evaluators.binary_segmentation_evaluator dacapo.experiments.tasks.evaluators.dummy_evaluation_scores dacapo.experiments.tasks.evaluators.dummy_evaluator dacapo.experiments.tasks.evaluators.evaluation_scores dacapo.experiments.tasks.evaluators.evaluator dacapo.experiments.tasks.evaluators.instance_evaluation_scores dacapo.experiments.tasks.evaluators.instance_evaluator dacapo.experiments.tasks.hot_distance_task dacapo.experiments.tasks.hot_distance_task_config dacapo.experiments.tasks.inner_distance_task dacapo.experiments.tasks.inner_distance_task_config dacapo.experiments.tasks.losses dacapo.experiments.tasks.losses.affinities_loss dacapo.experiments.tasks.losses.dummy_loss dacapo.experiments.tasks.losses.hot_distance_loss dacapo.experiments.tasks.losses.loss dacapo.experiments.tasks.losses.mse_loss dacapo.experiments.tasks.one_hot_task dacapo.experiments.tasks.one_hot_task_config dacapo.experiments.tasks.post_processors dacapo.experiments.tasks.post_processors.argmax_post_processor dacapo.experiments.tasks.post_processors.argmax_post_processor_parameters dacapo.experiments.tasks.post_processors.dummy_post_processor dacapo.experiments.tasks.post_processors.dummy_post_processor_parameters dacapo.experiments.tasks.post_processors.post_processor dacapo.experiments.tasks.post_processors.post_processor_parameters dacapo.experiments.tasks.post_processors.threshold_post_processor dacapo.experiments.tasks.post_processors.threshold_post_processor_parameters dacapo.experiments.tasks.post_processors.watershed_post_processor dacapo.experiments.tasks.post_processors.watershed_post_processor_parameters dacapo.experiments.tasks.predictors dacapo.experiments.tasks.predictors.affinities_predictor dacapo.experiments.tasks.predictors.distance_predictor dacapo.experiments.tasks.predictors.dummy_predictor dacapo.experiments.tasks.predictors.hot_distance_predictor dacapo.experiments.tasks.predictors.inner_distance_predictor dacapo.experiments.tasks.predictors.one_hot_predictor dacapo.experiments.tasks.predictors.predictor dacapo.experiments.tasks.pretrained_task dacapo.experiments.tasks.pretrained_task_config dacapo.experiments.tasks.task dacapo.experiments.tasks.task_config dacapo.experiments.trainers dacapo.experiments.trainers.dummy_trainer dacapo.experiments.trainers.dummy_trainer_config dacapo.experiments.trainers.gp_augments dacapo.experiments.trainers.gp_augments.augment_config dacapo.experiments.trainers.gp_augments.elastic_config dacapo.experiments.trainers.gp_augments.gamma_config dacapo.experiments.trainers.gp_augments.intensity_config dacapo.experiments.trainers.gp_augments.intensity_scale_shift_config dacapo.experiments.trainers.gp_augments.simple_config dacapo.experiments.trainers.gunpowder_trainer dacapo.experiments.trainers.gunpowder_trainer_config dacapo.experiments.trainers.optimizers dacapo.experiments.trainers.trainer dacapo.experiments.trainers.trainer_config dacapo.experiments.training_iteration_stats dacapo.experiments.training_stats dacapo.experiments.validation_iteration_scores dacapo.experiments.validation_scores dacapo.ext dacapo.gp dacapo.gp.copy dacapo.gp.dacapo_create_target dacapo.gp.dacapo_points_source dacapo.gp.elastic_augment_fuse dacapo.gp.gamma_noise dacapo.gp.product dacapo.gp.reject_if_empty dacapo.options dacapo.plot dacapo.predict dacapo.predict_local dacapo.store dacapo.store.array_store dacapo.store.config_store dacapo.store.conversion_hooks dacapo.store.converter dacapo.store.create_store dacapo.store.file_config_store dacapo.store.file_stats_store dacapo.store.local_array_store dacapo.store.local_weights_store dacapo.store.mongo_config_store dacapo.store.mongo_stats_store dacapo.store.stats_store dacapo.store.weights_store dacapo.tmp dacapo.train dacapo.utils dacapo.utils.affinities dacapo.utils.array_utils dacapo.utils.balance_weights dacapo.utils.pipeline dacapo.utils.view dacapo.utils.voi dacapo.validate

module() (dacapo.experiments.architectures.cnnectome_unet.CNNectomeUNet method) (dacapo.experiments.architectures.CNNectomeUNet method) mongo_db_host (dacapo.options.DaCapoConfig attribute), [1] mongo_db_name (dacapo.options.DaCapoConfig attribute), [1] MongoConfigStore (class in dacapo.store.mongo_config_store) MongoStatsStore (class in dacapo.store.mongo_stats_store) most_recent_iteration (dacapo.utils.view.NeuroglancerRunViewer attribute) move_optimizer() (dacapo.experiments.run.Run method) moving_counts (dacapo.gp.dacapo_create_target.DaCapoTargetFilter attribute) (dacapo.gp.DaCapoTargetFilter attribute) MSELoss (class in dacapo.experiments.tasks.losses) (class in dacapo.experiments.tasks.losses.mse_loss) MultiChannelBinarySegmentationEvaluationScores (class in dacapo.experiments.tasks.evaluators) (class in dacapo.experiments.tasks.evaluators.binary_segmentation_evaluation_scores)

N

name (dacapo.experiments.architectures.architecture_config.ArchitectureConfig attribute), [1] (dacapo.experiments.architectures.ArchitectureConfig attribute), [1] (dacapo.experiments.datasplits.datasets.arrays.array_config.ArrayConfig attribute), [1] (dacapo.experiments.datasplits.datasets.arrays.ArrayConfig attribute), [1] (dacapo.experiments.datasplits.datasets.Dataset attribute), [1] (dacapo.experiments.datasplits.datasets.dataset.Dataset attribute), [1] (dacapo.experiments.datasplits.datasets.dataset_config.DatasetConfig attribute), [1] (dacapo.experiments.datasplits.datasets.DatasetConfig attribute), [1] (dacapo.experiments.datasplits.datasets.dummy_dataset.DummyDataset attribute) (dacapo.experiments.datasplits.datasets.DummyDataset attribute) (dacapo.experiments.datasplits.datasets.raw_gt_dataset.RawGTDataset attribute) (dacapo.experiments.datasplits.datasets.RawGTDataset attribute) (dacapo.experiments.datasplits.datasets.simple.SimpleDataset attribute) (dacapo.experiments.datasplits.datasets.SimpleDataset attribute) (dacapo.experiments.datasplits.datasplit_config.DataSplitConfig attribute), [1] (dacapo.experiments.datasplits.datasplit_generator.DataSplitGenerator attribute), [1] (dacapo.experiments.datasplits.DataSplitConfig attribute), [1] (dacapo.experiments.datasplits.DataSplitGenerator attribute), [1] (dacapo.experiments.datasplits.simple_config.SimpleDataSplitConfig attribute) (dacapo.experiments.datasplits.SimpleDataSplitConfig attribute) (dacapo.experiments.run.Run attribute), [1] (dacapo.experiments.run_config.RunConfig attribute) (dacapo.experiments.RunConfig attribute) (dacapo.experiments.starts.cosem_start.CosemStart attribute), [1] (dacapo.experiments.starts.CosemStart attribute), [1] (dacapo.experiments.tasks.losses.dummy_loss.DummyLoss attribute) (dacapo.experiments.tasks.losses.DummyLoss attribute) (dacapo.experiments.tasks.task_config.TaskConfig attribute), [1] (dacapo.experiments.tasks.TaskConfig attribute), [1] (dacapo.experiments.trainers.trainer_config.TrainerConfig attribute), [1] (dacapo.experiments.trainers.TrainerConfig attribute), [1] neighborhood (dacapo.experiments.tasks.affinities_task_config.AffinitiesTaskConfig attribute), [1] (dacapo.experiments.tasks.AffinitiesTaskConfig attribute), [1] (dacapo.experiments.tasks.predictors.affinities_predictor.AffinitiesPredictor attribute), [1] (dacapo.experiments.tasks.predictors.AffinitiesPredictor attribute), [1] NeuroglancerRunViewer (class in dacapo.utils.view) new_validation_checker() (dacapo.utils.view.NeuroglancerRunViewer method), [1] next() (dacapo.experiments.trainers.gunpowder_trainer.GunpowderTrainer method), [1] (dacapo.experiments.trainers.GunpowderTrainer method), [1] next_conv_kernel_sizes (dacapo.experiments.architectures.cnnectome_unet.Upsample attribute), [1] node() (dacapo.experiments.trainers.AugmentConfig method), [1] (dacapo.experiments.trainers.gp_augments.augment_config.AugmentConfig method), [1] (dacapo.experiments.trainers.gp_augments.AugmentConfig method), [1] (dacapo.experiments.trainers.gp_augments.elastic_config.ElasticAugmentConfig method), [1] (dacapo.experiments.trainers.gp_augments.ElasticAugmentConfig method), [1] (dacapo.experiments.trainers.gp_augments.gamma_config.GammaAugmentConfig method), [1] (dacapo.experiments.trainers.gp_augments.GammaAugmentConfig method), [1] (dacapo.experiments.trainers.gp_augments.intensity_config.IntensityAugmentConfig method), [1] (dacapo.experiments.trainers.gp_augments.intensity_scale_shift_config.IntensityScaleShiftAugmentConfig method), [1] (dacapo.experiments.trainers.gp_augments.IntensityAugmentConfig method), [1] (dacapo.experiments.trainers.gp_augments.IntensityScaleShiftAugmentConfig method), [1] (dacapo.experiments.trainers.gp_augments.simple_config.SimpleAugmentConfig method), [1] (dacapo.experiments.trainers.gp_augments.SimpleAugmentConfig method), [1] NON_EMPTY (dacapo.experiments.datasplits.keys.ArrayKey attribute), [1] (dacapo.experiments.datasplits.keys.DataKey attribute) (dacapo.experiments.datasplits.keys.keys.ArrayKey attribute), [1] (dacapo.experiments.datasplits.keys.keys.DataKey attribute) None() (dacapo.experiments.tasks.one_hot_task_config.OneHotTaskConfig method) (dacapo.experiments.tasks.OneHotTaskConfig method) norm (dacapo.experiments.tasks.predictors.distance_predictor.DistancePredictor attribute) (dacapo.experiments.tasks.predictors.DistancePredictor attribute) (dacapo.experiments.tasks.predictors.hot_distance_predictor.HotDistancePredictor attribute), [1] (dacapo.experiments.tasks.predictors.HotDistancePredictor attribute), [1] (dacapo.experiments.tasks.predictors.inner_distance_predictor.InnerDistancePredictor attribute) (dacapo.experiments.tasks.predictors.InnerDistancePredictor attribute)

NoSuchModule (class in dacapo.ext) np_to_funlib_array() (in module dacapo.tmp) num_affinities (dacapo.experiments.tasks.losses.affinities_loss.AffinitiesLoss attribute), [1] (dacapo.experiments.tasks.losses.AffinitiesLoss attribute), [1] num_channels() (dacapo.experiments.tasks.predictors.affinities_predictor.AffinitiesPredictor method) (dacapo.experiments.tasks.predictors.AffinitiesPredictor method) num_channels_from_array() (in module dacapo.tmp) num_classes (dacapo.experiments.arraytypes.arraytype.ArrayType attribute) num_cpus (dacapo.compute_context.Bsub attribute), [1] (dacapo.compute_context.bsub.Bsub attribute), [1] num_data_fetchers (dacapo.experiments.trainers.gunpowder_trainer.GunpowderTrainer attribute), [1] (dacapo.experiments.trainers.gunpowder_trainer_config.GunpowderTrainerConfig attribute), [1] (dacapo.experiments.trainers.GunpowderTrainer attribute), [1] (dacapo.experiments.trainers.GunpowderTrainerConfig attribute), [1] num_fmaps (dacapo.experiments.architectures.cnnectome_unet.CNNectomeUNet attribute), [1] (dacapo.experiments.architectures.cnnectome_unet_config.CNNectomeUNetConfig attribute), [1] (dacapo.experiments.architectures.CNNectomeUNet attribute), [1] (dacapo.experiments.architectures.CNNectomeUNetConfig attribute), [1] num_gpus (dacapo.compute_context.Bsub attribute), [1] (dacapo.compute_context.bsub.Bsub attribute), [1] num_heads (dacapo.experiments.architectures.cnnectome_unet.CNNectomeUNet attribute) (dacapo.experiments.architectures.cnnectome_unet.CNNectomeUNetModule attribute), [1] (dacapo.experiments.architectures.CNNectomeUNet attribute) num_in_channels (dacapo.experiments.architectures.Architecture attribute) (dacapo.experiments.architectures.Architecture property) (dacapo.experiments.architectures.architecture.Architecture attribute) (dacapo.experiments.architectures.architecture.Architecture property) (dacapo.experiments.architectures.cnnectome_unet.CNNectomeUNet property) (dacapo.experiments.architectures.CNNectomeUNet property) (dacapo.experiments.architectures.dummy_architecture.DummyArchitecture property) (dacapo.experiments.architectures.dummy_architecture_config.DummyArchitectureConfig attribute), [1] (dacapo.experiments.architectures.DummyArchitecture property) (dacapo.experiments.architectures.DummyArchitectureConfig attribute), [1] (dacapo.experiments.Model attribute), [1] (dacapo.experiments.model.Model attribute), [1] num_in_channels() (dacapo.experiments.architectures.dummy_architecture.DummyArchitecture method) (dacapo.experiments.architectures.DummyArchitecture method) num_iterations (dacapo.experiments.run_config.RunConfig attribute) (dacapo.experiments.RunConfig attribute) num_levels (dacapo.experiments.architectures.cnnectome_unet.CNNectomeUNetModule attribute), [1] num_lsd_voxels (dacapo.experiments.tasks.affinities_task_config.AffinitiesTaskConfig attribute), [1] (dacapo.experiments.tasks.AffinitiesTaskConfig attribute), [1] num_out_channels (dacapo.experiments.architectures.Architecture attribute) (dacapo.experiments.architectures.Architecture property) (dacapo.experiments.architectures.architecture.Architecture attribute) (dacapo.experiments.architectures.architecture.Architecture property) (dacapo.experiments.architectures.cnnectome_unet.CNNectomeUNet property) (dacapo.experiments.architectures.CNNectomeUNet property) (dacapo.experiments.architectures.dummy_architecture.DummyArchitecture property) (dacapo.experiments.architectures.dummy_architecture_config.DummyArchitectureConfig attribute), [1] (dacapo.experiments.architectures.DummyArchitecture property) (dacapo.experiments.architectures.DummyArchitectureConfig attribute), [1] (dacapo.experiments.Model attribute), [1] (dacapo.experiments.model.Model attribute), [1] num_out_channels() (dacapo.experiments.architectures.dummy_architecture.DummyArchitecture method) (dacapo.experiments.architectures.DummyArchitecture method) num_points (dacapo.utils.pipeline.CreatePoints attribute), [1] num_voxels (dacapo.experiments.tasks.predictors.affinities_predictor.AffinitiesPredictor attribute), [1] (dacapo.experiments.tasks.predictors.AffinitiesPredictor attribute), [1] num_workers (dacapo.blockwise.blockwise_task.DaCapoBlockwiseTask attribute) (dacapo.blockwise.DaCapoBlockwiseTask attribute)

O

offset (dacapo.experiments.datasplits.datasets.arrays.tiff_array_config.TiffArrayConfig attribute), [1] offsets (dacapo.experiments.tasks.post_processors.watershed_post_processor.WatershedPostProcessor attribute), [1] (dacapo.experiments.tasks.post_processors.watershed_post_processor_parameters.WatershedPostProcessorParameters attribute) (dacapo.experiments.tasks.post_processors.WatershedPostProcessor attribute), [1] (dacapo.experiments.tasks.post_processors.WatershedPostProcessorParameters attribute) OneHotPredictor (class in dacapo.experiments.tasks.predictors) (class in dacapo.experiments.tasks.predictors.one_hot_predictor) OneHotTask (class in dacapo.experiments.tasks) (class in dacapo.experiments.tasks.one_hot_task) OneHotTaskConfig (class in dacapo.experiments.tasks) (class in dacapo.experiments.tasks.one_hot_task_config) OnesArrayConfig (class in dacapo.experiments.datasplits.datasets.arrays) (class in dacapo.experiments.datasplits.datasets.arrays.ones_array_config) oom_limit (dacapo.compute_context.local_torch.LocalTorch attribute), [1] (dacapo.compute_context.LocalTorch attribute), [1] open_from_array_identitifier() (dacapo.utils.view.NeuroglancerRunViewer method), [1] open_from_identifier() (in module dacapo.tmp) optimizer (dacapo.experiments.run.Run attribute), [1] (dacapo.store.weights_store.Weights attribute), [1] Options (class in dacapo) (class in dacapo.options) orthoplane_inference() (in module dacapo.blockwise.empanada_function) out_channels (dacapo.experiments.architectures.cnnectome_unet.CNNectomeUNetModule attribute), [1] output_array_type (dacapo.experiments.tasks.predictors.affinities_predictor.AffinitiesPredictor property) (dacapo.experiments.tasks.predictors.AffinitiesPredictor property) (dacapo.experiments.tasks.predictors.distance_predictor.DistancePredictor property) (dacapo.experiments.tasks.predictors.DistancePredictor property) (dacapo.experiments.tasks.predictors.dummy_predictor.DummyPredictor property) (dacapo.experiments.tasks.predictors.DummyPredictor property) (dacapo.experiments.tasks.predictors.hot_distance_predictor.HotDistancePredictor property) (dacapo.experiments.tasks.predictors.HotDistancePredictor property) (dacapo.experiments.tasks.predictors.inner_distance_predictor.InnerDistancePredictor property) (dacapo.experiments.tasks.predictors.InnerDistancePredictor property) (dacapo.experiments.tasks.predictors.one_hot_predictor.OneHotPredictor property) (dacapo.experiments.tasks.predictors.OneHotPredictor property) (dacapo.experiments.tasks.predictors.Predictor property) (dacapo.experiments.tasks.predictors.predictor.Predictor property)

output_array_type() (dacapo.experiments.tasks.predictors.affinities_predictor.AffinitiesPredictor method) (dacapo.experiments.tasks.predictors.AffinitiesPredictor method) (dacapo.experiments.tasks.predictors.distance_predictor.DistancePredictor method) (dacapo.experiments.tasks.predictors.DistancePredictor method) (dacapo.experiments.tasks.predictors.dummy_predictor.DummyPredictor method) (dacapo.experiments.tasks.predictors.DummyPredictor method) (dacapo.experiments.tasks.predictors.inner_distance_predictor.InnerDistancePredictor method) (dacapo.experiments.tasks.predictors.InnerDistancePredictor method) (dacapo.experiments.tasks.predictors.one_hot_predictor.OneHotPredictor method) (dacapo.experiments.tasks.predictors.OneHotPredictor method) output_resolution (dacapo.experiments.datasplits.datasplit_generator.DataSplitGenerator attribute), [1] (dacapo.experiments.datasplits.DataSplitGenerator attribute), [1] output_shape (dacapo.experiments.Model attribute) (dacapo.experiments.model.Model attribute) OutputIdentifier (in module dacapo.experiments.tasks.evaluators.evaluator) overlap_measures_filter() (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluator.ArrayEvaluator method)

P

p (dacapo.gp.reject_if_empty.RejectIfEmpty attribute), [1] (dacapo.gp.RejectIfEmpty attribute), [1] padding (dacapo.experiments.architectures.cnnectome_unet.CNNectomeUNet attribute), [1] (dacapo.experiments.architectures.cnnectome_unet.CNNectomeUNetModule attribute) (dacapo.experiments.architectures.cnnectome_unet_config.CNNectomeUNetConfig attribute), [1] (dacapo.experiments.architectures.CNNectomeUNet attribute), [1] (dacapo.experiments.architectures.CNNectomeUNetConfig attribute), [1] padding() (dacapo.experiments.tasks.predictors.distance_predictor.DistancePredictor method) (dacapo.experiments.tasks.predictors.DistancePredictor method) (dacapo.experiments.tasks.predictors.hot_distance_predictor.HotDistancePredictor method), [1] (dacapo.experiments.tasks.predictors.HotDistancePredictor method), [1] (dacapo.experiments.tasks.predictors.inner_distance_predictor.InnerDistancePredictor method) (dacapo.experiments.tasks.predictors.InnerDistancePredictor method) (dacapo.experiments.tasks.predictors.Predictor method) (dacapo.experiments.tasks.predictors.predictor.Predictor method) (in module dacapo.utils.affinities) parameter (dacapo.utils.view.BestScore attribute), [1] parameter_names (dacapo.experiments.tasks.post_processors.post_processor_parameters.PostProcessorParameters property) (dacapo.experiments.tasks.post_processors.PostProcessorParameters property) (dacapo.experiments.validation_scores.ValidationScores property) (dacapo.experiments.ValidationScores property) parameter_names() (dacapo.experiments.tasks.post_processors.argmax_post_processor_parameters.ArgmaxPostProcessorParameters method) (dacapo.experiments.tasks.post_processors.ArgmaxPostProcessorParameters method) (dacapo.experiments.tasks.post_processors.dummy_post_processor_parameters.DummyPostProcessorParameters method) (dacapo.experiments.tasks.post_processors.DummyPostProcessorParameters method) (dacapo.experiments.tasks.post_processors.post_processor_parameters.PostProcessorParameters method) (dacapo.experiments.tasks.post_processors.PostProcessorParameters method) (dacapo.experiments.validation_scores.ValidationScores method) (dacapo.experiments.ValidationScores method) parameters (dacapo.experiments.tasks.Task property) (dacapo.experiments.tasks.task.Task property) (dacapo.experiments.validation_scores.ValidationScores attribute), [1] (dacapo.experiments.ValidationScores attribute), [1] path (dacapo.experiments.datasplits.datasets.simple.SimpleDataset attribute) (dacapo.experiments.datasplits.datasets.SimpleDataset attribute) (dacapo.experiments.datasplits.simple_config.SimpleDataSplitConfig attribute) (dacapo.experiments.datasplits.SimpleDataSplitConfig attribute) (dacapo.store.file_config_store.FileConfigStore attribute), [1] (dacapo.store.file_stats_store.FileStatsStore attribute) (in module dacapo.blockwise.argmax_worker) (in module dacapo.blockwise.predict_worker) (in module dacapo.blockwise.relabel_worker) (in module dacapo.blockwise.segment_worker) (in module dacapo.blockwise.threshold_worker) plot_runs() (in module dacapo.plot) post_processor (dacapo.experiments.tasks.affinities_task.AffinitiesTask attribute), [1] (dacapo.experiments.tasks.AffinitiesTask attribute), [1] (dacapo.experiments.tasks.distance_task.DistanceTask attribute), [1] (dacapo.experiments.tasks.DistanceTask attribute), [1] (dacapo.experiments.tasks.dummy_task.DummyTask attribute), [1] (dacapo.experiments.tasks.DummyTask attribute), [1] (dacapo.experiments.tasks.hot_distance_task.HotDistanceTask attribute), [1] (dacapo.experiments.tasks.HotDistanceTask attribute), [1] (dacapo.experiments.tasks.inner_distance_task.InnerDistanceTask attribute), [1] (dacapo.experiments.tasks.InnerDistanceTask attribute), [1] (dacapo.experiments.tasks.one_hot_task.OneHotTask attribute) (dacapo.experiments.tasks.OneHotTask attribute) (dacapo.experiments.tasks.pretrained_task.PretrainedTask attribute) (dacapo.experiments.tasks.PretrainedTask attribute) (dacapo.experiments.tasks.Task attribute) (dacapo.experiments.tasks.task.Task attribute) PostProcessor (class in dacapo.experiments.tasks.post_processors) (class in dacapo.experiments.tasks.post_processors.post_processor) PostProcessorParameters (class in dacapo.experiments.tasks.post_processors) (class in dacapo.experiments.tasks.post_processors.post_processor_parameters) precision (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluation_scores.BinarySegmentationEvaluationScores attribute), [1] (dacapo.experiments.tasks.evaluators.BinarySegmentationEvaluationScores attribute), [1] precision() (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluator.ArrayEvaluator method), [1] precision_with_tolerance (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluation_scores.BinarySegmentationEvaluationScores attribute), [1] (dacapo.experiments.tasks.evaluators.BinarySegmentationEvaluationScores attribute), [1] precision_with_tolerance() (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluator.ArrayEvaluator method), [1] (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluator.CremiEvaluator method), [1] predict() (in module dacapo) (in module dacapo.predict) (in module dacapo.predict_local) prediction_array (dacapo.experiments.tasks.post_processors.argmax_post_processor.ArgmaxPostProcessor attribute) (dacapo.experiments.tasks.post_processors.ArgmaxPostProcessor attribute) (dacapo.experiments.tasks.post_processors.threshold_post_processor.ThresholdPostProcessor attribute) (dacapo.experiments.tasks.post_processors.ThresholdPostProcessor attribute) prediction_array_identifier (dacapo.experiments.tasks.post_processors.post_processor.PostProcessor attribute) (dacapo.experiments.tasks.post_processors.PostProcessor attribute) (dacapo.experiments.tasks.post_processors.threshold_post_processor.ThresholdPostProcessor attribute) (dacapo.experiments.tasks.post_processors.ThresholdPostProcessor attribute)

prediction_head (dacapo.experiments.Model attribute), [1] (dacapo.experiments.model.Model attribute), [1] Predictor (class in dacapo.experiments.tasks.predictors) (class in dacapo.experiments.tasks.predictors.predictor) predictor (dacapo.experiments.tasks.affinities_task.AffinitiesTask attribute), [1] (dacapo.experiments.tasks.AffinitiesTask attribute), [1] (dacapo.experiments.tasks.distance_task.DistanceTask attribute), [1] (dacapo.experiments.tasks.DistanceTask attribute), [1] (dacapo.experiments.tasks.dummy_task.DummyTask attribute), [1] (dacapo.experiments.tasks.DummyTask attribute), [1] (dacapo.experiments.tasks.hot_distance_task.HotDistanceTask attribute), [1] (dacapo.experiments.tasks.HotDistanceTask attribute), [1] (dacapo.experiments.tasks.inner_distance_task.InnerDistanceTask attribute), [1] (dacapo.experiments.tasks.InnerDistanceTask attribute), [1] (dacapo.experiments.tasks.one_hot_task.OneHotTask attribute) (dacapo.experiments.tasks.OneHotTask attribute) (dacapo.experiments.tasks.pretrained_task.PretrainedTask attribute) (dacapo.experiments.tasks.PretrainedTask attribute) (dacapo.experiments.tasks.Task attribute) (dacapo.experiments.tasks.task.Task attribute) Predictor (dacapo.gp.dacapo_create_target.DaCapoTargetFilter attribute) predictor (dacapo.gp.dacapo_create_target.DaCapoTargetFilter attribute) Predictor (dacapo.gp.DaCapoTargetFilter attribute) predictor (dacapo.gp.DaCapoTargetFilter attribute) prepare() (dacapo.gp.copy.CopyMask method), [1] (dacapo.gp.CopyMask method), [1] (dacapo.gp.dacapo_create_target.DaCapoTargetFilter method), [1] (dacapo.gp.DaCapoTargetFilter method), [1] (dacapo.gp.elastic_augment_fuse.ElasticAugment method) (dacapo.gp.ElasticAugment method) (dacapo.gp.Product method) (dacapo.gp.product.Product method) PretrainedTask (class in dacapo.experiments.tasks) (class in dacapo.experiments.tasks.pretrained_task) PretrainedTaskConfig (class in dacapo.experiments.tasks) (class in dacapo.experiments.tasks.pretrained_task_config) print_profiling (dacapo.experiments.trainers.gunpowder_trainer.GunpowderTrainer attribute), [1] (dacapo.experiments.trainers.GunpowderTrainer attribute), [1] ProbabilityArray (class in dacapo.experiments.arraytypes) (class in dacapo.experiments.arraytypes.probabilities) process() (dacapo.experiments.tasks.post_processors.argmax_post_processor.ArgmaxPostProcessor method), [1] (dacapo.experiments.tasks.post_processors.ArgmaxPostProcessor method), [1] (dacapo.experiments.tasks.post_processors.dummy_post_processor.DummyPostProcessor method), [1] (dacapo.experiments.tasks.post_processors.DummyPostProcessor method), [1] (dacapo.experiments.tasks.post_processors.post_processor.PostProcessor method), [1] (dacapo.experiments.tasks.post_processors.PostProcessor method), [1] (dacapo.experiments.tasks.post_processors.threshold_post_processor.ThresholdPostProcessor method), [1] (dacapo.experiments.tasks.post_processors.ThresholdPostProcessor method), [1] (dacapo.experiments.tasks.post_processors.watershed_post_processor.WatershedPostProcessor method), [1] (dacapo.experiments.tasks.post_processors.WatershedPostProcessor method), [1] (dacapo.experiments.tasks.predictors.distance_predictor.DistancePredictor method), [1] (dacapo.experiments.tasks.predictors.DistancePredictor method), [1] (dacapo.experiments.tasks.predictors.hot_distance_predictor.HotDistancePredictor method), [1] (dacapo.experiments.tasks.predictors.HotDistancePredictor method), [1] (dacapo.experiments.tasks.predictors.inner_distance_predictor.InnerDistancePredictor method) (dacapo.experiments.tasks.predictors.InnerDistancePredictor method) (dacapo.experiments.tasks.predictors.one_hot_predictor.OneHotPredictor method) (dacapo.experiments.tasks.predictors.OneHotPredictor method) (dacapo.gp.copy.CopyMask method), [1] (dacapo.gp.CopyMask method), [1] (dacapo.gp.dacapo_create_target.DaCapoTargetFilter method), [1] (dacapo.gp.DaCapoTargetFilter method), [1] (dacapo.gp.elastic_augment_fuse.ElasticAugment method) (dacapo.gp.ElasticAugment method) (dacapo.gp.gamma_noise.GammaAugment method), [1] (dacapo.gp.GammaAugment method), [1] (dacapo.gp.Product method) (dacapo.gp.product.Product method) (dacapo.utils.pipeline.CreatePoints method), [1] (dacapo.utils.pipeline.DilatePoints method), [1] (dacapo.utils.pipeline.ExpandLabels method), [1] (dacapo.utils.pipeline.MakeRaw method), [1] (dacapo.utils.pipeline.RandomDilateLabels method), [1] (dacapo.utils.pipeline.Relabel method), [1] Product (class in dacapo.gp) (class in dacapo.gp.product) provide() (dacapo.gp.dacapo_points_source.GraphSource method), [1] (dacapo.gp.GraphSource method), [1] (dacapo.gp.reject_if_empty.RejectIfEmpty method) (dacapo.gp.RejectIfEmpty method) (dacapo.utils.pipeline.ZerosSource method), [1] psi (dacapo.experiments.architectures.cnnectome_unet.AttentionBlockModule attribute)

Q

queue (dacapo.compute_context.Bsub attribute), [1] (dacapo.compute_context.bsub.Bsub attribute), [1]

R

r_conv (dacapo.experiments.architectures.cnnectome_unet.CNNectomeUNetModule attribute), [1] r_up (dacapo.experiments.architectures.cnnectome_unet.CNNectomeUNetModule attribute), [1] random_source_pipeline() (in module dacapo.utils.pipeline) RandomDilateLabels (class in dacapo.utils.pipeline) raw (dacapo.experiments.datasplits.datasets.Dataset attribute), [1] (dacapo.experiments.datasplits.datasets.dataset.Dataset attribute), [1] (dacapo.experiments.datasplits.datasets.dummy_dataset.DummyDataset attribute), [1] (dacapo.experiments.datasplits.datasets.DummyDataset attribute), [1] (dacapo.experiments.datasplits.datasets.raw_gt_dataset.RawGTDataset attribute), [1] (dacapo.experiments.datasplits.datasets.RawGTDataset attribute), [1] (dacapo.experiments.datasplits.datasets.simple.SimpleDataset property) (dacapo.experiments.datasplits.datasets.SimpleDataset property) RAW (dacapo.experiments.datasplits.keys.ArrayKey attribute), [1] (dacapo.experiments.datasplits.keys.DataKey attribute) (dacapo.experiments.datasplits.keys.keys.ArrayKey attribute), [1] (dacapo.experiments.datasplits.keys.keys.DataKey attribute) raw (dacapo.utils.pipeline.MakeRaw attribute) (dacapo.utils.pipeline.MakeRaw.Pipeline attribute) (dacapo.utils.view.NeuroglancerRunViewer attribute) raw_config (dacapo.experiments.datasplits.datasets.dummy_dataset_config.DummyDatasetConfig attribute), [1] (dacapo.experiments.datasplits.datasets.DummyDatasetConfig attribute), [1] (dacapo.experiments.datasplits.datasets.raw_gt_dataset_config.RawGTDatasetConfig attribute), [1] (dacapo.experiments.datasplits.datasets.RawGTDatasetConfig attribute), [1] raw_container (dacapo.experiments.datasplits.DatasetSpec attribute), [1] (dacapo.experiments.datasplits.datasplit_generator.DatasetSpec attribute), [1] raw_dataset (dacapo.experiments.datasplits.DatasetSpec attribute), [1] (dacapo.experiments.datasplits.datasplit_generator.DatasetSpec attribute), [1] raw_max (dacapo.experiments.datasplits.datasplit_generator.DataSplitGenerator attribute), [1] (dacapo.experiments.datasplits.DataSplitGenerator attribute), [1] raw_min (dacapo.experiments.datasplits.datasplit_generator.DataSplitGenerator attribute), [1] (dacapo.experiments.datasplits.DataSplitGenerator attribute), [1] raw_name (dacapo.experiments.datasplits.datasets.simple.SimpleDataset attribute) (dacapo.experiments.datasplits.datasets.SimpleDataset attribute) (dacapo.experiments.datasplits.simple_config.SimpleDataSplitConfig attribute) (dacapo.experiments.datasplits.SimpleDataSplitConfig attribute) RawGTDataset (class in dacapo.experiments.datasplits.datasets) (class in dacapo.experiments.datasplits.datasets.raw_gt_dataset) RawGTDatasetConfig (class in dacapo.experiments.datasplits.datasets) (class in dacapo.experiments.datasplits.datasets.raw_gt_dataset_config) read_cross_block_merges() (in module dacapo.blockwise.relabel_worker) read_roi (dacapo.blockwise.blockwise_task.DaCapoBlockwiseTask attribute) (dacapo.blockwise.DaCapoBlockwiseTask attribute) read_write_conflict (in module dacapo.blockwise.argmax_worker) (in module dacapo.blockwise.predict_worker) (in module dacapo.blockwise.relabel_worker) (in module dacapo.blockwise.segment_worker) (in module dacapo.blockwise.threshold_worker) rec_forward() (dacapo.experiments.architectures.cnnectome_unet.CNNectomeUNetModule method), [1] recall (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluation_scores.BinarySegmentationEvaluationScores attribute), [1] (dacapo.experiments.tasks.evaluators.BinarySegmentationEvaluationScores attribute), [1] recall() (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluator.ArrayEvaluator method), [1] recall_with_tolerance (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluation_scores.BinarySegmentationEvaluationScores attribute), [1] (dacapo.experiments.tasks.evaluators.BinarySegmentationEvaluationScores attribute), [1] recall_with_tolerance() (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluator.ArrayEvaluator method), [1] (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluator.CremiEvaluator method), [1] register_hierarchy() (dacapo.store.converter.TypedConverter method), [1] register_hierarchy_hooks() (in module dacapo.store.conversion_hooks) register_hooks() (in module dacapo.store.conversion_hooks) RejectIfEmpty (class in dacapo.gp) (class in dacapo.gp.reject_if_empty) Relabel (class in dacapo.utils.pipeline) relabel() (in module dacapo.experiments.tasks.evaluators.instance_evaluator) relabel_in_block() (in module dacapo.blockwise.relabel_worker) relu (dacapo.experiments.architectures.cnnectome_unet.AttentionBlockModule attribute) remove() (dacapo.store.array_store.ArrayStore method) (dacapo.store.local_array_store.LocalArrayStore method), [1] (dacapo.store.local_weights_store.LocalWeightsStore method), [1] (dacapo.store.weights_store.WeightsStore method), [1] repetition (dacapo.experiments.run_config.RunConfig attribute) (dacapo.experiments.RunConfig attribute) ResampledArrayConfig (class in dacapo.experiments.datasplits.datasets.arrays) (class in dacapo.experiments.datasplits.datasets.arrays.resampled_array_config) resize_if_needed() (in module dacapo.experiments.datasplits.datasplit_generator) resolution (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluator.ArrayEvaluator attribute), [1] retrieve_architecture_config() (dacapo.store.config_store.ConfigStore method), [1] (dacapo.store.file_config_store.FileConfigStore method), [1] (dacapo.store.mongo_config_store.MongoConfigStore method), [1]

retrieve_architecture_config_names() (dacapo.store.config_store.ConfigStore method), [1] (dacapo.store.file_config_store.FileConfigStore method), [1] (dacapo.store.mongo_config_store.MongoConfigStore method), [1] retrieve_array_config() (dacapo.store.config_store.ConfigStore method), [1] (dacapo.store.file_config_store.FileConfigStore method), [1] (dacapo.store.mongo_config_store.MongoConfigStore method), [1] retrieve_array_config_names() (dacapo.store.config_store.ConfigStore method), [1] (dacapo.store.file_config_store.FileConfigStore method), [1] (dacapo.store.mongo_config_store.MongoConfigStore method), [1] retrieve_best() (dacapo.store.local_weights_store.LocalWeightsStore method), [1] (dacapo.store.weights_store.WeightsStore method), [1] retrieve_dataset_config() (dacapo.store.mongo_config_store.MongoConfigStore method), [1] retrieve_dataset_config_names() (dacapo.store.mongo_config_store.MongoConfigStore method), [1] retrieve_datasplit_config() (dacapo.store.config_store.ConfigStore method), [1] (dacapo.store.file_config_store.FileConfigStore method), [1] (dacapo.store.mongo_config_store.MongoConfigStore method), [1] retrieve_datasplit_config_names() (dacapo.store.config_store.ConfigStore method), [1] (dacapo.store.file_config_store.FileConfigStore method), [1] (dacapo.store.mongo_config_store.MongoConfigStore method), [1] retrieve_run_config() (dacapo.store.config_store.ConfigStore method), [1] (dacapo.store.file_config_store.FileConfigStore method), [1] (dacapo.store.mongo_config_store.MongoConfigStore method), [1] retrieve_run_config_names() (dacapo.store.config_store.ConfigStore method), [1] (dacapo.store.file_config_store.FileConfigStore method), [1] (dacapo.store.mongo_config_store.MongoConfigStore method), [1] retrieve_task_config() (dacapo.store.config_store.ConfigStore method), [1] (dacapo.store.file_config_store.FileConfigStore method), [1] (dacapo.store.mongo_config_store.MongoConfigStore method), [1] retrieve_task_config_names() (dacapo.store.config_store.ConfigStore method), [1] (dacapo.store.file_config_store.FileConfigStore method), [1] (dacapo.store.mongo_config_store.MongoConfigStore method), [1] retrieve_trainer_config() (dacapo.store.config_store.ConfigStore method), [1] (dacapo.store.file_config_store.FileConfigStore method), [1] (dacapo.store.mongo_config_store.MongoConfigStore method), [1] retrieve_trainer_config_names() (dacapo.store.config_store.ConfigStore method), [1] (dacapo.store.file_config_store.FileConfigStore method), [1] (dacapo.store.mongo_config_store.MongoConfigStore method), [1] retrieve_training_stats() (dacapo.store.file_stats_store.FileStatsStore method) (dacapo.store.mongo_stats_store.MongoStatsStore method), [1] (dacapo.store.stats_store.StatsStore method), [1] retrieve_validation_iteration_scores() (dacapo.store.file_stats_store.FileStatsStore method) (dacapo.store.mongo_stats_store.MongoStatsStore method), [1] (dacapo.store.stats_store.StatsStore method), [1] retrieve_weights() (dacapo.store.local_weights_store.LocalWeightsStore method), [1] (dacapo.store.weights_store.WeightsStore method), [1] roi (dacapo.experiments.datasplits.datasets.arrays.crop_array_config.CropArrayConfig attribute), [1] (dacapo.experiments.datasplits.datasets.arrays.CropArrayConfig attribute), [1] rotation_interval (dacapo.experiments.trainers.gp_augments.elastic_config.ElasticAugmentConfig attribute), [1] (dacapo.experiments.trainers.gp_augments.ElasticAugmentConfig attribute), [1] rotation_max_amount (dacapo.gp.elastic_augment_fuse.ElasticAugment attribute) (dacapo.gp.ElasticAugment attribute) rotation_start (dacapo.gp.elastic_augment_fuse.ElasticAugment attribute) (dacapo.gp.ElasticAugment attribute) Run (class in dacapo.experiments.run) run (dacapo.experiments.starts.cosem_start.CosemStart attribute), [1] (dacapo.experiments.starts.cosem_start_config.CosemStartConfig attribute) (dacapo.experiments.starts.CosemStart attribute), [1] (dacapo.experiments.starts.CosemStartConfig attribute) (dacapo.experiments.starts.Start attribute) (dacapo.experiments.starts.start.Start attribute) (dacapo.experiments.starts.start_config.StartConfig attribute), [1] (dacapo.experiments.starts.StartConfig attribute), [1] (dacapo.utils.view.BestScore attribute), [1] (dacapo.utils.view.NeuroglancerRunViewer attribute), [1] run_blockwise() (in module dacapo.blockwise.scheduler) run_thread (dacapo.utils.view.NeuroglancerRunViewer attribute) RunConfig (class in dacapo.experiments) (class in dacapo.experiments.run_config) RunInfo (in module dacapo.plot) runs (dacapo.store.config_store.ConfigStore attribute), [1] (dacapo.store.file_config_store.FileConfigStore property) (dacapo.store.mongo_config_store.MongoConfigStore attribute) runs_base_dir (dacapo.options.DaCapoConfig attribute), [1]

S

sample_points (dacapo.experiments.datasplits.datasets.Dataset attribute), [1] (dacapo.experiments.datasplits.datasets.dataset.Dataset attribute), [1] (dacapo.experiments.datasplits.datasets.raw_gt_dataset.RawGTDataset attribute), [1] (dacapo.experiments.datasplits.datasets.raw_gt_dataset_config.RawGTDatasetConfig attribute), [1] (dacapo.experiments.datasplits.datasets.RawGTDataset attribute), [1] (dacapo.experiments.datasplits.datasets.RawGTDatasetConfig attribute), [1] (dacapo.experiments.datasplits.datasets.simple.SimpleDataset property) (dacapo.experiments.datasplits.datasets.SimpleDataset property) sampling (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluator.CremiEvaluator attribute), [1] save_ndarray() (in module dacapo.utils.array_utils) scale (dacapo.experiments.trainers.gp_augments.intensity_config.IntensityAugmentConfig attribute), [1] (dacapo.experiments.trainers.gp_augments.intensity_scale_shift_config.IntensityScaleShiftAugmentConfig attribute), [1] (dacapo.experiments.trainers.gp_augments.IntensityAugmentConfig attribute), [1] (dacapo.experiments.trainers.gp_augments.IntensityScaleShiftAugmentConfig attribute), [1] scale() (dacapo.experiments.architectures.Architecture method), [1] (dacapo.experiments.architectures.architecture.Architecture method), [1] (dacapo.experiments.architectures.cnnectome_unet.CNNectomeUNet method) (dacapo.experiments.architectures.CNNectomeUNet method) (dacapo.experiments.Model method) (dacapo.experiments.model.Model method) scale_factor (dacapo.experiments.tasks.distance_task_config.DistanceTaskConfig attribute), [1] (dacapo.experiments.tasks.DistanceTaskConfig attribute), [1] (dacapo.experiments.tasks.hot_distance_task_config.HotDistanceTaskConfig attribute), [1] (dacapo.experiments.tasks.HotDistanceTaskConfig attribute), [1] (dacapo.experiments.tasks.inner_distance_task_config.InnerDistanceTaskConfig attribute), [1] (dacapo.experiments.tasks.InnerDistanceTaskConfig attribute), [1] (dacapo.experiments.tasks.predictors.distance_predictor.DistancePredictor attribute) (dacapo.experiments.tasks.predictors.DistancePredictor attribute) (dacapo.experiments.tasks.predictors.hot_distance_predictor.HotDistancePredictor attribute) (dacapo.experiments.tasks.predictors.HotDistancePredictor attribute) (dacapo.experiments.tasks.predictors.inner_distance_predictor.InnerDistancePredictor attribute) (dacapo.experiments.tasks.predictors.InnerDistancePredictor attribute) scheduler (dacapo.experiments.trainers.gunpowder_trainer.GunpowderTrainer attribute), [1] (dacapo.experiments.trainers.GunpowderTrainer attribute), [1] score (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluator.BinarySegmentationEvaluator property) (dacapo.experiments.tasks.evaluators.BinarySegmentationEvaluator property) (dacapo.experiments.tasks.evaluators.dummy_evaluator.DummyEvaluator property) (dacapo.experiments.tasks.evaluators.DummyEvaluator property) (dacapo.experiments.tasks.evaluators.Evaluator property) (dacapo.experiments.tasks.evaluators.evaluator.Evaluator property) (dacapo.experiments.tasks.evaluators.instance_evaluator.InstanceEvaluator property) (dacapo.experiments.tasks.evaluators.InstanceEvaluator property) (dacapo.utils.view.BestScore attribute), [1] Score (in module dacapo.experiments.tasks.evaluators.evaluator) score() (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluator.BinarySegmentationEvaluator method) (dacapo.experiments.tasks.evaluators.BinarySegmentationEvaluator method) (dacapo.experiments.tasks.evaluators.dummy_evaluator.DummyEvaluator method) (dacapo.experiments.tasks.evaluators.DummyEvaluator method) (dacapo.experiments.tasks.evaluators.instance_evaluator.InstanceEvaluator method) (dacapo.experiments.tasks.evaluators.InstanceEvaluator method) scores (dacapo.experiments.validation_iteration_scores.ValidationIterationScores attribute), [1] (dacapo.experiments.validation_scores.ValidationScores attribute), [1] (dacapo.experiments.ValidationIterationScores attribute), [1] (dacapo.experiments.ValidationScores attribute), [1] seg_to_affgraph() (in module dacapo.utils.affinities) segment_blockwise() (in module dacapo.blockwise.scheduler) segment_function() (in module dacapo.blockwise.empanada_function) (in module dacapo.blockwise.watershed_function) segmentation (dacapo.utils.view.NeuroglancerRunViewer attribute) segmentation_type (dacapo.experiments.datasplits.datasplit_generator.DataSplitGenerator attribute), [1] (dacapo.experiments.datasplits.DataSplitGenerator attribute), [1] SegmentationType (class in dacapo.experiments.datasplits.datasplit_generator) semantic (dacapo.experiments.datasplits.datasplit_generator.SegmentationType attribute), [1] serialize() (dacapo.options.DaCapoConfig method), [1] set_best() (dacapo.experiments.tasks.evaluators.Evaluator method), [1] (dacapo.experiments.tasks.evaluators.evaluator.Evaluator method), [1] set_prediction() (dacapo.experiments.tasks.post_processors.argmax_post_processor.ArgmaxPostProcessor method), [1] (dacapo.experiments.tasks.post_processors.ArgmaxPostProcessor method), [1] (dacapo.experiments.tasks.post_processors.dummy_post_processor.DummyPostProcessor method), [1] (dacapo.experiments.tasks.post_processors.DummyPostProcessor method), [1] (dacapo.experiments.tasks.post_processors.post_processor.PostProcessor method), [1] (dacapo.experiments.tasks.post_processors.PostProcessor method), [1] (dacapo.experiments.tasks.post_processors.threshold_post_processor.ThresholdPostProcessor method), [1] (dacapo.experiments.tasks.post_processors.ThresholdPostProcessor method), [1] (dacapo.experiments.tasks.post_processors.watershed_post_processor.WatershedPostProcessor method), [1] (dacapo.experiments.tasks.post_processors.WatershedPostProcessor method), [1] setup() (dacapo.gp.copy.CopyMask method), [1] (dacapo.gp.CopyMask method), [1] (dacapo.gp.dacapo_create_target.DaCapoTargetFilter method), [1] (dacapo.gp.dacapo_points_source.GraphSource method), [1] (dacapo.gp.DaCapoTargetFilter method), [1] (dacapo.gp.elastic_augment_fuse.ElasticAugment method) (dacapo.gp.ElasticAugment method) (dacapo.gp.gamma_noise.GammaAugment method), [1] (dacapo.gp.GammaAugment method), [1] (dacapo.gp.GraphSource method), [1] (dacapo.gp.Product method) (dacapo.gp.product.Product method) (dacapo.gp.reject_if_empty.RejectIfEmpty method) (dacapo.gp.RejectIfEmpty method) (dacapo.utils.pipeline.MakeRaw method), [1] (dacapo.utils.pipeline.ZerosSource method), [1] shift (dacapo.experiments.trainers.gp_augments.intensity_config.IntensityAugmentConfig attribute), [1] (dacapo.experiments.trainers.gp_augments.intensity_scale_shift_config.IntensityScaleShiftAugmentConfig attribute), [1] (dacapo.experiments.trainers.gp_augments.IntensityAugmentConfig attribute), [1] (dacapo.experiments.trainers.gp_augments.IntensityScaleShiftAugmentConfig attribute), [1] sigma (dacapo.experiments.tasks.post_processors.watershed_post_processor_parameters.WatershedPostProcessorParameters attribute) (dacapo.experiments.tasks.post_processors.WatershedPostProcessorParameters attribute) sigma() (dacapo.experiments.tasks.predictors.affinities_predictor.AffinitiesPredictor method), [1] (dacapo.experiments.tasks.predictors.AffinitiesPredictor method), [1] SimpleAugmentConfig (class in dacapo.experiments.trainers.gp_augments) (class in dacapo.experiments.trainers.gp_augments.simple_config) SimpleDataset (class in dacapo.experiments.datasplits.datasets) (class in dacapo.experiments.datasplits.datasets.simple) SimpleDataSplitConfig (class in dacapo.experiments.datasplits) (class in dacapo.experiments.datasplits.simple_config) smooth_values() (in module dacapo.plot) snap_to_grid (dacapo.experiments.datasplits.datasets.arrays.zarr_array_config.ZarrArrayConfig attribute), [1] (dacapo.experiments.datasplits.datasets.arrays.ZarrArrayConfig attribute), [1] snapshot_container() (dacapo.store.array_store.ArrayStore method) (dacapo.store.local_array_store.LocalArrayStore method), [1] snapshot_interval (dacapo.experiments.trainers.gunpowder_trainer_config.GunpowderTrainerConfig attribute), [1] (dacapo.experiments.trainers.GunpowderTrainerConfig attribute), [1] snapshot_iteration (dacapo.experiments.trainers.gunpowder_trainer.GunpowderTrainer attribute), [1] (dacapo.experiments.trainers.GunpowderTrainer attribute), [1] source (dacapo.experiments.datasplits.datasets.arrays.dvid_array_config.DVIDArrayConfig attribute), [1] (dacapo.experiments.datasplits.datasets.arrays.DVIDArrayConfig attribute), [1] source_array_config (dacapo.experiments.datasplits.datasets.arrays.binarize_array_config.BinarizeArrayConfig attribute), [1] (dacapo.experiments.datasplits.datasets.arrays.BinarizeArrayConfig attribute), [1] (dacapo.experiments.datasplits.datasets.arrays.constant_array_config.ConstantArrayConfig attribute), [1] (dacapo.experiments.datasplits.datasets.arrays.ConstantArrayConfig attribute), [1] (dacapo.experiments.datasplits.datasets.arrays.crop_array_config.CropArrayConfig attribute), [1] (dacapo.experiments.datasplits.datasets.arrays.CropArrayConfig attribute), [1] (dacapo.experiments.datasplits.datasets.arrays.IntensitiesArrayConfig attribute), [1] (dacapo.experiments.datasplits.datasets.arrays.intensity_array_config.IntensitiesArrayConfig attribute), [1] (dacapo.experiments.datasplits.datasets.arrays.logical_or_array_config.LogicalOrArrayConfig attribute), [1] (dacapo.experiments.datasplits.datasets.arrays.LogicalOrArrayConfig attribute), [1] (dacapo.experiments.datasplits.datasets.arrays.missing_annotations_mask_config.MissingAnnotationsMaskConfig attribute), [1] (dacapo.experiments.datasplits.datasets.arrays.MissingAnnotationsMaskConfig attribute), [1] (dacapo.experiments.datasplits.datasets.arrays.ones_array_config.OnesArrayConfig attribute), [1] (dacapo.experiments.datasplits.datasets.arrays.OnesArrayConfig attribute), [1] (dacapo.experiments.datasplits.datasets.arrays.resampled_array_config.ResampledArrayConfig attribute), [1] (dacapo.experiments.datasplits.datasets.arrays.ResampledArrayConfig attribute), [1]

source_array_configs (dacapo.experiments.datasplits.datasets.arrays.concat_array_config.ConcatArrayConfig attribute), [1] (dacapo.experiments.datasplits.datasets.arrays.ConcatArrayConfig attribute), [1] (dacapo.experiments.datasplits.datasets.arrays.merge_instances_array_config.MergeInstancesArrayConfig attribute), [1] (dacapo.experiments.datasplits.datasets.arrays.MergeInstancesArrayConfig attribute), [1] (dacapo.experiments.datasplits.datasets.arrays.sum_array_config.SumArrayConfig attribute), [1] (dacapo.experiments.datasplits.datasets.arrays.SumArrayConfig attribute), [1] spawn_worker() (in module dacapo.blockwise.argmax_worker) (in module dacapo.blockwise.predict_worker) (in module dacapo.blockwise.relabel_worker) (in module dacapo.blockwise.segment_worker) (in module dacapo.blockwise.threshold_worker) SPECIFIED_LOCATIONS (dacapo.experiments.datasplits.keys.DataKey attribute) (dacapo.experiments.datasplits.keys.GraphKey attribute), [1] (dacapo.experiments.datasplits.keys.keys.DataKey attribute) (dacapo.experiments.datasplits.keys.keys.GraphKey attribute), [1] split() (dacapo.experiments.tasks.losses.hot_distance_loss.HotDistanceLoss method), [1] (dacapo.experiments.tasks.losses.HotDistanceLoss method), [1] split_vi() (in module dacapo.utils.voi) stack_inference() (in module dacapo.blockwise.empanada_function) stack_postprocessing() (in module dacapo.blockwise.empanada_function) Start (class in dacapo.experiments.starts) (class in dacapo.experiments.starts.start) start (dacapo.experiments.run.Run attribute), [1] start() (dacapo.utils.view.NeuroglancerRunViewer method), [1] start_config (dacapo.experiments.run_config.RunConfig attribute) (dacapo.experiments.RunConfig attribute) start_neuroglancer() (dacapo.utils.view.NeuroglancerRunViewer method), [1] start_type (dacapo.experiments.starts.cosem_start_config.CosemStartConfig attribute) (dacapo.experiments.starts.CosemStartConfig attribute) (dacapo.experiments.starts.start_config.StartConfig attribute) (dacapo.experiments.starts.StartConfig attribute) start_worker() (in module dacapo.blockwise.argmax_worker) (in module dacapo.blockwise.predict_worker) (in module dacapo.blockwise.relabel_worker) (in module dacapo.blockwise.segment_worker) (in module dacapo.blockwise.threshold_worker) start_worker_fn() (in module dacapo.blockwise.argmax_worker) (in module dacapo.blockwise.predict_worker) (in module dacapo.blockwise.relabel_worker) (in module dacapo.blockwise.segment_worker) (in module dacapo.blockwise.threshold_worker) StartConfig (class in dacapo.experiments.starts) (class in dacapo.experiments.starts.start_config) stats_store (dacapo.utils.view.BestScore attribute), [1] StatsStore (class in dacapo.store.stats_store) stop() (dacapo.utils.view.NeuroglancerRunViewer method), [1] store_architecture_config() (dacapo.store.config_store.ConfigStore method), [1] (dacapo.store.file_config_store.FileConfigStore method), [1] (dacapo.store.mongo_config_store.MongoConfigStore method), [1] store_array_config() (dacapo.store.config_store.ConfigStore method), [1] (dacapo.store.file_config_store.FileConfigStore method), [1] (dacapo.store.mongo_config_store.MongoConfigStore method), [1] store_best() (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluation_scores.BinarySegmentationEvaluationScores static method) (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluation_scores.MultiChannelBinarySegmentationEvaluationScores static method) (dacapo.experiments.tasks.evaluators.BinarySegmentationEvaluationScores static method) (dacapo.experiments.tasks.evaluators.dummy_evaluation_scores.DummyEvaluationScores method) (dacapo.experiments.tasks.evaluators.dummy_evaluation_scores.DummyEvaluationScores static method) (dacapo.experiments.tasks.evaluators.DummyEvaluationScores method) (dacapo.experiments.tasks.evaluators.DummyEvaluationScores static method) (dacapo.experiments.tasks.evaluators.evaluation_scores.EvaluationScores method) (dacapo.experiments.tasks.evaluators.evaluation_scores.EvaluationScores static method) (dacapo.experiments.tasks.evaluators.EvaluationScores method) (dacapo.experiments.tasks.evaluators.EvaluationScores static method) (dacapo.experiments.tasks.evaluators.Evaluator method), [1] (dacapo.experiments.tasks.evaluators.evaluator.Evaluator method), [1] (dacapo.experiments.tasks.evaluators.instance_evaluation_scores.InstanceEvaluationScores method) (dacapo.experiments.tasks.evaluators.instance_evaluation_scores.InstanceEvaluationScores static method) (dacapo.experiments.tasks.evaluators.InstanceEvaluationScores method) (dacapo.experiments.tasks.evaluators.InstanceEvaluationScores static method) (dacapo.experiments.tasks.evaluators.MultiChannelBinarySegmentationEvaluationScores static method) (dacapo.store.local_weights_store.LocalWeightsStore method), [1] store_dataset_config() (dacapo.store.mongo_config_store.MongoConfigStore method), [1] store_datasplit_config() (dacapo.store.config_store.ConfigStore method), [1] (dacapo.store.file_config_store.FileConfigStore method), [1] (dacapo.store.mongo_config_store.MongoConfigStore method), [1] store_run_config() (dacapo.store.config_store.ConfigStore method), [1] (dacapo.store.file_config_store.FileConfigStore method), [1] (dacapo.store.mongo_config_store.MongoConfigStore method), [1] store_task_config() (dacapo.store.config_store.ConfigStore method), [1] (dacapo.store.file_config_store.FileConfigStore method), [1] (dacapo.store.mongo_config_store.MongoConfigStore method), [1] store_trainer_config() (dacapo.store.config_store.ConfigStore method), [1] (dacapo.store.file_config_store.FileConfigStore method), [1] (dacapo.store.mongo_config_store.MongoConfigStore method), [1] store_training_stats() (dacapo.store.file_stats_store.FileStatsStore method) (dacapo.store.mongo_stats_store.MongoStatsStore method), [1] (dacapo.store.stats_store.StatsStore method), [1] store_type (dacapo.experiments.datasplits.datasets.graphstores.graph_source_config.GraphStoreConfig attribute) (dacapo.experiments.datasplits.datasets.graphstores.GraphStoreConfig attribute) store_validation_iteration_scores() (dacapo.store.file_stats_store.FileStatsStore method) (dacapo.store.mongo_stats_store.MongoStatsStore method), [1] (dacapo.store.stats_store.StatsStore method), [1] store_weights() (dacapo.store.local_weights_store.LocalWeightsStore method), [1] (dacapo.store.weights_store.WeightsStore method), [1] sub_task_config (dacapo.experiments.tasks.pretrained_task_config.PretrainedTaskConfig attribute), [1] (dacapo.experiments.tasks.PretrainedTaskConfig attribute), [1] subsample (dacapo.experiments.trainers.gp_augments.elastic_config.ElasticAugmentConfig attribute), [1] (dacapo.experiments.trainers.gp_augments.ElasticAugmentConfig attribute), [1] (dacapo.gp.elastic_augment_fuse.ElasticAugment attribute) (dacapo.gp.ElasticAugment attribute) subscores() (dacapo.experiments.validation_scores.ValidationScores method), [1] (dacapo.experiments.ValidationScores method), [1] SumArrayConfig (class in dacapo.experiments.datasplits.datasets.arrays) (class in dacapo.experiments.datasplits.datasets.arrays.sum_array_config)

T

target_key (dacapo.gp.dacapo_create_target.DaCapoTargetFilter attribute), [1] (dacapo.gp.DaCapoTargetFilter attribute), [1] target_rois (dacapo.gp.elastic_augment_fuse.ElasticAugment attribute) (dacapo.gp.ElasticAugment attribute) targets (dacapo.experiments.datasplits.datasplit_generator.DataSplitGenerator attribute), [1] (dacapo.experiments.datasplits.DataSplitGenerator attribute), [1] Task (class in dacapo.experiments.tasks) (class in dacapo.experiments.tasks.task) task (dacapo.experiments.run.Run attribute), [1] task_config (dacapo.experiments.run_config.RunConfig attribute) (dacapo.experiments.RunConfig attribute) (dacapo.experiments.tasks.inner_distance_task.InnerDistanceTask attribute) (dacapo.experiments.tasks.InnerDistanceTask attribute) task_type (dacapo.experiments.tasks.affinities_task_config.AffinitiesTaskConfig attribute) (dacapo.experiments.tasks.AffinitiesTaskConfig attribute) (dacapo.experiments.tasks.distance_task_config.DistanceTaskConfig attribute) (dacapo.experiments.tasks.DistanceTaskConfig attribute) (dacapo.experiments.tasks.dummy_task_config.DummyTaskConfig attribute), [1] (dacapo.experiments.tasks.DummyTaskConfig attribute), [1] (dacapo.experiments.tasks.hot_distance_task_config.HotDistanceTaskConfig attribute), [1] (dacapo.experiments.tasks.HotDistanceTaskConfig attribute), [1] (dacapo.experiments.tasks.inner_distance_task_config.InnerDistanceTaskConfig attribute) (dacapo.experiments.tasks.InnerDistanceTaskConfig attribute) (dacapo.experiments.tasks.one_hot_task_config.OneHotTaskConfig attribute), [1] (dacapo.experiments.tasks.OneHotTaskConfig attribute), [1] (dacapo.experiments.tasks.pretrained_task_config.PretrainedTaskConfig attribute) (dacapo.experiments.tasks.PretrainedTaskConfig attribute) TaskConfig (class in dacapo.experiments.tasks) (class in dacapo.experiments.tasks.task_config) tasks (dacapo.store.config_store.ConfigStore attribute), [1] (dacapo.store.file_config_store.FileConfigStore property) (dacapo.store.mongo_config_store.MongoConfigStore attribute) test (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluator.ArrayEvaluator attribute), [1] (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluator.CremiEvaluator attribute), [1] test_edt() (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluator.CremiEvaluator method) test_empty (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluator.ArrayEvaluator attribute), [1] test_itk() (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluator.ArrayEvaluator method) test_mask() (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluator.CremiEvaluator method) threshold (dacapo.experiments.tasks.post_processors.threshold_post_processor_parameters.ThresholdPostProcessorParameters attribute), [1] (dacapo.experiments.tasks.post_processors.ThresholdPostProcessorParameters attribute), [1] (dacapo.experiments.tasks.post_processors.watershed_post_processor_parameters.WatershedPostProcessorParameters attribute) (dacapo.experiments.tasks.post_processors.WatershedPostProcessorParameters attribute) (dacapo.experiments.tasks.predictors.distance_predictor.DistancePredictor attribute) (dacapo.experiments.tasks.predictors.DistancePredictor attribute) (dacapo.experiments.tasks.predictors.hot_distance_predictor.HotDistancePredictor attribute), [1] (dacapo.experiments.tasks.predictors.HotDistancePredictor attribute), [1] (dacapo.experiments.tasks.predictors.inner_distance_predictor.InnerDistancePredictor attribute) (dacapo.experiments.tasks.predictors.InnerDistancePredictor attribute) ThresholdPostProcessor (class in dacapo.experiments.tasks.post_processors) (class in dacapo.experiments.tasks.post_processors.threshold_post_processor) ThresholdPostProcessorParameters (class in dacapo.experiments.tasks.post_processors) (class in dacapo.experiments.tasks.post_processors.threshold_post_processor_parameters) TiffArrayConfig (class in dacapo.experiments.datasplits.datasets.arrays.tiff_array_config) time (dacapo.experiments.training_iteration_stats.TrainingIterationStats attribute), [1] (dacapo.experiments.TrainingIterationStats attribute), [1] timeout (dacapo.blockwise.blockwise_task.DaCapoBlockwiseTask attribute) (dacapo.blockwise.DaCapoBlockwiseTask attribute) to_array() (dacapo.experiments.datasplits.datasets.arrays.dummy_array_config.DummyArrayConfig method) (dacapo.experiments.datasplits.datasets.arrays.DummyArrayConfig method) (dacapo.experiments.datasplits.datasets.arrays.dvid_array_config.DVIDArrayConfig method) (dacapo.experiments.datasplits.datasets.arrays.DVIDArrayConfig method) (dacapo.experiments.datasplits.datasets.arrays.IntensitiesArrayConfig method) (dacapo.experiments.datasplits.datasets.arrays.intensity_array_config.IntensitiesArrayConfig method) (dacapo.experiments.datasplits.datasets.arrays.logical_or_array_config.LogicalOrArrayConfig method) (dacapo.experiments.datasplits.datasets.arrays.LogicalOrArrayConfig method) to_ndarray() (in module dacapo.utils.array_utils) to_xarray() (dacapo.experiments.training_stats.TrainingStats method), [1] (dacapo.experiments.TrainingStats method), [1] (dacapo.experiments.validation_scores.ValidationScores method), [1] (dacapo.experiments.ValidationScores method), [1]

tol_distance (dacapo.experiments.tasks.distance_task_config.DistanceTaskConfig attribute), [1] (dacapo.experiments.tasks.DistanceTaskConfig attribute), [1] (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluator.BinarySegmentationEvaluator attribute), [1] (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluator.CremiEvaluator attribute), [1] (dacapo.experiments.tasks.evaluators.BinarySegmentationEvaluator attribute), [1] (dacapo.experiments.tasks.hot_distance_task_config.HotDistanceTaskConfig attribute), [1] (dacapo.experiments.tasks.HotDistanceTaskConfig attribute), [1] (dacapo.experiments.tasks.inner_distance_task_config.InnerDistanceTaskConfig attribute), [1] (dacapo.experiments.tasks.InnerDistanceTaskConfig attribute), [1] total_roi (dacapo.blockwise.blockwise_task.DaCapoBlockwiseTask attribute) (dacapo.blockwise.DaCapoBlockwiseTask attribute) tracker_consensus() (in module dacapo.blockwise.empanada_function) train (dacapo.experiments.datasplits.DataSplit attribute), [1] (dacapo.experiments.datasplits.datasplit.DataSplit attribute), [1] (dacapo.experiments.datasplits.datasplit_generator.DatasetType attribute), [1] (dacapo.experiments.datasplits.dummy_datasplit.DummyDataSplit attribute), [1] (dacapo.experiments.datasplits.DummyDataSplit attribute), [1] (dacapo.experiments.datasplits.simple_config.SimpleDataSplitConfig property) (dacapo.experiments.datasplits.SimpleDataSplitConfig property) (dacapo.experiments.datasplits.train_validate_datasplit.TrainValidateDataSplit attribute), [1] (dacapo.experiments.datasplits.TrainValidateDataSplit attribute), [1] train() (in module dacapo) (in module dacapo.train) train_config (dacapo.experiments.datasplits.dummy_datasplit_config.DummyDataSplitConfig attribute), [1] (dacapo.experiments.datasplits.DummyDataSplitConfig attribute), [1] train_configs (dacapo.experiments.datasplits.train_validate_datasplit_config.TrainValidateDataSplitConfig attribute), [1] (dacapo.experiments.datasplits.TrainValidateDataSplitConfig attribute), [1] train_group_name (dacapo.experiments.datasplits.simple_config.SimpleDataSplitConfig attribute) (dacapo.experiments.datasplits.SimpleDataSplitConfig attribute) train_run() (in module dacapo.train) train_until (dacapo.experiments.run.Run attribute), [1] trained_until() (dacapo.experiments.training_stats.TrainingStats method), [1] (dacapo.experiments.TrainingStats method), [1] Trainer (class in dacapo.experiments.trainers) (class in dacapo.experiments.trainers.trainer) trainer (dacapo.experiments.run.Run attribute), [1] trainer_config (dacapo.experiments.run_config.RunConfig attribute) (dacapo.experiments.RunConfig attribute) trainer_type (dacapo.experiments.trainers.dummy_trainer_config.DummyTrainerConfig attribute) (dacapo.experiments.trainers.DummyTrainerConfig attribute) (dacapo.experiments.trainers.gunpowder_trainer_config.GunpowderTrainerConfig attribute), [1] (dacapo.experiments.trainers.GunpowderTrainerConfig attribute), [1] TrainerConfig (class in dacapo.experiments.trainers) (class in dacapo.experiments.trainers.trainer_config) trainers (dacapo.store.config_store.ConfigStore attribute), [1] (dacapo.store.file_config_store.FileConfigStore property) (dacapo.store.mongo_config_store.MongoConfigStore attribute) training_stats (dacapo.experiments.run.Run attribute), [1] (dacapo.store.mongo_stats_store.MongoStatsStore attribute) TrainingIterationStats (class in dacapo.experiments) (class in dacapo.experiments.training_iteration_stats) TrainingStats (class in dacapo.experiments) (class in dacapo.experiments.training_stats) TrainValidateDataSplit (class in dacapo.experiments.datasplits) (class in dacapo.experiments.datasplits.train_validate_datasplit) TrainValidateDataSplitConfig (class in dacapo.experiments.datasplits) (class in dacapo.experiments.datasplits.train_validate_datasplit_config) transformations (dacapo.gp.elastic_augment_fuse.ElasticAugment attribute) (dacapo.gp.ElasticAugment attribute) true_positives_with_tolerance() (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluator.CremiEvaluator method), [1] truth (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluator.ArrayEvaluator attribute), [1] (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluator.CremiEvaluator attribute), [1] truth_edt() (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluator.CremiEvaluator method) truth_empty (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluator.ArrayEvaluator attribute), [1] truth_itk() (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluator.ArrayEvaluator method) truth_mask() (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluator.CremiEvaluator method) type (dacapo.options.DaCapoConfig attribute), [1] TypedConverter (class in dacapo.store.converter)

U

unet (dacapo.experiments.architectures.cnnectome_unet.CNNectomeUNet attribute) (dacapo.experiments.architectures.CNNectomeUNet attribute) uniform_3d_rotation (dacapo.experiments.trainers.gp_augments.elastic_config.ElasticAugmentConfig attribute), [1] (dacapo.experiments.trainers.gp_augments.ElasticAugmentConfig attribute), [1] (dacapo.gp.elastic_augment_fuse.ElasticAugment attribute) (dacapo.gp.ElasticAugment attribute) units (dacapo.experiments.datasplits.datasets.arrays.tiff_array_config.TiffArrayConfig attribute) up (dacapo.experiments.architectures.cnnectome_unet.AttentionBlockModule attribute) (dacapo.experiments.architectures.cnnectome_unet.Upsample attribute) update_best_info() (dacapo.utils.view.NeuroglancerRunViewer method), [1] update_best_layer() (dacapo.utils.view.NeuroglancerRunViewer method), [1] update_neuroglancer() (dacapo.utils.view.NeuroglancerRunViewer method), [1] update_with_new_validation_if_possible() (dacapo.utils.view.NeuroglancerRunViewer method), [1] updated_neuroglancer_layer() (dacapo.utils.view.NeuroglancerRunViewer method), [1] Upsample (class in dacapo.experiments.architectures.cnnectome_unet) upsample (dacapo.experiments.datasplits.datasets.arrays.resampled_array_config.ResampledArrayConfig attribute), [1] (dacapo.experiments.datasplits.datasets.arrays.ResampledArrayConfig attribute), [1]

upsample_channel_contraction (dacapo.experiments.architectures.cnnectome_unet.CNNectomeUNet attribute) (dacapo.experiments.architectures.cnnectome_unet.CNNectomeUNetModule attribute) (dacapo.experiments.architectures.CNNectomeUNet attribute) upsample_factors (dacapo.experiments.architectures.cnnectome_unet.CNNectomeUNet attribute) (dacapo.experiments.architectures.cnnectome_unet_config.CNNectomeUNetConfig attribute), [1] (dacapo.experiments.architectures.CNNectomeUNet attribute) (dacapo.experiments.architectures.CNNectomeUNetConfig attribute), [1] upstream_tasks (dacapo.blockwise.blockwise_task.DaCapoBlockwiseTask attribute) (dacapo.blockwise.DaCapoBlockwiseTask attribute) use_attention (dacapo.experiments.architectures.cnnectome_unet.CNNectomeUNet attribute), [1] (dacapo.experiments.architectures.cnnectome_unet.CNNectomeUNetModule attribute), [1], [2] (dacapo.experiments.architectures.cnnectome_unet_config.CNNectomeUNetConfig attribute), [1] (dacapo.experiments.architectures.CNNectomeUNet attribute), [1] (dacapo.experiments.architectures.CNNectomeUNetConfig attribute), [1] use_negative_class (dacapo.experiments.datasplits.datasplit_generator.DataSplitGenerator attribute) (dacapo.experiments.datasplits.DataSplitGenerator attribute) users (dacapo.store.file_config_store.FileConfigStore property) (dacapo.store.mongo_config_store.MongoConfigStore attribute)

V

val (dacapo.experiments.datasplits.datasplit_generator.DatasetType attribute), [1] validate (dacapo.experiments.datasplits.DataSplit attribute), [1] (dacapo.experiments.datasplits.datasplit.DataSplit attribute), [1] (dacapo.experiments.datasplits.dummy_datasplit.DummyDataSplit attribute), [1] (dacapo.experiments.datasplits.DummyDataSplit attribute), [1] (dacapo.experiments.datasplits.simple_config.SimpleDataSplitConfig property) (dacapo.experiments.datasplits.SimpleDataSplitConfig property) (dacapo.experiments.datasplits.train_validate_datasplit.TrainValidateDataSplit attribute), [1] (dacapo.experiments.datasplits.TrainValidateDataSplit attribute), [1] validate() (in module dacapo.validate) validate_configs (dacapo.experiments.datasplits.train_validate_datasplit_config.TrainValidateDataSplitConfig attribute), [1] (dacapo.experiments.datasplits.TrainValidateDataSplitConfig attribute), [1] validate_group_name (dacapo.experiments.datasplits.simple_config.SimpleDataSplitConfig attribute) (dacapo.experiments.datasplits.SimpleDataSplitConfig attribute) validate_run() (in module dacapo.validate) validated_until() (dacapo.experiments.validation_scores.ValidationScores method), [1] (dacapo.experiments.ValidationScores method), [1] validation_container() (dacapo.store.array_store.ArrayStore method) (dacapo.store.local_array_store.LocalArrayStore method), [1] validation_input_arrays() (dacapo.store.array_store.ArrayStore method) (dacapo.store.local_array_store.LocalArrayStore method), [1] validation_interval (dacapo.experiments.run.Run attribute), [1] (dacapo.experiments.run_config.RunConfig attribute) (dacapo.experiments.RunConfig attribute) validation_output_array() (dacapo.store.array_store.ArrayStore method) (dacapo.store.local_array_store.LocalArrayStore method), [1] validation_parameters (dacapo.utils.view.BestScore attribute), [1] validation_prediction_array() (dacapo.store.array_store.ArrayStore method) (dacapo.store.local_array_store.LocalArrayStore method), [1] validation_scores (dacapo.experiments.run.Run attribute) (dacapo.experiments.run.Run property) (dacapo.store.mongo_stats_store.MongoStatsStore attribute) ValidationIterationScores (class in dacapo.experiments) (class in dacapo.experiments.validation_iteration_scores) ValidationScores (class in dacapo.experiments) (class in dacapo.experiments.validation_scores) verify() (dacapo.experiments.architectures.architecture_config.ArchitectureConfig method), [1] (dacapo.experiments.architectures.ArchitectureConfig method), [1] (dacapo.experiments.architectures.dummy_architecture_config.DummyArchitectureConfig method), [1] (dacapo.experiments.architectures.DummyArchitectureConfig method), [1] (dacapo.experiments.datasplits.datasets.arrays.array_config.ArrayConfig method), [1] (dacapo.experiments.datasplits.datasets.arrays.ArrayConfig method), [1] (dacapo.experiments.datasplits.datasets.arrays.dummy_array_config.DummyArrayConfig method), [1] (dacapo.experiments.datasplits.datasets.arrays.DummyArrayConfig method), [1] (dacapo.experiments.datasplits.datasets.arrays.dvid_array_config.DVIDArrayConfig method) (dacapo.experiments.datasplits.datasets.arrays.DVIDArrayConfig method) (dacapo.experiments.datasplits.datasets.arrays.zarr_array_config.ZarrArrayConfig method), [1] (dacapo.experiments.datasplits.datasets.arrays.ZarrArrayConfig method), [1] (dacapo.experiments.datasplits.datasets.dataset_config.DatasetConfig method), [1] (dacapo.experiments.datasplits.datasets.DatasetConfig method), [1] (dacapo.experiments.datasplits.datasets.dummy_dataset_config.DummyDatasetConfig method), [1] (dacapo.experiments.datasplits.datasets.DummyDatasetConfig method), [1] (dacapo.experiments.datasplits.datasets.graphstores.graph_source_config.GraphStoreConfig method) (dacapo.experiments.datasplits.datasets.graphstores.GraphStoreConfig method) (dacapo.experiments.datasplits.datasets.raw_gt_dataset_config.RawGTDatasetConfig method) (dacapo.experiments.datasplits.datasets.RawGTDatasetConfig method) (dacapo.experiments.datasplits.datasets.simple.SimpleDataset method) (dacapo.experiments.datasplits.datasets.SimpleDataset method) (dacapo.experiments.datasplits.datasplit_config.DataSplitConfig method), [1] (dacapo.experiments.datasplits.DataSplitConfig method), [1] (dacapo.experiments.datasplits.dummy_datasplit_config.DummyDataSplitConfig method), [1] (dacapo.experiments.datasplits.DummyDataSplitConfig method), [1] (dacapo.experiments.tasks.affinities_task_config.AffinitiesTaskConfig method) (dacapo.experiments.tasks.AffinitiesTaskConfig method) (dacapo.experiments.tasks.distance_task_config.DistanceTaskConfig method) (dacapo.experiments.tasks.DistanceTaskConfig method) (dacapo.experiments.tasks.dummy_task_config.DummyTaskConfig method), [1] (dacapo.experiments.tasks.DummyTaskConfig method), [1] (dacapo.experiments.tasks.hot_distance_task_config.HotDistanceTaskConfig method) (dacapo.experiments.tasks.HotDistanceTaskConfig method) (dacapo.experiments.tasks.pretrained_task_config.PretrainedTaskConfig method) (dacapo.experiments.tasks.PretrainedTaskConfig method) (dacapo.experiments.tasks.task_config.TaskConfig method), [1] (dacapo.experiments.tasks.TaskConfig method), [1] (dacapo.experiments.trainers.dummy_trainer_config.DummyTrainerConfig method), [1] (dacapo.experiments.trainers.DummyTrainerConfig method), [1] (dacapo.experiments.trainers.trainer_config.TrainerConfig method), [1] (dacapo.experiments.trainers.TrainerConfig method), [1]

vi_tables() (in module dacapo.utils.voi) viewer (dacapo.utils.view.NeuroglancerRunViewer attribute) visualize_pipeline() (dacapo.experiments.run.Run method) (dacapo.experiments.trainers.gunpowder_trainer.GunpowderTrainer method) (dacapo.experiments.trainers.GunpowderTrainer method) voi (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluation_scores.BinarySegmentationEvaluationScores attribute), [1] (dacapo.experiments.tasks.evaluators.BinarySegmentationEvaluationScores attribute), [1] (dacapo.experiments.tasks.evaluators.instance_evaluation_scores.InstanceEvaluationScores attribute) (dacapo.experiments.tasks.evaluators.instance_evaluation_scores.InstanceEvaluationScores property) (dacapo.experiments.tasks.evaluators.InstanceEvaluationScores attribute) (dacapo.experiments.tasks.evaluators.InstanceEvaluationScores property) voi() (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluator.ArrayEvaluator method), [1] (in module dacapo.experiments.tasks.evaluators.instance_evaluator) (in module dacapo.utils.voi) voi_merge (dacapo.experiments.tasks.evaluators.instance_evaluation_scores.InstanceEvaluationScores attribute), [1] (dacapo.experiments.tasks.evaluators.InstanceEvaluationScores attribute), [1] voi_split (dacapo.experiments.tasks.evaluators.instance_evaluation_scores.InstanceEvaluationScores attribute), [1] (dacapo.experiments.tasks.evaluators.InstanceEvaluationScores attribute), [1] voxel_size (dacapo.experiments.architectures.cnnectome_unet.CNNectomeUNet attribute) (dacapo.experiments.architectures.CNNectomeUNet attribute) (dacapo.experiments.datasplits.datasets.arrays.tiff_array_config.TiffArrayConfig attribute), [1]

W

W_g (dacapo.experiments.architectures.cnnectome_unet.AttentionBlockModule attribute) W_x (dacapo.experiments.architectures.cnnectome_unet.AttentionBlockModule attribute) WatershedPostProcessor (class in dacapo.experiments.tasks.post_processors) (class in dacapo.experiments.tasks.post_processors.watershed_post_processor) WatershedPostProcessorParameters (class in dacapo.experiments.tasks.post_processors) (class in dacapo.experiments.tasks.post_processors.watershed_post_processor_parameters) weight (dacapo.experiments.datasplits.datasets.Dataset attribute), [1] (dacapo.experiments.datasplits.datasets.dataset.Dataset attribute), [1] (dacapo.experiments.datasplits.datasets.dataset_config.DatasetConfig attribute), [1] (dacapo.experiments.datasplits.datasets.DatasetConfig attribute), [1] (dacapo.experiments.datasplits.datasets.raw_gt_dataset.RawGTDataset attribute), [1] (dacapo.experiments.datasplits.datasets.RawGTDataset attribute), [1] (dacapo.experiments.datasplits.datasets.simple.SimpleDataset attribute), [1] (dacapo.experiments.datasplits.datasets.SimpleDataset attribute), [1] Weights (class in dacapo.store.weights_store) weights (dacapo.experiments.tasks.one_hot_task.OneHotTask attribute) (dacapo.experiments.tasks.OneHotTask attribute) (dacapo.experiments.tasks.pretrained_task.PretrainedTask attribute), [1] (dacapo.experiments.tasks.pretrained_task_config.PretrainedTaskConfig attribute), [1] (dacapo.experiments.tasks.PretrainedTask attribute), [1] (dacapo.experiments.tasks.PretrainedTaskConfig attribute), [1]

weights_key (dacapo.gp.dacapo_create_target.DaCapoTargetFilter attribute), [1] (dacapo.gp.DaCapoTargetFilter attribute), [1] WeightsStore (class in dacapo.store.weights_store) worker_file (dacapo.blockwise.blockwise_task.DaCapoBlockwiseTask attribute) (dacapo.blockwise.DaCapoBlockwiseTask attribute) wrap_command() (dacapo.compute_context.compute_context.ComputeContext method), [1] (dacapo.compute_context.ComputeContext method), [1] (dacapo.compute_context.local_torch.LocalTorch method) (dacapo.compute_context.LocalTorch method) write_roi (dacapo.blockwise.blockwise_task.DaCapoBlockwiseTask attribute) (dacapo.blockwise.DaCapoBlockwiseTask attribute)

X

x1_key (dacapo.gp.Product attribute), [1] (dacapo.gp.product.Product attribute), [1]

x2_key (dacapo.gp.Product attribute), [1] (dacapo.gp.product.Product attribute), [1] xlogx() (in module dacapo.utils.voi)

Y

y_key (dacapo.gp.Product attribute), [1] (dacapo.gp.product.Product attribute), [1]

Z

ZarrArrayConfig (class in dacapo.experiments.datasplits.datasets.arrays) (class in dacapo.experiments.datasplits.datasets.arrays.zarr_array_config)

ZerosSource (class in dacapo.utils.pipeline)