Index

_

__call__() (PostProcessor method) __class_vars__ (cellmap_flow.models.cellmap_models.ModelMetadata attribute) __private_attributes__ (cellmap_flow.models.cellmap_models.ModelMetadata attribute) __pydantic_complete__ (cellmap_flow.models.cellmap_models.ModelMetadata attribute) __pydantic_computed_fields__ (cellmap_flow.models.cellmap_models.ModelMetadata attribute) __pydantic_core_schema__ (cellmap_flow.models.cellmap_models.ModelMetadata attribute) __pydantic_custom_init__ (cellmap_flow.models.cellmap_models.ModelMetadata attribute) __pydantic_decorators__ (cellmap_flow.models.cellmap_models.ModelMetadata attribute) __pydantic_extra__ (cellmap_flow.models.cellmap_models.ModelMetadata attribute) __pydantic_fields__ (cellmap_flow.models.cellmap_models.ModelMetadata attribute)

__pydantic_fields_set__ (cellmap_flow.models.cellmap_models.ModelMetadata attribute) __pydantic_generic_metadata__ (cellmap_flow.models.cellmap_models.ModelMetadata attribute) __pydantic_parent_namespace__ (cellmap_flow.models.cellmap_models.ModelMetadata attribute) __pydantic_post_init__ (cellmap_flow.models.cellmap_models.ModelMetadata attribute) __pydantic_private__ (cellmap_flow.models.cellmap_models.ModelMetadata attribute) __pydantic_root_model__ (cellmap_flow.models.cellmap_models.ModelMetadata attribute) __pydantic_serializer__ (cellmap_flow.models.cellmap_models.ModelMetadata attribute) __pydantic_validator__ (cellmap_flow.models.cellmap_models.ModelMetadata attribute) __signature__ (cellmap_flow.models.cellmap_models.ModelMetadata attribute) _process() (PostProcessor method)

A

access_parent() (in module cellmap_flow.utils.ds) activation (cellmap_flow.norm.input_normalize.EuclideanDistance attribute) AffinityPostprocessor (built-in class) (class in cellmap_flow.post.postprocessors) analyze_script() (in module cellmap_flow.utils.load_py) AndModelMerger (class in cellmap_flow.models.model_merger) anisotropy (cellmap_flow.norm.input_normalize.EuclideanDistance attribute) app (cellmap_flow.server.CellMapFlowServer attribute) (in module cellmap_flow.dashboard.app)

apply_norms() (in module cellmap_flow.utils.ds) apply_pipeline() (in module cellmap_flow.dashboard.app) apply_postprocess() (in module cellmap_flow.inferencer) ARGS_KEY (in module cellmap_flow.utils.web_utils) author (cellmap_flow.models.cellmap_models.ModelMetadata attribute) AWSBatchJob (class in cellmap_flow.utils.job_extensions) axes (cellmap_flow.server.CellMapFlowServer attribute) axes_names (cellmap_flow.utils.serialize_config.Config attribute) AzureBatchJob (class in cellmap_flow.utils.job_extensions)

B

batch_account (cellmap_flow.utils.job_extensions.AzureBatchJob attribute) bbx_generator_state (in module cellmap_flow.dashboard.app) BBXGenerator (class in cellmap_flow.dashboard.bbx_generator) bias (cellmap_flow.post.postprocessors.AffinityPostprocessor attribute) (cellmap_flow.post.postprocessors.DefaultPostprocessor attribute) BioModelConfig (class in cellmap_flow.models.models_config) black_border (cellmap_flow.norm.input_normalize.EuclideanDistance attribute) block_shape (cellmap_flow.blockwise.blockwise_processor.CellMapFlowBlockwiseProcessor attribute) (cellmap_flow.blockwise.CellMapFlowBlockwiseProcessor attribute)

blockwise_config_api() (in module cellmap_flow.dashboard.app) blockwise_tasks_dir (cellmap_flow.globals.Flow attribute) bounding_boxes (cellmap_flow.blockwise.blockwise_processor.CellMapFlowBlockwiseProcessor attribute) (cellmap_flow.blockwise.CellMapFlowBlockwiseProcessor attribute) (cellmap_flow.dashboard.bbx_generator.BBXGenerator attribute) build_model_from_entry() (in module cellmap_flow.utils.config_utils) build_models() (in module cellmap_flow.utils.config_utils)

C

calculate_equivalences() (cellmap_flow.post.postprocessors.SimpleBlockwiseMerger method) cellmap_flow module cellmap_flow.blockwise module cellmap_flow.blockwise.blockwise_processor module cellmap_flow.blockwise.cli module cellmap_flow.blockwise.multiple_cli module cellmap_flow.cli module cellmap_flow.cli.cli module cellmap_flow.cli.server_cli module cellmap_flow.cli.yaml_cli module cellmap_flow.dashboard module cellmap_flow.dashboard.app module cellmap_flow.dashboard.bbx_generator module cellmap_flow.globals module cellmap_flow.image_data_interface module cellmap_flow.inferencer module cellmap_flow.models module cellmap_flow.models.cellmap_models module cellmap_flow.models.model_merger module cellmap_flow.models.model_registry module cellmap_flow.models.models_config module cellmap_flow.models.run module cellmap_flow.norm module cellmap_flow.norm.input_normalize module cellmap_flow.post module cellmap_flow.post.postprocessors module cellmap_flow.server module cellmap_flow.utils module cellmap_flow.utils.bsub_utils module cellmap_flow.utils.cli_utils module cellmap_flow.utils.config_utils module cellmap_flow.utils.ds module cellmap_flow.utils.generate_neuroglancer module cellmap_flow.utils.import_utils module cellmap_flow.utils.job_extensions module cellmap_flow.utils.load_py module cellmap_flow.utils.neuroglancer_utils module

cellmap_flow.utils.scale_pyramid module cellmap_flow.utils.serialize_config module cellmap_flow.utils.serilization_utils module cellmap_flow.utils.web_utils module cellmap_model (cellmap_flow.models.models_config.CellMapModelConfig attribute) CellMapFlowBlockwiseProcessor (class in cellmap_flow.blockwise) (class in cellmap_flow.blockwise.blockwise_processor) CellMapFlowServer (class in cellmap_flow.server) CellmapModel (class in cellmap_flow.models.cellmap_models) CellMapModelConfig (class in cellmap_flow.models.models_config) CellmapModels (class in cellmap_flow.models.cellmap_models) channel (cellmap_flow.post.postprocessors.LabelPostprocessor attribute) (cellmap_flow.post.postprocessors.MortonSegmentationRelabeling attribute) (cellmap_flow.post.postprocessors.SimpleBlockwiseMerger attribute) channels (cellmap_flow.blockwise.blockwise_processor.CellMapFlowBlockwiseProcessor attribute) (cellmap_flow.blockwise.CellMapFlowBlockwiseProcessor attribute) (cellmap_flow.models.models_config.FlyModelConfig attribute) (cellmap_flow.post.postprocessors.ChannelSelection attribute) channels_names (cellmap_flow.models.cellmap_models.ModelMetadata attribute) ChannelSelection (built-in class) (class in cellmap_flow.post.postprocessors) charge_group (cellmap_flow.blockwise.blockwise_processor.CellMapFlowBlockwiseProcessor attribute) (cellmap_flow.blockwise.CellMapFlowBlockwiseProcessor attribute) (cellmap_flow.globals.Flow attribute) check_block() (in module cellmap_flow.blockwise.blockwise_processor) check_dependencies() (in module cellmap_flow.utils.import_utils) check_for_attrs_multiscale() (in module cellmap_flow.utils.ds) check_for_multiscale() (in module cellmap_flow.utils.ds) check_for_offset() (in module cellmap_flow.utils.ds) check_for_units() (in module cellmap_flow.utils.ds) check_for_voxel_size() (in module cellmap_flow.utils.ds) checkpoint_path (cellmap_flow.models.models_config.FlyModelConfig attribute) chunk_encoder (cellmap_flow.server.CellMapFlowServer attribute) chunk_slice_position_to_coords_id_dict (cellmap_flow.post.postprocessors.SimpleBlockwiseMerger attribute) cleanup_handler() (in module cellmap_flow.utils.bsub_utils) cli() (in module cellmap_flow.blockwise.cli) (in module cellmap_flow.blockwise.multiple_cli) (in module cellmap_flow.cli.cli) (in module cellmap_flow.cli.server_cli) client() (cellmap_flow.blockwise.blockwise_processor.CellMapFlowBlockwiseProcessor method) (cellmap_flow.blockwise.CellMapFlowBlockwiseProcessor method) clip_max (cellmap_flow.post.postprocessors.DefaultPostprocessor attribute) clip_min (cellmap_flow.post.postprocessors.DefaultPostprocessor attribute) close() (cellmap_flow.dashboard.bbx_generator.BBXGenerator method) command (cellmap_flow.models.models_config.BioModelConfig property) (cellmap_flow.models.models_config.CellMapModelConfig property) (cellmap_flow.models.models_config.DaCapoModelConfig property) (cellmap_flow.models.models_config.FlyModelConfig property) (cellmap_flow.models.models_config.ScriptModelConfig property) COMPLETED (cellmap_flow.utils.bsub_utils.JobStatus attribute) concat_along_c() (in module cellmap_flow.models.models_config) concurrency_limit (cellmap_flow.image_data_interface.ImageDataInterface attribute) config (cellmap_flow.blockwise.blockwise_processor.CellMapFlowBlockwiseProcessor attribute) (cellmap_flow.blockwise.CellMapFlowBlockwiseProcessor attribute) (cellmap_flow.models.models_config.ModelConfig property) Config (class in cellmap_flow.utils.serialize_config) cpu_workers (cellmap_flow.blockwise.blockwise_processor.CellMapFlowBlockwiseProcessor attribute) (cellmap_flow.blockwise.CellMapFlowBlockwiseProcessor attribute) create_and_run_app() (in module cellmap_flow.dashboard.app) create_bounding_boxes_interactive() (in module cellmap_flow.dashboard.bbx_generator) create_click_option_from_param() (in module cellmap_flow.utils.cli_utils) create_dynamic_command() (in module cellmap_flow.cli.cli) create_dynamic_server_command() (in module cellmap_flow.cli.server_cli) create_job_for_environment() (in module cellmap_flow.utils.job_extensions) create_model_config() (in module cellmap_flow.dashboard.app) cross_channels_mode (cellmap_flow.blockwise.blockwise_processor.CellMapFlowBlockwiseProcessor attribute) (cellmap_flow.blockwise.CellMapFlowBlockwiseProcessor attribute) CUSTOM_CODE_FOLDER (in module cellmap_flow.dashboard.app) custom_fill_value (cellmap_flow.image_data_interface.ImageDataInterface attribute)

D

DaCapoModelConfig (class in cellmap_flow.models.models_config) dataset_path (cellmap_flow.globals.Flow attribute) dataset_path_api() (in module cellmap_flow.dashboard.app) decode_to_json() (in module cellmap_flow.utils.web_utils) DEFAULT_AXES_NAMES (in module cellmap_flow.utils.serialize_config) DEFAULT_CHARGE_GROUP (in module cellmap_flow.utils.bsub_utils) DEFAULT_QUEUE (in module cellmap_flow.utils.bsub_utils) DEFAULT_SECURITY (in module cellmap_flow.utils.bsub_utils) DEFAULT_SERVER_QUEUE (in module cellmap_flow.utils.config_utils) DefaultPostprocessor (built-in class) (class in cellmap_flow.post.postprocessors) delete() (cellmap_flow.globals.Flow class method) description (cellmap_flow.models.cellmap_models.ModelMetadata attribute) deserialize_list() (in module cellmap_flow.norm.input_normalize) Dilate (class in cellmap_flow.norm.input_normalize) dims (cellmap_flow.utils.scale_pyramid.ScalePyramid attribute)

DISALLOWED_FUNCTIONS (in module cellmap_flow.utils.load_py) DISALLOWED_IMPORTS (in module cellmap_flow.utils.load_py) dtype (cellmap_flow.blockwise.blockwise_processor.CellMapFlowBlockwiseProcessor attribute) (cellmap_flow.blockwise.CellMapFlowBlockwiseProcessor attribute) (cellmap_flow.norm.input_normalize.EuclideanDistance property) (cellmap_flow.norm.input_normalize.LambdaNormalizer property) (cellmap_flow.norm.input_normalize.MinMaxNormalizer property) (cellmap_flow.norm.input_normalize.SerializableInterface property) (cellmap_flow.norm.input_normalize.ZScoreNormalizer property) (cellmap_flow.post.postprocessors.AffinityPostprocessor property) (cellmap_flow.post.postprocessors.DefaultPostprocessor property) (cellmap_flow.post.postprocessors.LabelPostprocessor property) (cellmap_flow.post.postprocessors.LambdaPostprocessor property) (cellmap_flow.post.postprocessors.MortonSegmentationRelabeling property) (cellmap_flow.post.postprocessors.SimpleBlockwiseMerger property) (cellmap_flow.post.postprocessors.ThresholdPostprocessor property) (PostProcessor attribute)

E

emit() (cellmap_flow.dashboard.app.LogHandler method) encode_to_str() (in module cellmap_flow.utils.web_utils) ends_with_scale() (in module cellmap_flow.utils.ds) equivalences (cellmap_flow.post.postprocessors.SimpleBlockwiseMerger attribute)

EuclideanDistance (class in cellmap_flow.norm.input_normalize) expression (cellmap_flow.norm.input_normalize.LambdaNormalizer attribute) (cellmap_flow.post.postprocessors.LambdaPostprocessor attribute) extract_host_from_output() (in module cellmap_flow.utils.bsub_utils)

F

face_erosion_iterations (cellmap_flow.post.postprocessors.SimpleBlockwiseMerger attribute) FAILED (cellmap_flow.utils.bsub_utils.JobStatus attribute) finalize_bbx_generation() (in module cellmap_flow.dashboard.app) find_closest_scale() (in module cellmap_flow.utils.ds) find_target_scale() (in module cellmap_flow.utils.ds)

fix_all() (in module cellmap_flow.utils.generate_neuroglancer) Flow (class in cellmap_flow.globals) FlyModelConfig (class in cellmap_flow.models.models_config) folder_path (cellmap_flow.models.cellmap_models.CellmapModel attribute) format_output_bioimage() (in module cellmap_flow.models.models_config) framework (cellmap_flow.models.cellmap_models.ModelMetadata attribute)

G

g (in module cellmap_flow.globals) generate_blockwise_task() (in module cellmap_flow.dashboard.app) generate_neuroglancer() (in module cellmap_flow.utils.generate_neuroglancer) generate_neuroglancer_url() (in module cellmap_flow.utils.neuroglancer_utils) generate_singlescale_metadata() (in module cellmap_flow.utils.ds) get() (cellmap_flow.utils.serialize_config.Config method) get_all_model_configs() (in module cellmap_flow.models.model_registry) (in module cellmap_flow.utils.cli_utils) get_all_subclasses() (in module cellmap_flow.utils.cli_utils) get_array_path_if_needed() (in module cellmap_flow.utils.ds) get_available_models() (in module cellmap_flow.dashboard.app) get_axes_and_dims() (cellmap_flow.models.models_config.BioModelConfig method) get_bbox_json_template() (in module cellmap_flow.dashboard.app) get_bbx_generator_status() (in module cellmap_flow.dashboard.app) get_blockwise_tasks_dir() (in module cellmap_flow.dashboard.app) get_ds_info() (in module cellmap_flow.utils.ds) get_encoded_subvolume() (cellmap_flow.utils.scale_pyramid.ScalePyramid method) get_free_port() (in module cellmap_flow.utils.web_utils) get_input_normalizers() (in module cellmap_flow.norm.input_normalize) get_input_slicer() (cellmap_flow.models.models_config.BioModelConfig method) get_model_config_types() (in module cellmap_flow.dashboard.app) get_model_merger() (in module cellmap_flow.models.model_merger) get_model_mergers_list() (in module cellmap_flow.models.model_merger)

get_model_type_mapping() (in module cellmap_flow.utils.config_utils) get_normalizations() (in module cellmap_flow.norm.input_normalize) get_norms_post_args() (in module cellmap_flow.utils.web_utils) get_object_mesh() (cellmap_flow.utils.scale_pyramid.ScalePyramid method) get_output_dtype() (cellmap_flow.globals.Flow method) get_parameter_info() (in module cellmap_flow.models.model_registry) get_postprocessors() (in module cellmap_flow.post.postprocessors) get_postprocessors_list() (in module cellmap_flow.post.postprocessors) get_process_dataset() (in module cellmap_flow.utils.serilization_utils) get_process_dataset_url() (in module cellmap_flow.utils.serilization_utils) get_public_ip() (in module cellmap_flow.utils.web_utils) get_raw_layer() (in module cellmap_flow.utils.scale_pyramid) get_scale_info() (in module cellmap_flow.utils.ds) get_spatial_dims() (cellmap_flow.models.models_config.BioModelConfig method) get_status() (cellmap_flow.utils.bsub_utils.Job method) (cellmap_flow.utils.bsub_utils.LocalJob method) (cellmap_flow.utils.bsub_utils.LSFJob method) (cellmap_flow.utils.job_extensions.AWSBatchJob method) (cellmap_flow.utils.job_extensions.AzureBatchJob method) (cellmap_flow.utils.job_extensions.GoogleCloudJob method) (cellmap_flow.utils.job_extensions.SlurmJob method) get_url() (in module cellmap_flow.utils.ds) GoogleCloudJob (class in cellmap_flow.utils.job_extensions)

H

host (cellmap_flow.utils.bsub_utils.Job attribute)

I

idi_raw (cellmap_flow.blockwise.blockwise_processor.CellMapFlowBlockwiseProcessor attribute) (cellmap_flow.blockwise.CellMapFlowBlockwiseProcessor attribute) (cellmap_flow.server.CellMapFlowServer attribute) image_path (cellmap_flow.dashboard.bbx_generator.BBXGenerator attribute) ImageDataInterface (class in cellmap_flow.image_data_interface) in_channels (cellmap_flow.models.cellmap_models.ModelMetadata attribute) index() (in module cellmap_flow.dashboard.app) inference_input_shape (cellmap_flow.models.cellmap_models.ModelMetadata attribute) inference_output_shape (cellmap_flow.models.cellmap_models.ModelMetadata attribute) INFERENCE_SERVER (in module cellmap_flow.dashboard.app) inferencer (cellmap_flow.blockwise.blockwise_processor.CellMapFlowBlockwiseProcessor attribute) (cellmap_flow.blockwise.CellMapFlowBlockwiseProcessor attribute) (cellmap_flow.server.CellMapFlowServer attribute) Inferencer (class in cellmap_flow.inferencer) inferencers (cellmap_flow.blockwise.blockwise_processor.CellMapFlowBlockwiseProcessor attribute) (cellmap_flow.blockwise.CellMapFlowBlockwiseProcessor attribute) info (cellmap_flow.image_data_interface.ImageDataInterface property) info() (cellmap_flow.utils.scale_pyramid.ScalePyramid method) INPUT_NORM_DICT_KEY (in module cellmap_flow.utils.web_utils) input_norms (cellmap_flow.globals.Flow attribute) (in module cellmap_flow.globals) input_path (cellmap_flow.blockwise.blockwise_processor.CellMapFlowBlockwiseProcessor attribute) (cellmap_flow.blockwise.CellMapFlowBlockwiseProcessor attribute)

input_shape (cellmap_flow.models.cellmap_models.ModelMetadata attribute) input_size (cellmap_flow.models.models_config.FlyModelConfig attribute) input_voxel_size (cellmap_flow.blockwise.blockwise_processor.CellMapFlowBlockwiseProcessor attribute) (cellmap_flow.blockwise.CellMapFlowBlockwiseProcessor attribute) (cellmap_flow.models.cellmap_models.ModelMetadata attribute) (cellmap_flow.models.models_config.FlyModelConfig attribute) (cellmap_flow.server.CellMapFlowServer attribute) InputNormalizer (class in cellmap_flow.norm.input_normalize) instantiate_model_config() (in module cellmap_flow.models.model_registry) invalidate() (cellmap_flow.utils.scale_pyramid.ScalePyramid method) IP_PATTERN (in module cellmap_flow.utils.web_utils) is_bsub_available() (in module cellmap_flow.utils.bsub_utils) is_output_segmentation() (in module cellmap_flow.dashboard.app) is_running() (cellmap_flow.utils.bsub_utils.Job method) is_segmentation (cellmap_flow.post.postprocessors.AffinityPostprocessor property) (cellmap_flow.post.postprocessors.DefaultPostprocessor property) (cellmap_flow.post.postprocessors.LabelPostprocessor property) (cellmap_flow.post.postprocessors.MortonSegmentationRelabeling property) (cellmap_flow.post.postprocessors.PostProcessor property) (cellmap_flow.post.postprocessors.SimpleBlockwiseMerger property) (cellmap_flow.post.postprocessors.ThresholdPostprocessor property) (PostProcessor attribute) iteration (cellmap_flow.models.cellmap_models.ModelMetadata attribute) (cellmap_flow.models.models_config.DaCapoModelConfig attribute)

J

Job (class in cellmap_flow.utils.bsub_utils) job_id (cellmap_flow.utils.bsub_utils.LSFJob attribute) (cellmap_flow.utils.job_extensions.AWSBatchJob attribute) (cellmap_flow.utils.job_extensions.AzureBatchJob attribute) (cellmap_flow.utils.job_extensions.GoogleCloudJob attribute) (cellmap_flow.utils.job_extensions.SlurmJob attribute)

job_queue (cellmap_flow.utils.job_extensions.AWSBatchJob attribute) jobs (cellmap_flow.globals.Flow attribute) JobStatus (class in cellmap_flow.utils.bsub_utils)

K

keys_to_skip (cellmap_flow.post.postprocessors.SimpleBlockwiseMerger attribute) kill() (cellmap_flow.utils.bsub_utils.Job method) (cellmap_flow.utils.bsub_utils.LocalJob method) (cellmap_flow.utils.bsub_utils.LSFJob method) (cellmap_flow.utils.job_extensions.AWSBatchJob method) (cellmap_flow.utils.job_extensions.AzureBatchJob method) (cellmap_flow.utils.job_extensions.GoogleCloudJob method) (cellmap_flow.utils.job_extensions.SlurmJob method)

kill_n_remove_from_neuroglancer() (in module cellmap_flow.utils.web_utils) KILLED (cellmap_flow.utils.bsub_utils.JobStatus attribute) kwargs (cellmap_flow.utils.serialize_config.Config attribute)

L

LabelPostprocessor (built-in class) (class in cellmap_flow.post.postprocessors) LambdaNormalizer (class in cellmap_flow.norm.input_normalize) LambdaPostprocessor (built-in class) (class in cellmap_flow.post.postprocessors) LazyNormalization (class in cellmap_flow.utils.ds) list_cls_to_dict() (in module cellmap_flow.utils.web_utils) list_models() (cellmap_flow.models.cellmap_models.CellmapModels method) (in module cellmap_flow.cli.cli) (in module cellmap_flow.cli.server_cli) load_config() (in module cellmap_flow.utils.config_utils) load_eval_model() (cellmap_flow.models.models_config.FlyModelConfig method) load_input_information() (cellmap_flow.models.models_config.BioModelConfig method) load_output_information() (cellmap_flow.models.models_config.BioModelConfig method) load_safe_config() (in module cellmap_flow.utils.load_py) LocalJob (class in cellmap_flow.utils.bsub_utils) log_buffer (in module cellmap_flow.dashboard.app) log_clients (in module cellmap_flow.dashboard.app) log_handler (in module cellmap_flow.dashboard.app) logger (in module cellmap_flow.blockwise.blockwise_processor) (in module cellmap_flow.blockwise.cli) (in module cellmap_flow.blockwise.multiple_cli) (in module cellmap_flow.cli.cli) (in module cellmap_flow.cli.server_cli) (in module cellmap_flow.cli.yaml_cli) (in module cellmap_flow.dashboard.app) (in module cellmap_flow.dashboard.bbx_generator) (in module cellmap_flow.globals) (in module cellmap_flow.image_data_interface) (in module cellmap_flow.inferencer) (in module cellmap_flow.models.model_merger) (in module cellmap_flow.models.models_config) (in module cellmap_flow.models.run) (in module cellmap_flow.norm.input_normalize) (in module cellmap_flow.post.postprocessors) (in module cellmap_flow.server) (in module cellmap_flow.utils.bsub_utils) (in module cellmap_flow.utils.config_utils) (in module cellmap_flow.utils.ds) (in module cellmap_flow.utils.job_extensions) (in module cellmap_flow.utils.neuroglancer_utils) (in module cellmap_flow.utils.scale_pyramid) (in module cellmap_flow.utils.serilization_utils)

LogHandler (class in cellmap_flow.dashboard.app) LSFJob (class in cellmap_flow.utils.bsub_utils)

M

main() (in module cellmap_flow.cli.cli) (in module cellmap_flow.cli.server_cli) (in module cellmap_flow.cli.yaml_cli) max_value (cellmap_flow.norm.input_normalize.MinMaxNormalizer attribute) max_voxel_size (cellmap_flow.utils.scale_pyramid.ScalePyramid attribute) mean (cellmap_flow.norm.input_normalize.ZScoreNormalizer attribute) merge() (cellmap_flow.models.model_merger.AndModelMerger method) (cellmap_flow.models.model_merger.ModelMerger method) (cellmap_flow.models.model_merger.OrModelMerger method) (cellmap_flow.models.model_merger.SumModelMerger method) MERGE_MODE_MAP (in module cellmap_flow.models.model_merger) metadata (cellmap_flow.models.cellmap_models.CellmapModel property) min_value (cellmap_flow.norm.input_normalize.MinMaxNormalizer attribute) min_voxel_size (cellmap_flow.utils.scale_pyramid.ScalePyramid attribute) MinMaxNormalizer (class in cellmap_flow.norm.input_normalize) model (cellmap_flow.models.models_config.FlyModelConfig property) model_catalog (cellmap_flow.globals.Flow attribute) model_config (cellmap_flow.blockwise.blockwise_processor.CellMapFlowBlockwiseProcessor attribute) (cellmap_flow.blockwise.CellMapFlowBlockwiseProcessor attribute) (cellmap_flow.inferencer.Inferencer attribute) MODEL_CONFIG_CLASSES (in module cellmap_flow.models.model_registry) model_mode_str (cellmap_flow.blockwise.blockwise_processor.CellMapFlowBlockwiseProcessor attribute) (cellmap_flow.blockwise.CellMapFlowBlockwiseProcessor attribute) model_name (cellmap_flow.models.cellmap_models.ModelMetadata attribute) (cellmap_flow.models.models_config.BioModelConfig attribute) (cellmap_flow.utils.bsub_utils.Job attribute) model_type (cellmap_flow.models.cellmap_models.ModelMetadata attribute) ModelConfig (class in cellmap_flow.models.models_config) ModelMerger (class in cellmap_flow.models.model_merger) ModelMetadata (class in cellmap_flow.models.cellmap_models) models (cellmap_flow.blockwise.blockwise_processor.CellMapFlowBlockwiseProcessor attribute) (cellmap_flow.blockwise.CellMapFlowBlockwiseProcessor attribute) models_config (cellmap_flow.globals.Flow attribute) module cellmap_flow cellmap_flow.blockwise cellmap_flow.blockwise.blockwise_processor cellmap_flow.blockwise.cli cellmap_flow.blockwise.multiple_cli cellmap_flow.cli cellmap_flow.cli.cli cellmap_flow.cli.server_cli cellmap_flow.cli.yaml_cli cellmap_flow.dashboard cellmap_flow.dashboard.app cellmap_flow.dashboard.bbx_generator cellmap_flow.globals cellmap_flow.image_data_interface cellmap_flow.inferencer cellmap_flow.models cellmap_flow.models.cellmap_models cellmap_flow.models.model_merger cellmap_flow.models.model_registry cellmap_flow.models.models_config cellmap_flow.models.run cellmap_flow.norm cellmap_flow.norm.input_normalize cellmap_flow.post cellmap_flow.post.postprocessors cellmap_flow.server cellmap_flow.utils cellmap_flow.utils.bsub_utils cellmap_flow.utils.cli_utils cellmap_flow.utils.config_utils cellmap_flow.utils.ds cellmap_flow.utils.generate_neuroglancer cellmap_flow.utils.import_utils cellmap_flow.utils.job_extensions cellmap_flow.utils.load_py cellmap_flow.utils.neuroglancer_utils cellmap_flow.utils.scale_pyramid cellmap_flow.utils.serialize_config cellmap_flow.utils.serilization_utils cellmap_flow.utils.web_utils

MortonSegmentationRelabeling (built-in class) (class in cellmap_flow.post.postprocessors) multiplier (cellmap_flow.post.postprocessors.DefaultPostprocessor attribute)

N

name (cellmap_flow.models.models_config.BioModelConfig attribute) (cellmap_flow.models.models_config.CellMapModelConfig attribute) (cellmap_flow.models.models_config.DaCapoModelConfig attribute) (cellmap_flow.models.models_config.FlyModelConfig attribute) (cellmap_flow.models.models_config.ScriptModelConfig attribute) name() (cellmap_flow.norm.input_normalize.SerializableInterface class method) (PostProcessor method) nb_cores_master (cellmap_flow.globals.Flow attribute) nb_cores_worker (cellmap_flow.globals.Flow attribute)

nb_workers (cellmap_flow.globals.Flow attribute) neighborhood (cellmap_flow.post.postprocessors.AffinityPostprocessor attribute) neuroglancer_thread (cellmap_flow.globals.Flow attribute) NEUROGLANCER_URL (in module cellmap_flow.dashboard.app) normalize (cellmap_flow.image_data_interface.ImageDataInterface attribute) num_boxes (cellmap_flow.dashboard.bbx_generator.BBXGenerator attribute) num_channels (cellmap_flow.post.postprocessors.AffinityPostprocessor property) (cellmap_flow.post.postprocessors.ChannelSelection property) num_previous_segments (cellmap_flow.post.postprocessors.AffinityPostprocessor attribute) (cellmap_flow.post.postprocessors.MortonSegmentationRelabeling attribute)

O

offset (cellmap_flow.image_data_interface.ImageDataInterface attribute) onnx_model (cellmap_flow.models.cellmap_models.CellmapModel property) open_ds_tensorstore() (in module cellmap_flow.utils.ds) optimize_model() (cellmap_flow.inferencer.Inferencer method) OrModelMerger (class in cellmap_flow.models.model_merger) ort (in module cellmap_flow.models.cellmap_models) out_channels (cellmap_flow.models.cellmap_models.ModelMetadata attribute) output_arrays (cellmap_flow.blockwise.blockwise_processor.CellMapFlowBlockwiseProcessor attribute) (cellmap_flow.blockwise.CellMapFlowBlockwiseProcessor attribute) output_channels (cellmap_flow.server.CellMapFlowServer attribute) output_channels_is_dict (cellmap_flow.blockwise.blockwise_processor.CellMapFlowBlockwiseProcessor attribute) (cellmap_flow.blockwise.CellMapFlowBlockwiseProcessor attribute)

output_dtype (cellmap_flow.models.models_config.ModelConfig property) (cellmap_flow.server.CellMapFlowServer attribute) output_path (cellmap_flow.blockwise.blockwise_processor.CellMapFlowBlockwiseProcessor attribute) (cellmap_flow.blockwise.CellMapFlowBlockwiseProcessor attribute) output_shape (cellmap_flow.models.cellmap_models.ModelMetadata attribute) output_size (cellmap_flow.models.models_config.FlyModelConfig attribute) output_voxel_size (cellmap_flow.blockwise.blockwise_processor.CellMapFlowBlockwiseProcessor attribute) (cellmap_flow.blockwise.CellMapFlowBlockwiseProcessor attribute) (cellmap_flow.models.cellmap_models.ModelMetadata attribute) (cellmap_flow.models.models_config.FlyModelConfig attribute) (cellmap_flow.server.CellMapFlowServer attribute)

P

parallel (cellmap_flow.norm.input_normalize.EuclideanDistance attribute) parse_comma_separated_values() (in module cellmap_flow.utils.cli_utils) parse_type_annotation() (in module cellmap_flow.utils.cli_utils) path (cellmap_flow.image_data_interface.ImageDataInterface attribute) PENDING (cellmap_flow.utils.bsub_utils.JobStatus attribute) pipeline_builder() (in module cellmap_flow.dashboard.app) pipeline_edges (cellmap_flow.globals.Flow attribute) pipeline_inputs (cellmap_flow.globals.Flow attribute) pipeline_models (cellmap_flow.globals.Flow attribute) pipeline_normalizers (cellmap_flow.globals.Flow attribute) pipeline_outputs (cellmap_flow.globals.Flow attribute) pipeline_postprocessors (cellmap_flow.globals.Flow attribute) pool_id (cellmap_flow.utils.job_extensions.AzureBatchJob attribute) postprocess (cellmap_flow.globals.Flow attribute) (in module cellmap_flow.globals) POSTPROCESS_DICT_KEY (in module cellmap_flow.utils.web_utils) postprocessing_lock (in module cellmap_flow.post.postprocessors) PostProcessor (built-in class) (class in cellmap_flow.post.postprocessors)

PostProcessorMethods (in module cellmap_flow.post.postprocessors) precheck_blockwise_task() (in module cellmap_flow.dashboard.app) predict() (in module cellmap_flow.inferencer) previous_refresh_time (cellmap_flow.server.CellMapFlowServer attribute) print_available_models() (in module cellmap_flow.utils.cli_utils) process (cellmap_flow.utils.bsub_utils.LocalJob attribute) process() (cellmap_flow.norm.input_normalize.SerializableInterface method) (in module cellmap_flow.dashboard.app) (PostProcessor method) process_chunk() (cellmap_flow.inferencer.Inferencer method) process_chunk_basic() (cellmap_flow.inferencer.Inferencer method) process_chunk_bioimage() (in module cellmap_flow.models.models_config) process_constructor_args() (in module cellmap_flow.utils.cli_utils) process_fn() (cellmap_flow.blockwise.blockwise_processor.CellMapFlowBlockwiseProcessor method) (cellmap_flow.blockwise.CellMapFlowBlockwiseProcessor method) process_only (cellmap_flow.blockwise.blockwise_processor.CellMapFlowBlockwiseProcessor attribute) (cellmap_flow.blockwise.CellMapFlowBlockwiseProcessor attribute) project_id (cellmap_flow.utils.job_extensions.GoogleCloudJob attribute) pytorch_model (cellmap_flow.models.cellmap_models.CellmapModel property)

Q

queue (cellmap_flow.blockwise.blockwise_processor.CellMapFlowBlockwiseProcessor attribute) (cellmap_flow.blockwise.CellMapFlowBlockwiseProcessor attribute) (cellmap_flow.globals.Flow attribute)

R

raw (cellmap_flow.globals.Flow attribute) readme (cellmap_flow.models.cellmap_models.CellmapModel property) refresh_dataset() (cellmap_flow.server.CellMapFlowServer method) refresh_rate_seconds (cellmap_flow.server.CellMapFlowServer attribute) region (cellmap_flow.utils.job_extensions.GoogleCloudJob attribute) register_all_model_commands() (in module cellmap_flow.cli.cli) register_all_server_commands() (in module cellmap_flow.cli.server_cli) regularize_offset() (in module cellmap_flow.utils.ds) reorder_axes() (in module cellmap_flow.models.models_config) root_dir (cellmap_flow.models.cellmap_models.CellmapModels attribute) run() (cellmap_flow.blockwise.blockwise_processor.CellMapFlowBlockwiseProcessor method) (cellmap_flow.blockwise.CellMapFlowBlockwiseProcessor method) (cellmap_flow.globals.Flow class method) (cellmap_flow.server.CellMapFlowServer method)

run_generic() (in module cellmap_flow.cli.cli) run_locally() (in module cellmap_flow.utils.bsub_utils) run_model() (in module cellmap_flow.models.run) run_multiple() (in module cellmap_flow.cli.yaml_cli) run_name (cellmap_flow.models.models_config.DaCapoModelConfig attribute) run_server() (in module cellmap_flow.cli.server_cli) run_ui_server() (in module cellmap_flow.cli.server_cli) RUNNING (cellmap_flow.utils.bsub_utils.JobStatus attribute)

S

scale (cellmap_flow.models.models_config.BioModelConfig attribute) (cellmap_flow.models.models_config.CellMapModelConfig attribute) (cellmap_flow.models.models_config.DaCapoModelConfig attribute) (cellmap_flow.models.models_config.FlyModelConfig attribute) (cellmap_flow.models.models_config.ScriptModelConfig attribute) ScalePyramid (class in cellmap_flow.utils.scale_pyramid) script_path (cellmap_flow.models.models_config.ScriptModelConfig attribute) ScriptModelConfig (class in cellmap_flow.models.models_config) separate_store_path() (in module cellmap_flow.utils.ds) separate_zarrs (cellmap_flow.blockwise.blockwise_processor.CellMapFlowBlockwiseProcessor attribute) (cellmap_flow.blockwise.CellMapFlowBlockwiseProcessor attribute) SerializableInterface (class in cellmap_flow.norm.input_normalize) serialize() (cellmap_flow.utils.serialize_config.Config method) serialize_norms_posts_to_json() (in module cellmap_flow.utils.serilization_utils) SERVER_COMMAND (in module cellmap_flow.utils.bsub_utils) servers (cellmap_flow.globals.Flow attribute) show() (in module cellmap_flow.utils.neuroglancer_utils) SimpleBlockwiseMerger (built-in class) (class in cellmap_flow.post.postprocessors)

size (cellmap_flow.norm.input_normalize.Dilate attribute) slices (cellmap_flow.post.postprocessors.SimpleBlockwiseMerger attribute) SlurmJob (class in cellmap_flow.utils.job_extensions) spatial_dims (cellmap_flow.models.cellmap_models.ModelMetadata attribute) spawn_worker() (in module cellmap_flow.blockwise.blockwise_processor) split_dataset_path() (in module cellmap_flow.utils.ds) start_bbx_generator() (in module cellmap_flow.dashboard.app) start_hosts() (in module cellmap_flow.utils.bsub_utils) start_viewer() (cellmap_flow.dashboard.bbx_generator.BBXGenerator method) static_dir (in module cellmap_flow.dashboard.app) status (cellmap_flow.utils.bsub_utils.Job attribute) std (cellmap_flow.norm.input_normalize.ZScoreNormalizer attribute) stop() (cellmap_flow.globals.Flow class method) stream_logs() (in module cellmap_flow.dashboard.app) submit_blockwise_task() (in module cellmap_flow.dashboard.app) submit_bsub_job() (in module cellmap_flow.utils.bsub_utils) submit_models() (in module cellmap_flow.dashboard.app) SumModelMerger (class in cellmap_flow.models.model_merger)

T

task_name (cellmap_flow.blockwise.blockwise_processor.CellMapFlowBlockwiseProcessor attribute) (cellmap_flow.blockwise.CellMapFlowBlockwiseProcessor attribute) template_dir (in module cellmap_flow.dashboard.app) threshold (cellmap_flow.post.postprocessors.ThresholdPostprocessor attribute) ThresholdPostprocessor (built-in class) (class in cellmap_flow.post.postprocessors) tmp_dir (cellmap_flow.blockwise.blockwise_processor.CellMapFlowBlockwiseProcessor attribute) (cellmap_flow.blockwise.CellMapFlowBlockwiseProcessor attribute) (cellmap_flow.globals.Flow attribute) to_dict() (cellmap_flow.globals.Flow method) (cellmap_flow.models.models_config.BioModelConfig method) (cellmap_flow.models.models_config.CellMapModelConfig method) (cellmap_flow.models.models_config.DaCapoModelConfig method) (cellmap_flow.models.models_config.FlyModelConfig method) (cellmap_flow.models.models_config.ModelConfig method) (cellmap_flow.models.models_config.ScriptModelConfig method) (cellmap_flow.norm.input_normalize.SerializableInterface method) (cellmap_flow.utils.serialize_config.Config method) (PostProcessor method)

to_ndarray_tensorstore() (in module cellmap_flow.utils.ds) to_ndarray_ts() (cellmap_flow.image_data_interface.ImageDataInterface method) token (cellmap_flow.utils.scale_pyramid.ScalePyramid property) torch (in module cellmap_flow.models.cellmap_models) ts (cellmap_flow.image_data_interface.ImageDataInterface property) ts_dataset (cellmap_flow.utils.ds.LazyNormalization attribute) ts_model (cellmap_flow.models.cellmap_models.CellmapModel property)

U

update_equivalences() (in module cellmap_flow.dashboard.app) update_run_models() (in module cellmap_flow.models.run) use_exact (cellmap_flow.post.postprocessors.AffinityPostprocessor attribute) (cellmap_flow.post.postprocessors.MortonSegmentationRelabeling attribute) (cellmap_flow.post.postprocessors.SimpleBlockwiseMerger attribute)

use_half_prediction (cellmap_flow.inferencer.Inferencer attribute)

V

validate_blockwise() (in module cellmap_flow.dashboard.app) validate_pipeline() (in module cellmap_flow.dashboard.app) validate_pipeline_config() (in module cellmap_flow.dashboard.app) verbose (cellmap_flow.dashboard.bbx_generator.BBXGenerator attribute) version (cellmap_flow.models.cellmap_models.ModelMetadata attribute) viewer (cellmap_flow.dashboard.bbx_generator.BBXGenerator attribute) (cellmap_flow.globals.Flow attribute) (in module cellmap_flow.globals)

vol_shape (cellmap_flow.server.CellMapFlowServer attribute) volume_layers (cellmap_flow.utils.scale_pyramid.ScalePyramid attribute) volume_type (cellmap_flow.utils.scale_pyramid.ScalePyramid property) voxel_size (cellmap_flow.models.models_config.BioModelConfig attribute) voxels_to_process (cellmap_flow.models.models_config.BioModelConfig attribute)

W

wait_for_boxes() (cellmap_flow.dashboard.bbx_generator.BBXGenerator method) wait_for_host() (cellmap_flow.utils.bsub_utils.Job method) (cellmap_flow.utils.bsub_utils.LocalJob method) (cellmap_flow.utils.bsub_utils.LSFJob method) (cellmap_flow.utils.job_extensions.AWSBatchJob method) (cellmap_flow.utils.job_extensions.AzureBatchJob method) (cellmap_flow.utils.job_extensions.GoogleCloudJob method) (cellmap_flow.utils.job_extensions.SlurmJob method)

workers (cellmap_flow.blockwise.blockwise_processor.CellMapFlowBlockwiseProcessor attribute) (cellmap_flow.blockwise.CellMapFlowBlockwiseProcessor attribute)

Y

yaml_config (cellmap_flow.blockwise.blockwise_processor.CellMapFlowBlockwiseProcessor attribute) (cellmap_flow.blockwise.CellMapFlowBlockwiseProcessor attribute)

Z

zarr_block_shape (cellmap_flow.server.CellMapFlowServer attribute)

ZScoreNormalizer (class in cellmap_flow.norm.input_normalize)