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 --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

_

__augment() (dacapo.gp.gamma_noise.GammaAugment method) (dacapo.gp.GammaAugment method)

_device (dacapo.compute_context.local_torch.LocalTorch attribute) (dacapo.compute_context.LocalTorch attribute)

A

add_iteration_scores() (dacapo.experiments.validation_scores.ValidationScores method) (dacapo.experiments.ValidationScores method) add_iteration_stats() (dacapo.experiments.training_stats.TrainingStats method) (dacapo.experiments.TrainingStats method) add_metadata() (dacapo.experiments.datasplits.datasets.arrays.dvid_array.DVIDArray method) (dacapo.experiments.datasplits.datasets.arrays.DVIDArray method) (dacapo.experiments.datasplits.datasets.arrays.zarr_array.ZarrArray method) (dacapo.experiments.datasplits.datasets.arrays.ZarrArray 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) (dacapo.experiments.tasks.AffinitiesTaskConfig attribute) affs_weight_clipmin (dacapo.experiments.tasks.affinities_task_config.AffinitiesTaskConfig attribute) (dacapo.experiments.tasks.AffinitiesTaskConfig attribute) 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.run.Run attribute) 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] ArchitectureConfig (class in dacapo.experiments.architectures) (class in dacapo.experiments.architectures.architecture_config) architectures (dacapo.store.config_store.ConfigStore attribute) (dacapo.store.file_config_store.FileConfigStore property) 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 (class in dacapo.experiments.datasplits.datasets.arrays) (class in dacapo.experiments.datasplits.datasets.arrays.array) array_identifier() (dacapo.store.array_store.LocalContainerIdentifier method) array_key (dacapo.gp.copy.CopyMask attribute) (dacapo.gp.CopyMask attribute) array_type (dacapo.experiments.datasplits.datasets.arrays.binarize_array_config.BinarizeArrayConfig attribute) (dacapo.experiments.datasplits.datasets.arrays.BinarizeArrayConfig attribute) (dacapo.experiments.datasplits.datasets.arrays.concat_array_config.ConcatArrayConfig attribute) (dacapo.experiments.datasplits.datasets.arrays.ConcatArrayConfig attribute) (dacapo.experiments.datasplits.datasets.arrays.crop_array_config.CropArrayConfig attribute) (dacapo.experiments.datasplits.datasets.arrays.CropArrayConfig attribute) (dacapo.experiments.datasplits.datasets.arrays.dummy_array_config.DummyArrayConfig attribute) (dacapo.experiments.datasplits.datasets.arrays.DummyArrayConfig attribute) (dacapo.experiments.datasplits.datasets.arrays.dvid_array_config.DVIDArrayConfig attribute) (dacapo.experiments.datasplits.datasets.arrays.DVIDArrayConfig attribute) (dacapo.experiments.datasplits.datasets.arrays.IntensitiesArrayConfig attribute) (dacapo.experiments.datasplits.datasets.arrays.intensity_array_config.IntensitiesArrayConfig attribute) (dacapo.experiments.datasplits.datasets.arrays.logical_or_array_config.LogicalOrArrayConfig attribute) (dacapo.experiments.datasplits.datasets.arrays.LogicalOrArrayConfig attribute) (dacapo.experiments.datasplits.datasets.arrays.merge_instances_array_config.MergeInstancesArrayConfig attribute) (dacapo.experiments.datasplits.datasets.arrays.MergeInstancesArrayConfig attribute) (dacapo.experiments.datasplits.datasets.arrays.missing_annotations_mask_config.MissingAnnotationsMaskConfig attribute) (dacapo.experiments.datasplits.datasets.arrays.MissingAnnotationsMaskConfig attribute) (dacapo.experiments.datasplits.datasets.arrays.ones_array_config.OnesArrayConfig attribute) (dacapo.experiments.datasplits.datasets.arrays.OnesArrayConfig attribute) (dacapo.experiments.datasplits.datasets.arrays.resampled_array_config.ResampledArrayConfig attribute) (dacapo.experiments.datasplits.datasets.arrays.ResampledArrayConfig attribute) (dacapo.experiments.datasplits.datasets.arrays.sum_array_config.SumArrayConfig attribute) (dacapo.experiments.datasplits.datasets.arrays.SumArrayConfig attribute) (dacapo.experiments.datasplits.datasets.arrays.tiff_array_config.ZarrArrayConfig attribute) (dacapo.experiments.datasplits.datasets.arrays.zarr_array_config.ZarrArrayConfig attribute) (dacapo.experiments.datasplits.datasets.arrays.ZarrArrayConfig 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) (dacapo.gp.GammaAugment attribute) (dacapo.store.config_store.ConfigStore attribute) (dacapo.store.file_config_store.FileConfigStore property) ArrayStore (class in dacapo.store.array_store) ArrayType (class in dacapo.experiments.arraytypes.arraytype) AttentionBlockModule (class in dacapo.experiments.architectures.cnnectome_unet) attrs (dacapo.experiments.datasplits.datasets.arrays.Array property) (dacapo.experiments.datasplits.datasets.arrays.array.Array property) (dacapo.experiments.datasplits.datasets.arrays.binarize_array.BinarizeArray property) (dacapo.experiments.datasplits.datasets.arrays.BinarizeArray property) (dacapo.experiments.datasplits.datasets.arrays.concat_array.ConcatArray property) (dacapo.experiments.datasplits.datasets.arrays.ConcatArray property) (dacapo.experiments.datasplits.datasets.arrays.crop_array.CropArray property) (dacapo.experiments.datasplits.datasets.arrays.CropArray property) (dacapo.experiments.datasplits.datasets.arrays.dummy_array.DummyArray property) (dacapo.experiments.datasplits.datasets.arrays.DummyArray property) (dacapo.experiments.datasplits.datasets.arrays.IntensitiesArray property) (dacapo.experiments.datasplits.datasets.arrays.intensity_array.IntensitiesArray property) (dacapo.experiments.datasplits.datasets.arrays.logical_or_array.LogicalOrArray property) (dacapo.experiments.datasplits.datasets.arrays.LogicalOrArray property) (dacapo.experiments.datasplits.datasets.arrays.merge_instances_array.MergeInstancesArray property) (dacapo.experiments.datasplits.datasets.arrays.MergeInstancesArray property) (dacapo.experiments.datasplits.datasets.arrays.missing_annotations_mask.MissingAnnotationsMask property) (dacapo.experiments.datasplits.datasets.arrays.MissingAnnotationsMask property) (dacapo.experiments.datasplits.datasets.arrays.numpy_array.NumpyArray property) (dacapo.experiments.datasplits.datasets.arrays.NumpyArray property) (dacapo.experiments.datasplits.datasets.arrays.ones_array.OnesArray property) (dacapo.experiments.datasplits.datasets.arrays.OnesArray property) (dacapo.experiments.datasplits.datasets.arrays.resampled_array.ResampledArray property) (dacapo.experiments.datasplits.datasets.arrays.ResampledArray property) (dacapo.experiments.datasplits.datasets.arrays.sum_array.SumArray property) (dacapo.experiments.datasplits.datasets.arrays.SumArray property) (dacapo.experiments.datasplits.datasets.arrays.tiff_array.TiffArray property) (dacapo.experiments.datasplits.datasets.arrays.zarr_array.ZarrArray property) (dacapo.experiments.datasplits.datasets.arrays.ZarrArray property) attrs() (dacapo.experiments.datasplits.datasets.arrays.dvid_array.DVIDArray method) (dacapo.experiments.datasplits.datasets.arrays.DVIDArray method) 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_config.GunpowderTrainerConfig attribute), [1] (dacapo.experiments.trainers.GunpowderTrainerConfig attribute), [1] axes (dacapo.experiments.datasplits.datasets.arrays.Array property) (dacapo.experiments.datasplits.datasets.arrays.array.Array property) (dacapo.experiments.datasplits.datasets.arrays.binarize_array.BinarizeArray property) (dacapo.experiments.datasplits.datasets.arrays.BinarizeArray property) (dacapo.experiments.datasplits.datasets.arrays.concat_array.ConcatArray property) (dacapo.experiments.datasplits.datasets.arrays.ConcatArray property) (dacapo.experiments.datasplits.datasets.arrays.crop_array.CropArray property) (dacapo.experiments.datasplits.datasets.arrays.CropArray property) (dacapo.experiments.datasplits.datasets.arrays.dummy_array.DummyArray property) (dacapo.experiments.datasplits.datasets.arrays.DummyArray property) (dacapo.experiments.datasplits.datasets.arrays.dvid_array.DVIDArray property) (dacapo.experiments.datasplits.datasets.arrays.DVIDArray property) (dacapo.experiments.datasplits.datasets.arrays.IntensitiesArray property) (dacapo.experiments.datasplits.datasets.arrays.intensity_array.IntensitiesArray property) (dacapo.experiments.datasplits.datasets.arrays.logical_or_array.LogicalOrArray property) (dacapo.experiments.datasplits.datasets.arrays.LogicalOrArray property) (dacapo.experiments.datasplits.datasets.arrays.merge_instances_array.MergeInstancesArray property) (dacapo.experiments.datasplits.datasets.arrays.MergeInstancesArray property) (dacapo.experiments.datasplits.datasets.arrays.missing_annotations_mask.MissingAnnotationsMask property) (dacapo.experiments.datasplits.datasets.arrays.MissingAnnotationsMask property) (dacapo.experiments.datasplits.datasets.arrays.numpy_array.NumpyArray property) (dacapo.experiments.datasplits.datasets.arrays.NumpyArray property) (dacapo.experiments.datasplits.datasets.arrays.ones_array.OnesArray property) (dacapo.experiments.datasplits.datasets.arrays.OnesArray property) (dacapo.experiments.datasplits.datasets.arrays.resampled_array.ResampledArray property) (dacapo.experiments.datasplits.datasets.arrays.ResampledArray property) (dacapo.experiments.datasplits.datasets.arrays.sum_array.SumArray property) (dacapo.experiments.datasplits.datasets.arrays.SumArray property) (dacapo.experiments.datasplits.datasets.arrays.tiff_array.TiffArray property) (dacapo.experiments.datasplits.datasets.arrays.tiff_array_config.ZarrArrayConfig attribute) (dacapo.experiments.datasplits.datasets.arrays.zarr_array.ZarrArray property) (dacapo.experiments.datasplits.datasets.arrays.ZarrArray property)

B

background (dacapo.experiments.datasplits.datasets.arrays.binarize_array_config.BinarizeArrayConfig attribute) (dacapo.experiments.datasplits.datasets.arrays.BinarizeArrayConfig attribute) background_as_object (dacapo.experiments.tasks.affinities_task_config.AffinitiesTaskConfig attribute) (dacapo.experiments.tasks.AffinitiesTaskConfig attribute) balance_weights() (in module dacapo.utils.balance_weights) batch_size (dacapo.experiments.trainers.Trainer attribute) (dacapo.experiments.trainers.trainer.Trainer attribute) (dacapo.experiments.trainers.trainer_config.TrainerConfig attribute), [1] (dacapo.experiments.trainers.TrainerConfig attribute), [1] best_scores (dacapo.experiments.tasks.evaluators.Evaluator property) (dacapo.experiments.tasks.evaluators.evaluator.Evaluator property) best_validation_array() (dacapo.store.local_array_store.LocalArrayStore method) 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) (dacapo.experiments.tasks.post_processors.WatershedPostProcessorParameters attribute) billing (dacapo.compute_context.Bsub attribute) (dacapo.compute_context.bsub.Bsub attribute) BinarizeArray (class in dacapo.experiments.datasplits.datasets.arrays) (class in dacapo.experiments.datasplits.datasets.arrays.binarize_array) 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) (dacapo.experiments.tasks.evaluators.DummyEvaluationScores attribute) 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 static method) (dacapo.experiments.tasks.evaluators.DummyEvaluationScores static method) (dacapo.experiments.tasks.evaluators.evaluation_scores.EvaluationScores static method) (dacapo.experiments.tasks.evaluators.EvaluationScores static method) (dacapo.experiments.tasks.evaluators.Evaluator method) (dacapo.experiments.tasks.evaluators.evaluator.Evaluator method) (dacapo.experiments.tasks.evaluators.instance_evaluation_scores.InstanceEvaluationScores static 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) (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)

C

calculate_and_apply_padding() (dacapo.experiments.architectures.cnnectome_unet.AttentionBlockModule method) can_train() (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) channel_scores (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluation_scores.MultiChannelBinarySegmentationEvaluationScores attribute) (dacapo.experiments.tasks.evaluators.MultiChannelBinarySegmentationEvaluationScores attribute) channels (dacapo.experiments.arraytypes.binary.BinaryArray attribute), [1] (dacapo.experiments.arraytypes.intensities.IntensitiesArray attribute) (dacapo.experiments.arraytypes.IntensitiesArray attribute) (dacapo.experiments.datasplits.datasets.arrays.binarize_array.BinarizeArray property) (dacapo.experiments.datasplits.datasets.arrays.BinarizeArray property) (dacapo.experiments.datasplits.datasets.arrays.concat_array_config.ConcatArrayConfig attribute) (dacapo.experiments.datasplits.datasets.arrays.ConcatArrayConfig attribute) (dacapo.experiments.datasplits.datasets.arrays.crop_array.CropArray property) (dacapo.experiments.datasplits.datasets.arrays.CropArray property) (dacapo.experiments.datasplits.datasets.arrays.missing_annotations_mask.MissingAnnotationsMask property) (dacapo.experiments.datasplits.datasets.arrays.MissingAnnotationsMask property) (dacapo.experiments.tasks.distance_task_config.DistanceTaskConfig attribute) (dacapo.experiments.tasks.DistanceTaskConfig attribute) (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) channels_in (dacapo.experiments.architectures.dummy_architecture.DummyArchitecture attribute) (dacapo.experiments.architectures.DummyArchitecture attribute) channels_out (dacapo.experiments.architectures.dummy_architecture.DummyArchitecture attribute) (dacapo.experiments.architectures.DummyArchitecture attribute) check() (dacapo.experiments.starts.cosem_start.CosemStart method) (dacapo.experiments.starts.CosemStart method) check_class_name() (dacapo.experiments.datasplits.datasplit_generator.DataSplitGenerator method) (dacapo.experiments.datasplits.DataSplitGenerator method) class_name (dacapo.experiments.datasplits.datasplit_generator.DataSplitGenerator property) (dacapo.experiments.datasplits.DataSplitGenerator property) classes (dacapo.experiments.arraytypes.AnnotationArray attribute) (dacapo.experiments.arraytypes.annotations.AnnotationArray attribute) (dacapo.experiments.arraytypes.DistanceArray attribute) (dacapo.experiments.arraytypes.distances.DistanceArray attribute) (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) 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) clip (dacapo.experiments.trainers.gp_augments.intensity_config.IntensityAugmentConfig attribute) (dacapo.experiments.trainers.gp_augments.IntensityAugmentConfig attribute) clip_distance (dacapo.experiments.tasks.distance_task_config.DistanceTaskConfig attribute) (dacapo.experiments.tasks.DistanceTaskConfig attribute) (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) clip_raw (dacapo.experiments.trainers.gunpowder_trainer_config.GunpowderTrainerConfig attribute), [1] (dacapo.experiments.trainers.GunpowderTrainerConfig attribute), [1] clipmax (dacapo.experiments.tasks.distance_task_config.DistanceTaskConfig attribute) (dacapo.experiments.tasks.DistanceTaskConfig attribute) clipmin (dacapo.experiments.tasks.distance_task_config.DistanceTaskConfig attribute) (dacapo.experiments.tasks.DistanceTaskConfig attribute) 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) (dacapo.experiments.tasks.evaluators.evaluator.Evaluator method) (dacapo.experiments.validation_scores.ValidationScores method) (dacapo.experiments.ValidationScores method) compute() (dacapo.experiments.datasplits.datasplit_generator.DataSplitGenerator method) (dacapo.experiments.datasplits.DataSplitGenerator method) (dacapo.experiments.tasks.losses.affinities_loss.AffinitiesLoss method) (dacapo.experiments.tasks.losses.AffinitiesLoss method) (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) (dacapo.experiments.tasks.losses.HotDistanceLoss method) (dacapo.experiments.tasks.losses.Loss method) (dacapo.experiments.tasks.losses.loss.Loss method) (dacapo.experiments.tasks.losses.mse_loss.MSELoss method) (dacapo.experiments.tasks.losses.MSELoss method) compute_context (dacapo.options.DaCapoConfig attribute) 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) ConcatArray (class in dacapo.experiments.datasplits.datasets.arrays) (class in dacapo.experiments.datasplits.datasets.arrays.concat_array) 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.Options class method) ConfigStore (class in dacapo.store.config_store) constant_upsample (dacapo.experiments.architectures.cnnectome_unet_config.CNNectomeUNetConfig attribute) (dacapo.experiments.architectures.CNNectomeUNetConfig attribute) container (dacapo.store.array_store.LocalArrayIdentifier attribute) (dacapo.store.array_store.LocalContainerIdentifier attribute) context (dacapo.experiments.tasks.post_processors.watershed_post_processor_parameters.WatershedPostProcessorParameters attribute) (dacapo.experiments.tasks.post_processors.WatershedPostProcessorParameters attribute) 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] control_point_spacing (dacapo.experiments.trainers.gp_augments.elastic_config.ElasticAugmentConfig attribute), [1] (dacapo.experiments.trainers.gp_augments.ElasticAugmentConfig attribute), [1] conv (dacapo.experiments.architectures.dummy_architecture.DummyArchitecture attribute) (dacapo.experiments.architectures.DummyArchitecture attribute)

converter (in module dacapo.store.converter) ConvPass (class in dacapo.experiments.architectures.cnnectome_unet) copy_key (dacapo.gp.copy.CopyMask attribute) (dacapo.gp.CopyMask attribute) 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_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) (dacapo.experiments.tasks.predictors.DistancePredictor method) (dacapo.experiments.tasks.predictors.hot_distance_predictor.HotDistancePredictor method) (dacapo.experiments.tasks.predictors.HotDistancePredictor method) create_from_array_identifier() (dacapo.experiments.datasplits.datasets.arrays.zarr_array.ZarrArray class method) (dacapo.experiments.datasplits.datasets.arrays.ZarrArray class method) create_model() (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.hot_distance_predictor.HotDistancePredictor method) (dacapo.experiments.tasks.predictors.HotDistancePredictor 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) (dacapo.experiments.tasks.predictors.Predictor method) (dacapo.experiments.tasks.predictors.predictor.Predictor method) (dacapo.experiments.tasks.pretrained_task.PretrainedTask method) (dacapo.experiments.tasks.PretrainedTask method) (dacapo.experiments.tasks.Task method) (dacapo.experiments.tasks.task.Task method) create_optimizer() (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) create_stats_store() (in module dacapo.store.create_store) create_target() (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.hot_distance_predictor.HotDistancePredictor method) (dacapo.experiments.tasks.predictors.HotDistancePredictor 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) (dacapo.experiments.tasks.predictors.Predictor method) (dacapo.experiments.tasks.predictors.predictor.Predictor method) create_weight() (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.hot_distance_predictor.HotDistancePredictor method) (dacapo.experiments.tasks.predictors.HotDistancePredictor 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) (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) 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) (dacapo.experiments.tasks.evaluators.BinarySegmentationEvaluationScores attribute) (dacapo.experiments.tasks.evaluators.BinarySegmentationEvaluator attribute) (dacapo.experiments.tasks.evaluators.dummy_evaluation_scores.DummyEvaluationScores attribute) (dacapo.experiments.tasks.evaluators.dummy_evaluator.DummyEvaluator attribute) (dacapo.experiments.tasks.evaluators.DummyEvaluationScores attribute) (dacapo.experiments.tasks.evaluators.DummyEvaluator attribute) (dacapo.experiments.tasks.evaluators.evaluation_scores.EvaluationScores property) (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) (dacapo.experiments.tasks.evaluators.InstanceEvaluationScores attribute) (dacapo.experiments.tasks.evaluators.InstanceEvaluator attribute) (dacapo.experiments.tasks.evaluators.MultiChannelBinarySegmentationEvaluationScores property) (dacapo.experiments.validation_scores.ValidationScores property) (dacapo.experiments.ValidationScores property) criterion (dacapo.experiments.starts.cosem_start.CosemStart attribute) (dacapo.experiments.starts.CosemStart 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) crop_to_factor() (dacapo.experiments.architectures.cnnectome_unet.Upsample method) CropArray (class in dacapo.experiments.datasplits.datasets.arrays) (class in dacapo.experiments.datasplits.datasets.arrays.crop_array) 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] 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 --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 module dacapo.experiments.datasplits.datasets.arrays.array_config module dacapo.experiments.datasplits.datasets.arrays.binarize_array module dacapo.experiments.datasplits.datasets.arrays.binarize_array_config module dacapo.experiments.datasplits.datasets.arrays.concat_array module dacapo.experiments.datasplits.datasets.arrays.concat_array_config module dacapo.experiments.datasplits.datasets.arrays.crop_array module dacapo.experiments.datasplits.datasets.arrays.crop_array_config module dacapo.experiments.datasplits.datasets.arrays.dummy_array module dacapo.experiments.datasplits.datasets.arrays.dummy_array_config module dacapo.experiments.datasplits.datasets.arrays.dvid_array module dacapo.experiments.datasplits.datasets.arrays.dvid_array_config module dacapo.experiments.datasplits.datasets.arrays.intensity_array module dacapo.experiments.datasplits.datasets.arrays.intensity_array_config module dacapo.experiments.datasplits.datasets.arrays.logical_or_array module dacapo.experiments.datasplits.datasets.arrays.logical_or_array_config module dacapo.experiments.datasplits.datasets.arrays.merge_instances_array module dacapo.experiments.datasplits.datasets.arrays.merge_instances_array_config module dacapo.experiments.datasplits.datasets.arrays.missing_annotations_mask module dacapo.experiments.datasplits.datasets.arrays.missing_annotations_mask_config module dacapo.experiments.datasplits.datasets.arrays.numpy_array module dacapo.experiments.datasplits.datasets.arrays.ones_array module dacapo.experiments.datasplits.datasets.arrays.ones_array_config module dacapo.experiments.datasplits.datasets.arrays.resampled_array module dacapo.experiments.datasplits.datasets.arrays.resampled_array_config module dacapo.experiments.datasplits.datasets.arrays.sum_array module dacapo.experiments.datasplits.datasets.arrays.sum_array_config module dacapo.experiments.datasplits.datasets.arrays.tiff_array module dacapo.experiments.datasplits.datasets.arrays.tiff_array_config module dacapo.experiments.datasplits.datasets.arrays.zarr_array 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.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.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_array_source 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.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.train module dacapo.utils module dacapo.utils.affinities module dacapo.utils.balance_weights module dacapo.utils.pipeline module dacapo.utils.view module dacapo.utils.voi module dacapo.validate module DaCapoArraySource (class in dacapo.gp) (class in dacapo.gp.dacapo_array_source) 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) data (dacapo.experiments.datasplits.datasets.arrays.Array property) (dacapo.experiments.datasplits.datasets.arrays.array.Array property) (dacapo.experiments.datasplits.datasets.arrays.binarize_array.BinarizeArray property) (dacapo.experiments.datasplits.datasets.arrays.BinarizeArray property) (dacapo.experiments.datasplits.datasets.arrays.concat_array.ConcatArray property) (dacapo.experiments.datasplits.datasets.arrays.ConcatArray property) (dacapo.experiments.datasplits.datasets.arrays.crop_array.CropArray property) (dacapo.experiments.datasplits.datasets.arrays.CropArray property) (dacapo.experiments.datasplits.datasets.arrays.dummy_array.DummyArray property) (dacapo.experiments.datasplits.datasets.arrays.DummyArray property) (dacapo.experiments.datasplits.datasets.arrays.dvid_array.DVIDArray property) (dacapo.experiments.datasplits.datasets.arrays.DVIDArray property) (dacapo.experiments.datasplits.datasets.arrays.IntensitiesArray property) (dacapo.experiments.datasplits.datasets.arrays.intensity_array.IntensitiesArray property) (dacapo.experiments.datasplits.datasets.arrays.logical_or_array.LogicalOrArray property) (dacapo.experiments.datasplits.datasets.arrays.LogicalOrArray property) (dacapo.experiments.datasplits.datasets.arrays.merge_instances_array.MergeInstancesArray property) (dacapo.experiments.datasplits.datasets.arrays.MergeInstancesArray property) (dacapo.experiments.datasplits.datasets.arrays.missing_annotations_mask.MissingAnnotationsMask property) (dacapo.experiments.datasplits.datasets.arrays.MissingAnnotationsMask property) (dacapo.experiments.datasplits.datasets.arrays.numpy_array.NumpyArray property) (dacapo.experiments.datasplits.datasets.arrays.NumpyArray property) (dacapo.experiments.datasplits.datasets.arrays.ones_array.OnesArray property) (dacapo.experiments.datasplits.datasets.arrays.OnesArray property) (dacapo.experiments.datasplits.datasets.arrays.resampled_array.ResampledArray property) (dacapo.experiments.datasplits.datasets.arrays.ResampledArray property) (dacapo.experiments.datasplits.datasets.arrays.sum_array.SumArray property) (dacapo.experiments.datasplits.datasets.arrays.SumArray property) (dacapo.experiments.datasplits.datasets.arrays.zarr_array.ZarrArray property) (dacapo.experiments.datasplits.datasets.arrays.ZarrArray property) data() (dacapo.experiments.datasplits.datasets.arrays.tiff_array.TiffArray method) 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) (dacapo.experiments.datasplits.datasets.arrays.ZarrArrayConfig attribute) (dacapo.store.array_store.LocalArrayIdentifier attribute) 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] DatasetConfig (class in dacapo.experiments.datasplits.datasets) (class in dacapo.experiments.datasplits.datasets.dataset_config) datasets (dacapo.experiments.validation_scores.ValidationScores attribute) (dacapo.experiments.ValidationScores attribute) (dacapo.store.config_store.ConfigStore attribute) (dacapo.store.file_config_store.FileConfigStore property) DatasetSpec (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) 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) 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) (dacapo.store.file_config_store.FileConfigStore property) default_config (dacapo.experiments.datasplits.datasets.arrays.concat_array_config.ConcatArrayConfig attribute) (dacapo.experiments.datasplits.datasets.arrays.ConcatArrayConfig attribute) 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) (dacapo.experiments.ValidationScores method) delete_architecture_config() (dacapo.store.config_store.ConfigStore method) delete_array_config() (dacapo.store.config_store.ConfigStore method) delete_config() (dacapo.store.config_store.ConfigStore method) (dacapo.store.file_config_store.FileConfigStore method) (dacapo.store.mongo_config_store.MongoConfigStore method) delete_datasplit_config() (dacapo.store.config_store.ConfigStore method) delete_run_config() (dacapo.store.config_store.ConfigStore method) (dacapo.store.mongo_config_store.MongoConfigStore method) delete_task_config() (dacapo.store.config_store.ConfigStore method) delete_trainer_config() (dacapo.store.config_store.ConfigStore method) delete_training_stats() (dacapo.store.file_stats_store.FileStatsStore method) (dacapo.store.mongo_stats_store.MongoStatsStore method) (dacapo.store.stats_store.StatsStore method) delete_validation_scores() (dacapo.store.mongo_stats_store.MongoStatsStore method) deprecated_start_neuroglancer() (dacapo.utils.view.NeuroglancerRunViewer method) detection_threshold (dacapo.experiments.tasks.dummy_task_config.DummyTaskConfig attribute), [1] (dacapo.experiments.tasks.DummyTaskConfig attribute), [1] device (dacapo.compute_context.Bsub property) (dacapo.compute_context.bsub.Bsub property) (dacapo.compute_context.compute_context.ComputeContext property) (dacapo.compute_context.ComputeContext property) (dacapo.compute_context.local_torch.LocalTorch property) (dacapo.compute_context.LocalTorch property) dice (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluation_scores.BinarySegmentationEvaluationScores attribute) (dacapo.experiments.tasks.evaluators.BinarySegmentationEvaluationScores attribute) dice() (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluator.ArrayEvaluator method) DilatePoints (class in dacapo.utils.pipeline) dims (dacapo.experiments.architectures.Architecture property) (dacapo.experiments.architectures.architecture.Architecture property) (dacapo.experiments.datasplits.datasets.arrays.Array property) (dacapo.experiments.datasplits.datasets.arrays.array.Array property) (dacapo.experiments.datasplits.datasets.arrays.binarize_array.BinarizeArray property) (dacapo.experiments.datasplits.datasets.arrays.BinarizeArray property) (dacapo.experiments.datasplits.datasets.arrays.concat_array.ConcatArray property) (dacapo.experiments.datasplits.datasets.arrays.ConcatArray property) (dacapo.experiments.datasplits.datasets.arrays.crop_array.CropArray property) (dacapo.experiments.datasplits.datasets.arrays.CropArray property) (dacapo.experiments.datasplits.datasets.arrays.dummy_array.DummyArray property) (dacapo.experiments.datasplits.datasets.arrays.DummyArray property) (dacapo.experiments.datasplits.datasets.arrays.dvid_array.DVIDArray property) (dacapo.experiments.datasplits.datasets.arrays.DVIDArray property) (dacapo.experiments.datasplits.datasets.arrays.IntensitiesArray property) (dacapo.experiments.datasplits.datasets.arrays.intensity_array.IntensitiesArray property) (dacapo.experiments.datasplits.datasets.arrays.logical_or_array.LogicalOrArray property) (dacapo.experiments.datasplits.datasets.arrays.LogicalOrArray property) (dacapo.experiments.datasplits.datasets.arrays.merge_instances_array.MergeInstancesArray property) (dacapo.experiments.datasplits.datasets.arrays.MergeInstancesArray property) (dacapo.experiments.datasplits.datasets.arrays.missing_annotations_mask.MissingAnnotationsMask property) (dacapo.experiments.datasplits.datasets.arrays.MissingAnnotationsMask property) (dacapo.experiments.datasplits.datasets.arrays.numpy_array.NumpyArray property) (dacapo.experiments.datasplits.datasets.arrays.NumpyArray property) (dacapo.experiments.datasplits.datasets.arrays.ones_array.OnesArray property) (dacapo.experiments.datasplits.datasets.arrays.OnesArray property) (dacapo.experiments.datasplits.datasets.arrays.resampled_array.ResampledArray property) (dacapo.experiments.datasplits.datasets.arrays.ResampledArray property) (dacapo.experiments.datasplits.datasets.arrays.sum_array.SumArray property) (dacapo.experiments.datasplits.datasets.arrays.SumArray property) (dacapo.experiments.datasplits.datasets.arrays.tiff_array.TiffArray property) (dacapo.experiments.datasplits.datasets.arrays.zarr_array.ZarrArray property) (dacapo.experiments.datasplits.datasets.arrays.ZarrArray property) (dacapo.experiments.tasks.predictors.affinities_predictor.AffinitiesPredictor property) (dacapo.experiments.tasks.predictors.AffinitiesPredictor property) 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) divide_columns() (in module dacapo.utils.voi) divide_rows() (in module dacapo.utils.voi) does_new_best_exist() (dacapo.utils.view.BestScore method) Downsample (class in dacapo.experiments.architectures.cnnectome_unet) downsample (dacapo.experiments.datasplits.datasets.arrays.resampled_array_config.ResampledArrayConfig attribute) (dacapo.experiments.datasplits.datasets.arrays.ResampledArrayConfig attribute) downsample_factors (dacapo.experiments.architectures.cnnectome_unet_config.CNNectomeUNetConfig attribute) (dacapo.experiments.architectures.CNNectomeUNetConfig attribute) drop_channels (dacapo.gp.copy.CopyMask attribute) (dacapo.gp.CopyMask attribute) dtype (dacapo.experiments.datasplits.datasets.arrays.Array property) (dacapo.experiments.datasplits.datasets.arrays.array.Array property) (dacapo.experiments.datasplits.datasets.arrays.binarize_array.BinarizeArray property) (dacapo.experiments.datasplits.datasets.arrays.BinarizeArray property) (dacapo.experiments.datasplits.datasets.arrays.concat_array.ConcatArray property) (dacapo.experiments.datasplits.datasets.arrays.ConcatArray property) (dacapo.experiments.datasplits.datasets.arrays.crop_array.CropArray property) (dacapo.experiments.datasplits.datasets.arrays.CropArray property) (dacapo.experiments.datasplits.datasets.arrays.dummy_array.DummyArray property) (dacapo.experiments.datasplits.datasets.arrays.DummyArray property) (dacapo.experiments.datasplits.datasets.arrays.dvid_array.DVIDArray property) (dacapo.experiments.datasplits.datasets.arrays.DVIDArray property) (dacapo.experiments.datasplits.datasets.arrays.IntensitiesArray property) (dacapo.experiments.datasplits.datasets.arrays.intensity_array.IntensitiesArray property) (dacapo.experiments.datasplits.datasets.arrays.logical_or_array.LogicalOrArray property) (dacapo.experiments.datasplits.datasets.arrays.LogicalOrArray property) (dacapo.experiments.datasplits.datasets.arrays.merge_instances_array.MergeInstancesArray property) (dacapo.experiments.datasplits.datasets.arrays.MergeInstancesArray property) (dacapo.experiments.datasplits.datasets.arrays.missing_annotations_mask.MissingAnnotationsMask property) (dacapo.experiments.datasplits.datasets.arrays.MissingAnnotationsMask property) (dacapo.experiments.datasplits.datasets.arrays.numpy_array.NumpyArray property) (dacapo.experiments.datasplits.datasets.arrays.NumpyArray property) (dacapo.experiments.datasplits.datasets.arrays.ones_array.OnesArray property) (dacapo.experiments.datasplits.datasets.arrays.OnesArray property) (dacapo.experiments.datasplits.datasets.arrays.resampled_array.ResampledArray property) (dacapo.experiments.datasplits.datasets.arrays.ResampledArray property) (dacapo.experiments.datasplits.datasets.arrays.sum_array.SumArray property) (dacapo.experiments.datasplits.datasets.arrays.SumArray property) (dacapo.experiments.datasplits.datasets.arrays.tiff_array.TiffArray property) (dacapo.experiments.datasplits.datasets.arrays.zarr_array.ZarrArray property) (dacapo.experiments.datasplits.datasets.arrays.ZarrArray property) 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) DummyArray (class in dacapo.experiments.datasplits.datasets.arrays) (class in dacapo.experiments.datasplits.datasets.arrays.dummy_array) 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 DVIDArray (class in dacapo.experiments.datasplits.datasets.arrays) (class in dacapo.experiments.datasplits.datasets.arrays.dvid_array) 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) embedding_dims (dacapo.experiments.arraytypes.embedding.EmbeddingArray attribute) (dacapo.experiments.arraytypes.EmbeddingArray attribute) (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.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) (dacapo.experiments.tasks.post_processors.ArgmaxPostProcessor method) (dacapo.experiments.tasks.post_processors.dummy_post_processor.DummyPostProcessor method) (dacapo.experiments.tasks.post_processors.DummyPostProcessor method) (dacapo.experiments.tasks.post_processors.post_processor.PostProcessor method) (dacapo.experiments.tasks.post_processors.PostProcessor method) (dacapo.experiments.tasks.post_processors.threshold_post_processor.ThresholdPostProcessor method) (dacapo.experiments.tasks.post_processors.ThresholdPostProcessor method) (dacapo.experiments.tasks.post_processors.watershed_post_processor.WatershedPostProcessor method) (dacapo.experiments.tasks.post_processors.WatershedPostProcessor method) eval_shape_increase (dacapo.experiments.architectures.Architecture property) (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) (dacapo.experiments.tasks.evaluators.BinarySegmentationEvaluator method) (dacapo.experiments.tasks.evaluators.dummy_evaluator.DummyEvaluator method) (dacapo.experiments.tasks.evaluators.DummyEvaluator method) (dacapo.experiments.tasks.evaluators.Evaluator method) (dacapo.experiments.tasks.evaluators.evaluator.Evaluator method) (dacapo.experiments.tasks.evaluators.instance_evaluator.InstanceEvaluator method) (dacapo.experiments.tasks.evaluators.InstanceEvaluator method) evaluation_scores (dacapo.experiments.tasks.Task property) (dacapo.experiments.tasks.task.Task property) (dacapo.experiments.validation_scores.ValidationScores attribute) (dacapo.experiments.ValidationScores attribute) 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.distance_task.DistanceTask attribute) (dacapo.experiments.tasks.DistanceTask attribute) (dacapo.experiments.tasks.dummy_task.DummyTask attribute) (dacapo.experiments.tasks.DummyTask attribute) (dacapo.experiments.tasks.hot_distance_task.HotDistanceTask attribute) (dacapo.experiments.tasks.HotDistanceTask attribute) (dacapo.experiments.tasks.inner_distance_task.InnerDistanceTask attribute) (dacapo.experiments.tasks.InnerDistanceTask attribute) (dacapo.experiments.tasks.Task attribute) (dacapo.experiments.tasks.task.Task attribute) execute() (dacapo.compute_context.compute_context.ComputeContext method) (dacapo.compute_context.ComputeContext method) ExpandLabels (class in dacapo.utils.pipeline) extractor() (dacapo.experiments.tasks.predictors.affinities_predictor.AffinitiesPredictor method) (dacapo.experiments.tasks.predictors.AffinitiesPredictor method)

F

f1_score (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluation_scores.BinarySegmentationEvaluationScores attribute) (dacapo.experiments.tasks.evaluators.BinarySegmentationEvaluationScores attribute) f1_score() (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluator.ArrayEvaluator method) f1_score_with_tolerance (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluation_scores.BinarySegmentationEvaluationScores attribute) (dacapo.experiments.tasks.evaluators.BinarySegmentationEvaluationScores attribute) f1_score_with_tolerance() (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluator.ArrayEvaluator method) (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluator.CremiEvaluator method) false_discovery_rate (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluation_scores.BinarySegmentationEvaluationScores attribute) (dacapo.experiments.tasks.evaluators.BinarySegmentationEvaluationScores attribute) false_discovery_rate() (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluator.ArrayEvaluator method) false_negative_distances() (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluator.CremiEvaluator method) false_negative_rate (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluation_scores.BinarySegmentationEvaluationScores attribute) (dacapo.experiments.tasks.evaluators.BinarySegmentationEvaluationScores attribute) false_negative_rate() (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluator.ArrayEvaluator method) false_negative_rate_with_tolerance (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluation_scores.BinarySegmentationEvaluationScores attribute) (dacapo.experiments.tasks.evaluators.BinarySegmentationEvaluationScores attribute) false_negative_rate_with_tolerance() (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluator.ArrayEvaluator method) (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluator.CremiEvaluator method) false_negatives_with_tolerance() (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluator.CremiEvaluator method) false_positive_distances() (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluator.CremiEvaluator method) false_positive_rate (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluation_scores.BinarySegmentationEvaluationScores attribute) (dacapo.experiments.tasks.evaluators.BinarySegmentationEvaluationScores attribute) false_positive_rate() (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluator.ArrayEvaluator method) false_positive_rate_with_tolerance (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluation_scores.BinarySegmentationEvaluationScores attribute) (dacapo.experiments.tasks.evaluators.BinarySegmentationEvaluationScores attribute) false_positive_rate_with_tolerance() (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluator.ArrayEvaluator method) (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluator.CremiEvaluator method) false_positives_with_tolerance() (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluator.CremiEvaluator method) fetch_info (in module dacapo.experiments.datasplits.datasets.arrays.dvid_array) file_name (dacapo.experiments.datasplits.datasets.arrays.tiff_array_config.ZarrArrayConfig attribute) (dacapo.experiments.datasplits.datasets.arrays.zarr_array_config.ZarrArrayConfig attribute) (dacapo.experiments.datasplits.datasets.arrays.ZarrArrayConfig attribute)

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_config.CNNectomeUNetConfig attribute) (dacapo.experiments.architectures.CNNectomeUNetConfig attribute) fmaps_in (dacapo.experiments.architectures.cnnectome_unet_config.CNNectomeUNetConfig attribute) (dacapo.experiments.architectures.CNNectomeUNetConfig attribute) fmaps_out (dacapo.experiments.architectures.cnnectome_unet_config.CNNectomeUNetConfig attribute) (dacapo.experiments.architectures.CNNectomeUNetConfig attribute) 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) (dacapo.experiments.architectures.cnnectome_unet.ConvPass method) (dacapo.experiments.architectures.cnnectome_unet.Downsample method) (dacapo.experiments.architectures.cnnectome_unet.Upsample method) (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) frizz_level (dacapo.experiments.tasks.evaluators.dummy_evaluation_scores.DummyEvaluationScores attribute) (dacapo.experiments.tasks.evaluators.DummyEvaluationScores attribute) from_gp_array() (dacapo.experiments.datasplits.datasets.arrays.numpy_array.NumpyArray class method) (dacapo.experiments.datasplits.datasets.arrays.NumpyArray class method) from_np_array() (dacapo.experiments.datasplits.datasets.arrays.numpy_array.NumpyArray class method) (dacapo.experiments.datasplits.datasets.arrays.NumpyArray class method)

G

gamma_max (dacapo.gp.gamma_noise.GammaAugment attribute) (dacapo.gp.GammaAugment attribute) gamma_min (dacapo.gp.gamma_noise.GammaAugment attribute) (dacapo.gp.GammaAugment attribute) 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) generate_dataspec_from_csv() (in module dacapo.experiments.datasplits.datasplit_generator) generate_from_csv() (dacapo.experiments.datasplits.datasplit_generator.DataSplitGenerator static method) (dacapo.experiments.datasplits.DataSplitGenerator static method) get_best() (dacapo.experiments.validation_scores.ValidationScores method) (dacapo.experiments.ValidationScores method) get_datasets() (dacapo.utils.view.NeuroglancerRunViewer method) get_ds() (dacapo.utils.view.BestScore method) get_model_setup() (in module dacapo.experiments.starts.cosem_start) get_overall_best() (dacapo.experiments.tasks.evaluators.Evaluator method) (dacapo.experiments.tasks.evaluators.evaluator.Evaluator method) get_overall_best_parameters() (dacapo.experiments.tasks.evaluators.Evaluator method) (dacapo.experiments.tasks.evaluators.evaluator.Evaluator 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 static method) get_viewer() (in module dacapo.utils.view) graph (dacapo.gp.dacapo_points_source.GraphSource attribute) (dacapo.gp.GraphSource attribute) 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) (dacapo.experiments.datasplits.datasets.arrays.BinarizeArrayConfig attribute) (dacapo.experiments.datasplits.datasets.arrays.missing_annotations_mask_config.MissingAnnotationsMaskConfig attribute) (dacapo.experiments.datasplits.datasets.arrays.MissingAnnotationsMaskConfig attribute) 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] GT (dacapo.experiments.datasplits.keys.ArrayKey attribute), [1] (dacapo.experiments.datasplits.keys.keys.ArrayKey attribute), [1] gt_config (dacapo.experiments.datasplits.datasets.raw_gt_dataset_config.RawGTDatasetConfig attribute), [1] (dacapo.experiments.datasplits.datasets.RawGTDatasetConfig attribute), [1] gt_region_for_roi() (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.hot_distance_predictor.HotDistancePredictor method) (dacapo.experiments.tasks.predictors.HotDistancePredictor method) (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) 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) (dacapo.experiments.tasks.evaluators.BinarySegmentationEvaluationScores attribute) hausdorff() (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluator.ArrayEvaluator method) 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 static method) (dacapo.experiments.tasks.evaluators.DummyEvaluationScores static method) (dacapo.experiments.tasks.evaluators.evaluation_scores.EvaluationScores static method) (dacapo.experiments.tasks.evaluators.EvaluationScores static method) (dacapo.experiments.tasks.evaluators.Evaluator method) (dacapo.experiments.tasks.evaluators.evaluator.Evaluator method) (dacapo.experiments.tasks.evaluators.instance_evaluation_scores.InstanceEvaluationScores static method) (dacapo.experiments.tasks.evaluators.InstanceEvaluationScores static method) (dacapo.experiments.tasks.evaluators.MultiChannelBinarySegmentationEvaluationScores static method)

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) (dacapo.experiments.tasks.post_processors.PostProcessorParameters attribute) initialize_weights() (dacapo.experiments.starts.cosem_start.CosemStart method) (dacapo.experiments.starts.CosemStart method) (dacapo.experiments.starts.Start method) (dacapo.experiments.starts.start.Start method) 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_shape (dacapo.experiments.architectures.Architecture property) (dacapo.experiments.architectures.architecture.Architecture property) (dacapo.experiments.architectures.cnnectome_unet.CNNectomeUNet property) (dacapo.experiments.architectures.cnnectome_unet_config.CNNectomeUNetConfig attribute) (dacapo.experiments.architectures.CNNectomeUNet property) (dacapo.experiments.architectures.CNNectomeUNetConfig attribute) (dacapo.experiments.architectures.dummy_architecture.DummyArchitecture attribute) (dacapo.experiments.architectures.dummy_architecture.DummyArchitecture property) (dacapo.experiments.architectures.DummyArchitecture attribute) (dacapo.experiments.architectures.DummyArchitecture property) instance (dacapo.experiments.datasplits.datasplit_generator.SegmentationType attribute) instance() (dacapo.Options class method) (dacapo.options.Options class 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) (class in dacapo.experiments.datasplits.datasets.arrays) (class in dacapo.experiments.datasplits.datasets.arrays.intensity_array) 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) (dacapo.experiments.datasplits.datasets.arrays.ResampledArrayConfig attribute) 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.binary.BinaryArray method) is_best() (dacapo.experiments.tasks.evaluators.Evaluator method) (dacapo.experiments.tasks.evaluators.evaluator.Evaluator method) 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) (dacapo.experiments.trainers.trainer.Trainer attribute) (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] 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) (dacapo.experiments.tasks.evaluators.BinarySegmentationEvaluationScores attribute)

jaccard() (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluator.ArrayEvaluator method)

K

kernel_size_down (dacapo.experiments.architectures.cnnectome_unet_config.CNNectomeUNetConfig attribute) (dacapo.experiments.architectures.CNNectomeUNetConfig attribute) kernel_size_up (dacapo.experiments.architectures.cnnectome_unet_config.CNNectomeUNetConfig attribute) (dacapo.experiments.architectures.CNNectomeUNetConfig attribute)

key (dacapo.gp.dacapo_points_source.GraphSource attribute) (dacapo.gp.GraphSource attribute)

L

latest_iteration() (dacapo.store.local_weights_store.LocalWeightsStore method) (dacapo.store.weights_store.WeightsStore method) learning_rate (dacapo.experiments.trainers.Trainer attribute) (dacapo.experiments.trainers.trainer.Trainer attribute) (dacapo.experiments.trainers.trainer_config.TrainerConfig attribute), [1] (dacapo.experiments.trainers.TrainerConfig attribute), [1] like() (dacapo.experiments.datasplits.datasets.arrays.ones_array.OnesArray class method) (dacapo.experiments.datasplits.datasets.arrays.OnesArray class method) load_best() (dacapo.store.weights_store.WeightsStore method) load_weights() (dacapo.store.weights_store.WeightsStore method) 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.datasets.arrays.concat_array) (in module dacapo.experiments.datasplits.datasets.arrays.dvid_array) (in module dacapo.experiments.datasplits.datasets.arrays.tiff_array) (in module dacapo.experiments.datasplits.datasets.arrays.zarr_array) (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.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.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.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)

LogicalOrArray (class in dacapo.experiments.datasplits.datasets.arrays) (class in dacapo.experiments.datasplits.datasets.arrays.logical_or_array) 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.distance_task.DistanceTask attribute) (dacapo.experiments.tasks.DistanceTask attribute) (dacapo.experiments.tasks.dummy_task.DummyTask attribute) (dacapo.experiments.tasks.DummyTask attribute) (dacapo.experiments.tasks.hot_distance_task.HotDistanceTask attribute) (dacapo.experiments.tasks.HotDistanceTask attribute) (dacapo.experiments.tasks.inner_distance_task.InnerDistanceTask attribute) (dacapo.experiments.tasks.InnerDistanceTask 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) (dacapo.experiments.tasks.predictors.AffinitiesPredictor method) lsd_weight_clipmax (dacapo.experiments.tasks.affinities_task_config.AffinitiesTaskConfig attribute) (dacapo.experiments.tasks.AffinitiesTaskConfig attribute) lsd_weight_clipmin (dacapo.experiments.tasks.affinities_task_config.AffinitiesTaskConfig attribute) (dacapo.experiments.tasks.AffinitiesTaskConfig attribute) lsds (dacapo.experiments.tasks.affinities_task_config.AffinitiesTaskConfig attribute) (dacapo.experiments.tasks.AffinitiesTaskConfig attribute) lsds_to_affs_weight_ratio (dacapo.experiments.tasks.affinities_task_config.AffinitiesTaskConfig attribute) (dacapo.experiments.tasks.AffinitiesTaskConfig attribute)

M

MakeRaw (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] MASK (dacapo.experiments.datasplits.keys.ArrayKey attribute), [1] (dacapo.experiments.datasplits.keys.keys.ArrayKey attribute), [1] 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) (dacapo.experiments.tasks.DistanceTaskConfig attribute) (dacapo.experiments.tasks.hot_distance_task_config.HotDistanceTaskConfig attribute), [1] (dacapo.experiments.tasks.HotDistanceTaskConfig attribute), [1] match_heads() (in module dacapo.experiments.starts.start) max (dacapo.experiments.arraytypes.intensities.IntensitiesArray attribute) (dacapo.experiments.arraytypes.IntensitiesArray attribute) (dacapo.experiments.datasplits.datasets.arrays.IntensitiesArrayConfig attribute) (dacapo.experiments.datasplits.datasets.arrays.intensity_array_config.IntensitiesArrayConfig attribute) mean_false_distance (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluation_scores.BinarySegmentationEvaluationScores attribute) (dacapo.experiments.tasks.evaluators.BinarySegmentationEvaluationScores attribute) mean_false_distance() (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluator.ArrayEvaluator method) (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluator.CremiEvaluator method) mean_false_distance_clipped (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluation_scores.BinarySegmentationEvaluationScores attribute) (dacapo.experiments.tasks.evaluators.BinarySegmentationEvaluationScores attribute) mean_false_distance_clipped() (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluator.ArrayEvaluator method) (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluator.CremiEvaluator method) mean_false_negative_distance (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluation_scores.BinarySegmentationEvaluationScores attribute) (dacapo.experiments.tasks.evaluators.BinarySegmentationEvaluationScores attribute) mean_false_negative_distance() (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluator.ArrayEvaluator method) (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluator.CremiEvaluator method) mean_false_negative_distance_clipped (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluation_scores.BinarySegmentationEvaluationScores attribute) (dacapo.experiments.tasks.evaluators.BinarySegmentationEvaluationScores attribute) mean_false_negative_distance_clipped() (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluator.ArrayEvaluator method) mean_false_negative_distances_clipped() (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluator.CremiEvaluator method) mean_false_positive_distance (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluation_scores.BinarySegmentationEvaluationScores attribute) (dacapo.experiments.tasks.evaluators.BinarySegmentationEvaluationScores attribute) mean_false_positive_distance() (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluator.ArrayEvaluator method) (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluator.CremiEvaluator method) mean_false_positive_distance_clipped (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluation_scores.BinarySegmentationEvaluationScores attribute) (dacapo.experiments.tasks.evaluators.BinarySegmentationEvaluationScores attribute) mean_false_positive_distance_clipped() (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluator.ArrayEvaluator method) mean_false_positive_distances_clipped() (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluator.CremiEvaluator method) MergeInstancesArray (class in dacapo.experiments.datasplits.datasets.arrays) (class in dacapo.experiments.datasplits.datasets.arrays.merge_instances_array) MergeInstancesArrayConfig (class in dacapo.experiments.datasplits.datasets.arrays) (class in dacapo.experiments.datasplits.datasets.arrays.merge_instances_array_config) min (dacapo.experiments.arraytypes.intensities.IntensitiesArray attribute) (dacapo.experiments.arraytypes.IntensitiesArray attribute) (dacapo.experiments.datasplits.datasets.arrays.IntensitiesArrayConfig attribute) (dacapo.experiments.datasplits.datasets.arrays.intensity_array_config.IntensitiesArrayConfig attribute) min_masked (dacapo.experiments.trainers.gunpowder_trainer_config.GunpowderTrainerConfig attribute), [1] (dacapo.experiments.trainers.GunpowderTrainerConfig attribute), [1] min_size (dacapo.experiments.tasks.post_processors.dummy_post_processor_parameters.DummyPostProcessorParameters attribute) (dacapo.experiments.tasks.post_processors.DummyPostProcessorParameters attribute) mirror_augment (dacapo.experiments.trainers.dummy_trainer_config.DummyTrainerConfig attribute) (dacapo.experiments.trainers.DummyTrainerConfig attribute) MissingAnnotationsMask (class in dacapo.experiments.datasplits.datasets.arrays) (class in dacapo.experiments.datasplits.datasets.arrays.missing_annotations_mask) MissingAnnotationsMaskConfig (class in dacapo.experiments.datasplits.datasets.arrays) (class in dacapo.experiments.datasplits.datasets.arrays.missing_annotations_mask_config) Model (class in dacapo.experiments) (class in dacapo.experiments.model) model (dacapo.experiments.run.Run attribute) (dacapo.store.weights_store.Weights attribute) model_configs (in module dacapo.blockwise.empanada_function) module dacapo, [1] 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 dacapo.experiments.datasplits.datasets.arrays.array_config dacapo.experiments.datasplits.datasets.arrays.binarize_array dacapo.experiments.datasplits.datasets.arrays.binarize_array_config dacapo.experiments.datasplits.datasets.arrays.concat_array dacapo.experiments.datasplits.datasets.arrays.concat_array_config dacapo.experiments.datasplits.datasets.arrays.crop_array dacapo.experiments.datasplits.datasets.arrays.crop_array_config dacapo.experiments.datasplits.datasets.arrays.dummy_array dacapo.experiments.datasplits.datasets.arrays.dummy_array_config dacapo.experiments.datasplits.datasets.arrays.dvid_array dacapo.experiments.datasplits.datasets.arrays.dvid_array_config dacapo.experiments.datasplits.datasets.arrays.intensity_array dacapo.experiments.datasplits.datasets.arrays.intensity_array_config dacapo.experiments.datasplits.datasets.arrays.logical_or_array dacapo.experiments.datasplits.datasets.arrays.logical_or_array_config dacapo.experiments.datasplits.datasets.arrays.merge_instances_array dacapo.experiments.datasplits.datasets.arrays.merge_instances_array_config dacapo.experiments.datasplits.datasets.arrays.missing_annotations_mask dacapo.experiments.datasplits.datasets.arrays.missing_annotations_mask_config dacapo.experiments.datasplits.datasets.arrays.numpy_array dacapo.experiments.datasplits.datasets.arrays.ones_array dacapo.experiments.datasplits.datasets.arrays.ones_array_config dacapo.experiments.datasplits.datasets.arrays.resampled_array dacapo.experiments.datasplits.datasets.arrays.resampled_array_config dacapo.experiments.datasplits.datasets.arrays.sum_array dacapo.experiments.datasplits.datasets.arrays.sum_array_config dacapo.experiments.datasplits.datasets.arrays.tiff_array dacapo.experiments.datasplits.datasets.arrays.tiff_array_config dacapo.experiments.datasplits.datasets.arrays.zarr_array 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.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.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_array_source 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.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.train dacapo.utils dacapo.utils.affinities 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) mongo_db_name (dacapo.options.DaCapoConfig attribute) MongoConfigStore (class in dacapo.store.mongo_config_store) MongoStatsStore (class in dacapo.store.mongo_stats_store) move_optimizer() (dacapo.experiments.run.Run method) 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) (dacapo.experiments.datasplits.datasets.arrays.ArrayConfig attribute) (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) (dacapo.experiments.datasplits.datasets.RawGTDataset attribute) (dacapo.experiments.datasplits.datasplit_config.DataSplitConfig attribute), [1] (dacapo.experiments.datasplits.DataSplitConfig attribute), [1] (dacapo.experiments.run.Run attribute) (dacapo.experiments.run_config.RunConfig attribute) (dacapo.experiments.RunConfig attribute) (dacapo.experiments.tasks.task_config.TaskConfig attribute) (dacapo.experiments.tasks.TaskConfig attribute) (dacapo.experiments.trainers.trainer_config.TrainerConfig attribute), [1] (dacapo.experiments.trainers.TrainerConfig attribute), [1] neighborhood (dacapo.experiments.tasks.affinities_task_config.AffinitiesTaskConfig attribute) (dacapo.experiments.tasks.AffinitiesTaskConfig attribute) NeuroglancerRunViewer (class in dacapo.utils.view) new_validation_checker() (dacapo.utils.view.NeuroglancerRunViewer method) next() (dacapo.experiments.trainers.gunpowder_trainer.GunpowderTrainer method) (dacapo.experiments.trainers.GunpowderTrainer method) node() (dacapo.experiments.trainers.AugmentConfig method) (dacapo.experiments.trainers.gp_augments.augment_config.AugmentConfig method) (dacapo.experiments.trainers.gp_augments.AugmentConfig method) (dacapo.experiments.trainers.gp_augments.elastic_config.ElasticAugmentConfig method) (dacapo.experiments.trainers.gp_augments.ElasticAugmentConfig method) (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) (dacapo.experiments.trainers.gp_augments.intensity_scale_shift_config.IntensityScaleShiftAugmentConfig method) (dacapo.experiments.trainers.gp_augments.IntensityAugmentConfig method) (dacapo.experiments.trainers.gp_augments.IntensityScaleShiftAugmentConfig method) (dacapo.experiments.trainers.gp_augments.simple_config.SimpleAugmentConfig method) (dacapo.experiments.trainers.gp_augments.SimpleAugmentConfig method) NON_EMPTY (dacapo.experiments.datasplits.keys.ArrayKey attribute), [1] (dacapo.experiments.datasplits.keys.keys.ArrayKey attribute), [1] None (dacapo.experiments.tasks.losses.mse_loss.MSELoss attribute) (dacapo.experiments.tasks.losses.MSELoss attribute) None() (dacapo.experiments.tasks.one_hot_task_config.OneHotTaskConfig method) (dacapo.experiments.tasks.OneHotTaskConfig method) NoSuchModule (class in dacapo.ext) num_channels (dacapo.experiments.datasplits.datasets.arrays.Array property) (dacapo.experiments.datasplits.datasets.arrays.array.Array property) (dacapo.experiments.datasplits.datasets.arrays.binarize_array.BinarizeArray property) (dacapo.experiments.datasplits.datasets.arrays.BinarizeArray property) (dacapo.experiments.datasplits.datasets.arrays.concat_array.ConcatArray property) (dacapo.experiments.datasplits.datasets.arrays.ConcatArray property) (dacapo.experiments.datasplits.datasets.arrays.crop_array.CropArray property) (dacapo.experiments.datasplits.datasets.arrays.CropArray property) (dacapo.experiments.datasplits.datasets.arrays.dummy_array.DummyArray property) (dacapo.experiments.datasplits.datasets.arrays.DummyArray property) (dacapo.experiments.datasplits.datasets.arrays.dvid_array.DVIDArray property) (dacapo.experiments.datasplits.datasets.arrays.DVIDArray property) (dacapo.experiments.datasplits.datasets.arrays.IntensitiesArray property) (dacapo.experiments.datasplits.datasets.arrays.intensity_array.IntensitiesArray property) (dacapo.experiments.datasplits.datasets.arrays.logical_or_array.LogicalOrArray property) (dacapo.experiments.datasplits.datasets.arrays.LogicalOrArray property) (dacapo.experiments.datasplits.datasets.arrays.merge_instances_array.MergeInstancesArray property) (dacapo.experiments.datasplits.datasets.arrays.MergeInstancesArray property) (dacapo.experiments.datasplits.datasets.arrays.missing_annotations_mask.MissingAnnotationsMask property) (dacapo.experiments.datasplits.datasets.arrays.MissingAnnotationsMask property) (dacapo.experiments.datasplits.datasets.arrays.numpy_array.NumpyArray property) (dacapo.experiments.datasplits.datasets.arrays.NumpyArray property) (dacapo.experiments.datasplits.datasets.arrays.ones_array.OnesArray property) (dacapo.experiments.datasplits.datasets.arrays.OnesArray property) (dacapo.experiments.datasplits.datasets.arrays.resampled_array.ResampledArray property) (dacapo.experiments.datasplits.datasets.arrays.ResampledArray property) (dacapo.experiments.datasplits.datasets.arrays.sum_array.SumArray property) (dacapo.experiments.datasplits.datasets.arrays.SumArray property) (dacapo.experiments.datasplits.datasets.arrays.tiff_array.TiffArray property) (dacapo.experiments.datasplits.datasets.arrays.zarr_array.ZarrArray property) (dacapo.experiments.datasplits.datasets.arrays.ZarrArray property) (dacapo.experiments.tasks.predictors.affinities_predictor.AffinitiesPredictor property) (dacapo.experiments.tasks.predictors.AffinitiesPredictor property)

num_cpus (dacapo.compute_context.Bsub attribute) (dacapo.compute_context.bsub.Bsub attribute) num_data_fetchers (dacapo.experiments.trainers.gunpowder_trainer_config.GunpowderTrainerConfig attribute), [1] (dacapo.experiments.trainers.GunpowderTrainerConfig attribute), [1] num_fmaps (dacapo.experiments.architectures.cnnectome_unet_config.CNNectomeUNetConfig attribute) (dacapo.experiments.architectures.CNNectomeUNetConfig attribute) num_gpus (dacapo.compute_context.Bsub attribute) (dacapo.compute_context.bsub.Bsub attribute) num_in_channels (dacapo.experiments.architectures.Architecture property) (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) (dacapo.experiments.model.Model attribute) num_iterations (dacapo.experiments.run_config.RunConfig attribute) (dacapo.experiments.RunConfig attribute) num_out_channels (dacapo.experiments.architectures.Architecture property) (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) (dacapo.experiments.model.Model attribute) NumpyArray (class in dacapo.experiments.datasplits.datasets.arrays) (class in dacapo.experiments.datasplits.datasets.arrays.numpy_array)

O

offset (dacapo.experiments.datasplits.datasets.arrays.tiff_array_config.ZarrArrayConfig 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) OnesArray (class in dacapo.experiments.datasplits.datasets.arrays) (class in dacapo.experiments.datasplits.datasets.arrays.ones_array) 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) (dacapo.compute_context.LocalTorch attribute) open_from_array_identifier() (dacapo.experiments.datasplits.datasets.arrays.zarr_array.ZarrArray class method) (dacapo.experiments.datasplits.datasets.arrays.ZarrArray class method) open_from_array_identitifier() (dacapo.utils.view.NeuroglancerRunViewer method) optimizer (dacapo.experiments.run.Run attribute) (dacapo.store.weights_store.Weights attribute)

Options (class in dacapo) (class in dacapo.options) orthoplane_inference() (in module dacapo.blockwise.empanada_function) 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) OutputIdentifier (in module dacapo.experiments.tasks.evaluators.evaluator) overlap_measures_filter() (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluator.ArrayEvaluator method)

P

padding (dacapo.experiments.architectures.cnnectome_unet_config.CNNectomeUNetConfig attribute) (dacapo.experiments.architectures.CNNectomeUNetConfig attribute) padding() (dacapo.experiments.tasks.predictors.distance_predictor.DistancePredictor method) (dacapo.experiments.tasks.predictors.DistancePredictor method) (dacapo.experiments.tasks.predictors.hot_distance_predictor.HotDistancePredictor method) (dacapo.experiments.tasks.predictors.HotDistancePredictor method) (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_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) parameters (dacapo.experiments.tasks.Task property) (dacapo.experiments.tasks.task.Task property) (dacapo.experiments.validation_scores.ValidationScores attribute) (dacapo.experiments.ValidationScores attribute) parser (in module dacapo.validate) path (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.distance_task.DistanceTask attribute) (dacapo.experiments.tasks.DistanceTask attribute) (dacapo.experiments.tasks.dummy_task.DummyTask attribute) (dacapo.experiments.tasks.DummyTask attribute) (dacapo.experiments.tasks.hot_distance_task.HotDistanceTask attribute) (dacapo.experiments.tasks.HotDistanceTask attribute) (dacapo.experiments.tasks.inner_distance_task.InnerDistanceTask attribute) (dacapo.experiments.tasks.InnerDistanceTask 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) (dacapo.experiments.tasks.evaluators.BinarySegmentationEvaluationScores attribute) precision() (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluator.ArrayEvaluator method) precision_with_tolerance (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluation_scores.BinarySegmentationEvaluationScores attribute) (dacapo.experiments.tasks.evaluators.BinarySegmentationEvaluationScores attribute) precision_with_tolerance() (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluator.ArrayEvaluator method) (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluator.CremiEvaluator method) predict() (in module dacapo.predict) Predictor (class in dacapo.experiments.tasks.predictors) (class in dacapo.experiments.tasks.predictors.predictor) predictor (dacapo.experiments.tasks.distance_task.DistanceTask attribute) (dacapo.experiments.tasks.DistanceTask attribute) (dacapo.experiments.tasks.dummy_task.DummyTask attribute) (dacapo.experiments.tasks.DummyTask attribute) (dacapo.experiments.tasks.hot_distance_task.HotDistanceTask attribute) (dacapo.experiments.tasks.HotDistanceTask attribute) (dacapo.experiments.tasks.inner_distance_task.InnerDistanceTask attribute) (dacapo.experiments.tasks.InnerDistanceTask attribute) (dacapo.experiments.tasks.Task attribute) (dacapo.experiments.tasks.task.Task attribute)

prepare() (dacapo.gp.copy.CopyMask method), [1] (dacapo.gp.CopyMask method), [1] (dacapo.gp.dacapo_create_target.DaCapoTargetFilter method) (dacapo.gp.DaCapoTargetFilter method) (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) ProbabilityArray (class in dacapo.experiments.arraytypes) (class in dacapo.experiments.arraytypes.probabilities) process() (dacapo.experiments.tasks.post_processors.argmax_post_processor.ArgmaxPostProcessor method) (dacapo.experiments.tasks.post_processors.ArgmaxPostProcessor method) (dacapo.experiments.tasks.post_processors.dummy_post_processor.DummyPostProcessor method) (dacapo.experiments.tasks.post_processors.DummyPostProcessor method) (dacapo.experiments.tasks.post_processors.post_processor.PostProcessor method) (dacapo.experiments.tasks.post_processors.PostProcessor method) (dacapo.experiments.tasks.post_processors.threshold_post_processor.ThresholdPostProcessor method) (dacapo.experiments.tasks.post_processors.ThresholdPostProcessor method) (dacapo.experiments.tasks.post_processors.watershed_post_processor.WatershedPostProcessor method) (dacapo.experiments.tasks.post_processors.WatershedPostProcessor method) (dacapo.experiments.tasks.predictors.distance_predictor.DistancePredictor method) (dacapo.experiments.tasks.predictors.DistancePredictor method) (dacapo.experiments.tasks.predictors.hot_distance_predictor.HotDistancePredictor method) (dacapo.experiments.tasks.predictors.HotDistancePredictor 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) (dacapo.gp.copy.CopyMask method), [1] (dacapo.gp.CopyMask method), [1] (dacapo.gp.dacapo_create_target.DaCapoTargetFilter method) (dacapo.gp.DaCapoTargetFilter method) (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) (dacapo.utils.pipeline.DilatePoints method) (dacapo.utils.pipeline.ExpandLabels method) (dacapo.utils.pipeline.MakeRaw method) (dacapo.utils.pipeline.RandomDilateLabels method) (dacapo.utils.pipeline.Relabel method) Product (class in dacapo.gp) (class in dacapo.gp.product) provide() (dacapo.gp.dacapo_array_source.DaCapoArraySource method) (dacapo.gp.dacapo_points_source.GraphSource method) (dacapo.gp.DaCapoArraySource method) (dacapo.gp.GraphSource method) (dacapo.gp.reject_if_empty.RejectIfEmpty method) (dacapo.gp.RejectIfEmpty method) (dacapo.utils.pipeline.ZerosSource method)

Q

queue (dacapo.compute_context.Bsub attribute) (dacapo.compute_context.bsub.Bsub attribute)

R

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) (dacapo.experiments.datasplits.datasets.DummyDataset attribute) (dacapo.experiments.datasplits.datasets.raw_gt_dataset.RawGTDataset attribute), [1] (dacapo.experiments.datasplits.datasets.RawGTDataset attribute), [1] RAW (dacapo.experiments.datasplits.keys.ArrayKey attribute), [1] (dacapo.experiments.datasplits.keys.keys.ArrayKey attribute), [1] 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] 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_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) recall (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluation_scores.BinarySegmentationEvaluationScores attribute) (dacapo.experiments.tasks.evaluators.BinarySegmentationEvaluationScores attribute) recall() (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluator.ArrayEvaluator method) recall_with_tolerance (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluation_scores.BinarySegmentationEvaluationScores attribute) (dacapo.experiments.tasks.evaluators.BinarySegmentationEvaluationScores attribute) recall_with_tolerance() (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluator.ArrayEvaluator method) (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluator.CremiEvaluator method) register_hierarchy() (dacapo.store.converter.TypedConverter method) 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) remove() (dacapo.store.array_store.ArrayStore method) (dacapo.store.local_array_store.LocalArrayStore method) (dacapo.store.local_weights_store.LocalWeightsStore method) (dacapo.store.weights_store.WeightsStore method) repetition (dacapo.experiments.run_config.RunConfig attribute) (dacapo.experiments.RunConfig attribute) ResampledArray (class in dacapo.experiments.datasplits.datasets.arrays) (class in dacapo.experiments.datasplits.datasets.arrays.resampled_array) 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) retrieve_architecture_config() (dacapo.store.config_store.ConfigStore method) (dacapo.store.file_config_store.FileConfigStore method) (dacapo.store.mongo_config_store.MongoConfigStore method) retrieve_architecture_config_names() (dacapo.store.config_store.ConfigStore method) (dacapo.store.file_config_store.FileConfigStore method) (dacapo.store.mongo_config_store.MongoConfigStore method) retrieve_array_config() (dacapo.store.config_store.ConfigStore method) (dacapo.store.file_config_store.FileConfigStore method) (dacapo.store.mongo_config_store.MongoConfigStore method) retrieve_array_config_names() (dacapo.store.config_store.ConfigStore method) (dacapo.store.file_config_store.FileConfigStore method) (dacapo.store.mongo_config_store.MongoConfigStore method) retrieve_best() (dacapo.store.local_weights_store.LocalWeightsStore method) (dacapo.store.weights_store.WeightsStore method) retrieve_dataset_config() (dacapo.store.mongo_config_store.MongoConfigStore method) retrieve_dataset_config_names() (dacapo.store.mongo_config_store.MongoConfigStore method) retrieve_datasplit_config() (dacapo.store.config_store.ConfigStore method) (dacapo.store.file_config_store.FileConfigStore method) (dacapo.store.mongo_config_store.MongoConfigStore method) retrieve_datasplit_config_names() (dacapo.store.config_store.ConfigStore method) (dacapo.store.file_config_store.FileConfigStore method) (dacapo.store.mongo_config_store.MongoConfigStore method) retrieve_run_config() (dacapo.store.config_store.ConfigStore method) (dacapo.store.file_config_store.FileConfigStore method) (dacapo.store.mongo_config_store.MongoConfigStore method)

retrieve_run_config_names() (dacapo.store.config_store.ConfigStore method) (dacapo.store.file_config_store.FileConfigStore method) (dacapo.store.mongo_config_store.MongoConfigStore method) retrieve_task_config() (dacapo.store.config_store.ConfigStore method) (dacapo.store.file_config_store.FileConfigStore method) (dacapo.store.mongo_config_store.MongoConfigStore method) retrieve_task_config_names() (dacapo.store.config_store.ConfigStore method) (dacapo.store.file_config_store.FileConfigStore method) (dacapo.store.mongo_config_store.MongoConfigStore method) retrieve_trainer_config() (dacapo.store.config_store.ConfigStore method) (dacapo.store.file_config_store.FileConfigStore method) (dacapo.store.mongo_config_store.MongoConfigStore method) retrieve_trainer_config_names() (dacapo.store.config_store.ConfigStore method) (dacapo.store.file_config_store.FileConfigStore method) (dacapo.store.mongo_config_store.MongoConfigStore method) retrieve_training_stats() (dacapo.store.file_stats_store.FileStatsStore method) (dacapo.store.mongo_stats_store.MongoStatsStore method) (dacapo.store.stats_store.StatsStore method) retrieve_validation_iteration_scores() (dacapo.store.file_stats_store.FileStatsStore method) (dacapo.store.mongo_stats_store.MongoStatsStore method) (dacapo.store.stats_store.StatsStore method) retrieve_weights() (dacapo.store.local_weights_store.LocalWeightsStore method) (dacapo.store.weights_store.WeightsStore method) roi (dacapo.experiments.datasplits.datasets.arrays.Array property) (dacapo.experiments.datasplits.datasets.arrays.array.Array property) (dacapo.experiments.datasplits.datasets.arrays.binarize_array.BinarizeArray property) (dacapo.experiments.datasplits.datasets.arrays.BinarizeArray property) (dacapo.experiments.datasplits.datasets.arrays.concat_array.ConcatArray property) (dacapo.experiments.datasplits.datasets.arrays.ConcatArray property) (dacapo.experiments.datasplits.datasets.arrays.crop_array.CropArray property) (dacapo.experiments.datasplits.datasets.arrays.crop_array_config.CropArrayConfig attribute) (dacapo.experiments.datasplits.datasets.arrays.CropArray property) (dacapo.experiments.datasplits.datasets.arrays.CropArrayConfig attribute) (dacapo.experiments.datasplits.datasets.arrays.dummy_array.DummyArray property) (dacapo.experiments.datasplits.datasets.arrays.DummyArray property) (dacapo.experiments.datasplits.datasets.arrays.IntensitiesArray property) (dacapo.experiments.datasplits.datasets.arrays.intensity_array.IntensitiesArray property) (dacapo.experiments.datasplits.datasets.arrays.logical_or_array.LogicalOrArray property) (dacapo.experiments.datasplits.datasets.arrays.LogicalOrArray property) (dacapo.experiments.datasplits.datasets.arrays.merge_instances_array.MergeInstancesArray property) (dacapo.experiments.datasplits.datasets.arrays.MergeInstancesArray property) (dacapo.experiments.datasplits.datasets.arrays.missing_annotations_mask.MissingAnnotationsMask property) (dacapo.experiments.datasplits.datasets.arrays.MissingAnnotationsMask property) (dacapo.experiments.datasplits.datasets.arrays.numpy_array.NumpyArray property) (dacapo.experiments.datasplits.datasets.arrays.NumpyArray property) (dacapo.experiments.datasplits.datasets.arrays.ones_array.OnesArray property) (dacapo.experiments.datasplits.datasets.arrays.OnesArray property) (dacapo.experiments.datasplits.datasets.arrays.resampled_array.ResampledArray property) (dacapo.experiments.datasplits.datasets.arrays.ResampledArray property) (dacapo.experiments.datasplits.datasets.arrays.sum_array.SumArray property) (dacapo.experiments.datasplits.datasets.arrays.SumArray property) roi() (dacapo.experiments.datasplits.datasets.arrays.dvid_array.DVIDArray method) (dacapo.experiments.datasplits.datasets.arrays.DVIDArray method) (dacapo.experiments.datasplits.datasets.arrays.tiff_array.TiffArray method) (dacapo.experiments.datasplits.datasets.arrays.zarr_array.ZarrArray method) (dacapo.experiments.datasplits.datasets.arrays.ZarrArray method) rotation_interval (dacapo.experiments.trainers.gp_augments.elastic_config.ElasticAugmentConfig attribute), [1] (dacapo.experiments.trainers.gp_augments.ElasticAugmentConfig attribute), [1] Run (class in dacapo.experiments.run) run (dacapo.experiments.starts.cosem_start.CosemStart attribute) (dacapo.experiments.starts.CosemStart 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] run_blockwise() (in module dacapo.blockwise) (in module dacapo.blockwise.scheduler) RunConfig (class in dacapo.experiments) (class in dacapo.experiments.run_config) RunInfo (in module dacapo.plot) runs (dacapo.store.config_store.ConfigStore attribute) (dacapo.store.file_config_store.FileConfigStore property) runs_base_dir (dacapo.options.DaCapoConfig attribute)

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] scale (dacapo.experiments.datasplits.datasets.arrays.resampled_array.ResampledArray property) (dacapo.experiments.datasplits.datasets.arrays.ResampledArray property) (dacapo.experiments.trainers.gp_augments.intensity_config.IntensityAugmentConfig attribute) (dacapo.experiments.trainers.gp_augments.intensity_scale_shift_config.IntensityScaleShiftAugmentConfig attribute) (dacapo.experiments.trainers.gp_augments.IntensityAugmentConfig attribute) (dacapo.experiments.trainers.gp_augments.IntensityScaleShiftAugmentConfig attribute) scale() (dacapo.experiments.architectures.Architecture method) (dacapo.experiments.architectures.architecture.Architecture method) (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) (dacapo.experiments.tasks.DistanceTaskConfig attribute) (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) 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) Score (in module dacapo.experiments.tasks.evaluators.evaluator) scores (dacapo.experiments.validation_iteration_scores.ValidationIterationScores attribute), [1] (dacapo.experiments.validation_scores.ValidationScores attribute) (dacapo.experiments.ValidationIterationScores attribute), [1] (dacapo.experiments.ValidationScores attribute) seg_to_affgraph() (in module dacapo.utils.affinities) segment_blockwise() (in module dacapo.blockwise) (in module dacapo.blockwise.scheduler) segment_function() (in module dacapo.blockwise.empanada_function) (in module dacapo.blockwise.watershed_function) SegmentationType (class in dacapo.experiments.datasplits.datasplit_generator) semantic (dacapo.experiments.datasplits.datasplit_generator.SegmentationType attribute) serialize() (dacapo.options.DaCapoConfig method) set_best() (dacapo.experiments.tasks.evaluators.Evaluator method) (dacapo.experiments.tasks.evaluators.evaluator.Evaluator method) set_prediction() (dacapo.experiments.tasks.post_processors.argmax_post_processor.ArgmaxPostProcessor method) (dacapo.experiments.tasks.post_processors.ArgmaxPostProcessor method) (dacapo.experiments.tasks.post_processors.dummy_post_processor.DummyPostProcessor method) (dacapo.experiments.tasks.post_processors.DummyPostProcessor method) (dacapo.experiments.tasks.post_processors.post_processor.PostProcessor method) (dacapo.experiments.tasks.post_processors.PostProcessor method) (dacapo.experiments.tasks.post_processors.threshold_post_processor.ThresholdPostProcessor method) (dacapo.experiments.tasks.post_processors.ThresholdPostProcessor method) (dacapo.experiments.tasks.post_processors.watershed_post_processor.WatershedPostProcessor method) (dacapo.experiments.tasks.post_processors.WatershedPostProcessor method) setup() (dacapo.gp.copy.CopyMask method), [1] (dacapo.gp.CopyMask method), [1] (dacapo.gp.dacapo_array_source.DaCapoArraySource method) (dacapo.gp.dacapo_create_target.DaCapoTargetFilter method) (dacapo.gp.dacapo_points_source.GraphSource method) (dacapo.gp.DaCapoArraySource method) (dacapo.gp.DaCapoTargetFilter method) (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) (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) (dacapo.utils.pipeline.ZerosSource method) shape() (dacapo.experiments.datasplits.datasets.arrays.tiff_array.TiffArray method) shift (dacapo.experiments.trainers.gp_augments.intensity_config.IntensityAugmentConfig attribute) (dacapo.experiments.trainers.gp_augments.intensity_scale_shift_config.IntensityScaleShiftAugmentConfig attribute) (dacapo.experiments.trainers.gp_augments.IntensityAugmentConfig attribute) (dacapo.experiments.trainers.gp_augments.IntensityScaleShiftAugmentConfig attribute) sigma() (dacapo.experiments.tasks.predictors.affinities_predictor.AffinitiesPredictor method) (dacapo.experiments.tasks.predictors.AffinitiesPredictor method) SimpleAugmentConfig (class in dacapo.experiments.trainers.gp_augments) (class in dacapo.experiments.trainers.gp_augments.simple_config) smooth_values() (in module dacapo.plot) snap_to_grid (dacapo.experiments.datasplits.datasets.arrays.zarr_array_config.ZarrArrayConfig attribute) (dacapo.experiments.datasplits.datasets.arrays.ZarrArrayConfig attribute) snapshot_container() (dacapo.store.array_store.ArrayStore method) (dacapo.store.local_array_store.LocalArrayStore method) snapshot_interval (dacapo.experiments.trainers.gunpowder_trainer_config.GunpowderTrainerConfig attribute), [1] (dacapo.experiments.trainers.GunpowderTrainerConfig attribute), [1] source (dacapo.experiments.datasplits.datasets.arrays.dvid_array_config.DVIDArrayConfig attribute) (dacapo.experiments.datasplits.datasets.arrays.DVIDArrayConfig attribute) source_array (dacapo.experiments.datasplits.datasets.arrays.concat_array.ConcatArray property) (dacapo.experiments.datasplits.datasets.arrays.ConcatArray property) (dacapo.experiments.datasplits.datasets.arrays.ones_array.OnesArray property) (dacapo.experiments.datasplits.datasets.arrays.OnesArray property) source_array_config (dacapo.experiments.datasplits.datasets.arrays.binarize_array_config.BinarizeArrayConfig attribute) (dacapo.experiments.datasplits.datasets.arrays.BinarizeArrayConfig attribute) (dacapo.experiments.datasplits.datasets.arrays.crop_array_config.CropArrayConfig attribute) (dacapo.experiments.datasplits.datasets.arrays.CropArrayConfig attribute) (dacapo.experiments.datasplits.datasets.arrays.IntensitiesArrayConfig attribute) (dacapo.experiments.datasplits.datasets.arrays.intensity_array_config.IntensitiesArrayConfig attribute) (dacapo.experiments.datasplits.datasets.arrays.logical_or_array_config.LogicalOrArrayConfig attribute) (dacapo.experiments.datasplits.datasets.arrays.LogicalOrArrayConfig attribute) (dacapo.experiments.datasplits.datasets.arrays.missing_annotations_mask_config.MissingAnnotationsMaskConfig attribute) (dacapo.experiments.datasplits.datasets.arrays.MissingAnnotationsMaskConfig attribute) (dacapo.experiments.datasplits.datasets.arrays.ones_array_config.OnesArrayConfig attribute) (dacapo.experiments.datasplits.datasets.arrays.OnesArrayConfig attribute) (dacapo.experiments.datasplits.datasets.arrays.resampled_array_config.ResampledArrayConfig attribute) (dacapo.experiments.datasplits.datasets.arrays.ResampledArrayConfig attribute)

source_array_configs (dacapo.experiments.datasplits.datasets.arrays.concat_array_config.ConcatArrayConfig attribute) (dacapo.experiments.datasplits.datasets.arrays.ConcatArrayConfig attribute) (dacapo.experiments.datasplits.datasets.arrays.merge_instances_array_config.MergeInstancesArrayConfig attribute) (dacapo.experiments.datasplits.datasets.arrays.MergeInstancesArrayConfig attribute) (dacapo.experiments.datasplits.datasets.arrays.sum_array_config.SumArrayConfig attribute) (dacapo.experiments.datasplits.datasets.arrays.SumArrayConfig attribute) source_arrays (dacapo.experiments.datasplits.datasets.arrays.concat_array.ConcatArray property) (dacapo.experiments.datasplits.datasets.arrays.ConcatArray property) spatial_axes (dacapo.experiments.datasplits.datasets.arrays.dvid_array.DVIDArray property) (dacapo.experiments.datasplits.datasets.arrays.DVIDArray property) (dacapo.experiments.datasplits.datasets.arrays.tiff_array.TiffArray property) (dacapo.experiments.datasplits.datasets.arrays.zarr_array.ZarrArray property) (dacapo.experiments.datasplits.datasets.arrays.ZarrArray property) 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.GraphKey attribute), [1] (dacapo.experiments.datasplits.keys.keys.GraphKey attribute), [1] split() (dacapo.experiments.tasks.losses.hot_distance_loss.HotDistanceLoss method) (dacapo.experiments.tasks.losses.HotDistanceLoss method) 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.utils.view.NeuroglancerRunViewer method) start_config (dacapo.experiments.run_config.RunConfig attribute) (dacapo.experiments.RunConfig attribute) start_neuroglancer() (dacapo.utils.view.NeuroglancerRunViewer method) 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) StartConfig (class in dacapo.experiments.starts) (class in dacapo.experiments.starts.start_config) StatsStore (class in dacapo.store.stats_store) stop() (dacapo.utils.view.NeuroglancerRunViewer method) store_architecture_config() (dacapo.store.config_store.ConfigStore method) (dacapo.store.file_config_store.FileConfigStore method) (dacapo.store.mongo_config_store.MongoConfigStore method) store_array_config() (dacapo.store.config_store.ConfigStore method) (dacapo.store.file_config_store.FileConfigStore method) (dacapo.store.mongo_config_store.MongoConfigStore method) 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 static method) (dacapo.experiments.tasks.evaluators.DummyEvaluationScores static method) (dacapo.experiments.tasks.evaluators.evaluation_scores.EvaluationScores static method) (dacapo.experiments.tasks.evaluators.EvaluationScores static method) (dacapo.experiments.tasks.evaluators.Evaluator method) (dacapo.experiments.tasks.evaluators.evaluator.Evaluator method) (dacapo.experiments.tasks.evaluators.instance_evaluation_scores.InstanceEvaluationScores static method) (dacapo.experiments.tasks.evaluators.InstanceEvaluationScores static method) (dacapo.experiments.tasks.evaluators.MultiChannelBinarySegmentationEvaluationScores static method) (dacapo.store.local_weights_store.LocalWeightsStore method) store_dataset_config() (dacapo.store.mongo_config_store.MongoConfigStore method) store_datasplit_config() (dacapo.store.config_store.ConfigStore method) (dacapo.store.file_config_store.FileConfigStore method) (dacapo.store.mongo_config_store.MongoConfigStore method) store_run_config() (dacapo.store.config_store.ConfigStore method) (dacapo.store.file_config_store.FileConfigStore method) (dacapo.store.mongo_config_store.MongoConfigStore method) store_task_config() (dacapo.store.config_store.ConfigStore method) (dacapo.store.file_config_store.FileConfigStore method) (dacapo.store.mongo_config_store.MongoConfigStore method) store_trainer_config() (dacapo.store.config_store.ConfigStore method) (dacapo.store.file_config_store.FileConfigStore method) (dacapo.store.mongo_config_store.MongoConfigStore method) store_training_stats() (dacapo.store.file_stats_store.FileStatsStore method) (dacapo.store.mongo_stats_store.MongoStatsStore method) (dacapo.store.stats_store.StatsStore method) store_validation_iteration_scores() (dacapo.store.file_stats_store.FileStatsStore method) (dacapo.store.mongo_stats_store.MongoStatsStore method) (dacapo.store.stats_store.StatsStore method) store_weights() (dacapo.store.local_weights_store.LocalWeightsStore method) (dacapo.store.weights_store.WeightsStore method) sub_task_config (dacapo.experiments.tasks.pretrained_task_config.PretrainedTaskConfig attribute) (dacapo.experiments.tasks.PretrainedTaskConfig attribute) subsample (dacapo.experiments.trainers.gp_augments.elastic_config.ElasticAugmentConfig attribute), [1] (dacapo.experiments.trainers.gp_augments.ElasticAugmentConfig attribute), [1] subscores() (dacapo.experiments.validation_scores.ValidationScores method) (dacapo.experiments.ValidationScores method) SumArray (class in dacapo.experiments.datasplits.datasets.arrays) (class in dacapo.experiments.datasplits.datasets.arrays.sum_array) SumArrayConfig (class in dacapo.experiments.datasplits.datasets.arrays) (class in dacapo.experiments.datasplits.datasets.arrays.sum_array_config)

T

Task (class in dacapo.experiments.tasks) (class in dacapo.experiments.tasks.task) task (dacapo.experiments.run.Run attribute) 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) (dacapo.store.file_config_store.FileConfigStore property) test_edt() (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluator.CremiEvaluator method) 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) (dacapo.experiments.tasks.post_processors.ThresholdPostProcessorParameters 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) TiffArray (class in dacapo.experiments.datasplits.datasets.arrays.tiff_array) time (dacapo.experiments.training_iteration_stats.TrainingIterationStats attribute), [1] (dacapo.experiments.TrainingIterationStats attribute), [1] to_xarray() (dacapo.experiments.training_stats.TrainingStats method), [1] (dacapo.experiments.TrainingStats method), [1] (dacapo.experiments.validation_scores.ValidationScores method) (dacapo.experiments.ValidationScores method) tol_distance (dacapo.experiments.tasks.distance_task_config.DistanceTaskConfig attribute) (dacapo.experiments.tasks.DistanceTaskConfig attribute) (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)

tracker_consensus() (in module dacapo.blockwise.empanada_function) train (dacapo.experiments.datasplits.DataSplit attribute) (dacapo.experiments.datasplits.datasplit.DataSplit attribute) (dacapo.experiments.datasplits.datasplit_generator.DatasetType attribute) (dacapo.experiments.datasplits.dummy_datasplit.DummyDataSplit attribute) (dacapo.experiments.datasplits.DummyDataSplit attribute) (dacapo.experiments.datasplits.train_validate_datasplit.TrainValidateDataSplit attribute) (dacapo.experiments.datasplits.TrainValidateDataSplit attribute) 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) (dacapo.experiments.datasplits.TrainValidateDataSplitConfig attribute) train_run() (in module dacapo.train) train_until (dacapo.experiments.run.Run attribute) 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) 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) (dacapo.store.file_config_store.FileConfigStore property) training_stats (dacapo.experiments.run.Run 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) true_positives_with_tolerance() (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluator.CremiEvaluator method) truth_edt() (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluator.CremiEvaluator method) 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) TypedConverter (class in dacapo.store.converter)

U

uniform_3d_rotation (dacapo.experiments.trainers.gp_augments.elastic_config.ElasticAugmentConfig attribute), [1] (dacapo.experiments.trainers.gp_augments.ElasticAugmentConfig attribute), [1] update_best_info() (dacapo.utils.view.NeuroglancerRunViewer method) update_best_layer() (dacapo.utils.view.NeuroglancerRunViewer method) update_neuroglancer() (dacapo.utils.view.NeuroglancerRunViewer method) update_with_new_validation_if_possible() (dacapo.utils.view.NeuroglancerRunViewer method) updated_neuroglancer_layer() (dacapo.utils.view.NeuroglancerRunViewer method)

Upsample (class in dacapo.experiments.architectures.cnnectome_unet) upsample (dacapo.experiments.datasplits.datasets.arrays.resampled_array_config.ResampledArrayConfig attribute) (dacapo.experiments.datasplits.datasets.arrays.ResampledArrayConfig attribute) upsample_factors (dacapo.experiments.architectures.cnnectome_unet_config.CNNectomeUNetConfig attribute) (dacapo.experiments.architectures.CNNectomeUNetConfig attribute) use_attention (dacapo.experiments.architectures.cnnectome_unet_config.CNNectomeUNetConfig attribute) (dacapo.experiments.architectures.CNNectomeUNetConfig attribute) users (dacapo.store.file_config_store.FileConfigStore property)

V

val (dacapo.experiments.datasplits.datasplit_generator.DatasetType attribute) validate (dacapo.experiments.datasplits.DataSplit attribute) (dacapo.experiments.datasplits.datasplit.DataSplit attribute) (dacapo.experiments.datasplits.dummy_datasplit.DummyDataSplit attribute), [1] (dacapo.experiments.datasplits.DummyDataSplit attribute), [1] (dacapo.experiments.datasplits.train_validate_datasplit.TrainValidateDataSplit attribute) (dacapo.experiments.datasplits.TrainValidateDataSplit attribute) validate() (in module dacapo) (in module dacapo.validate) validate_configs (dacapo.experiments.datasplits.train_validate_datasplit_config.TrainValidateDataSplitConfig attribute) (dacapo.experiments.datasplits.TrainValidateDataSplitConfig attribute) validate_run() (in module dacapo.validate) validated_until() (dacapo.experiments.validation_scores.ValidationScores method) (dacapo.experiments.ValidationScores method) validation_container() (dacapo.store.array_store.ArrayStore method) (dacapo.store.local_array_store.LocalArrayStore method) validation_input_arrays() (dacapo.store.array_store.ArrayStore method) (dacapo.store.local_array_store.LocalArrayStore method) validation_interval (dacapo.experiments.run.Run attribute) (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) validation_prediction_array() (dacapo.store.array_store.ArrayStore method) (dacapo.store.local_array_store.LocalArrayStore method) validation_scores (dacapo.experiments.run.Run 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) (dacapo.experiments.architectures.DummyArchitectureConfig method) (dacapo.experiments.datasplits.datasets.arrays.array_config.ArrayConfig method) (dacapo.experiments.datasplits.datasets.arrays.ArrayConfig 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.zarr_array_config.ZarrArrayConfig method) (dacapo.experiments.datasplits.datasets.arrays.ZarrArrayConfig method) (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.datasplit_config.DataSplitConfig method), [1] (dacapo.experiments.datasplits.DataSplitConfig method), [1] (dacapo.experiments.datasplits.dummy_datasplit_config.DummyDataSplitConfig method) (dacapo.experiments.datasplits.DummyDataSplitConfig method) (dacapo.experiments.tasks.dummy_task_config.DummyTaskConfig method) (dacapo.experiments.tasks.DummyTaskConfig method) (dacapo.experiments.tasks.task_config.TaskConfig method) (dacapo.experiments.tasks.TaskConfig method) (dacapo.experiments.trainers.dummy_trainer_config.DummyTrainerConfig method) (dacapo.experiments.trainers.DummyTrainerConfig method) (dacapo.experiments.trainers.trainer_config.TrainerConfig method) (dacapo.experiments.trainers.TrainerConfig method)

vi_tables() (in module dacapo.utils.voi) voi (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluation_scores.BinarySegmentationEvaluationScores attribute) (dacapo.experiments.tasks.evaluators.BinarySegmentationEvaluationScores attribute) (dacapo.experiments.tasks.evaluators.instance_evaluation_scores.InstanceEvaluationScores property) (dacapo.experiments.tasks.evaluators.InstanceEvaluationScores property) voi() (dacapo.experiments.tasks.evaluators.binary_segmentation_evaluator.ArrayEvaluator method) (in module dacapo.experiments.tasks.evaluators.instance_evaluator) (in module dacapo.utils.voi) voi_merge (dacapo.experiments.tasks.evaluators.instance_evaluation_scores.InstanceEvaluationScores attribute) (dacapo.experiments.tasks.evaluators.InstanceEvaluationScores attribute) voi_split (dacapo.experiments.tasks.evaluators.instance_evaluation_scores.InstanceEvaluationScores attribute) (dacapo.experiments.tasks.evaluators.InstanceEvaluationScores attribute) voxel_size (dacapo.experiments.datasplits.datasets.arrays.Array property) (dacapo.experiments.datasplits.datasets.arrays.array.Array property) (dacapo.experiments.datasplits.datasets.arrays.binarize_array.BinarizeArray property) (dacapo.experiments.datasplits.datasets.arrays.BinarizeArray property) (dacapo.experiments.datasplits.datasets.arrays.concat_array.ConcatArray property) (dacapo.experiments.datasplits.datasets.arrays.ConcatArray property) (dacapo.experiments.datasplits.datasets.arrays.crop_array.CropArray property) (dacapo.experiments.datasplits.datasets.arrays.CropArray property) (dacapo.experiments.datasplits.datasets.arrays.dummy_array.DummyArray property) (dacapo.experiments.datasplits.datasets.arrays.DummyArray property) (dacapo.experiments.datasplits.datasets.arrays.IntensitiesArray property) (dacapo.experiments.datasplits.datasets.arrays.intensity_array.IntensitiesArray property) (dacapo.experiments.datasplits.datasets.arrays.logical_or_array.LogicalOrArray property) (dacapo.experiments.datasplits.datasets.arrays.LogicalOrArray property) (dacapo.experiments.datasplits.datasets.arrays.merge_instances_array.MergeInstancesArray property) (dacapo.experiments.datasplits.datasets.arrays.MergeInstancesArray property) (dacapo.experiments.datasplits.datasets.arrays.missing_annotations_mask.MissingAnnotationsMask property) (dacapo.experiments.datasplits.datasets.arrays.MissingAnnotationsMask property) (dacapo.experiments.datasplits.datasets.arrays.numpy_array.NumpyArray property) (dacapo.experiments.datasplits.datasets.arrays.NumpyArray property) (dacapo.experiments.datasplits.datasets.arrays.ones_array.OnesArray property) (dacapo.experiments.datasplits.datasets.arrays.OnesArray property) (dacapo.experiments.datasplits.datasets.arrays.resampled_array.ResampledArray property) (dacapo.experiments.datasplits.datasets.arrays.ResampledArray property) (dacapo.experiments.datasplits.datasets.arrays.sum_array.SumArray property) (dacapo.experiments.datasplits.datasets.arrays.SumArray property) (dacapo.experiments.datasplits.datasets.arrays.tiff_array_config.ZarrArrayConfig attribute) voxel_size() (dacapo.experiments.datasplits.datasets.arrays.dvid_array.DVIDArray method) (dacapo.experiments.datasplits.datasets.arrays.DVIDArray method) (dacapo.experiments.datasplits.datasets.arrays.tiff_array.TiffArray method) (dacapo.experiments.datasplits.datasets.arrays.zarr_array.ZarrArray method) (dacapo.experiments.datasplits.datasets.arrays.ZarrArray method)

W

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) (dacapo.experiments.datasplits.datasets.RawGTDataset attribute) Weights (class in dacapo.store.weights_store) weights (dacapo.experiments.tasks.pretrained_task_config.PretrainedTaskConfig attribute) (dacapo.experiments.tasks.PretrainedTaskConfig attribute) WeightsStore (class in dacapo.store.weights_store) wrap_command() (dacapo.compute_context.compute_context.ComputeContext method) (dacapo.compute_context.ComputeContext method) writable (dacapo.experiments.datasplits.datasets.arrays.Array property) (dacapo.experiments.datasplits.datasets.arrays.array.Array property) (dacapo.experiments.datasplits.datasets.arrays.binarize_array.BinarizeArray property) (dacapo.experiments.datasplits.datasets.arrays.BinarizeArray property) (dacapo.experiments.datasplits.datasets.arrays.concat_array.ConcatArray property) (dacapo.experiments.datasplits.datasets.arrays.ConcatArray property) (dacapo.experiments.datasplits.datasets.arrays.crop_array.CropArray property) (dacapo.experiments.datasplits.datasets.arrays.CropArray property) (dacapo.experiments.datasplits.datasets.arrays.dummy_array.DummyArray property) (dacapo.experiments.datasplits.datasets.arrays.DummyArray property) (dacapo.experiments.datasplits.datasets.arrays.dvid_array.DVIDArray property) (dacapo.experiments.datasplits.datasets.arrays.DVIDArray property) (dacapo.experiments.datasplits.datasets.arrays.IntensitiesArray property) (dacapo.experiments.datasplits.datasets.arrays.intensity_array.IntensitiesArray property) (dacapo.experiments.datasplits.datasets.arrays.logical_or_array.LogicalOrArray property) (dacapo.experiments.datasplits.datasets.arrays.LogicalOrArray property) (dacapo.experiments.datasplits.datasets.arrays.merge_instances_array.MergeInstancesArray property) (dacapo.experiments.datasplits.datasets.arrays.MergeInstancesArray property) (dacapo.experiments.datasplits.datasets.arrays.missing_annotations_mask.MissingAnnotationsMask property) (dacapo.experiments.datasplits.datasets.arrays.MissingAnnotationsMask property) (dacapo.experiments.datasplits.datasets.arrays.numpy_array.NumpyArray property) (dacapo.experiments.datasplits.datasets.arrays.NumpyArray property) (dacapo.experiments.datasplits.datasets.arrays.ones_array.OnesArray property) (dacapo.experiments.datasplits.datasets.arrays.OnesArray property) (dacapo.experiments.datasplits.datasets.arrays.resampled_array.ResampledArray property) (dacapo.experiments.datasplits.datasets.arrays.ResampledArray property) (dacapo.experiments.datasplits.datasets.arrays.sum_array.SumArray property) (dacapo.experiments.datasplits.datasets.arrays.SumArray property) (dacapo.experiments.datasplits.datasets.arrays.tiff_array.TiffArray property) (dacapo.experiments.datasplits.datasets.arrays.zarr_array.ZarrArray property) (dacapo.experiments.datasplits.datasets.arrays.ZarrArray property)

X

xlogx() (in module dacapo.utils.voi)

Z

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

ZerosSource (class in dacapo.utils.pipeline)