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) anisotropy (cellmap_flow.norm.input_normalize.EuclideanDistance attribute)

app (cellmap_flow.server.CellMapFlowServer attribute) (in module cellmap_flow.dashboard.app) AppInput (class in cellmap_flow.models.model_app_config) apply_norms() (in module cellmap_flow.utils.ds) apply_postprocess() (in module cellmap_flow.inferencer) ARGS_KEY (in module cellmap_flow.utils.web_utils) author (cellmap_flow.models.cellmap_models.ModelMetadata attribute)

B

bias (cellmap_flow.post.postprocessors.AffinityPostprocessor attribute) (cellmap_flow.post.postprocessors.DefaultPostprocessor attribute) bioimage() (in module cellmap_flow.cli.cli) (in module cellmap_flow.cli.server_cli) BioModelConfig (class in cellmap_flow.utils.data)

black_border (cellmap_flow.norm.input_normalize.EuclideanDistance attribute) block_shape (cellmap_flow.blockwise.blockwise_processor.CellMapFlowBlockwiseProcessor attribute) (cellmap_flow.blockwise.CellMapFlowBlockwiseProcessor attribute) (cellmap_flow.server.DummyConfig attribute) 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.cli module cellmap_flow.cli.cli module cellmap_flow.cli.fly_model module cellmap_flow.cli.multiple_cli module cellmap_flow.cli.multiple_yaml_cli module cellmap_flow.cli.server_cli module cellmap_flow.dashboard module cellmap_flow.dashboard.app 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_app_config module cellmap_flow.models.model_yaml 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.config_utils module cellmap_flow.utils.data module cellmap_flow.utils.ds module cellmap_flow.utils.import_utils module cellmap_flow.utils.load_py module

cellmap_flow.utils.neuroglancer_utils module cellmap_flow.utils.scale_pyramid module cellmap_flow.utils.serilization_utils module cellmap_flow.utils.web_utils module cellmap_model (cellmap_flow.utils.data.CellMapModelConfig attribute) cellmap_model() (in module cellmap_flow.cli.cli) (in module cellmap_flow.cli.server_cli) 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.utils.data) 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.post.postprocessors.ChannelSelection attribute) (cellmap_flow.utils.data.FlyModelConfig 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) (in module cellmap_flow.cli.fly_model) charge_group_arg (in module cellmap_flow.cli.multiple_cli) check_config() (in module cellmap_flow.utils.data) 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.utils.data.FlyModelConfig attribute) chunk_encoder (cellmap_flow.server.CellMapFlowServer attribute) chunk_slice_position_to_coords_id_dict (cellmap_flow.post.postprocessors.SimpleBlockwiseMerger attribute) cleanup() (in module cellmap_flow.utils.bsub_utils) cli() (in module cellmap_flow.blockwise.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) command (cellmap_flow.utils.data.BioModelConfig property) (cellmap_flow.utils.data.CellMapModelConfig property) (cellmap_flow.utils.data.DaCapoModelConfig property) (cellmap_flow.utils.data.FlyModelConfig property) (cellmap_flow.utils.data.ScriptModelConfig property) concat_along_c() (in module cellmap_flow.utils.data) concurrency_limit (cellmap_flow.image_data_interface.ImageDataInterface attribute) config (cellmap_flow.blockwise.blockwise_processor.CellMapFlowBlockwiseProcessor attribute) (cellmap_flow.blockwise.CellMapFlowBlockwiseProcessor attribute) (cellmap_flow.utils.data.ModelConfig property) Config (class in cellmap_flow.utils.data) (class in cellmap_flow.utils.load_py) create_and_run_app() (in module cellmap_flow.dashboard.app) custom_fill_value (cellmap_flow.image_data_interface.ImageDataInterface attribute) CustomCodeFolder (in module cellmap_flow.dashboard.app)

D

dacapo() (in module cellmap_flow.cli.cli) (in module cellmap_flow.cli.server_cli) DaCapoModelConfig (class in cellmap_flow.utils.data) data_args (in module cellmap_flow.cli.multiple_cli) decode_to_json() (in module cellmap_flow.utils.web_utils) DEFAULT_SERVER_QUEUE (in module cellmap_flow.cli.multiple_cli) (in module cellmap_flow.utils.config_utils) default_value (cellmap_flow.models.model_app_config.FileInput attribute) (cellmap_flow.models.model_app_config.ListInput attribute) (cellmap_flow.models.model_app_config.SelectInput attribute) (cellmap_flow.models.model_app_config.TextInput attribute) 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) (cellmap_flow.models.model_app_config.FileInput attribute) (cellmap_flow.models.model_app_config.ListInput attribute) (cellmap_flow.models.model_app_config.SelectInput attribute) (cellmap_flow.models.model_app_config.TextInput 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) DummyConfig (class in cellmap_flow.server)

E

elemns (cellmap_flow.models.model_app_config.MyModelConfig attribute) 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) extra_args (in module cellmap_flow.cli.multiple_cli)

F

face_erosion_iterations (cellmap_flow.post.postprocessors.SimpleBlockwiseMerger attribute) FileInput (class in cellmap_flow.models.model_app_config) filetype (cellmap_flow.image_data_interface.ImageDataInterface attribute) find_target_scale() (in module cellmap_flow.utils.ds) Flow (class in cellmap_flow.globals)

fly() (in module cellmap_flow.cli.server_cli) FlyModelConfig (class in cellmap_flow.utils.data) folder_path (cellmap_flow.models.cellmap_models.CellmapModel attribute) format_output_bioimage() (in module cellmap_flow.utils.data) framework (cellmap_flow.models.cellmap_models.ModelMetadata attribute)

G

g (in module cellmap_flow.globals) generate_neuroglancer_url() (in module cellmap_flow.utils.neuroglancer_utils) get_axes_and_dims() (cellmap_flow.utils.data.BioModelConfig method) get_dacapo_channels() (in module cellmap_flow.utils.data) get_dacapo_run_model() (in module cellmap_flow.utils.data) 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_host_from_stdout() (in module cellmap_flow.utils.bsub_utils) get_input_normalizers() (in module cellmap_flow.norm.input_normalize) get_input_slicer() (cellmap_flow.utils.data.BioModelConfig method) 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_postprocessors() (in module cellmap_flow.post.postprocessors) get_postprocessors_list() (in module cellmap_flow.post.postprocessors) get_process_dataset() (in module cellmap_flow.server) (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.utils.data.BioModelConfig method) get_url() (in module cellmap_flow.utils.ds)

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) 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) info() (cellmap_flow.utils.scale_pyramid.ScalePyramid method) INPUT_NORM_DICT_KEY (in module cellmap_flow.utils.web_utils) input_norms (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.utils.data.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.server.CellMapFlowServer attribute) (cellmap_flow.utils.data.FlyModelConfig attribute) InputNormalizer (class in cellmap_flow.norm.input_normalize) 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_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.utils.data.DaCapoModelConfig attribute)

J

Job (class in cellmap_flow.utils.bsub_utils)

job_id (cellmap_flow.utils.bsub_utils.Job attribute)

K

keys_to_skip (cellmap_flow.post.postprocessors.SimpleBlockwiseMerger attribute)

kill() (cellmap_flow.utils.bsub_utils.Job method) kill_n_remove_from_neuroglancer() (in module cellmap_flow.utils.web_utils)

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) ListInput (class in cellmap_flow.models.model_app_config) load_config() (in module cellmap_flow.utils.config_utils) load_eval_model() (in module cellmap_flow.utils.data) load_input_information() (cellmap_flow.utils.data.BioModelConfig method) load_model_paths() (in module cellmap_flow.models.model_yaml) load_output_information() (cellmap_flow.utils.data.BioModelConfig method) load_safe_config() (in module cellmap_flow.utils.load_py) logger (in module cellmap_flow.blockwise.blockwise_processor) (in module cellmap_flow.blockwise.cli) (in module cellmap_flow.cli.cli), [1] (in module cellmap_flow.cli.multiple_cli) (in module cellmap_flow.cli.multiple_yaml_cli) (in module cellmap_flow.cli.server_cli) (in module cellmap_flow.dashboard.app) (in module cellmap_flow.inferencer) (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), [1] (in module cellmap_flow.utils.config_utils) (in module cellmap_flow.utils.data) (in module cellmap_flow.utils.ds) (in module cellmap_flow.utils.neuroglancer_utils) (in module cellmap_flow.utils.scale_pyramid) (in module cellmap_flow.utils.serilization_utils)

M

main() (in module cellmap_flow.cli.fly_model) (in module cellmap_flow.cli.multiple_cli) (in module cellmap_flow.cli.multiple_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) 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.utils.data.FlyModelConfig property) model_config (cellmap_flow.blockwise.blockwise_processor.CellMapFlowBlockwiseProcessor attribute) (cellmap_flow.blockwise.CellMapFlowBlockwiseProcessor attribute) (cellmap_flow.inferencer.Inferencer attribute) model_name (cellmap_flow.models.cellmap_models.ModelMetadata attribute) (cellmap_flow.utils.bsub_utils.Job attribute) (cellmap_flow.utils.data.BioModelConfig attribute) model_type (cellmap_flow.models.cellmap_models.ModelMetadata attribute) ModelConfig (class in cellmap_flow.utils.data) ModelDashboardConfig (class in cellmap_flow.models.model_app_config) ModelMetadata (class in cellmap_flow.models.cellmap_models) module cellmap_flow cellmap_flow.blockwise cellmap_flow.blockwise.blockwise_processor cellmap_flow.blockwise.cli cellmap_flow.cli cellmap_flow.cli.cli cellmap_flow.cli.fly_model cellmap_flow.cli.multiple_cli cellmap_flow.cli.multiple_yaml_cli cellmap_flow.cli.server_cli cellmap_flow.dashboard cellmap_flow.dashboard.app cellmap_flow.globals cellmap_flow.image_data_interface cellmap_flow.inferencer cellmap_flow.models cellmap_flow.models.cellmap_models cellmap_flow.models.model_app_config cellmap_flow.models.model_yaml 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.config_utils cellmap_flow.utils.data cellmap_flow.utils.ds cellmap_flow.utils.import_utils cellmap_flow.utils.load_py cellmap_flow.utils.neuroglancer_utils cellmap_flow.utils.scale_pyramid 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) MyModelConfig (class in cellmap_flow.models.model_app_config)

N

n5_block_shape (cellmap_flow.server.CellMapFlowServer attribute) name (cellmap_flow.models.model_app_config.FileInput attribute) (cellmap_flow.models.model_app_config.ListInput attribute) (cellmap_flow.models.model_app_config.SelectInput attribute) (cellmap_flow.models.model_app_config.TextInput attribute) (cellmap_flow.utils.data.BioModelConfig attribute) (cellmap_flow.utils.data.CellMapModelConfig attribute) (cellmap_flow.utils.data.DaCapoModelConfig attribute) (cellmap_flow.utils.data.FlyModelConfig attribute) (cellmap_flow.utils.data.ScriptModelConfig attribute)

name() (cellmap_flow.norm.input_normalize.SerializableInterface class method) (PostProcessor method) neighborhood (cellmap_flow.post.postprocessors.AffinityPostprocessor attribute) NEUROGLANCER_URL (in module cellmap_flow.dashboard.app) normalize (cellmap_flow.image_data_interface.ImageDataInterface attribute) normalize() (cellmap_flow.norm.input_normalize.ZScoreNormalizer method) 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) options (cellmap_flow.models.model_app_config.ListInput attribute) (cellmap_flow.models.model_app_config.SelectInput attribute) 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.blockwise.blockwise_processor.CellMapFlowBlockwiseProcessor attribute) (cellmap_flow.blockwise.CellMapFlowBlockwiseProcessor attribute) (cellmap_flow.server.CellMapFlowServer attribute) (cellmap_flow.server.DummyConfig attribute)

output_dtype (cellmap_flow.utils.data.ModelConfig property) 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.utils.data.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.server.CellMapFlowServer attribute) (cellmap_flow.server.DummyConfig attribute) (cellmap_flow.utils.data.FlyModelConfig attribute)

P

parallel (cellmap_flow.norm.input_normalize.EuclideanDistance attribute) parse_bpeek_output() (in module cellmap_flow.utils.bsub_utils) parse_model_configs() (in module cellmap_flow.utils.data) path (cellmap_flow.image_data_interface.ImageDataInterface attribute) postprocess (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) predict() (in module cellmap_flow.inferencer)

previous_refresh_time (cellmap_flow.server.CellMapFlowServer attribute) process (cellmap_flow.utils.bsub_utils.Job 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.utils.data) process_chunk_bioimage_test() (in module cellmap_flow.utils.data) process_fn() (cellmap_flow.blockwise.blockwise_processor.CellMapFlowBlockwiseProcessor method) (cellmap_flow.blockwise.CellMapFlowBlockwiseProcessor method) pytorch_model (cellmap_flow.models.cellmap_models.CellmapModel property)

Q

queue (cellmap_flow.blockwise.blockwise_processor.CellMapFlowBlockwiseProcessor attribute) (cellmap_flow.blockwise.CellMapFlowBlockwiseProcessor attribute) (in module cellmap_flow.cli.fly_model)

R

read_block_shape (cellmap_flow.server.CellMapFlowServer attribute) readme (cellmap_flow.models.cellmap_models.CellmapModel property) refresh_rate_seconds (cellmap_flow.server.CellMapFlowServer attribute) regularize_offset() (in module cellmap_flow.utils.ds) reorder_axes() (in module cellmap_flow.utils.data) 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) (in module cellmap_flow.blockwise.cli) (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.multiple_cli) (in module cellmap_flow.cli.multiple_yaml_cli) run_name (cellmap_flow.utils.data.DaCapoModelConfig attribute) run_server() (in module cellmap_flow.cli.server_cli) run_ui_server() (in module cellmap_flow.cli.server_cli)

S

scale (cellmap_flow.utils.data.CellMapModelConfig attribute) (cellmap_flow.utils.data.ScriptModelConfig attribute) ScalePyramid (class in cellmap_flow.utils.scale_pyramid) script() (in module cellmap_flow.cli.cli) (in module cellmap_flow.cli.server_cli) script_path (cellmap_flow.utils.data.ScriptModelConfig attribute) script_server_check() (in module cellmap_flow.cli.cli) ScriptModelConfig (class in cellmap_flow.utils.data) security (in module cellmap_flow.utils.bsub_utils) SelectInput (class in cellmap_flow.models.model_app_config) separate_store_path() (in module cellmap_flow.utils.ds) SerializableInterface (class in cellmap_flow.norm.input_normalize) serialize_norms_posts_to_json() (in module cellmap_flow.utils.serilization_utils) SERVER_COMMAND (in module cellmap_flow.utils.bsub_utils) server_queue_arg (in module cellmap_flow.cli.multiple_cli)

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) 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_hosts() (in module cellmap_flow.utils.bsub_utils) status (cellmap_flow.utils.bsub_utils.Job attribute) std (cellmap_flow.norm.input_normalize.ZScoreNormalizer attribute) stop() (cellmap_flow.globals.Flow class method) submit_bsub_job() (in module cellmap_flow.utils.bsub_utils) submit_models() (in module cellmap_flow.dashboard.app) swap_axes (cellmap_flow.image_data_interface.ImageDataInterface attribute)

T

task_name (cellmap_flow.blockwise.blockwise_processor.CellMapFlowBlockwiseProcessor attribute) (cellmap_flow.blockwise.CellMapFlowBlockwiseProcessor attribute) TextInput (class in cellmap_flow.models.model_app_config) threshold (cellmap_flow.post.postprocessors.ThresholdPostprocessor attribute) ThresholdPostprocessor (built-in class) (class in cellmap_flow.post.postprocessors) to_dict() (cellmap_flow.globals.Flow method) (cellmap_flow.norm.input_normalize.SerializableInterface 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

version (cellmap_flow.models.cellmap_models.ModelMetadata attribute) viewer (in module cellmap_flow.globals) volume_layers (cellmap_flow.utils.scale_pyramid.ScalePyramid attribute)

volume_type (cellmap_flow.utils.scale_pyramid.ScalePyramid property) voxel_size (cellmap_flow.utils.data.BioModelConfig attribute) voxels_to_process (cellmap_flow.utils.data.BioModelConfig attribute)

W

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

ZScoreNormalizer (class in cellmap_flow.norm.input_normalize)