Index

_

__call__() (PostProcessor method)

_process() (PostProcessor method)

A

activation (cellmap_flow.norm.input_normalize.EuclideanDistance attribute) actual_voxel_size (cellmap_flow.image_data_interface.ImageDataInterface attribute) AdaptationStrategy (class in cellmap_flow.finetune.adaptation) ADAPTER_CONFIG (in module cellmap_flow.models.resolve) add() (cellmap_flow.finetune.job_manager.listener.Listeners method) (in module cellmap_flow.cli.add_cli) (in module cellmap_flow.inference.timing) add_annotation_layer() (in module cellmap_flow.dashboard.routes.finetune.overlay) add_crop_to_viewer() (in module cellmap_flow.dashboard.routes.finetune.overlay) add_finetuned_layer() (in module cellmap_flow.dashboard.finetune_layers) add_image_layer_to_viewer() (in module cellmap_flow.dashboard.routes.finetune.layers) add_listener() (cellmap_flow.finetune.job_manager.manager.FinetuneJobManager method) add_model() (in module cellmap_flow.dashboard.routes.model_resolve) add_segmentation_layer_to_viewer() (in module cellmap_flow.dashboard.routes.finetune.layers) AddModel (class in cellmap_flow.dashboard.routes.model_resolve) AffinityPostprocessor (built-in class) (class in cellmap_flow.post.postprocessors) AffinityTargetTransform (class in cellmap_flow.finetune.target_transforms) aliases() (in module cellmap_flow.models.envs) aliases_file() (in module cellmap_flow.models.envs) ALIASES_FILE_ENV (in module cellmap_flow.models.envs) alpha (cellmap_flow.finetune.adaptation.LoraStrategy attribute) amp_dtype (cellmap_flow.finetune.lora_trainer.LoRAFinetuner attribute) analyze_script() (in module cellmap_flow.plugins) ANCHOR_SHARE (in module cellmap_flow.finetune.data.sampler) AndModelMerger (class in cellmap_flow.models.model_merger) anisotropy (cellmap_flow.norm.input_normalize.EuclideanDistance attribute) annotated_chunks (cellmap_flow.finetune.data.sampler.PatchSampler attribute) annotation() (cellmap_flow.finetune.data.reader.PatchReader method) annotation_dtype_for() (in module cellmap_flow.dashboard.routes.finetune.common) ANNOTATION_TOOL_BINDINGS (in module cellmap_flow.dashboard.routes.finetune.overlay) annotation_volumes (cellmap_flow.dashboard.state.Session attribute) app (cellmap_flow.server.CellMapFlowServer attribute) (cellmap_flow.serving.chunkmirage_server.ChunkmirageServer attribute) (in module cellmap_flow.cli.aliases) (in module cellmap_flow.dashboard.app) applied_restarts (cellmap_flow.finetune.session_loop.TrainingSession attribute)

apply_at() (cellmap_flow.serving.chunkmirage_ops.InferenceOp method) (cellmap_flow.serving.chunkmirage_ops.PostprocessOp method) apply_finetune() (in module cellmap_flow.finetune.export_merged) apply_norms() (in module cellmap_flow.image_data_interface) apply_pipeline() (in module cellmap_flow.dashboard.routes.pipeline) apply_postprocess() (in module cellmap_flow.inferencer) apply_restart_params() (in module cellmap_flow.finetune.cli) apply_sigmoid (cellmap_flow.finetune.losses.DiceLoss attribute) (cellmap_flow.finetune.losses.MarginLoss attribute) apply_viewer_defaults() (in module cellmap_flow.viewer.bootstrap) args (cellmap_flow.finetune.session_loop.TrainingSession attribute) ARGS_KEY (in module cellmap_flow.serving.protocol) argv (cellmap_flow.jobs.spec.JobSpec attribute) ARRAY_ATTRIBUTES (in module cellmap_flow.norm.safe_expression) ARRAY_METHODS (in module cellmap_flow.norm.safe_expression) ArrayMeta (class in cellmap_flow.io.metadata) ArraySource (class in cellmap_flow.io.source) as_bool() (in module cellmap_flow.post.segment) as_connectivity() (in module cellmap_flow.post.segment) as_dict() (cellmap_flow.jobs.settings.LauncherSettings method) as_logits() (in module cellmap_flow.finetune.losses) as_probabilities() (in module cellmap_flow.finetune.losses) attrs_from_meta() (in module cellmap_flow.io.metadata) augment (cellmap_flow.dashboard.requests.FinetuneSubmit attribute) (cellmap_flow.finetune.data.dataset.VirtualPatchDataset attribute) (cellmap_flow.finetune.data.VirtualPatchDataset attribute) augmentation (cellmap_flow.finetune.data.dataset.VirtualPatchDataset attribute) (cellmap_flow.finetune.data.VirtualPatchDataset attribute) Augmentation (class in cellmap_flow.finetune.data.augment) auto_serve (cellmap_flow.dashboard.requests.FinetuneSubmit attribute) autocast_dtype (cellmap_flow.inference.runner.ModelRunner attribute) autodetect_output_type() (in module cellmap_flow.dashboard.routes.finetune.common) available() (in module cellmap_flow.jobs.lsf) axes (cellmap_flow.io.metadata.ArrayMeta attribute) (cellmap_flow.server.CellMapFlowServer attribute) (cellmap_flow.serving.chunkmirage_server.ChunkmirageServer attribute) axes_names (cellmap_flow.models.configs.base.Config attribute) (cellmap_flow.models.models_config.Config attribute)

B

balance_classes (cellmap_flow.dashboard.requests.FinetuneSubmit attribute) (cellmap_flow.finetune.lora_trainer.LoRAFinetuner attribute) (cellmap_flow.finetune.losses.IntervalLoss attribute) (cellmap_flow.finetune.losses.MarginLoss attribute) balanced_mean() (in module cellmap_flow.finetune.losses) base_model_config (cellmap_flow.models.configs.finetune.FinetuneModelConfig property) (cellmap_flow.models.models_config.FinetuneModelConfig property) base_model_dict (cellmap_flow.models.configs.finetune.FinetuneModelConfig attribute) (cellmap_flow.models.models_config.FinetuneModelConfig attribute) batch_size (cellmap_flow.dashboard.requests.FinetuneSubmit attribute) (cellmap_flow.models.configs.cellpose.CellposeModelConfig attribute) (cellmap_flow.models.models_config.CellposeModelConfig attribute) BatchLoopWrapper (class in cellmap_flow.finetune.lora_wrapper) BBOX_LAYER_NAME (in module cellmap_flow.dashboard.routes.bbx_generator) bbx_bp (in module cellmap_flow.dashboard.routes.bbx_generator) bbx_generator_state (cellmap_flow.dashboard.state.Session attribute) BbxGenerator (class in cellmap_flow.dashboard.requests) bce_loss (cellmap_flow.finetune.losses.CombinedLoss attribute) bce_weight (cellmap_flow.finetune.losses.CombinedLoss attribute) begin (cellmap_flow.io.geometry.Box attribute) best_loss (cellmap_flow.finetune.lora_trainer.LoRAFinetuner attribute) bg_ids (cellmap_flow.finetune.crop_loader.CropEntry attribute) bias (cellmap_flow.post.postprocessors.AffinityPostprocessor attribute) (cellmap_flow.post.postprocessors.DefaultPostprocessor attribute) BinaryTargetTransform (class in cellmap_flow.finetune.target_transforms) BIOIMAGE_CACHE_DIR (in module cellmap_flow.models.bioimage_catalog) BIOIMAGE_CACHE_FILE (in module cellmap_flow.models.bioimage_catalog) bioimage_entry() (in module cellmap_flow.models.bioimage_catalog) bioimage_job_name() (in module cellmap_flow.dashboard.services.launch) bioimage_params() (in module cellmap_flow.models.resolve) BioimageSelection (class in cellmap_flow.dashboard.requests) BioModelConfig (class in cellmap_flow.models.configs.bio) (class in cellmap_flow.models.models_config) block (cellmap_flow.serving.chunkmirage_ops.BlockInput attribute) (cellmap_flow.serving.chunkmirage_ops.ServedModel attribute) block_shape (cellmap_flow.blockwise.blockwise_processor.CellMapFlowBlockwiseProcessor attribute) block_shape() (cellmap_flow.models.geometry.ModelGeometry method) block_start (cellmap_flow.serving.chunkmirage_ops.BlockInput attribute) BlockInput (class in cellmap_flow.serving.chunkmirage_ops) blockwise (in module cellmap_flow.cli.aliases) blockwise_bp (in module cellmap_flow.dashboard.routes.blockwise) blockwise_config (cellmap_flow.dashboard.requests.BlockwisePipeline attribute)

blockwise_config_api() (in module cellmap_flow.dashboard.routes.pipeline) blockwise_multiple (in module cellmap_flow.cli.aliases) blockwise_tasks_dir (cellmap_flow.dashboard.requests.BlockwiseSettings attribute) (cellmap_flow.dashboard.state.Session attribute) BlockwiseConfigNode (class in cellmap_flow.dashboard.requests) BlockwiseGenerate (class in cellmap_flow.dashboard.requests) BlockwisePipeline (class in cellmap_flow.dashboard.requests) BlockwisePrecheck (class in cellmap_flow.dashboard.requests) BlockwiseSettings (class in cellmap_flow.dashboard.requests) BlockwiseSubmit (class in cellmap_flow.dashboard.requests) BlockwiseTaskSettings (class in cellmap_flow.dashboard.requests) BlockwiseValidate (class in cellmap_flow.dashboard.requests) BLOSC (in module cellmap_flow.serving.virtual_zarr) bounding_boxes (cellmap_flow.blockwise.blockwise_processor.CellMapFlowBlockwiseProcessor attribute) BoundingBox (class in cellmap_flow.dashboard.requests) bounds_term() (cellmap_flow.finetune.losses.IntervalLoss method) Box (class in cellmap_flow.io.geometry) box_to_world() (cellmap_flow.io.geometry.Grid method) box_voxels() (in module cellmap_flow.finetune.session.fill) BroadcastBinaryTargetTransform (class in cellmap_flow.finetune.target_transforms) bsub_argv() (in module cellmap_flow.jobs.lsf) bsub_timeout_seconds (cellmap_flow.jobs.site.SiteProfile attribute) BSUB_TIMEOUT_SECONDS (in module cellmap_flow.jobs.lsf) BsubTimeoutError bucket_key() (in module cellmap_flow.finetune.session.instance) build() (cellmap_flow.pipeline_spec.PipelineSpec method) build_arg_parser() (in module cellmap_flow.finetune.cli) build_command() (in module cellmap_flow.finetune.job_manager.submit) build_corrections() (in module cellmap_flow.finetune.build_corrections) build_extra_layers() (in module cellmap_flow.cli.yaml_cli) build_here() (in module cellmap_flow.models.geometry_cache) build_index() (in module cellmap_flow.review_index) build_manifest() (in module cellmap_flow.finetune.session.volume) build_model() (in module cellmap_flow.models.registry) build_models() (in module cellmap_flow.models.registry) build_restart_params() (in module cellmap_flow.dashboard.routes.finetune.common) build_target_transform() (in module cellmap_flow.finetune.cli) builder (cellmap_flow.dashboard.routes.pipeline.PipelineUpdate attribute) builder_model_configs (cellmap_flow.dashboard.state.Session attribute) builder_state (cellmap_flow.dashboard.state.Session property) builder_steps() (in module cellmap_flow.pipeline_spec) BuilderCanvas (class in cellmap_flow.dashboard.routes.pipeline)

C

cache (cellmap_flow.serving.chunkmirage_ops.InferenceOp attribute) cache_bytes (cellmap_flow.image_data_interface.ImageDataInterface attribute) (cellmap_flow.io.source.ArraySource attribute) CACHE_FORMAT (in module cellmap_flow.models.bioimage_catalog) cache_key() (in module cellmap_flow.models.geometry_cache) CACHE_PATH (in module cellmap_flow.models.geometry_cache) cache_token() (cellmap_flow.serving.chunkmirage_ops.InferenceOp method) CACHE_TTL_SECONDS (in module cellmap_flow.jobs.queues) cached (cellmap_flow.jobs.settings.LauncherSettings attribute) calculate_equivalences() (cellmap_flow.post.postprocessors.SimpleBlockwiseMerger method) can_restart() (in module cellmap_flow.finetune.job_manager.state) cancel_job() (cellmap_flow.finetune.job_manager.manager.FinetuneJobManager method) (in module cellmap_flow.dashboard.routes.finetune.training) cancel_requested (cellmap_flow.finetune.job_manager.state.FinetuneJob attribute) CANCELLED (cellmap_flow.finetune.job_manager.state.JobStatus attribute) candidates() (in module cellmap_flow.jobs.queues) cc3d_relabel() (in module cellmap_flow.finetune.session.instance) cc3d_relabel_annotation() (in module cellmap_flow.dashboard.routes.finetune.instance_correction) 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.add_cli module cellmap_flow.cli.aliases module cellmap_flow.cli.cli module cellmap_flow.cli.common module cellmap_flow.cli.doctor module cellmap_flow.cli.envs_cli module cellmap_flow.cli.infer module cellmap_flow.cli.main module cellmap_flow.cli.server_cli module cellmap_flow.cli.viewer_cli module cellmap_flow.cli.yaml_cli module cellmap_flow.config module cellmap_flow.config.yaml module cellmap_flow.dashboard module cellmap_flow.dashboard.app module cellmap_flow.dashboard.finetune_layers module cellmap_flow.dashboard.finetune_utils module cellmap_flow.dashboard.progress module cellmap_flow.dashboard.requests module cellmap_flow.dashboard.routes module cellmap_flow.dashboard.routes.bbx_generator module cellmap_flow.dashboard.routes.blockwise module cellmap_flow.dashboard.routes.finetune module cellmap_flow.dashboard.routes.finetune.annotation_core module cellmap_flow.dashboard.routes.finetune.annotation_sessions module cellmap_flow.dashboard.routes.finetune.blueprint module cellmap_flow.dashboard.routes.finetune.common module cellmap_flow.dashboard.routes.finetune.good_regions module cellmap_flow.dashboard.routes.finetune.instance_correction module cellmap_flow.dashboard.routes.finetune.layers module cellmap_flow.dashboard.routes.finetune.overlay module cellmap_flow.dashboard.routes.finetune.training module cellmap_flow.dashboard.routes.finetune.view_labels module cellmap_flow.dashboard.routes.finetune.yaml_crops module cellmap_flow.dashboard.routes.index_page module cellmap_flow.dashboard.routes.logging_routes module cellmap_flow.dashboard.routes.model_advice module cellmap_flow.dashboard.routes.model_resolve module cellmap_flow.dashboard.routes.models module cellmap_flow.dashboard.routes.pipeline module cellmap_flow.dashboard.routes.pipeline_builder_page module cellmap_flow.dashboard.routes.review_routes module cellmap_flow.dashboard.services module cellmap_flow.dashboard.services.launch module cellmap_flow.dashboard.services.startup module cellmap_flow.dashboard.state module cellmap_flow.finetune module cellmap_flow.finetune.adaptation module cellmap_flow.finetune.build_corrections module cellmap_flow.finetune.cli module cellmap_flow.finetune.crop_loader module cellmap_flow.finetune.data module cellmap_flow.finetune.data.augment module cellmap_flow.finetune.data.dataset module cellmap_flow.finetune.data.loader module cellmap_flow.finetune.data.reader module cellmap_flow.finetune.data.sampler module cellmap_flow.finetune.export_merged module cellmap_flow.finetune.finetune_cli module cellmap_flow.finetune.finetuned_model_templates module cellmap_flow.finetune.instance_flows module cellmap_flow.finetune.job_manager module cellmap_flow.finetune.job_manager.listener module cellmap_flow.finetune.job_manager.manager module cellmap_flow.finetune.job_manager.monitor module cellmap_flow.finetune.job_manager.persistence module cellmap_flow.finetune.job_manager.restart module cellmap_flow.finetune.job_manager.state module cellmap_flow.finetune.job_manager.submit module cellmap_flow.finetune.job_manager.tailer module cellmap_flow.finetune.json_files module cellmap_flow.finetune.lora_trainer module cellmap_flow.finetune.lora_wrapper module cellmap_flow.finetune.losses module cellmap_flow.finetune.markers module cellmap_flow.finetune.model_loading module cellmap_flow.finetune.run_outputs module cellmap_flow.finetune.session module cellmap_flow.finetune.session.fill module cellmap_flow.finetune.session.instance module cellmap_flow.finetune.session.manifest module cellmap_flow.finetune.session.minio module cellmap_flow.finetune.session.store module cellmap_flow.finetune.session.sync module cellmap_flow.finetune.session.volume module cellmap_flow.finetune.session_loop module cellmap_flow.finetune.target_transforms module cellmap_flow.finetune.trainable module cellmap_flow.globals module cellmap_flow.image_data_interface module cellmap_flow.inference module cellmap_flow.inference.runner module cellmap_flow.inference.timing module cellmap_flow.inferencer module cellmap_flow.io module cellmap_flow.io.geometry module cellmap_flow.io.metadata module cellmap_flow.io.multiscale module cellmap_flow.io.ome module cellmap_flow.io.paths module cellmap_flow.io.resample module cellmap_flow.io.source module cellmap_flow.io.store module cellmap_flow.jobs module cellmap_flow.jobs.launch module cellmap_flow.jobs.local module cellmap_flow.jobs.lsf module cellmap_flow.jobs.queues module cellmap_flow.jobs.ready module cellmap_flow.jobs.settings module cellmap_flow.jobs.site module cellmap_flow.jobs.spec module cellmap_flow.jobs.synced_tee module cellmap_flow.logging_setup module cellmap_flow.models module cellmap_flow.models.bioimage_catalog module cellmap_flow.models.configs module cellmap_flow.models.configs.base module cellmap_flow.models.configs.bio module cellmap_flow.models.configs.cellmap module cellmap_flow.models.configs.cellpose module

cellmap_flow.models.configs.dacapo module cellmap_flow.models.configs.finetune module cellmap_flow.models.configs.fly module cellmap_flow.models.configs.huggingface module cellmap_flow.models.configs.script module cellmap_flow.models.envs module cellmap_flow.models.geometry module cellmap_flow.models.geometry_cache module cellmap_flow.models.hf_catalog module cellmap_flow.models.model_merger module cellmap_flow.models.model_registry module cellmap_flow.models.models_config module cellmap_flow.models.registry module cellmap_flow.models.resolve module cellmap_flow.norm module cellmap_flow.norm.input_normalize module cellmap_flow.norm.safe_expression module cellmap_flow.pipeline_spec module cellmap_flow.plugins module cellmap_flow.post module cellmap_flow.post.postprocessors module cellmap_flow.post.segment module cellmap_flow.process_chain module cellmap_flow.review module cellmap_flow.review_index module cellmap_flow.server module cellmap_flow.serving module cellmap_flow.serving.chunkmirage_ops module cellmap_flow.serving.chunkmirage_server module cellmap_flow.serving.client module cellmap_flow.serving.engine module cellmap_flow.serving.launch module cellmap_flow.serving.probe module cellmap_flow.serving.protocol module cellmap_flow.serving.restart_token module cellmap_flow.serving.virtual_zarr module cellmap_flow.utils module cellmap_flow.utils.bsub_utils module cellmap_flow.utils.serialize_config module cellmap_flow.viewer module cellmap_flow.viewer.bootstrap module cellmap_flow.viewer.layers module cellmap_flow.viewer.raw module CELLMAP_HF_ORG (in module cellmap_flow.serving.probe) cellmap_model (cellmap_flow.models.configs.cellmap.CellMapModelConfig attribute) (cellmap_flow.models.models_config.CellMapModelConfig attribute) CELLMAP_MODEL_DIR (in module cellmap_flow.serving.probe) CellMapFlowBlockwiseProcessor (class in cellmap_flow.blockwise.blockwise_processor) CellMapFlowGroup (class in cellmap_flow.cli.main) CellMapFlowServer (class in cellmap_flow.server) CellMapModelConfig (class in cellmap_flow.models.configs.cellmap) (class in cellmap_flow.models.models_config) CELLPOSE_CELL_CHANNEL (in module cellmap_flow.dashboard.routes.finetune.view_labels) CELLPOSE_DIAMETER (in module cellmap_flow.models.configs.cellpose) cellpose_flows() (in module cellmap_flow.finetune.instance_flows) cellpose_job_name() (in module cellmap_flow.dashboard.services.launch) CELLPOSE_MODELS (in module cellmap_flow.dashboard.services.launch) cellpose_panel_data() (in module cellmap_flow.dashboard.routes.index_page) cellpose_panel_names() (in module cellmap_flow.dashboard.routes.index_page) CellposeMasksPostprocessor (built-in class) (class in cellmap_flow.post.postprocessors) CellposeModelConfig (class in cellmap_flow.models.configs.cellpose) (class in cellmap_flow.models.models_config) CellposeSelection (class in cellmap_flow.dashboard.requests) cellprob_threshold (cellmap_flow.models.configs.cellpose.CellposeModelConfig attribute) (cellmap_flow.models.models_config.CellposeModelConfig attribute) (cellmap_flow.post.postprocessors.CellposeMasksPostprocessor attribute) chain() (cellmap_flow.image_data_interface.LazyNormalization method) CHAIN_CACHE_SIZE (in module cellmap_flow.server) chain_for() (cellmap_flow.server.CellMapFlowServer method) chain_is_segmentation() (in module cellmap_flow.pipeline_spec) chain_items() (in module cellmap_flow.dashboard.routes.index_page) chain_num_channels() (in module cellmap_flow.pipeline_spec) chain_output_dtype() (in module cellmap_flow.pipeline_spec) ChainNode (class in cellmap_flow.dashboard.requests) channel (cellmap_flow.norm.input_normalize.ChannelSelector attribute) (cellmap_flow.post.postprocessors.LabelPostprocessor attribute) (cellmap_flow.post.postprocessors.MortonSegmentationRelabeling attribute) (cellmap_flow.post.postprocessors.SimpleBlockwiseMerger attribute) channel_axis (cellmap_flow.io.metadata.ArrayMeta property) CHANNEL_AXIS_NAMES (in module cellmap_flow.io.ome) channel_dim (cellmap_flow.finetune.trainable.ScaleLinear attribute) channel_names (cellmap_flow.models.geometry.ModelGeometry attribute) channel_names_of() (in module cellmap_flow.models.geometry) channels (cellmap_flow.blockwise.blockwise_processor.CellMapFlowBlockwiseProcessor attribute) (cellmap_flow.models.configs.fly.FlyModelConfig attribute) (cellmap_flow.models.models_config.FlyModelConfig attribute) (cellmap_flow.post.postprocessors.ChannelSelection attribute) ChannelSelection (built-in class) (class in cellmap_flow.post.postprocessors) ChannelSelector (class in cellmap_flow.norm.input_normalize) charge_group (cellmap_flow.blockwise.blockwise_processor.CellMapFlowBlockwiseProcessor attribute) (cellmap_flow.dashboard.requests.BlockwiseSettings attribute) (cellmap_flow.dashboard.requests.BlockwiseTaskSettings attribute) (cellmap_flow.dashboard.requests.FinetuneSubmit attribute) (cellmap_flow.jobs.spec.JobSpec attribute) check() (in module cellmap_flow.dashboard.requests) check_block() (in module cellmap_flow.blockwise.blockwise_processor) check_cmd() (in module cellmap_flow.cli.envs_cli) check_equivalence() (in module cellmap_flow.finetune.export_merged) check_export() (in module cellmap_flow.finetune.job_manager.persistence) check_output_shape() (cellmap_flow.models.configs.base.ModelConfig method) (cellmap_flow.models.models_config.ModelConfig method) check_server() (in module cellmap_flow.serving.engine) check_shapes_on_warmup (cellmap_flow.models.configs.base.ModelConfig attribute) (cellmap_flow.models.models_config.ModelConfig attribute) checkpoint() (cellmap_flow.finetune.adaptation.AdaptationStrategy method) (cellmap_flow.finetune.adaptation.FullStrategy method) (cellmap_flow.finetune.adaptation.LoraStrategy method) checkpoint_format() (in module cellmap_flow.models.configs.fly) checkpoint_path (cellmap_flow.dashboard.requests.FinetuneSubmit attribute) (cellmap_flow.models.configs.fly.FlyModelConfig attribute) (cellmap_flow.models.models_config.FlyModelConfig attribute) chunk_encoder (cellmap_flow.server.CellMapFlowServer attribute) chunk_encoder() (in module cellmap_flow.serving.virtual_zarr) CHUNK_KEY_RE (in module cellmap_flow.io.geometry) chunk_output_axes (cellmap_flow.models.configs.base.ModelConfig property) (cellmap_flow.models.geometry.ModelGeometry attribute) (cellmap_flow.models.models_config.ModelConfig property) chunk_roi() (in module cellmap_flow.serving.virtual_zarr) chunk_shape (cellmap_flow.io.metadata.ArrayMeta attribute) chunk_size (cellmap_flow.finetune.session.volume.VolumeGeometry attribute) chunk_slice_position_to_coords_id_dict (cellmap_flow.post.postprocessors.SimpleBlockwiseMerger attribute) chunk_version() (in module cellmap_flow.finetune.session.sync) ChunkCancelled CHUNKMIRAGE (in module cellmap_flow.viewer.layers) CHUNKMIRAGE_FORMAT (in module cellmap_flow.viewer.layers) ChunkmirageServer (class in cellmap_flow.serving.chunkmirage_server) CHUNKS_TIMED_AT_INFO (cellmap_flow.server.CellMapFlowServer attribute) claimed_input_voxel_size (cellmap_flow.finetune.session.volume.VolumeGeometry attribute) claimed_output_voxel_size (cellmap_flow.finetune.session.volume.VolumeGeometry attribute) class_name (cellmap_flow.dashboard.requests.CreateModelConfig attribute) classify_output_range() (in module cellmap_flow.serving.probe) cleanup_handler() (in module cellmap_flow.jobs.launch) cli() (in module cellmap_flow.blockwise.cli) (in module cellmap_flow.cli.main) (in module cellmap_flow.cli.server_cli) cli_name (cellmap_flow.models.configs.bio.BioModelConfig attribute) (cellmap_flow.models.configs.cellmap.CellMapModelConfig attribute) (cellmap_flow.models.configs.cellpose.CellposeModelConfig attribute) (cellmap_flow.models.configs.dacapo.DaCapoModelConfig attribute) (cellmap_flow.models.configs.finetune.FinetuneModelConfig attribute) (cellmap_flow.models.configs.fly.FlyModelConfig attribute) (cellmap_flow.models.configs.huggingface.HuggingFaceModelConfig attribute) (cellmap_flow.models.configs.script.ScriptModelConfig attribute) (cellmap_flow.models.models_config.BioModelConfig attribute) (cellmap_flow.models.models_config.CellMapModelConfig attribute) (cellmap_flow.models.models_config.CellposeModelConfig attribute) (cellmap_flow.models.models_config.DaCapoModelConfig attribute) (cellmap_flow.models.models_config.FinetuneModelConfig attribute) (cellmap_flow.models.models_config.FlyModelConfig attribute) (cellmap_flow.models.models_config.HuggingFaceModelConfig attribute) (cellmap_flow.models.models_config.ScriptModelConfig attribute) cli_name_of() (in module cellmap_flow.models.registry) click_options() (in module cellmap_flow.models.registry) client() (cellmap_flow.blockwise.blockwise_processor.CellMapFlowBlockwiseProcessor method) Clip (class in cellmap_flow.finetune.trainable) clip_max (cellmap_flow.post.postprocessors.DefaultPostprocessor attribute) clip_min (cellmap_flow.post.postprocessors.DefaultPostprocessor attribute) close() (cellmap_flow.dashboard.routes.review_routes.PickBoard method) (cellmap_flow.finetune.lora_trainer.LoRAFinetuner method) closed (cellmap_flow.dashboard.routes.review_routes.PickBoard attribute) closest_raw_scale() (in module cellmap_flow.io.multiscale) coarser_anywhere() (in module cellmap_flow.io.multiscale) coerce_cli_args() (in module cellmap_flow.models.registry) coerce_form_params() (in module cellmap_flow.models.registry) CombinedLoss (class in cellmap_flow.finetune.losses) command (cellmap_flow.models.configs.base.ModelConfig property) (cellmap_flow.models.models_config.ModelConfig property) command_argv() (in module cellmap_flow.models.configs.base) compile_expression() (in module cellmap_flow.norm.safe_expression) complete_job() (in module cellmap_flow.finetune.job_manager.monitor) COMPLETED (cellmap_flow.finetune.job_manager.state.JobStatus attribute) (cellmap_flow.jobs.spec.JobStatus attribute) concurrency_limit (cellmap_flow.image_data_interface.ImageDataInterface attribute) (cellmap_flow.io.source.ArraySource attribute) config (cellmap_flow.blockwise.blockwise_processor.CellMapFlowBlockwiseProcessor attribute) (cellmap_flow.dashboard.requests.ModelNode attribute) (cellmap_flow.models.configs.base.ModelConfig property) (cellmap_flow.models.models_config.ModelConfig property) Config (class in cellmap_flow.models.configs.base) (class in cellmap_flow.models.models_config) ConfigError configure_logging() (in module cellmap_flow.logging_setup) connected_components (cellmap_flow.finetune.crop_loader.CropEntry attribute) connected_components() (in module cellmap_flow.post.segment) CONNECTIVITIES (in module cellmap_flow.post.segment) connectivity (cellmap_flow.post.postprocessors.LabelPostprocessor attribute) context (cellmap_flow.inference.runner.ModelRunner attribute) (cellmap_flow.models.configs.bio.BioModelConfig attribute) (cellmap_flow.models.configs.cellpose.CellposeModelConfig attribute) (cellmap_flow.models.geometry.ModelGeometry property) (cellmap_flow.models.models_config.BioModelConfig attribute) (cellmap_flow.models.models_config.CellposeModelConfig attribute) CONTEXT (in module cellmap_flow.finetune.export_merged) coordinate_or_floats() (in module cellmap_flow.io.geometry) copy_chunks_parallel() (in module cellmap_flow.finetune.session.sync) corner_nm (cellmap_flow.finetune.data.reader.PatchReader attribute) corrections_path (cellmap_flow.dashboard.requests.FinetuneSubmit attribute) (cellmap_flow.finetune.job_manager.state.FinetuneJob attribute) count (cellmap_flow.finetune.job_manager.tailer.Iterations attribute) count_corrections() (in module cellmap_flow.finetune.job_manager.submit) count_instances() (in module cellmap_flow.review) cpu_state_copy() (in module cellmap_flow.finetune.adaptation) cpu_workers (cellmap_flow.blockwise.blockwise_processor.CellMapFlowBlockwiseProcessor attribute) cpus (cellmap_flow.jobs.spec.JobSpec attribute) create_and_run_app() (in module cellmap_flow.dashboard.app) create_annotation_volume() (in module cellmap_flow.dashboard.routes.finetune.annotation_core) create_dataloader() (in module cellmap_flow.finetune.data) (in module cellmap_flow.finetune.data.loader) create_dynamic_command() (in module cellmap_flow.cli.infer) create_dynamic_server_command() (in module cellmap_flow.cli.server_cli) create_instance_correction() (in module cellmap_flow.dashboard.routes.finetune.instance_correction) create_model_config() (in module cellmap_flow.dashboard.routes.models) create_volume_zarr() (in module cellmap_flow.finetune.session.volume) created_at (cellmap_flow.finetune.job_manager.state.FinetuneJob attribute) CreateModelConfig (class in cellmap_flow.dashboard.requests) CreateVolume (class in cellmap_flow.dashboard.requests) crop (cellmap_flow.finetune.trainable.Crop attribute) Crop (class in cellmap_flow.finetune.trainable) CropEntry (class in cellmap_flow.finetune.crop_loader) crops (cellmap_flow.finetune.crop_loader.CropsConfig attribute) CropsConfig (class in cellmap_flow.finetune.crop_loader) cross_channels_mode (cellmap_flow.blockwise.blockwise_processor.CellMapFlowBlockwiseProcessor attribute) CURRENT (in module cellmap_flow.models.envs) current_chain() (in module cellmap_flow.dashboard.routes.finetune.common) current_epoch (cellmap_flow.finetune.job_manager.state.FinetuneJob attribute) (cellmap_flow.finetune.lora_trainer.LoRAFinetuner attribute) current_site() (in module cellmap_flow.jobs.site) custom_fill_value (cellmap_flow.image_data_interface.ImageDataInterface attribute)

D

DACAPO_FRAMEWORKS (in module cellmap_flow.serving.probe) DaCapoModelConfig (class in cellmap_flow.models.configs.dacapo) (class in cellmap_flow.models.models_config) dashboard() (in module cellmap_flow.cli.main) dashboard_url (cellmap_flow.server.ServedChain attribute) dataloader (cellmap_flow.finetune.lora_trainer.LoRAFinetuner attribute) dataset (cellmap_flow.dashboard.requests.Equivalences attribute) dataset_from_manifest() (in module cellmap_flow.finetune.data) (in module cellmap_flow.finetune.data.loader) dataset_offset_nm (cellmap_flow.finetune.session.volume.VolumeGeometry attribute) dataset_path (cellmap_flow.dashboard.requests.BbxGenerator attribute) (cellmap_flow.dashboard.requests.SetData attribute) (cellmap_flow.dashboard.state.Session attribute) dataset_shape_voxels (cellmap_flow.finetune.session.volume.VolumeGeometry attribute) dataset_transforms() (in module cellmap_flow.io.metadata) db_path (cellmap_flow.dashboard.routes.review_routes.ReviewSession attribute) DB_SUFFIXES (in module cellmap_flow.review) decides_per_model() (in module cellmap_flow.models.envs) declared_block_shape (cellmap_flow.models.geometry.ModelGeometry attribute) declared_default() (in module cellmap_flow.models.envs) declared_output_type() (in module cellmap_flow.dashboard.routes.finetune.common) declared_voxel_size() (in module cellmap_flow.models.bioimage_catalog) decode_model_entry() (in module cellmap_flow.finetune.model_loading) decode_to_json() (in module cellmap_flow.serving.protocol) DEFAULT_AXES_NAMES (in module cellmap_flow.models.configs.base) DEFAULT_BATCH_SIZE (in module cellmap_flow.models.configs.cellpose) default_charge_group (cellmap_flow.jobs.site.SiteProfile attribute) DEFAULT_ENGINE (in module cellmap_flow.serving.engine) default_env (cellmap_flow.models.configs.base.ModelConfig attribute) (cellmap_flow.models.configs.bio.BioModelConfig attribute) (cellmap_flow.models.configs.cellpose.CellposeModelConfig attribute) (cellmap_flow.models.configs.finetune.FinetuneModelConfig property) (cellmap_flow.models.configs.fly.FlyModelConfig property) (cellmap_flow.models.models_config.BioModelConfig attribute) (cellmap_flow.models.models_config.CellposeModelConfig attribute) (cellmap_flow.models.models_config.FinetuneModelConfig property) (cellmap_flow.models.models_config.FlyModelConfig property) (cellmap_flow.models.models_config.ModelConfig attribute) DEFAULT_INPUT_NORM (in module cellmap_flow.finetune.build_corrections) DEFAULT_INPUT_SIZE (in module cellmap_flow.models.configs.bio) default_log_dir() (in module cellmap_flow.jobs.spec) DEFAULT_OUTPUT_AXES (in module cellmap_flow.models.geometry) default_queue (cellmap_flow.jobs.site.SiteProfile attribute) DEFAULT_QUEUES (in module cellmap_flow.review_index) DEFAULT_REGION_SIZE_NM (in module cellmap_flow.dashboard.routes.finetune.good_regions) DEFAULT_SLICES_PER_CHUNK (in module cellmap_flow.models.configs.bio) DEFAULT_TIMEOUT_SECONDS (in module cellmap_flow.serving.client) default_walltime (cellmap_flow.jobs.site.SiteProfile attribute) DefaultPostprocessor (built-in class) (class in cellmap_flow.post.postprocessors) delete_good_region() (in module cellmap_flow.dashboard.routes.finetune.good_regions) dense_to_sparse_ratio (cellmap_flow.finetune.crop_loader.CropsConfig attribute) (cellmap_flow.finetune.data.sampler.PatchSampler attribute) deprecated() (in module cellmap_flow.cli.common) deprecation_notice() (in module cellmap_flow.cli.common) describe_types() (in module cellmap_flow.models.registry)

deserialize_list() (in module cellmap_flow.norm.input_normalize) detail (cellmap_flow.cli.doctor.Result attribute) detect_adaptable_layers() (in module cellmap_flow.finetune.lora_wrapper) detect_sparse_annotations() (in module cellmap_flow.dashboard.routes.finetune.common) device_slots (cellmap_flow.inference.runner.ModelRunner attribute) DevicePostprocessOp (class in cellmap_flow.serving.chunkmirage_ops) DeviceSlots (class in cellmap_flow.inference.runner) diameter (cellmap_flow.models.configs.cellpose.CellposeModelConfig attribute) (cellmap_flow.models.models_config.CellposeModelConfig attribute) dice_loss (cellmap_flow.finetune.losses.CombinedLoss attribute) dice_weight (cellmap_flow.finetune.losses.CombinedLoss attribute) DiceLoss (class in cellmap_flow.finetune.losses) diff_and_sync_chunks() (in module cellmap_flow.finetune.session.sync) digest() (cellmap_flow.pipeline_spec.PipelineSpec method) Dilate (class in cellmap_flow.norm.input_normalize) dims (cellmap_flow.viewer.raw.ScalePyramid attribute) DINO_TILE_SIZE (in module cellmap_flow.models.configs.cellpose) DISALLOWED_FUNCTIONS (in module cellmap_flow.plugins) DISALLOWED_IMPORTS (in module cellmap_flow.plugins) display_channel (cellmap_flow.models.configs.base.ModelConfig attribute) (cellmap_flow.models.configs.cellpose.CellposeModelConfig property) (cellmap_flow.models.configs.finetune.FinetuneModelConfig property) (cellmap_flow.models.models_config.CellposeModelConfig property) (cellmap_flow.models.models_config.FinetuneModelConfig property) (cellmap_flow.models.models_config.ModelConfig attribute) display_channel() (in module cellmap_flow.viewer.layers) distance_bounds() (cellmap_flow.finetune.target_transforms.IntervalTargetTransform method) distance_watershed() (in module cellmap_flow.post.segment) DistanceTargetTransform (class in cellmap_flow.finetune.target_transforms) distillation_all_voxels (cellmap_flow.finetune.lora_trainer.LoRAFinetuner attribute) distillation_lambda (cellmap_flow.dashboard.requests.FinetuneSubmit attribute) (cellmap_flow.dashboard.routes.finetune.common.TrainingSettings attribute) (cellmap_flow.finetune.lora_trainer.LoRAFinetuner attribute) distillation_loss() (in module cellmap_flow.finetune.losses) distillation_scope (cellmap_flow.dashboard.requests.FinetuneSubmit attribute) draw() (cellmap_flow.finetune.data.sampler.PatchSampler method) dropout (cellmap_flow.finetune.adaptation.LoraStrategy attribute) dtype (cellmap_flow.blockwise.blockwise_processor.CellMapFlowBlockwiseProcessor attribute) (cellmap_flow.io.metadata.ArrayMeta 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.CellposeMasksPostprocessor property) (cellmap_flow.post.postprocessors.DefaultPostprocessor property) (cellmap_flow.post.postprocessors.FillHolesPostprocessor property) (cellmap_flow.post.postprocessors.LabelPostprocessor property) (cellmap_flow.post.postprocessors.LambdaPostprocessor property) (cellmap_flow.post.postprocessors.MortonSegmentationRelabeling property) (cellmap_flow.post.postprocessors.SigmoidPostprocessor property) (cellmap_flow.post.postprocessors.SimpleBlockwiseMerger property) (cellmap_flow.post.postprocessors.ThresholdPostprocessor property) (PostProcessor attribute) DTYPE_STRINGS (in module cellmap_flow.norm.safe_expression)

E

edges (cellmap_flow.dashboard.routes.pipeline.BuilderCanvas attribute) effective() (in module cellmap_flow.models.envs) effective_anchor_fraction (cellmap_flow.finetune.data.sampler.PatchSampler attribute) effective_dense_ratio (cellmap_flow.finetune.data.sampler.PatchSampler attribute) effective_env (cellmap_flow.models.configs.base.ModelConfig property) (cellmap_flow.models.models_config.ModelConfig property) effective_postprocess() (cellmap_flow.server.ServedChain method) effective_rehearsal_fraction (cellmap_flow.finetune.data.sampler.PatchSampler attribute) emit() (cellmap_flow.dashboard.routes.logging_routes.LogHandler method) (in module cellmap_flow.finetune.markers) emits_anchor (cellmap_flow.finetune.data.dataset.VirtualPatchDataset property) (cellmap_flow.finetune.data.VirtualPatchDataset property) encode_to_str() (in module cellmap_flow.serving.protocol) end (cellmap_flow.io.geometry.Box property) ENGINE (in module cellmap_flow.serving.chunkmirage_server) ENGINE_ENV (in module cellmap_flow.serving.engine) engine_name() (in module cellmap_flow.serving.engine) ENGINES (in module cellmap_flow.serving.engine) ensure_corrections_storage() (in module cellmap_flow.dashboard.routes.finetune.common) ensure_minio_serving() (in module cellmap_flow.dashboard.finetune_utils) ensure_serving() (cellmap_flow.finetune.session.minio.MinioServer method) entry (cellmap_flow.dashboard.routes.model_resolve.AddModel attribute) entry() (cellmap_flow.models.resolve.Resolved method) entry_model_id() (in module cellmap_flow.models.bioimage_catalog) entry_yaml() (in module cellmap_flow.cli.add_cli) env (cellmap_flow.jobs.spec.JobSpec attribute) (cellmap_flow.models.configs.base.ModelConfig attribute) (cellmap_flow.models.configs.finetune.FinetuneModelConfig property) (cellmap_flow.models.models_config.FinetuneModelConfig property) (cellmap_flow.models.models_config.ModelConfig attribute) (cellmap_flow.models.resolve.Resolved attribute), [1]

ENV_KEY (in module cellmap_flow.models.registry) envs_group() (in module cellmap_flow.cli.envs_cli) EPOCH_START_RE (in module cellmap_flow.finetune.markers) EPOCH_SUMMARY_RE (in module cellmap_flow.finetune.markers) equivalences (cellmap_flow.dashboard.requests.Equivalences attribute) (cellmap_flow.post.postprocessors.SimpleBlockwiseMerger attribute) Equivalences (class in cellmap_flow.dashboard.requests) EQUIVALENCES_EVERY_SECONDS (in module cellmap_flow.serving.chunkmirage_ops) equivalences_json() (cellmap_flow.post.postprocessors.SimpleBlockwiseMerger method) EQUIVALENCES_TIMEOUT_SECONDS (in module cellmap_flow.server) (in module cellmap_flow.serving.chunkmirage_ops) EuclideanDistance (class in cellmap_flow.norm.input_normalize) existing_bounding_boxes (cellmap_flow.dashboard.requests.BbxGenerator attribute) exists() (in module cellmap_flow.io.store) exists_now() (in module cellmap_flow.jobs.spec) export() (cellmap_flow.finetune.adaptation.AdaptationStrategy method) (cellmap_flow.finetune.adaptation.FullStrategy method) (cellmap_flow.finetune.adaptation.LoraStrategy method) export_config() (in module cellmap_flow.dashboard.routes.models) export_folder() (in module cellmap_flow.finetune.export_merged) export_name (cellmap_flow.finetune.adaptation.AdaptationStrategy attribute) (cellmap_flow.finetune.adaptation.FullStrategy attribute) (cellmap_flow.finetune.adaptation.LoraStrategy attribute) expression (cellmap_flow.norm.input_normalize.LambdaNormalizer attribute) (cellmap_flow.post.postprocessors.LambdaPostprocessor attribute) extra_layer_entries() (in module cellmap_flow.cli.yaml_cli) EXTRA_LAYER_TYPES (in module cellmap_flow.cli.yaml_cli) extra_layers (cellmap_flow.dashboard.state.Session attribute) extract_data_path_from_corrections() (in module cellmap_flow.finetune.job_manager.submit) extract_host_from_output() (in module cellmap_flow.jobs.spec)

F

face_erosion_iterations (cellmap_flow.post.postprocessors.SimpleBlockwiseMerger attribute) factor() (cellmap_flow.io.resample.Resampling method) FAIL (in module cellmap_flow.cli.doctor) FAILED (cellmap_flow.finetune.job_manager.state.JobStatus attribute) (cellmap_flow.jobs.spec.JobStatus attribute) failed_starts() (in module cellmap_flow.jobs.launch) FAILED_STARTS_KEPT (in module cellmap_flow.jobs.launch) feed() (cellmap_flow.finetune.job_manager.tailer.Iterations method) fetch_model_info() (in module cellmap_flow.serving.client) FETCH_TIMEOUT_S (in module cellmap_flow.models.bioimage_catalog) fg_ids (cellmap_flow.finetune.crop_loader.CropEntry attribute) fill_unpainted() (in module cellmap_flow.finetune.session.fill) fill_value (cellmap_flow.io.metadata.ArrayMeta attribute) FillHolesPostprocessor (class in cellmap_flow.post.postprocessors) finalize_bbx_generation() (in module cellmap_flow.dashboard.routes.bbx_generator) find_available_port() (in module cellmap_flow.finetune.session.minio) find_bioimage_model() (in module cellmap_flow.models.bioimage_catalog) find_checkpoint() (in module cellmap_flow.finetune.job_manager.submit) find_model_config() (in module cellmap_flow.dashboard.routes.finetune.common) find_v3_container() (in module cellmap_flow.io.paths) finetunable (cellmap_flow.models.configs.base.ModelConfig attribute) (cellmap_flow.models.configs.bio.BioModelConfig attribute) (cellmap_flow.models.configs.cellmap.CellMapModelConfig attribute) (cellmap_flow.models.configs.cellpose.CellposeModelConfig attribute) (cellmap_flow.models.configs.dacapo.DaCapoModelConfig attribute) (cellmap_flow.models.configs.finetune.FinetuneModelConfig attribute) (cellmap_flow.models.configs.fly.FlyModelConfig attribute) (cellmap_flow.models.configs.huggingface.HuggingFaceModelConfig attribute) (cellmap_flow.models.configs.script.ScriptModelConfig attribute) (cellmap_flow.models.models_config.BioModelConfig attribute) (cellmap_flow.models.models_config.CellMapModelConfig attribute) (cellmap_flow.models.models_config.CellposeModelConfig attribute) (cellmap_flow.models.models_config.DaCapoModelConfig attribute) (cellmap_flow.models.models_config.FinetuneModelConfig attribute) (cellmap_flow.models.models_config.FlyModelConfig attribute) (cellmap_flow.models.models_config.HuggingFaceModelConfig attribute) (cellmap_flow.models.models_config.ModelConfig attribute) (cellmap_flow.models.models_config.ScriptModelConfig attribute) finetune() (in module cellmap_flow.cli.main) finetune_bp (in module cellmap_flow.dashboard.routes.finetune) (in module cellmap_flow.dashboard.routes.finetune.blueprint) finetune_export_kwargs() (in module cellmap_flow.finetune.job_manager.persistence) finetune_job_manager (cellmap_flow.dashboard.state.Session property) finetune_modes() (cellmap_flow.models.configs.base.ModelConfig method) (cellmap_flow.models.configs.bio.BioModelConfig method) (cellmap_flow.models.configs.cellpose.CellposeModelConfig method) (cellmap_flow.models.configs.finetune.FinetuneModelConfig method) (cellmap_flow.models.models_config.BioModelConfig method) (cellmap_flow.models.models_config.CellposeModelConfig method) (cellmap_flow.models.models_config.FinetuneModelConfig method) (cellmap_flow.models.models_config.ModelConfig method) (in module cellmap_flow.finetune.trainable) finetune_output_type (cellmap_flow.models.configs.cellpose.CellposeModelConfig attribute) (cellmap_flow.models.models_config.CellposeModelConfig attribute) finetune_problem() (in module cellmap_flow.models.envs) finetuned_model_name (cellmap_flow.finetune.job_manager.state.FinetuneJob attribute) finetuned_model_name() (in module cellmap_flow.finetune.run_outputs) FINETUNED_MODEL_YAML (in module cellmap_flow.finetune.markers) FINETUNED_MODEL_YAML_MARKER (in module cellmap_flow.finetune.finetuned_model_templates)

FinetuneJob (class in cellmap_flow.finetune.job_manager.state) FinetuneJobListener (class in cellmap_flow.finetune.job_manager.listener) FinetuneJobManager (class in cellmap_flow.finetune.job_manager.manager) FinetuneLayerListener (class in cellmap_flow.dashboard.finetune_layers) FinetuneModelConfig (class in cellmap_flow.models.configs.finetune) (class in cellmap_flow.models.models_config) FinetuneRestart (class in cellmap_flow.dashboard.requests) FinetuneSubmit (class in cellmap_flow.dashboard.requests) finish() (in module cellmap_flow.inference.timing) finished_iterations() (in module cellmap_flow.finetune.job_manager.tailer) fix (cellmap_flow.cli.doctor.Result attribute) FixedZeroMeanUnitVariance (class in cellmap_flow.finetune.trainable) FLAG_MODEL_TYPES (in module cellmap_flow.finetune.job_manager.submit) Flow (class in cellmap_flow.globals) FLOW_CHANNELS (in module cellmap_flow.viewer.layers) flow_channels() (in module cellmap_flow.viewer.layers) flow_fn (cellmap_flow.finetune.instance_flows.FlowTargetTransform attribute) flow_scale (cellmap_flow.finetune.instance_flows.FlowTargetTransform attribute) FLOW_SCALE (in module cellmap_flow.finetune.instance_flows) FLOW_SHADER (in module cellmap_flow.viewer.raw) flow_shader() (in module cellmap_flow.viewer.raw) flow_targets() (in module cellmap_flow.finetune.instance_flows) flow_threshold (cellmap_flow.models.configs.cellpose.CellposeModelConfig attribute) (cellmap_flow.models.models_config.CellposeModelConfig attribute) (cellmap_flow.post.postprocessors.CellposeMasksPostprocessor attribute) FlowLoss (class in cellmap_flow.finetune.instance_flows) FlowTargetTransform (class in cellmap_flow.finetune.instance_flows) FlyModelConfig (class in cellmap_flow.models.configs.fly) (class in cellmap_flow.models.models_config) follow_jobs() (in module cellmap_flow.dashboard.finetune_layers) for_dashboard() (cellmap_flow.serving.chunkmirage_ops.PostprocessOp method) foreground_mask() (in module cellmap_flow.dashboard.routes.finetune.view_labels) FOREGROUND_SHARE (in module cellmap_flow.finetune.data.sampler) format (cellmap_flow.io.metadata.ArrayMeta attribute) FORMAT (in module cellmap_flow.serving.chunkmirage_server) forward() (cellmap_flow.finetune.instance_flows.FlowLoss method) (cellmap_flow.finetune.lora_wrapper.BatchLoopWrapper method) (cellmap_flow.finetune.lora_wrapper.SequentialWrapper method) (cellmap_flow.finetune.losses.CombinedLoss method) (cellmap_flow.finetune.losses.DiceLoss method) (cellmap_flow.finetune.losses.IntervalLoss method) (cellmap_flow.finetune.losses.MarginLoss method) (cellmap_flow.finetune.trainable.Clip method) (cellmap_flow.finetune.trainable.Crop method) (cellmap_flow.finetune.trainable.FixedZeroMeanUnitVariance method) (cellmap_flow.finetune.trainable.ScaleLinear method) (cellmap_flow.finetune.trainable.ScaleRange method) (cellmap_flow.finetune.trainable.SliceWise method) (cellmap_flow.finetune.trainable.ZeroMeanUnitVariance method) from_builder() (cellmap_flow.pipeline_spec.PipelineSpec class method) from_config() (cellmap_flow.models.geometry.ModelGeometry class method) from_env() (cellmap_flow.inference.runner.DeviceSlots class method) from_json_data() (cellmap_flow.pipeline_spec.PipelineSpec class method) from_steps() (cellmap_flow.pipeline_spec.PipelineSpec class method) from_url_blob() (cellmap_flow.pipeline_spec.PipelineSpec class method) frozen_teacher_copy() (in module cellmap_flow.finetune.adaptation) FULL_FINETUNE_WEIGHTS (in module cellmap_flow.models.resolve) full_output_roi (cellmap_flow.blockwise.blockwise_processor.CellMapFlowBlockwiseProcessor attribute) FullStrategy (class in cellmap_flow.finetune.adaptation)

G

g (in module cellmap_flow.globals) GCS_PUBLIC_URL (in module cellmap_flow.io.store) generate_blockwise_task() (in module cellmap_flow.dashboard.routes.blockwise) generate_current_config_yaml() (in module cellmap_flow.finetune.finetuned_model_templates) generate_finetuned_model_yaml() (in module cellmap_flow.finetune.finetuned_model_templates) generate_neuroglancer_url() (in module cellmap_flow.dashboard.services.startup) geometry (cellmap_flow.models.configs.base.ModelConfig property) (cellmap_flow.models.models_config.ModelConfig property) (cellmap_flow.server.CellMapFlowServer attribute) (cellmap_flow.serving.chunkmirage_server.ChunkmirageServer attribute) GEOMETRY_ATTRS (in module cellmap_flow.finetune.session.volume) GEOMETRY_FIELDS (in module cellmap_flow.serving.client) geometry_from_hf_metadata() (in module cellmap_flow.finetune.build_corrections) geometry_stand_in() (in module cellmap_flow.serving.client) get() (cellmap_flow.models.configs.base.Config method) (cellmap_flow.models.models_config.Config method) get_bbox_json_template() (in module cellmap_flow.dashboard.routes.logging_routes) get_bbx_generator_status() (in module cellmap_flow.dashboard.routes.bbx_generator) get_bioimage_models() (in module cellmap_flow.dashboard.routes.models) get_command() (cellmap_flow.cli.common.ModelTypeGroup method) (cellmap_flow.cli.main.CellMapFlowGroup method) get_encoded_subvolume() (cellmap_flow.viewer.raw.ScalePyramid method) get_finetune_models() (in module cellmap_flow.dashboard.routes.finetune.annotation_core) get_finetuning_jobs() (in module cellmap_flow.dashboard.routes.finetune.training) get_free_port() (in module cellmap_flow.server) get_huggingface_models() (in module cellmap_flow.dashboard.routes.models) get_if_triggered() (cellmap_flow.finetune.session_loop.RestartController method) get_input_normalizers() (in module cellmap_flow.norm.input_normalize) get_instance() (in module cellmap_flow.review) get_job() (cellmap_flow.finetune.job_manager.manager.FinetuneJobManager method) get_job_logs() (cellmap_flow.finetune.job_manager.manager.FinetuneJobManager method) (in module cellmap_flow.dashboard.routes.finetune.training) get_job_status() (cellmap_flow.finetune.job_manager.manager.FinetuneJobManager method) (in module cellmap_flow.dashboard.routes.finetune.training) get_load_crops_progress() (in module cellmap_flow.dashboard.routes.finetune.yaml_crops) get_local_ip() (in module cellmap_flow.finetune.session.minio) get_lsf_job_id() (in module cellmap_flow.dashboard.routes.finetune.common) get_meta() (in module cellmap_flow.review)

get_model_config_types() (in module cellmap_flow.dashboard.routes.models) get_model_merger() (in module cellmap_flow.models.model_merger) get_model_mergers_list() (in module cellmap_flow.models.model_merger) get_next() (in module cellmap_flow.review) get_normalizations() (in module cellmap_flow.norm.input_normalize) get_object_mesh() (cellmap_flow.viewer.raw.ScalePyramid method) get_or_create() (cellmap_flow.finetune.session.store.SessionStore method) get_output_dtype() (cellmap_flow.globals.Flow method) get_plugins_dir() (in module cellmap_flow.plugins) get_postprocessors() (in module cellmap_flow.post.postprocessors) get_postprocessors_list() (in module cellmap_flow.post.postprocessors) get_progress() (in module cellmap_flow.review) get_public_ip() (in module cellmap_flow.server) (in module cellmap_flow.serving.chunkmirage_server) get_raw_layer() (in module cellmap_flow.viewer.raw) get_server_config() (in module cellmap_flow.dashboard.routes.models) get_session() (in module cellmap_flow.dashboard.state) get_status() (cellmap_flow.jobs.local.LocalJob method) (cellmap_flow.jobs.lsf.LSFJob method) (cellmap_flow.jobs.spec.Job method) get_user_prefs() (in module cellmap_flow.dashboard.routes.finetune.annotation_core) global_step (cellmap_flow.finetune.lora_trainer.LoRAFinetuner attribute) good_regions (cellmap_flow.finetune.data.sampler.PatchSampler attribute) GOOD_REGIONS_FILENAME (in module cellmap_flow.finetune.session.manifest) GOOD_REGIONS_LAYER (in module cellmap_flow.dashboard.routes.finetune.good_regions) good_regions_path() (in module cellmap_flow.finetune.session.manifest) GPU_MEMORY_LIMIT (in module cellmap_flow.viewer.bootstrap) gpu_queue_availability() (in module cellmap_flow.jobs.queues) gpu_queues (cellmap_flow.jobs.site.SiteProfile attribute) GPU_QUEUES (in module cellmap_flow.jobs.queues) gpu_queues() (in module cellmap_flow.dashboard.routes.models) GPU_SLOTS_ENV (in module cellmap_flow.inference.runner) gpus (cellmap_flow.jobs.spec.JobSpec attribute) gradient_accumulation_steps (cellmap_flow.finetune.lora_trainer.LoRAFinetuner attribute) grid (cellmap_flow.serving.chunkmirage_ops.BlockInput attribute) (cellmap_flow.serving.chunkmirage_ops.ServedModel attribute) Grid (class in cellmap_flow.io.geometry) grid_origin (cellmap_flow.blockwise.blockwise_processor.CellMapFlowBlockwiseProcessor attribute)

H

half_precision (cellmap_flow.inference.runner.ModelRunner attribute) HALF_PRECISION_ENV (in module cellmap_flow.server) (in module cellmap_flow.serving.chunkmirage_server) HALF_PRECISION_TOLERANCE (in module cellmap_flow.inference.runner) halo (cellmap_flow.serving.chunkmirage_ops.InferenceOp property) (cellmap_flow.serving.chunkmirage_ops.ServedModel attribute) has_channel (cellmap_flow.server.CellMapFlowServer attribute) (cellmap_flow.serving.chunkmirage_ops.ServedModel attribute) (cellmap_flow.serving.chunkmirage_server.ChunkmirageServer attribute) has_channel_axis (cellmap_flow.models.geometry.ModelGeometry property) has_painted_annotations() (in module cellmap_flow.finetune.session.manifest)

has_pixi() (in module cellmap_flow.models.envs) HF_CACHE_DIR (in module cellmap_flow.models.hf_catalog) HF_CACHE_FILE (in module cellmap_flow.models.hf_catalog) hold() (cellmap_flow.inference.runner.DeviceSlots method) host (cellmap_flow.jobs.spec.Job attribute) how (cellmap_flow.models.resolve.Resolved attribute), [1] HUGGING_FACE_ORGS_NAME (in module cellmap_flow.models.hf_catalog) HuggingFaceModelConfig (class in cellmap_flow.models.configs.huggingface) (class in cellmap_flow.models.models_config) HYPHA_ARTIFACTS (in module cellmap_flow.models.bioimage_catalog) HYPHA_MODELS_URL (in module cellmap_flow.models.bioimage_catalog)

I

id (cellmap_flow.dashboard.requests.BioimageSelection attribute) idi_raw (cellmap_flow.blockwise.blockwise_processor.CellMapFlowBlockwiseProcessor attribute) (cellmap_flow.server.CellMapFlowServer attribute) (cellmap_flow.serving.chunkmirage_server.ChunkmirageServer attribute) ImageDataInterface (class in cellmap_flow.image_data_interface) index() (in module cellmap_flow.dashboard.routes.index_page) index_bp (in module cellmap_flow.dashboard.routes.index_page) infer (in module cellmap_flow.cli.infer) INFERENCE_PREFETCH (in module cellmap_flow.serving.chunkmirage_server) inference_server (cellmap_flow.finetune.session_loop.TrainingSession attribute) INFERENCE_SERVER_FAILED (in module cellmap_flow.finetune.markers) inference_server_ready (cellmap_flow.finetune.job_manager.state.FinetuneJob attribute) inference_server_url (cellmap_flow.finetune.job_manager.state.FinetuneJob attribute) InferenceOp (class in cellmap_flow.serving.chunkmirage_ops) inferencer (cellmap_flow.blockwise.blockwise_processor.CellMapFlowBlockwiseProcessor attribute) (cellmap_flow.server.CellMapFlowServer attribute) (cellmap_flow.serving.chunkmirage_server.ChunkmirageServer attribute) Inferencer (class in cellmap_flow.inferencer) inferencers (cellmap_flow.blockwise.blockwise_processor.CellMapFlowBlockwiseProcessor attribute) info (cellmap_flow.image_data_interface.ImageDataInterface property) info() (cellmap_flow.viewer.raw.ScalePyramid method) initial_state (cellmap_flow.finetune.lora_trainer.LoRAFinetuner attribute) (cellmap_flow.finetune.session_loop.TrainingSession attribute) initial_state() (cellmap_flow.finetune.adaptation.AdaptationStrategy method) (cellmap_flow.finetune.adaptation.FullStrategy method) (cellmap_flow.finetune.adaptation.LoraStrategy method) input_channels (cellmap_flow.models.geometry.ModelGeometry attribute) input_norm (cellmap_flow.dashboard.routes.pipeline.PipelineUpdate attribute) (cellmap_flow.pipeline_spec.PipelineSpec attribute) (cellmap_flow.serving.chunkmirage_ops.InferenceOp attribute) input_norm_config (cellmap_flow.finetune.data.reader.PatchReader attribute) (cellmap_flow.process_chain.ProcessChain attribute) INPUT_NORM_KEY (in module cellmap_flow.serving.protocol) input_normalizers() (in module cellmap_flow.finetune.data.reader) input_norms (cellmap_flow.dashboard.state.Session property) (cellmap_flow.image_data_interface.ImageDataInterface attribute) (cellmap_flow.image_data_interface.LazyNormalization attribute) (cellmap_flow.process_chain.ProcessChain attribute) (cellmap_flow.server.ServedChain attribute) (cellmap_flow.serving.chunkmirage_ops.BlockInput attribute) input_path (cellmap_flow.blockwise.blockwise_processor.CellMapFlowBlockwiseProcessor attribute) input_shape (cellmap_flow.models.geometry.ModelGeometry property) input_size (cellmap_flow.finetune.data.reader.PatchReader attribute) (cellmap_flow.finetune.session.volume.VolumeGeometry attribute) (cellmap_flow.models.configs.bio.BioModelConfig attribute) (cellmap_flow.models.configs.fly.FlyModelConfig attribute) (cellmap_flow.models.models_config.BioModelConfig attribute) (cellmap_flow.models.models_config.FlyModelConfig attribute) input_voxel_size (cellmap_flow.blockwise.blockwise_processor.CellMapFlowBlockwiseProcessor attribute) (cellmap_flow.finetune.data.reader.PatchReader attribute) (cellmap_flow.finetune.session.volume.VolumeGeometry attribute) (cellmap_flow.models.configs.finetune.FinetuneModelConfig attribute) (cellmap_flow.models.configs.fly.FlyModelConfig attribute) (cellmap_flow.models.geometry.ModelGeometry attribute) (cellmap_flow.models.models_config.FinetuneModelConfig attribute) (cellmap_flow.models.models_config.FlyModelConfig attribute) (cellmap_flow.server.CellMapFlowServer attribute) (cellmap_flow.serving.chunkmirage_ops.ServedModel attribute)

input_voxel_size() (cellmap_flow.serving.chunkmirage_ops.InferenceOp method) InputNormalizer (class in cellmap_flow.norm.input_normalize) inputs (cellmap_flow.dashboard.requests.BlockwisePipeline attribute) (cellmap_flow.dashboard.routes.pipeline.BuilderCanvas attribute) install_argv() (in module cellmap_flow.models.envs) install_cleanup_handlers() (in module cellmap_flow.jobs.launch) install_cmd() (in module cellmap_flow.cli.envs_cli) instance_components() (in module cellmap_flow.finetune.instance_flows) INSTANCE_TARGETS (in module cellmap_flow.dashboard.routes.finetune.common) instantiate_model_config() (in module cellmap_flow.models.registry) intensity() (cellmap_flow.finetune.data.augment.Augmentation method) IntervalLoss (class in cellmap_flow.finetune.losses) IntervalTargetTransform (class in cellmap_flow.finetune.target_transforms) invalidate() (cellmap_flow.viewer.raw.ScalePyramid method) IP_PATTERN (in module cellmap_flow.jobs.spec) is_empty() (cellmap_flow.pipeline_spec.PipelineSpec method) is_installed() (in module cellmap_flow.models.envs) is_integral() (in module cellmap_flow.io.metadata) is_label_dtype() (in module cellmap_flow.io.resample) is_path() (in module cellmap_flow.models.envs) is_peft_model() (in module cellmap_flow.finetune.adaptation) is_precomputed() (in module cellmap_flow.io.paths) is_remote() (in module cellmap_flow.io.paths) is_running() (cellmap_flow.jobs.spec.Job method) is_running_in() (in module cellmap_flow.models.envs) is_segmentation (cellmap_flow.post.postprocessors.AffinityPostprocessor property) (cellmap_flow.post.postprocessors.CellposeMasksPostprocessor property) (cellmap_flow.post.postprocessors.DefaultPostprocessor property) (cellmap_flow.post.postprocessors.FillHolesPostprocessor 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) is_url() (in module cellmap_flow.io.store) is_v3_container() (in module cellmap_flow.io.paths) is_zarr_container() (in module cellmap_flow.io.paths) iteration (cellmap_flow.finetune.session_loop.TrainingSession attribute) (cellmap_flow.models.configs.dacapo.DaCapoModelConfig attribute) (cellmap_flow.models.models_config.DaCapoModelConfig attribute) ITERATION_COMPLETE_RE (in module cellmap_flow.finetune.markers) iteration_dir() (in module cellmap_flow.finetune.run_outputs) Iterations (class in cellmap_flow.finetune.job_manager.tailer)

J

JANELIA (in module cellmap_flow.jobs.site) jitter (cellmap_flow.finetune.data.sampler.PatchSampler attribute) jitter_voxels (cellmap_flow.finetune.crop_loader.CropsConfig attribute) Job (class in cellmap_flow.jobs.spec) job_id (cellmap_flow.finetune.job_manager.state.FinetuneJob attribute) (cellmap_flow.jobs.lsf.LSFJob attribute) job_ids_named() (in module cellmap_flow.jobs.lsf) job_logs() (in module cellmap_flow.dashboard.routes.models)

job_name (cellmap_flow.dashboard.requests.BlockwiseGenerate attribute) JobIdMissingError jobs (cellmap_flow.dashboard.state.Session property) (cellmap_flow.finetune.job_manager.manager.FinetuneJobManager attribute) JobSpec (class in cellmap_flow.jobs.spec) JobStartError JobStatus (class in cellmap_flow.finetune.job_manager.state) (class in cellmap_flow.jobs.spec) join() (in module cellmap_flow.io.paths)

K

keys_to_skip (cellmap_flow.post.postprocessors.SimpleBlockwiseMerger attribute) KEYWORDS (in module cellmap_flow.norm.safe_expression) kill() (cellmap_flow.jobs.local.LocalJob method) (cellmap_flow.jobs.lsf.LSFJob method) (cellmap_flow.jobs.spec.Job method) kill_n_remove_from_neuroglancer() (in module cellmap_flow.dashboard.services.launch)

KILLED (cellmap_flow.jobs.spec.JobStatus attribute) kind (cellmap_flow.finetune.adaptation.AdaptationStrategy attribute) (cellmap_flow.finetune.adaptation.FullStrategy attribute) (cellmap_flow.finetune.adaptation.LoraStrategy attribute) kvstores() (in module cellmap_flow.io.store) kwargs (cellmap_flow.models.configs.base.Config attribute) (cellmap_flow.models.models_config.Config attribute)

L

label_id (cellmap_flow.dashboard.routes.review_routes.PickBoard attribute) label_smoothing (cellmap_flow.dashboard.requests.FinetuneSubmit attribute) (cellmap_flow.dashboard.routes.finetune.common.TrainingSettings attribute) (cellmap_flow.finetune.lora_trainer.LoRAFinetuner attribute) label_undo (cellmap_flow.dashboard.state.Session attribute) label_view_background() (in module cellmap_flow.dashboard.routes.finetune.view_labels) 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) LARGE_BOX_VOXELS (in module cellmap_flow.dashboard.routes.finetune.view_labels) last_supervised_loss (cellmap_flow.finetune.lora_trainer.LoRAFinetuner attribute) latest() (cellmap_flow.dashboard.routes.review_routes.PickBoard method) latest_loss (cellmap_flow.finetune.job_manager.state.FinetuneJob attribute) latest_on_disk() (cellmap_flow.finetune.session.store.SessionStore method) launch() (in module cellmap_flow.finetune.job_manager.submit) launch_entry (cellmap_flow.models.configs.base.ModelConfig property) (cellmap_flow.models.models_config.ModelConfig property) launcher_settings() (in module cellmap_flow.jobs.settings) LauncherSettings (class in cellmap_flow.jobs.settings) layer_ops() (in module cellmap_flow.serving.chunkmirage_ops) LazyNormalization (class in cellmap_flow.image_data_interface) learning_rate (cellmap_flow.dashboard.requests.FinetuneSubmit attribute) (cellmap_flow.finetune.lora_trainer.LoRAFinetuner attribute) legacy_attrs() (in module cellmap_flow.io.metadata) legacy_meta() (in module cellmap_flow.image_data_interface) Level (in module cellmap_flow.io.multiscale) level_shape (cellmap_flow.serving.chunkmirage_ops.BlockInput attribute) (cellmap_flow.serving.chunkmirage_ops.ServedModel attribute) lib_dir() (in module cellmap_flow.models.envs) list_bioimage_models() (in module cellmap_flow.models.bioimage_catalog) list_cmd() (in module cellmap_flow.cli.envs_cli) list_commands() (cellmap_flow.cli.common.ModelTypeGroup method) list_existing_sessions() (in module cellmap_flow.dashboard.routes.finetune.annotation_sessions) list_good_regions() (in module cellmap_flow.dashboard.routes.finetune.good_regions) list_huggingface_models() (in module cellmap_flow.models.hf_catalog) list_jobs() (cellmap_flow.finetune.job_manager.manager.FinetuneJobManager method) list_levels() (in module cellmap_flow.io.metadata) list_models() (in module cellmap_flow.cli.server_cli) list_plugins() (in module cellmap_flow.plugins) list_plugins_cmd() (in module cellmap_flow.cli.main) list_populated_chunks() (in module cellmap_flow.io.geometry) Listeners (class in cellmap_flow.finetune.job_manager.listener) load() (cellmap_flow.jobs.settings.LauncherSettings class method) load_cached_geometry() (in module cellmap_flow.models.geometry_cache) load_checkpoint() (cellmap_flow.finetune.lora_trainer.LoRAFinetuner method) load_config() (in module cellmap_flow.config.yaml) load_crops_from_yaml() (in module cellmap_flow.dashboard.routes.finetune.yaml_crops) load_eager_base() (in module cellmap_flow.finetune.export_merged) load_eval_model() (cellmap_flow.models.configs.fly.FlyModelConfig method) (cellmap_flow.models.models_config.FlyModelConfig method) load_existing_volume() (in module cellmap_flow.dashboard.routes.finetune.annotation_sessions) load_existing_volume_progress() (in module cellmap_flow.dashboard.routes.finetune.annotation_sessions) load_good_regions() (in module cellmap_flow.dashboard.routes.finetune.good_regions) (in module cellmap_flow.finetune.session.manifest) load_good_regions_for() (in module cellmap_flow.finetune.session.manifest) load_id (cellmap_flow.dashboard.requests.LoadCrops attribute) load_lora_adapter() (in module cellmap_flow.finetune.lora_wrapper) load_plugins() (in module cellmap_flow.plugins) load_safe_config() (in module cellmap_flow.models.configs.script) load_server_config_cache() (in module cellmap_flow.jobs.settings) load_trainable_model() (in module cellmap_flow.finetune.model_loading) load_user_prefs() (in module cellmap_flow.dashboard.routes.finetune.common) LoadCrops (class in cellmap_flow.dashboard.requests) LocalJob (class in cellmap_flow.jobs.local) log_buffer (cellmap_flow.dashboard.state.Session attribute) log_clients (cellmap_flow.dashboard.state.Session attribute) LOG_DATEFMT (in module cellmap_flow.logging_setup) log_dir (cellmap_flow.jobs.spec.JobSpec attribute) log_file (cellmap_flow.finetune.job_manager.state.FinetuneJob attribute) (cellmap_flow.jobs.local.LocalJob attribute) (cellmap_flow.jobs.lsf.LSFJob attribute) LOG_FILTER_PATTERNS (in module cellmap_flow.dashboard.routes.finetune.common) LOG_FORMAT (in module cellmap_flow.logging_setup) log_handler (in module cellmap_flow.dashboard.app) log_level_option() (in module cellmap_flow.cli.common) LOG_LEVELS (in module cellmap_flow.cli.common) log_pattern() (in module cellmap_flow.jobs.lsf) log_rehearsal_status() (cellmap_flow.finetune.data.sampler.PatchSampler method) log_stem() (in module cellmap_flow.jobs.spec) logger (in module cellmap_flow.blockwise.blockwise_processor) (in module cellmap_flow.blockwise.cli) (in module cellmap_flow.cli.infer) (in module cellmap_flow.cli.server_cli) (in module cellmap_flow.cli.viewer_cli) (in module cellmap_flow.cli.yaml_cli) (in module cellmap_flow.config.yaml) (in module cellmap_flow.dashboard.app) (in module cellmap_flow.dashboard.finetune_layers) (in module cellmap_flow.dashboard.routes.bbx_generator) (in module cellmap_flow.dashboard.routes.blockwise) (in module cellmap_flow.dashboard.routes.finetune.annotation_core) (in module cellmap_flow.dashboard.routes.finetune.annotation_sessions) (in module cellmap_flow.dashboard.routes.finetune.common) (in module cellmap_flow.dashboard.routes.finetune.good_regions) (in module cellmap_flow.dashboard.routes.finetune.instance_correction) (in module cellmap_flow.dashboard.routes.finetune.layers) (in module cellmap_flow.dashboard.routes.finetune.overlay) (in module cellmap_flow.dashboard.routes.finetune.training) (in module cellmap_flow.dashboard.routes.finetune.view_labels) (in module cellmap_flow.dashboard.routes.finetune.yaml_crops) (in module cellmap_flow.dashboard.routes.index_page) (in module cellmap_flow.dashboard.routes.logging_routes) (in module cellmap_flow.dashboard.routes.model_advice) (in module cellmap_flow.dashboard.routes.model_resolve) (in module cellmap_flow.dashboard.routes.models) (in module cellmap_flow.dashboard.routes.pipeline) (in module cellmap_flow.dashboard.routes.pipeline_builder_page) (in module cellmap_flow.dashboard.routes.review_routes) (in module cellmap_flow.dashboard.services.launch) (in module cellmap_flow.dashboard.services.startup) (in module cellmap_flow.finetune.build_corrections) (in module cellmap_flow.finetune.cli) (in module cellmap_flow.finetune.crop_loader) (in module cellmap_flow.finetune.data.augment) (in module cellmap_flow.finetune.data.dataset) (in module cellmap_flow.finetune.data.loader) (in module cellmap_flow.finetune.data.reader) (in module cellmap_flow.finetune.data.sampler) (in module cellmap_flow.finetune.export_merged) (in module cellmap_flow.finetune.finetune_cli) (in module cellmap_flow.finetune.finetuned_model_templates) (in module cellmap_flow.finetune.job_manager.listener) (in module cellmap_flow.finetune.job_manager.manager) (in module cellmap_flow.finetune.job_manager.monitor) (in module cellmap_flow.finetune.job_manager.persistence) (in module cellmap_flow.finetune.job_manager.restart) (in module cellmap_flow.finetune.job_manager.state) (in module cellmap_flow.finetune.job_manager.submit) (in module cellmap_flow.finetune.job_manager.tailer) (in module cellmap_flow.finetune.lora_trainer) (in module cellmap_flow.finetune.lora_wrapper) (in module cellmap_flow.finetune.model_loading) (in module cellmap_flow.finetune.run_outputs) (in module cellmap_flow.finetune.session.fill) (in module cellmap_flow.finetune.session.instance) (in module cellmap_flow.finetune.session.manifest) (in module cellmap_flow.finetune.session.minio) (in module cellmap_flow.finetune.session.store) (in module cellmap_flow.finetune.session.sync) (in module cellmap_flow.finetune.session.volume) (in module cellmap_flow.finetune.session_loop) (in module cellmap_flow.finetune.target_transforms) (in module cellmap_flow.image_data_interface) (in module cellmap_flow.inference.runner) (in module cellmap_flow.inferencer) (in module cellmap_flow.io.geometry) (in module cellmap_flow.io.metadata) (in module cellmap_flow.io.multiscale) (in module cellmap_flow.io.source) (in module cellmap_flow.io.store) (in module cellmap_flow.jobs.launch) (in module cellmap_flow.jobs.local) (in module cellmap_flow.jobs.lsf) (in module cellmap_flow.jobs.queues) (in module cellmap_flow.jobs.ready) (in module cellmap_flow.jobs.spec) (in module cellmap_flow.models.configs.base) (in module cellmap_flow.models.configs.bio) (in module cellmap_flow.models.configs.cellpose) (in module cellmap_flow.models.configs.fly) (in module cellmap_flow.models.configs.huggingface) (in module cellmap_flow.models.configs.script) (in module cellmap_flow.models.envs) (in module cellmap_flow.models.geometry_cache) (in module cellmap_flow.models.model_merger) (in module cellmap_flow.models.registry) (in module cellmap_flow.norm.input_normalize) (in module cellmap_flow.plugins) (in module cellmap_flow.post.postprocessors) (in module cellmap_flow.server) (in module cellmap_flow.serving.chunkmirage_ops) (in module cellmap_flow.serving.chunkmirage_server) (in module cellmap_flow.serving.client) (in module cellmap_flow.serving.engine) (in module cellmap_flow.serving.probe) (in module cellmap_flow.serving.virtual_zarr) (in module cellmap_flow.viewer.bootstrap) (in module cellmap_flow.viewer.layers) (in module cellmap_flow.viewer.raw)

logging_bp (in module cellmap_flow.dashboard.routes.logging_routes) LogHandler (class in cellmap_flow.dashboard.routes.logging_routes) LogTailer (class in cellmap_flow.finetune.job_manager.tailer) looks_like_affinities() (in module cellmap_flow.serving.probe) lora_adapter_path (cellmap_flow.models.configs.finetune.FinetuneModelConfig attribute) (cellmap_flow.models.models_config.FinetuneModelConfig attribute) lora_r (cellmap_flow.dashboard.requests.FinetuneSubmit attribute) LoRAFinetuner (class in cellmap_flow.finetune.lora_trainer) LoraStrategy (class in cellmap_flow.finetune.adaptation) loss_type (cellmap_flow.dashboard.requests.FinetuneSubmit attribute) (cellmap_flow.dashboard.routes.finetune.common.TrainingSettings attribute) (cellmap_flow.finetune.lora_trainer.LoRAFinetuner attribute) LOSS_TYPES (in module cellmap_flow.finetune.cli) lsf_job (cellmap_flow.finetune.job_manager.state.FinetuneJob attribute) LSFJob (class in cellmap_flow.jobs.lsf)

M

main() (in module cellmap_flow.cli.doctor) (in module cellmap_flow.cli.main) (in module cellmap_flow.cli.server_cli) (in module cellmap_flow.cli.viewer_cli) (in module cellmap_flow.cli.yaml_cli) (in module cellmap_flow.finetune.build_corrections) (in module cellmap_flow.finetune.export_merged) (in module cellmap_flow.finetune.finetune_cli) (in module cellmap_flow.review_index) majority_vote_downsample() (in module cellmap_flow.finetune.session.volume) make_s3_filesystem() (in module cellmap_flow.finetune.session.minio) make_server() (in module cellmap_flow.serving.engine) make_training_loader() (in module cellmap_flow.finetune.data) (in module cellmap_flow.finetune.data.loader) margin (cellmap_flow.dashboard.requests.FinetuneSubmit attribute) (cellmap_flow.finetune.lora_trainer.LoRAFinetuner attribute) (cellmap_flow.finetune.losses.MarginLoss attribute) MarginLoss (class in cellmap_flow.finetune.losses) mark_current_view_good() (in module cellmap_flow.dashboard.routes.finetune.good_regions) mask_unannotated (cellmap_flow.dashboard.routes.finetune.common.TrainingSettings attribute) (cellmap_flow.finetune.lora_trainer.LoRAFinetuner attribute) masked_mean() (in module cellmap_flow.finetune.losses) match_dataset() (in module cellmap_flow.io.metadata) MAX_ENTRIES (in module cellmap_flow.models.geometry_cache) MAX_EXPONENT (in module cellmap_flow.norm.safe_expression) MAX_LABEL (in module cellmap_flow.review_index) MAX_LENGTH (in module cellmap_flow.norm.safe_expression) MAX_POSITIONAL (in module cellmap_flow.norm.safe_expression) max_slope (cellmap_flow.finetune.losses.IntervalLoss attribute) max_value (cellmap_flow.norm.input_normalize.MinMaxNormalizer attribute) MC_ALIAS (in module cellmap_flow.finetune.session.minio) mc_env() (cellmap_flow.finetune.session.minio.MinioServer method) mean (cellmap_flow.norm.input_normalize.ZScoreNormalizer attribute) merge() (cellmap_flow.finetune.adaptation.AdaptationStrategy method) (cellmap_flow.finetune.adaptation.FullStrategy static method) (cellmap_flow.finetune.adaptation.LoraStrategy static method) (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) METADATA_FILE (in module cellmap_flow.finetune.job_manager.persistence) METADATA_RETRY_SECONDS (cellmap_flow.models.configs.huggingface.HuggingFaceModelConfig attribute) (cellmap_flow.models.models_config.HuggingFaceModelConfig attribute) METADATA_TIMEOUT_SECONDS (in module cellmap_flow.dashboard.routes.finetune.view_labels) methods() (cellmap_flow.io.resample.Resampling method) methods_for() (in module cellmap_flow.dashboard.routes.finetune.view_labels) MIN_BLOCK_EDGE (in module cellmap_flow.review_index) min_channels (cellmap_flow.finetune.adaptation.LoraStrategy attribute) min_size (cellmap_flow.post.postprocessors.CellposeMasksPostprocessor attribute) (cellmap_flow.post.postprocessors.LabelPostprocessor attribute) min_value (cellmap_flow.norm.input_normalize.MinMaxNormalizer attribute) MINIO_INSTALL (in module cellmap_flow.cli.doctor) MINIO_PROXY_URL_ENV (in module cellmap_flow.finetune.session.minio) MINIO_READY_TIMEOUT (in module cellmap_flow.finetune.session.minio) minio_root() (in module cellmap_flow.finetune.session.minio) minio_state (cellmap_flow.dashboard.state.Session attribute) MinioServer (class in cellmap_flow.finetune.session.minio) MinMaxNormalizer (class in cellmap_flow.norm.input_normalize) mode (cellmap_flow.finetune.crop_loader.CropEntry attribute) Mode (in module cellmap_flow.io.multiscale) model (cellmap_flow.dashboard.requests.CellposeSelection attribute) (cellmap_flow.finetune.lora_trainer.LoRAFinetuner attribute) (cellmap_flow.finetune.lora_wrapper.BatchLoopWrapper attribute) (cellmap_flow.finetune.lora_wrapper.SequentialWrapper attribute) (cellmap_flow.finetune.session_loop.TrainingSession attribute) (cellmap_flow.models.configs.bio.BioModelConfig attribute) (cellmap_flow.models.configs.fly.FlyModelConfig property) (cellmap_flow.models.models_config.BioModelConfig attribute) (cellmap_flow.models.models_config.FlyModelConfig property) (cellmap_flow.serving.chunkmirage_ops.InferenceOp attribute) (cellmap_flow.serving.chunkmirage_ops.PostprocessOp attribute) model_advice() (in module cellmap_flow.dashboard.routes.model_advice) model_advice_bp (in module cellmap_flow.dashboard.routes.model_advice) model_catalog (cellmap_flow.dashboard.state.Session attribute) model_classes() (in module cellmap_flow.models.registry) model_config (cellmap_flow.blockwise.blockwise_processor.CellMapFlowBlockwiseProcessor attribute) (cellmap_flow.dashboard.requests.ServerConfigUpdate attribute) (cellmap_flow.finetune.crop_loader.CropEntry attribute) (cellmap_flow.finetune.crop_loader.CropsConfig attribute) (cellmap_flow.finetune.session_loop.TrainingSession attribute) (cellmap_flow.inference.runner.ModelRunner attribute) model_config_from_args() (in module cellmap_flow.finetune.cli) model_config_from_entry() (in module cellmap_flow.finetune.model_loading) model_entry() (in module cellmap_flow.finetune.job_manager.submit) (in module cellmap_flow.models.configs.base) model_env() (in module cellmap_flow.models.envs) model_geometry() (in module cellmap_flow.serving.client) model_geometry_config() (in module cellmap_flow.serving.client) model_holds (cellmap_flow.finetune.session_loop.TrainingSession attribute) model_info() (cellmap_flow.serving.chunkmirage_server.ChunkmirageServer method) model_merger (cellmap_flow.blockwise.blockwise_processor.CellMapFlowBlockwiseProcessor attribute) model_mode (cellmap_flow.dashboard.requests.BlockwisePipeline attribute) model_mode_str (cellmap_flow.blockwise.blockwise_processor.CellMapFlowBlockwiseProcessor attribute) model_name (cellmap_flow.dashboard.requests.CreateVolume attribute) (cellmap_flow.dashboard.requests.FinetuneSubmit attribute) (cellmap_flow.dashboard.requests.LoadCrops attribute) (cellmap_flow.finetune.job_manager.state.FinetuneJob attribute) (cellmap_flow.jobs.spec.Job attribute) model_output() (in module cellmap_flow.dashboard.routes.finetune.view_labels) model_post_init() (cellmap_flow.serving.chunkmirage_ops.InferenceOp method) (cellmap_flow.serving.chunkmirage_ops.PostprocessOp method) model_resolve_bp (in module cellmap_flow.dashboard.routes.model_resolve) model_settings() (in module cellmap_flow.finetune.job_manager.submit) model_type() (in module cellmap_flow.models.registry) model_types() (in module cellmap_flow.models.registry) model_yaml_path (cellmap_flow.finetune.job_manager.state.FinetuneJob attribute) MODEL_YAML_RE (in module cellmap_flow.finetune.markers) ModelConfig (class in cellmap_flow.models.configs.base) (class in cellmap_flow.models.models_config) ModelEnvError ModelGeometry (class in cellmap_flow.models.geometry) ModelMerger (class in cellmap_flow.models.model_merger) ModelNode (class in cellmap_flow.dashboard.requests) ModelRunner (class in cellmap_flow.inference.runner) models (cellmap_flow.blockwise.blockwise_processor.CellMapFlowBlockwiseProcessor attribute) (cellmap_flow.dashboard.requests.BlockwisePipeline attribute) (cellmap_flow.dashboard.routes.pipeline.BuilderCanvas attribute) models() (in module cellmap_flow.cli.main) models_bp (in module cellmap_flow.dashboard.routes.models) models_config (cellmap_flow.dashboard.state.Session attribute) models_dir() (in module cellmap_flow.finetune.run_outputs) ModelTypeGroup (class in cellmap_flow.cli.common) 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.add_cli cellmap_flow.cli.aliases cellmap_flow.cli.cli cellmap_flow.cli.common cellmap_flow.cli.doctor cellmap_flow.cli.envs_cli cellmap_flow.cli.infer cellmap_flow.cli.main cellmap_flow.cli.server_cli cellmap_flow.cli.viewer_cli cellmap_flow.cli.yaml_cli cellmap_flow.config cellmap_flow.config.yaml cellmap_flow.dashboard cellmap_flow.dashboard.app cellmap_flow.dashboard.finetune_layers cellmap_flow.dashboard.finetune_utils cellmap_flow.dashboard.progress cellmap_flow.dashboard.requests cellmap_flow.dashboard.routes cellmap_flow.dashboard.routes.bbx_generator cellmap_flow.dashboard.routes.blockwise cellmap_flow.dashboard.routes.finetune cellmap_flow.dashboard.routes.finetune.annotation_core cellmap_flow.dashboard.routes.finetune.annotation_sessions cellmap_flow.dashboard.routes.finetune.blueprint cellmap_flow.dashboard.routes.finetune.common cellmap_flow.dashboard.routes.finetune.good_regions cellmap_flow.dashboard.routes.finetune.instance_correction cellmap_flow.dashboard.routes.finetune.layers cellmap_flow.dashboard.routes.finetune.overlay cellmap_flow.dashboard.routes.finetune.training cellmap_flow.dashboard.routes.finetune.view_labels cellmap_flow.dashboard.routes.finetune.yaml_crops cellmap_flow.dashboard.routes.index_page cellmap_flow.dashboard.routes.logging_routes cellmap_flow.dashboard.routes.model_advice cellmap_flow.dashboard.routes.model_resolve cellmap_flow.dashboard.routes.models cellmap_flow.dashboard.routes.pipeline cellmap_flow.dashboard.routes.pipeline_builder_page cellmap_flow.dashboard.routes.review_routes cellmap_flow.dashboard.services cellmap_flow.dashboard.services.launch cellmap_flow.dashboard.services.startup cellmap_flow.dashboard.state cellmap_flow.finetune cellmap_flow.finetune.adaptation cellmap_flow.finetune.build_corrections cellmap_flow.finetune.cli cellmap_flow.finetune.crop_loader cellmap_flow.finetune.data cellmap_flow.finetune.data.augment cellmap_flow.finetune.data.dataset cellmap_flow.finetune.data.loader cellmap_flow.finetune.data.reader cellmap_flow.finetune.data.sampler cellmap_flow.finetune.export_merged cellmap_flow.finetune.finetune_cli cellmap_flow.finetune.finetuned_model_templates cellmap_flow.finetune.instance_flows cellmap_flow.finetune.job_manager cellmap_flow.finetune.job_manager.listener cellmap_flow.finetune.job_manager.manager cellmap_flow.finetune.job_manager.monitor cellmap_flow.finetune.job_manager.persistence cellmap_flow.finetune.job_manager.restart cellmap_flow.finetune.job_manager.state cellmap_flow.finetune.job_manager.submit cellmap_flow.finetune.job_manager.tailer cellmap_flow.finetune.json_files cellmap_flow.finetune.lora_trainer cellmap_flow.finetune.lora_wrapper cellmap_flow.finetune.losses cellmap_flow.finetune.markers cellmap_flow.finetune.model_loading cellmap_flow.finetune.run_outputs cellmap_flow.finetune.session cellmap_flow.finetune.session.fill cellmap_flow.finetune.session.instance cellmap_flow.finetune.session.manifest cellmap_flow.finetune.session.minio cellmap_flow.finetune.session.store cellmap_flow.finetune.session.sync cellmap_flow.finetune.session.volume cellmap_flow.finetune.session_loop cellmap_flow.finetune.target_transforms cellmap_flow.finetune.trainable cellmap_flow.globals cellmap_flow.image_data_interface cellmap_flow.inference cellmap_flow.inference.runner cellmap_flow.inference.timing cellmap_flow.inferencer cellmap_flow.io cellmap_flow.io.geometry cellmap_flow.io.metadata cellmap_flow.io.multiscale cellmap_flow.io.ome cellmap_flow.io.paths cellmap_flow.io.resample cellmap_flow.io.source cellmap_flow.io.store cellmap_flow.jobs cellmap_flow.jobs.launch cellmap_flow.jobs.local cellmap_flow.jobs.lsf cellmap_flow.jobs.queues cellmap_flow.jobs.ready cellmap_flow.jobs.settings cellmap_flow.jobs.site cellmap_flow.jobs.spec cellmap_flow.jobs.synced_tee cellmap_flow.logging_setup cellmap_flow.models cellmap_flow.models.bioimage_catalog cellmap_flow.models.configs cellmap_flow.models.configs.base cellmap_flow.models.configs.bio cellmap_flow.models.configs.cellmap cellmap_flow.models.configs.cellpose cellmap_flow.models.configs.dacapo cellmap_flow.models.configs.finetune cellmap_flow.models.configs.fly cellmap_flow.models.configs.huggingface cellmap_flow.models.configs.script cellmap_flow.models.envs cellmap_flow.models.geometry cellmap_flow.models.geometry_cache cellmap_flow.models.hf_catalog cellmap_flow.models.model_merger cellmap_flow.models.model_registry cellmap_flow.models.models_config cellmap_flow.models.registry cellmap_flow.models.resolve cellmap_flow.norm cellmap_flow.norm.input_normalize cellmap_flow.norm.safe_expression cellmap_flow.pipeline_spec cellmap_flow.plugins cellmap_flow.post cellmap_flow.post.postprocessors cellmap_flow.post.segment cellmap_flow.process_chain cellmap_flow.review cellmap_flow.review_index cellmap_flow.server cellmap_flow.serving cellmap_flow.serving.chunkmirage_ops cellmap_flow.serving.chunkmirage_server cellmap_flow.serving.client cellmap_flow.serving.engine cellmap_flow.serving.launch cellmap_flow.serving.probe cellmap_flow.serving.protocol cellmap_flow.serving.restart_token cellmap_flow.serving.virtual_zarr cellmap_flow.utils cellmap_flow.utils.bsub_utils cellmap_flow.utils.serialize_config cellmap_flow.viewer cellmap_flow.viewer.bootstrap cellmap_flow.viewer.layers cellmap_flow.viewer.raw

monitor_job() (cellmap_flow.finetune.job_manager.manager.FinetuneJobManager method) (in module cellmap_flow.finetune.job_manager.monitor) MortonSegmentationRelabeling (built-in class) (class in cellmap_flow.post.postprocessors) multiplier (cellmap_flow.post.postprocessors.DefaultPostprocessor attribute) multiscales_attrs() (in module cellmap_flow.io.ome) multiscales_from_group() (in module cellmap_flow.io.metadata) mutex_watershed() (in module cellmap_flow.post.segment)

N

n (cellmap_flow.inference.runner.DeviceSlots attribute) n5_offset() (in module cellmap_flow.io.metadata) n5_units() (in module cellmap_flow.io.metadata) n5_voxel_size() (in module cellmap_flow.io.metadata) name (cellmap_flow.cli.doctor.Result attribute) (cellmap_flow.dashboard.requests.PipelineNode attribute) (cellmap_flow.dashboard.routes.model_resolve.ResolveModel attribute) (cellmap_flow.finetune.crop_loader.CropEntry attribute) (cellmap_flow.finetune.job_manager.tailer.Iterations attribute) (cellmap_flow.jobs.spec.JobSpec attribute) (cellmap_flow.models.configs.bio.BioModelConfig attribute) (cellmap_flow.models.configs.cellmap.CellMapModelConfig attribute) (cellmap_flow.models.configs.cellpose.CellposeModelConfig attribute) (cellmap_flow.models.configs.dacapo.DaCapoModelConfig attribute) (cellmap_flow.models.configs.finetune.FinetuneModelConfig attribute) (cellmap_flow.models.configs.fly.FlyModelConfig attribute) (cellmap_flow.models.configs.huggingface.HuggingFaceModelConfig attribute) (cellmap_flow.models.configs.script.ScriptModelConfig attribute) (cellmap_flow.models.models_config.BioModelConfig attribute) (cellmap_flow.models.models_config.CellMapModelConfig attribute) (cellmap_flow.models.models_config.CellposeModelConfig attribute) (cellmap_flow.models.models_config.DaCapoModelConfig attribute) (cellmap_flow.models.models_config.FinetuneModelConfig attribute) (cellmap_flow.models.models_config.FlyModelConfig attribute) (cellmap_flow.models.models_config.HuggingFaceModelConfig attribute) (cellmap_flow.models.models_config.ScriptModelConfig attribute) (cellmap_flow.models.resolve.Resolved attribute), [1] (cellmap_flow.serving.chunkmirage_ops.DevicePostprocessOp attribute) (cellmap_flow.serving.chunkmirage_ops.InferenceOp attribute) (cellmap_flow.serving.chunkmirage_ops.PostprocessOp attribute) (cellmap_flow.serving.chunkmirage_ops.ServedModel attribute) name() (cellmap_flow.norm.input_normalize.SerializableInterface class method) (PostProcessor method) NANOMETER (in module cellmap_flow.io.metadata) nb_cores_master (cellmap_flow.dashboard.requests.BlockwiseSettings attribute) (cellmap_flow.dashboard.requests.BlockwiseTaskSettings attribute) (cellmap_flow.dashboard.requests.ServerConfigUpdate attribute) nb_cores_worker (cellmap_flow.dashboard.requests.BlockwiseSettings attribute) (cellmap_flow.dashboard.requests.BlockwiseTaskSettings attribute) (cellmap_flow.dashboard.requests.ServerConfigUpdate attribute) nb_workers (cellmap_flow.dashboard.requests.BlockwiseSettings attribute) (cellmap_flow.dashboard.requests.BlockwiseTaskSettings attribute) (cellmap_flow.dashboard.requests.ServerConfigUpdate attribute) ndim (cellmap_flow.models.geometry.ModelGeometry property)

needs (cellmap_flow.models.resolve.Resolved attribute), [1] neighborhood (cellmap_flow.post.postprocessors.AffinityPostprocessor attribute) NEIGHBORHOOD_OFFSETS (in module cellmap_flow.serving.probe) net (cellmap_flow.finetune.trainable.SliceWise attribute) NEUROGLANCER_FORK_INSTALL (in module cellmap_flow.cli.doctor) NEUROGLANCER_FORK_MARKER (in module cellmap_flow.cli.doctor) neuroglancer_source() (in module cellmap_flow.viewer.raw) neuroglancer_url (cellmap_flow.dashboard.state.Session attribute) new_viewer() (in module cellmap_flow.viewer.bootstrap) new_volume_id() (in module cellmap_flow.finetune.session.volume) niter (cellmap_flow.post.postprocessors.CellposeMasksPostprocessor attribute) NM_PER_UNIT (in module cellmap_flow.models.configs.bio) nm_per_unit() (in module cellmap_flow.io.metadata) node_type() (in module cellmap_flow.io.metadata) normalise() (in module cellmap_flow.models.bioimage_catalog) normalise_artifact() (in module cellmap_flow.models.bioimage_catalog) normalize (cellmap_flow.image_data_interface.ImageDataInterface attribute) (cellmap_flow.image_data_interface.LazyNormalization attribute) normalize() (cellmap_flow.finetune.data.reader.PatchReader method) normalize_path() (in module cellmap_flow.io.paths) normalize_steps() (in module cellmap_flow.pipeline_spec) normalizers (cellmap_flow.dashboard.requests.BlockwisePipeline attribute) (cellmap_flow.dashboard.routes.pipeline.BuilderCanvas attribute) (cellmap_flow.finetune.data.augment.Augmentation attribute) (cellmap_flow.finetune.data.reader.PatchReader attribute) norms_to_apply() (cellmap_flow.image_data_interface.LazyNormalization method) NotAnAnnotationVolume note (cellmap_flow.dashboard.routes.finetune.common.TrainingSettings attribute) notes (cellmap_flow.models.resolve.Resolved attribute), [1] notify() (cellmap_flow.finetune.job_manager.listener.Listeners method) num_boxes (cellmap_flow.dashboard.requests.BbxGenerator attribute) num_channels (cellmap_flow.finetune.target_transforms.AffinityTargetTransform attribute) (cellmap_flow.finetune.target_transforms.BroadcastBinaryTargetTransform attribute) (cellmap_flow.finetune.target_transforms.DistanceTargetTransform attribute) (cellmap_flow.post.postprocessors.AffinityPostprocessor property) (cellmap_flow.post.postprocessors.CellposeMasksPostprocessor property) (cellmap_flow.post.postprocessors.ChannelSelection property) num_epochs (cellmap_flow.dashboard.requests.FinetuneSubmit attribute) (cellmap_flow.finetune.lora_trainer.LoRAFinetuner attribute) num_previous_segments (cellmap_flow.post.postprocessors.AffinityPostprocessor attribute) (cellmap_flow.post.postprocessors.MortonSegmentationRelabeling attribute) number() (in module cellmap_flow.models.geometry) NUMPY_CONSTANTS (in module cellmap_flow.norm.safe_expression) NUMPY_DTYPES (in module cellmap_flow.norm.safe_expression) NUMPY_FUNCTIONS (in module cellmap_flow.norm.safe_expression)

O

observed_status() (cellmap_flow.jobs.lsf.LSFJob method) offset (cellmap_flow.dashboard.requests.BoundingBox attribute) (cellmap_flow.image_data_interface.ImageDataInterface attribute) offsets (cellmap_flow.dashboard.requests.FinetuneSubmit attribute) (cellmap_flow.finetune.target_transforms.AffinityTargetTransform attribute) OK (in module cellmap_flow.cli.doctor) ome_corner() (in module cellmap_flow.io.ome) ome_translation() (in module cellmap_flow.io.ome) on_iteration_complete() (cellmap_flow.dashboard.finetune_layers.FinetuneLayerListener method) (cellmap_flow.finetune.job_manager.listener.FinetuneJobListener method) on_scheduler_status() (in module cellmap_flow.finetune.job_manager.state) on_server_ready() (cellmap_flow.dashboard.finetune_layers.FinetuneLayerListener method) (cellmap_flow.finetune.job_manager.listener.FinetuneJobListener method) on_status_marker() (in module cellmap_flow.finetune.job_manager.state) ON_VOXEL_SIZE_MISMATCH (in module cellmap_flow.image_data_interface) ONLINE_TIMEOUT (in module cellmap_flow.models.resolve) open_array() (in module cellmap_flow.io.source) open_db() (in module cellmap_flow.review) open_served_labels() (in module cellmap_flow.finetune.session.fill) optimize_model() (cellmap_flow.inference.runner.ModelRunner method) optimizer (cellmap_flow.finetune.lora_trainer.LoRAFinetuner attribute) OPTIONAL_FIELDS (in module cellmap_flow.serving.client) origin (cellmap_flow.server.CellMapFlowServer attribute) (cellmap_flow.serving.chunkmirage_ops.ServedModel attribute) OrModelMerger (class in cellmap_flow.models.model_merger) output (cellmap_flow.dashboard.requests.CellposeSelection attribute) (cellmap_flow.jobs.lsf.JobIdMissingError attribute) (cellmap_flow.models.configs.cellpose.CellposeModelConfig attribute) (cellmap_flow.models.models_config.CellposeModelConfig attribute) output_arrays (cellmap_flow.blockwise.blockwise_processor.CellMapFlowBlockwiseProcessor attribute) output_channels (cellmap_flow.models.geometry.ModelGeometry attribute) (cellmap_flow.server.CellMapFlowServer attribute) (cellmap_flow.serving.chunkmirage_ops.ServedModel attribute) OUTPUT_CHANNELS (in module cellmap_flow.models.configs.cellpose) output_channels_is_dict (cellmap_flow.blockwise.blockwise_processor.CellMapFlowBlockwiseProcessor attribute) output_class (cellmap_flow.inference.runner.ModelRunner attribute) output_dir (cellmap_flow.finetune.job_manager.state.FinetuneJob attribute) (cellmap_flow.finetune.lora_trainer.LoRAFinetuner attribute)

output_display_range() (in module cellmap_flow.serving.probe) output_dtype (cellmap_flow.models.configs.base.ModelConfig property) (cellmap_flow.models.geometry.ModelGeometry attribute) (cellmap_flow.models.models_config.ModelConfig property) (cellmap_flow.server.CellMapFlowServer attribute) (cellmap_flow.serving.chunkmirage_ops.ServedModel attribute) output_dtype() (cellmap_flow.process_chain.ProcessChain method) output_info() (cellmap_flow.norm.input_normalize.SerializableInterface method) (cellmap_flow.serving.chunkmirage_ops.InferenceOp method) (cellmap_flow.serving.chunkmirage_ops.PostprocessOp method) output_path (cellmap_flow.blockwise.blockwise_processor.CellMapFlowBlockwiseProcessor attribute) (cellmap_flow.dashboard.requests.CreateVolume attribute) (cellmap_flow.dashboard.requests.LoadCrops attribute) output_range (cellmap_flow.inference.runner.ModelRunner attribute) output_sessions (cellmap_flow.dashboard.state.Session attribute) output_shape (cellmap_flow.models.geometry.ModelGeometry property) output_size (cellmap_flow.finetune.data.reader.PatchReader attribute) (cellmap_flow.models.configs.fly.FlyModelConfig attribute) (cellmap_flow.models.models_config.FlyModelConfig attribute) output_type (cellmap_flow.dashboard.requests.FinetuneSubmit attribute) (cellmap_flow.dashboard.routes.finetune.common.TrainingSettings attribute) OUTPUT_TYPES (in module cellmap_flow.finetune.cli) output_voxel_size (cellmap_flow.blockwise.blockwise_processor.CellMapFlowBlockwiseProcessor attribute) (cellmap_flow.finetune.data.reader.PatchReader attribute) (cellmap_flow.finetune.data.sampler.PatchSampler attribute) (cellmap_flow.finetune.session.volume.VolumeGeometry attribute) (cellmap_flow.models.configs.finetune.FinetuneModelConfig attribute) (cellmap_flow.models.configs.fly.FlyModelConfig attribute) (cellmap_flow.models.geometry.ModelGeometry attribute) (cellmap_flow.models.models_config.FinetuneModelConfig attribute) (cellmap_flow.models.models_config.FlyModelConfig attribute) (cellmap_flow.server.CellMapFlowServer attribute) (cellmap_flow.serving.chunkmirage_ops.ServedModel attribute) outputs (cellmap_flow.dashboard.requests.BlockwisePipeline attribute) (cellmap_flow.dashboard.routes.pipeline.BuilderCanvas attribute) OUTPUTS (in module cellmap_flow.models.configs.cellpose)

P

package_logger (in module cellmap_flow.dashboard.app) parallel (cellmap_flow.norm.input_normalize.EuclideanDistance attribute) parameter_info() (in module cellmap_flow.models.registry) params (cellmap_flow.dashboard.requests.BlockwiseConfigNode attribute) (cellmap_flow.dashboard.requests.ChainNode attribute) (cellmap_flow.dashboard.requests.CreateModelConfig attribute) (cellmap_flow.dashboard.requests.PipelineNode attribute) (cellmap_flow.finetune.job_manager.state.FinetuneJob attribute) (cellmap_flow.models.resolve.Resolved attribute), [1] parent() (in module cellmap_flow.io.paths) parse() (in module cellmap_flow.dashboard.requests) parse_args() (in module cellmap_flow.finetune.cli) parse_crops_yaml() (in module cellmap_flow.finetune.crop_loader) parse_job_id() (in module cellmap_flow.jobs.lsf) patches_per_epoch (cellmap_flow.finetune.crop_loader.CropsConfig attribute) (cellmap_flow.finetune.data.dataset.VirtualPatchDataset attribute) (cellmap_flow.finetune.data.VirtualPatchDataset attribute) PatchReader (class in cellmap_flow.finetune.data.reader) PatchSampler (class in cellmap_flow.finetune.data.sampler) PatchVoxels (in module cellmap_flow.finetune.data.loader) path (cellmap_flow.finetune.crop_loader.CropEntry attribute) (cellmap_flow.finetune.job_manager.tailer.LogTailer attribute) (cellmap_flow.image_data_interface.ImageDataInterface attribute) (cellmap_flow.io.metadata.ArrayMeta attribute) (cellmap_flow.io.source.ArraySource attribute) peek() (cellmap_flow.jobs.local.LocalJob method) (cellmap_flow.jobs.lsf.LSFJob method) (cellmap_flow.jobs.spec.Job method) PENDING (cellmap_flow.finetune.job_manager.state.JobStatus attribute) (cellmap_flow.jobs.spec.JobStatus attribute) pending_fallback_seconds (cellmap_flow.jobs.site.SiteProfile attribute) PENDING_FALLBACK_SECONDS (in module cellmap_flow.jobs.launch) pending_reset (cellmap_flow.finetune.session_loop.TrainingSession attribute) per_slice (cellmap_flow.post.postprocessors.LabelPostprocessor attribute) periodic_sync() (in module cellmap_flow.finetune.session.sync) periodic_sync_once() (in module cellmap_flow.finetune.session.sync) PICK_STREAM_HEARTBEAT_S (in module cellmap_flow.dashboard.routes.review_routes) PickBoard (class in cellmap_flow.dashboard.routes.review_routes) picks (cellmap_flow.dashboard.routes.review_routes.ReviewSession attribute) pipeline (cellmap_flow.dashboard.requests.BlockwiseValidate attribute) pipeline_bp (in module cellmap_flow.dashboard.routes.pipeline) pipeline_builder() (in module cellmap_flow.dashboard.routes.pipeline_builder_page) pipeline_builder_bp (in module cellmap_flow.dashboard.routes.pipeline_builder_page) pipeline_for() (cellmap_flow.serving.chunkmirage_server.ChunkmirageServer method) pipeline_spec (cellmap_flow.dashboard.state.Session property) PipelineNode (class in cellmap_flow.dashboard.requests) PipelineSpec (class in cellmap_flow.pipeline_spec) PipelineUpdate (class in cellmap_flow.dashboard.routes.pipeline) pixi_env_of() (in module cellmap_flow.models.envs) pixi_environments() (in module cellmap_flow.models.envs) pixi_manifest() (in module cellmap_flow.models.envs) PIXI_MANIFEST_ENV (in module cellmap_flow.models.envs) pixi_program() (in module cellmap_flow.models.envs) PLACEHOLDER_DATA_PATHS (in module cellmap_flow.finetune.finetuned_model_templates) plan_volume() (in module cellmap_flow.finetune.session.volume) PLUGINS_DIR (in module cellmap_flow.plugins) plugins_group() (in module cellmap_flow.cli.main) point_latest_export() (in module cellmap_flow.finetune.run_outputs) POLL_SECONDS (cellmap_flow.inference.runner.DeviceSlots attribute) POOL_DTYPE (in module cellmap_flow.finetune.data.sampler) POOL_FACTOR (in module cellmap_flow.finetune.export_merged) populated_backing_store() (in module cellmap_flow.finetune.session.instance) post() (cellmap_flow.dashboard.routes.review_routes.PickBoard method)

postprocess (cellmap_flow.dashboard.routes.pipeline.PipelineUpdate attribute) (cellmap_flow.dashboard.state.Session property) (cellmap_flow.pipeline_spec.PipelineSpec attribute) (cellmap_flow.process_chain.ProcessChain attribute) (cellmap_flow.server.ServedChain attribute) postprocess_config (cellmap_flow.process_chain.ProcessChain attribute) POSTPROCESS_KEY (in module cellmap_flow.serving.protocol) PostprocessOp (class in cellmap_flow.serving.chunkmirage_ops) PostProcessor (built-in class) (class in cellmap_flow.post.postprocessors) postprocessors (cellmap_flow.dashboard.requests.BlockwisePipeline attribute) (cellmap_flow.dashboard.routes.pipeline.BuilderCanvas attribute) precheck() (in module cellmap_flow.blockwise.blockwise_processor) precheck_blockwise_task() (in module cellmap_flow.dashboard.routes.blockwise) precomputed_scale() (in module cellmap_flow.io.paths) precomputed_volume() (in module cellmap_flow.io.paths) predict() (cellmap_flow.inference.runner.ModelRunner method) (in module cellmap_flow.inference.runner) PREDICTION_CACHE_BYTES_DEFAULT (in module cellmap_flow.serving.chunkmirage_server) PREDICTION_CACHE_BYTES_ENV (in module cellmap_flow.serving.chunkmirage_server) PREDICTION_COLORS (in module cellmap_flow.viewer.raw) prediction_layer() (in module cellmap_flow.viewer.layers) PREDICTION_SHADER (in module cellmap_flow.viewer.raw) prediction_shader() (in module cellmap_flow.viewer.raw) prediction_shader_for() (in module cellmap_flow.viewer.layers) prediction_source() (in module cellmap_flow.viewer.layers) PREDICTION_TIMEOUT_SECONDS (in module cellmap_flow.dashboard.routes.finetune.view_labels) prediction_url() (in module cellmap_flow.viewer.layers) prediction_voxel_override() (in module cellmap_flow.viewer.layers) prefix() (in module cellmap_flow.models.envs) preflight (cellmap_flow.finetune.session.minio.MinioServer attribute) prepare() (cellmap_flow.finetune.adaptation.AdaptationStrategy method) (cellmap_flow.finetune.adaptation.FullStrategy method) (cellmap_flow.finetune.adaptation.LoraStrategy method) pretrained_model (cellmap_flow.models.configs.cellpose.CellposeModelConfig attribute) (cellmap_flow.models.models_config.CellposeModelConfig attribute) PRETRAINED_MODELS (in module cellmap_flow.models.configs.cellpose) previous_refresh_time (cellmap_flow.server.CellMapFlowServer attribute) print_available_models() (in module cellmap_flow.models.registry) print_lora_parameters() (in module cellmap_flow.finetune.lora_wrapper) probability() (in module cellmap_flow.dashboard.routes.finetune.view_labels) problem_with() (cellmap_flow.post.postprocessors.CellposeMasksPostprocessor method) (cellmap_flow.post.postprocessors.PostProcessor method) process (cellmap_flow.jobs.local.LocalJob attribute) process() (cellmap_flow.norm.input_normalize.SerializableInterface method) (in module cellmap_flow.dashboard.routes.pipeline) (PostProcessor method) process_chain() (in module cellmap_flow.process_chain) process_chunk() (cellmap_flow.inferencer.Inferencer method) (cellmap_flow.models.configs.bio.BioModelConfig method) (cellmap_flow.models.configs.cellpose.CellposeModelConfig method) (cellmap_flow.models.models_config.BioModelConfig method) (cellmap_flow.models.models_config.CellposeModelConfig method) process_chunk_basic() (cellmap_flow.inference.runner.ModelRunner method) process_fn() (cellmap_flow.blockwise.blockwise_processor.CellMapFlowBlockwiseProcessor method) process_only (cellmap_flow.blockwise.blockwise_processor.CellMapFlowBlockwiseProcessor attribute) ProcessChain (class in cellmap_flow.process_chain) Progress (class in cellmap_flow.dashboard.progress) progress_marker() (in module cellmap_flow.blockwise.blockwise_processor) proxied_url() (in module cellmap_flow.finetune.session.minio) public_server_url() (in module cellmap_flow.jobs.spec) put_pipeline() (in module cellmap_flow.dashboard.routes.pipeline) python() (in module cellmap_flow.models.envs) python_argv() (in module cellmap_flow.models.envs)

Q

queue (cellmap_flow.blockwise.blockwise_processor.CellMapFlowBlockwiseProcessor attribute) (cellmap_flow.dashboard.requests.BlockwiseSettings attribute) (cellmap_flow.dashboard.requests.BlockwiseTaskSettings attribute) (cellmap_flow.dashboard.requests.FinetuneSubmit attribute) (cellmap_flow.jobs.spec.Job attribute) (cellmap_flow.jobs.spec.JobSpec attribute)

QUEUES (in module cellmap_flow.review_index) queues() (in module cellmap_flow.review)

R

r (cellmap_flow.finetune.adaptation.AdaptationStrategy attribute) (cellmap_flow.finetune.adaptation.FullStrategy attribute) (cellmap_flow.finetune.adaptation.LoraStrategy attribute) RANK_PREFIX (in module cellmap_flow.review) ratio (cellmap_flow.serving.chunkmirage_ops.ServedModel attribute) raw (cellmap_flow.dashboard.state.Session attribute) raw() (cellmap_flow.finetune.data.reader.PatchReader method) RAW_CACHE_BYTES_DEFAULT (in module cellmap_flow.server) (in module cellmap_flow.serving.chunkmirage_server) RAW_CACHE_BYTES_ENV (in module cellmap_flow.server) (in module cellmap_flow.serving.chunkmirage_server) raw_dataset_path (cellmap_flow.finetune.data.dataset.VirtualPatchDataset attribute) (cellmap_flow.finetune.data.reader.PatchReader attribute) (cellmap_flow.finetune.data.VirtualPatchDataset attribute) raw_dimensions() (in module cellmap_flow.viewer.bootstrap) raw_layer() (in module cellmap_flow.viewer.layers) RAW_READ_CONCURRENCY_ENV (in module cellmap_flow.server) RAW_SHADER (in module cellmap_flow.viewer.raw) read() (cellmap_flow.finetune.job_manager.tailer.LogTailer method) (cellmap_flow.io.resample.Resampling method) (cellmap_flow.io.source.ArraySource method) (in module cellmap_flow.io.store) read_array_meta() (in module cellmap_flow.io.metadata) read_box() (cellmap_flow.image_data_interface.ImageDataInterface method) read_chunk() (cellmap_flow.serving.chunkmirage_server.ChunkmirageServer method) read_json() (in module cellmap_flow.io.store) read_manifest() (in module cellmap_flow.finetune.session.manifest) read_offsets_from_script() (in module cellmap_flow.finetune.target_transforms) read_or_create_restart_token() (in module cellmap_flow.serving.restart_token) read_padded() (in module cellmap_flow.io.source) read_prediction() (in module cellmap_flow.dashboard.routes.finetune.view_labels) read_ready_file() (in module cellmap_flow.jobs.ready) read_restart_token() (in module cellmap_flow.serving.restart_token) read_shape (cellmap_flow.models.geometry.ModelGeometry attribute) read_size (cellmap_flow.models.configs.cellpose.CellposeModelConfig property) (cellmap_flow.models.models_config.CellposeModelConfig property) read_volume() (in module cellmap_flow.finetune.session.volume) read_yaml() (in module cellmap_flow.dashboard.routes.finetune.yaml_crops) read_yaml_file() (in module cellmap_flow.finetune.crop_loader) read_zarr_json() (in module cellmap_flow.io.metadata) reader (cellmap_flow.finetune.data.dataset.VirtualPatchDataset attribute) (cellmap_flow.finetune.data.VirtualPatchDataset attribute) READY_ENV (in module cellmap_flow.jobs.ready) ready_file (cellmap_flow.jobs.lsf.LSFJob attribute) ready_path() (in module cellmap_flow.jobs.ready) rebuild_loader() (in module cellmap_flow.finetune.data) (in module cellmap_flow.finetune.data.loader) record() (cellmap_flow.finetune.session.volume.VolumeGeometry method) record_completion() (in module cellmap_flow.finetune.job_manager.persistence) record_verdict() (in module cellmap_flow.review) recorded_model_entry() (in module cellmap_flow.finetune.job_manager.persistence) ref (cellmap_flow.dashboard.routes.model_resolve.ResolveModel attribute) refresh_annotated_regions() (in module cellmap_flow.dashboard.routes.finetune.overlay) refresh_annotated_regions_layer() (in module cellmap_flow.dashboard.routes.finetune.overlay) refresh_annotation_layer() (in module cellmap_flow.dashboard.routes.finetune.overlay) refresh_bioimage_models() (in module cellmap_flow.models.bioimage_catalog) refresh_bioimage_models_route() (in module cellmap_flow.dashboard.routes.models) refresh_good_regions_layer() (in module cellmap_flow.dashboard.routes.finetune.good_regions) refresh_huggingface_models() (in module cellmap_flow.models.hf_catalog) refresh_huggingface_models_route() (in module cellmap_flow.dashboard.routes.models) refresh_rate_seconds (cellmap_flow.server.CellMapFlowServer attribute) register_cmd() (in module cellmap_flow.cli.main) register_finetuned_model() (in module cellmap_flow.dashboard.finetune_layers) register_plugin() (in module cellmap_flow.plugins) register_volume() (cellmap_flow.finetune.session.store.SessionStore method) registry (cellmap_flow.serving.chunkmirage_server.ChunkmirageServer attribute) regularize_offset() (in module cellmap_flow.io.metadata) rehearsal_centres (cellmap_flow.finetune.data.sampler.PatchSampler attribute) rehearsal_fraction (cellmap_flow.finetune.data.sampler.PatchSampler attribute) rehydrate() (in module cellmap_flow.finetune.job_manager.persistence) rehydrate_session() (cellmap_flow.finetune.job_manager.manager.FinetuneJobManager method) REL_TOL (in module cellmap_flow.finetune.export_merged) relabel_instances() (in module cellmap_flow.post.segment) relabel_objects() (in module cellmap_flow.finetune.session.fill) remap_labels() (in module cellmap_flow.finetune.crop_loader) remove() (cellmap_flow.finetune.job_manager.listener.Listeners method) remove_layer_from_viewer() (in module cellmap_flow.dashboard.routes.finetune.layers) remove_listener() (cellmap_flow.finetune.job_manager.manager.FinetuneJobManager method) remove_small() (in module cellmap_flow.post.segment) REMOVED_IN (in module cellmap_flow.cli.common) rename_layer_in_viewer() (in module cellmap_flow.dashboard.routes.finetune.layers) reorder_to_zarr_axes() (in module cellmap_flow.serving.virtual_zarr) repo (cellmap_flow.models.configs.huggingface.HuggingFaceModelConfig attribute) (cellmap_flow.models.models_config.HuggingFaceModelConfig attribute) report() (cellmap_flow.finetune.data.augment.Augmentation method) (in module cellmap_flow.cli.doctor)

request_restart() (cellmap_flow.finetune.session_loop.RestartController method) (in module cellmap_flow.finetune.job_manager.restart) requested_voxel_size (cellmap_flow.image_data_interface.ImageDataInterface attribute) required_params() (in module cellmap_flow.models.registry) REQUIRED_TABLES (in module cellmap_flow.review) resample (cellmap_flow.dashboard.requests.SubmitModels attribute) (cellmap_flow.dashboard.state.Session attribute) (cellmap_flow.finetune.data.reader.PatchReader attribute) (cellmap_flow.finetune.session.volume.VolumeGeometry attribute) (cellmap_flow.serving.chunkmirage_server.ChunkmirageServer attribute) RESAMPLE_HINT (in module cellmap_flow.image_data_interface) resample_option() (in module cellmap_flow.cli.common) resampled (cellmap_flow.image_data_interface.ImageDataInterface property) Resampling (class in cellmap_flow.io.resample) reset() (cellmap_flow.finetune.adaptation.AdaptationStrategy method) (cellmap_flow.finetune.adaptation.FullStrategy method) (cellmap_flow.finetune.adaptation.LoraStrategy method) resolve() (in module cellmap_flow.models.resolve) resolve_data_path() (in module cellmap_flow.config.yaml) resolve_db_path() (in module cellmap_flow.review) resolve_finetune_session() (in module cellmap_flow.dashboard.routes.finetune.common) resolve_model() (in module cellmap_flow.dashboard.routes.model_resolve) resolve_model_geometry() (in module cellmap_flow.models.geometry_cache) resolve_model_type() (in module cellmap_flow.finetune.job_manager.submit) Resolved (class in cellmap_flow.models.resolve) ResolveModel (class in cellmap_flow.dashboard.routes.model_resolve) response() (cellmap_flow.dashboard.progress.Progress method) restart() (cellmap_flow.finetune.adaptation.AdaptationStrategy method) (cellmap_flow.finetune.adaptation.FullStrategy method) (cellmap_flow.finetune.adaptation.LoraStrategy method) restart_callback (cellmap_flow.server.CellMapFlowServer attribute) (cellmap_flow.serving.chunkmirage_server.ChunkmirageServer attribute) restart_controller (cellmap_flow.finetune.session_loop.TrainingSession attribute) RESTART_FAILED (in module cellmap_flow.finetune.markers) restart_finetuning_job() (cellmap_flow.finetune.job_manager.manager.FinetuneJobManager method) (in module cellmap_flow.dashboard.routes.finetune.training) RESTART_PASSTHROUGH_KEYS (in module cellmap_flow.dashboard.routes.finetune.common) RESTART_STATUS (in module cellmap_flow.finetune.markers) restart_token (cellmap_flow.server.CellMapFlowServer attribute) (cellmap_flow.serving.chunkmirage_server.ChunkmirageServer attribute) RESTARTABLE_ARGS (in module cellmap_flow.finetune.cli) RestartController (class in cellmap_flow.finetune.session_loop) RESTARTING_TRAINING (in module cellmap_flow.finetune.markers) restore_box() (in module cellmap_flow.finetune.session.fill) Result (class in cellmap_flow.cli.doctor) review (cellmap_flow.dashboard.state.Session attribute) review_bp (in module cellmap_flow.dashboard.routes.review_routes) review_next() (in module cellmap_flow.dashboard.routes.review_routes) review_open() (in module cellmap_flow.dashboard.routes.review_routes) review_pick_stream() (in module cellmap_flow.dashboard.routes.review_routes) review_postprocess() (in module cellmap_flow.serving.probe) review_progress() (in module cellmap_flow.dashboard.routes.review_routes) review_show() (in module cellmap_flow.dashboard.routes.review_routes) review_status() (in module cellmap_flow.dashboard.routes.review_routes) review_undo() (in module cellmap_flow.dashboard.routes.review_routes) review_verdict() (in module cellmap_flow.dashboard.routes.review_routes) reviewer (cellmap_flow.dashboard.routes.review_routes.ReviewSession attribute) ReviewSession (class in cellmap_flow.dashboard.routes.review_routes) revision (cellmap_flow.models.configs.huggingface.HuggingFaceModelConfig attribute) (cellmap_flow.models.models_config.HuggingFaceModelConfig attribute) rewrite_foreground() (in module cellmap_flow.finetune.session.fill) rewrite_minio_url_for_proxy() (in module cellmap_flow.dashboard.routes.finetune.common) roi (cellmap_flow.image_data_interface.ImageDataInterface attribute) root_base_model_dict() (in module cellmap_flow.finetune.model_loading) run() (cellmap_flow.blockwise.blockwise_processor.CellMapFlowBlockwiseProcessor method) (cellmap_flow.finetune.session_loop.TrainingSession method) (cellmap_flow.server.CellMapFlowServer method) (cellmap_flow.serving.chunkmirage_server.ChunkmirageServer method) (in module cellmap_flow.jobs.local) run_bioimage_model() (in module cellmap_flow.dashboard.services.launch) run_cellpose_model() (in module cellmap_flow.dashboard.services.launch) run_checks() (in module cellmap_flow.cli.doctor) run_generic() (in module cellmap_flow.cli.infer) run_hf_model() (in module cellmap_flow.dashboard.services.launch) run_metadata() (in module cellmap_flow.models.configs.fly) run_model() (in module cellmap_flow.dashboard.services.launch) run_model_config() (in module cellmap_flow.dashboard.services.launch) run_multiple() (in module cellmap_flow.cli.yaml_cli) run_name (cellmap_flow.models.configs.dacapo.DaCapoModelConfig attribute) (cellmap_flow.models.models_config.DaCapoModelConfig attribute) run_server() (in module cellmap_flow.cli.server_cli) runner (cellmap_flow.serving.chunkmirage_ops.ServedModel attribute) RUNNING (cellmap_flow.finetune.job_manager.state.JobStatus attribute) (cellmap_flow.jobs.spec.JobStatus attribute) running() (cellmap_flow.finetune.session.minio.MinioServer method) running_job_host() (in module cellmap_flow.serving.client) running_names() (in module cellmap_flow.dashboard.services.launch)

S

SAM_TILE_SIZE (in module cellmap_flow.models.configs.cellpose) same_voxel_size() (in module cellmap_flow.io.multiscale) sampler (cellmap_flow.finetune.data.dataset.VirtualPatchDataset attribute) (cellmap_flow.finetune.data.VirtualPatchDataset attribute) saturation (cellmap_flow.finetune.losses.IntervalLoss attribute) SATURATION_SIGMAS (in module cellmap_flow.finetune.target_transforms) save() (cellmap_flow.jobs.settings.LauncherSettings method) save_adapter() (cellmap_flow.finetune.lora_trainer.LoRAFinetuner method) save_checkpoint() (cellmap_flow.finetune.lora_trainer.LoRAFinetuner method) save_good_regions() (in module cellmap_flow.dashboard.routes.finetune.good_regions) (in module cellmap_flow.finetune.session.manifest) save_lora_adapter() (in module cellmap_flow.finetune.lora_wrapper) save_server_config() (cellmap_flow.dashboard.state.Session method) (cellmap_flow.globals.Flow method) save_server_config_cache() (in module cellmap_flow.jobs.settings) save_user_prefs() (in module cellmap_flow.dashboard.routes.finetune.common) scale (cellmap_flow.models.configs.bio.BioModelConfig attribute) (cellmap_flow.models.configs.cellmap.CellMapModelConfig attribute) (cellmap_flow.models.configs.cellpose.CellposeModelConfig attribute) (cellmap_flow.models.configs.dacapo.DaCapoModelConfig attribute) (cellmap_flow.models.configs.finetune.FinetuneModelConfig attribute) (cellmap_flow.models.configs.fly.FlyModelConfig attribute) (cellmap_flow.models.configs.huggingface.HuggingFaceModelConfig attribute) (cellmap_flow.models.configs.script.ScriptModelConfig attribute) (cellmap_flow.models.models_config.BioModelConfig attribute) (cellmap_flow.models.models_config.CellMapModelConfig attribute) (cellmap_flow.models.models_config.CellposeModelConfig attribute) (cellmap_flow.models.models_config.DaCapoModelConfig attribute) (cellmap_flow.models.models_config.FinetuneModelConfig attribute) (cellmap_flow.models.models_config.FlyModelConfig attribute) (cellmap_flow.models.models_config.HuggingFaceModelConfig attribute) (cellmap_flow.models.models_config.ScriptModelConfig attribute) ScaleLinear (class in cellmap_flow.finetune.trainable) ScalePyramid (class in cellmap_flow.viewer.raw) scaler (cellmap_flow.finetune.lora_trainer.LoRAFinetuner attribute) ScaleRange (class in cellmap_flow.finetune.trainable) script_path (cellmap_flow.models.configs.script.ScriptModelConfig attribute) (cellmap_flow.models.models_config.ScriptModelConfig attribute) ScriptModelConfig (class in cellmap_flow.models.configs.script) (class in cellmap_flow.models.models_config) seed (cellmap_flow.finetune.crop_loader.CropsConfig attribute) (cellmap_flow.finetune.data.dataset.VirtualPatchDataset attribute) (cellmap_flow.finetune.data.VirtualPatchDataset attribute) seed_instance_volume() (in module cellmap_flow.finetune.session.instance) seed_labels() (in module cellmap_flow.finetune.session.fill) SEED_METHODS (in module cellmap_flow.dashboard.routes.finetune.view_labels) seed_methods() (in module cellmap_flow.dashboard.routes.finetune.view_labels) seed_sources() (in module cellmap_flow.dashboard.routes.finetune.view_labels) seed_view_from_prediction() (in module cellmap_flow.dashboard.routes.finetune.view_labels) segment_prediction() (in module cellmap_flow.dashboard.routes.finetune.view_labels) segmentation_layer (cellmap_flow.dashboard.routes.review_routes.ReviewSession attribute) select_channel (cellmap_flow.dashboard.requests.FinetuneSubmit attribute) (cellmap_flow.finetune.lora_trainer.LoRAFinetuner attribute) select_channel() (in module cellmap_flow.image_data_interface) select_dataset() (in module cellmap_flow.io.multiscale) select_level() (in module cellmap_flow.io.multiscale) selected() (cellmap_flow.image_data_interface.LazyNormalization method) selected_bioimage_models (cellmap_flow.dashboard.requests.SubmitModels attribute) selected_cellpose_models (cellmap_flow.dashboard.requests.SubmitModels attribute) selected_channel() (in module cellmap_flow.image_data_interface) selected_hf_models (cellmap_flow.dashboard.requests.SubmitModels attribute) selected_models (cellmap_flow.dashboard.requests.SubmitModels attribute) separate_zarrs (cellmap_flow.blockwise.blockwise_processor.CellMapFlowBlockwiseProcessor attribute) seq (cellmap_flow.dashboard.routes.review_routes.PickBoard attribute) SequentialWrapper (class in cellmap_flow.finetune.lora_wrapper) SerializableInterface (class in cellmap_flow.norm.input_normalize) serve() (in module cellmap_flow.cli.server_cli) serve_entry() (in module cellmap_flow.cli.server_cli) serve_model() (in module cellmap_flow.serving.chunkmirage_ops) serve_new_volume() (in module cellmap_flow.dashboard.routes.finetune.annotation_core) serve_trained() (cellmap_flow.models.configs.base.ModelConfig method) (cellmap_flow.models.configs.bio.BioModelConfig method) (cellmap_flow.models.configs.cellpose.CellposeModelConfig method) (cellmap_flow.models.models_config.BioModelConfig method) (cellmap_flow.models.models_config.CellposeModelConfig method) (cellmap_flow.models.models_config.ModelConfig method) served (cellmap_flow.serving.chunkmirage_ops.InferenceOp property) (cellmap_flow.serving.chunkmirage_ops.PostprocessOp property) (cellmap_flow.serving.chunkmirage_server.ChunkmirageServer attribute) served_dtype() (in module cellmap_flow.models.configs.bio) served_model() (in module cellmap_flow.serving.chunkmirage_ops) served_spatial_shape() (in module cellmap_flow.serving.virtual_zarr) ServedChain (class in cellmap_flow.server) ServedModel (class in cellmap_flow.serving.chunkmirage_ops) server_argv() (in module cellmap_flow.models.envs) (in module cellmap_flow.serving.launch) server_argv_for() (in module cellmap_flow.serving.launch) SERVER_COMMAND (in module cellmap_flow.jobs.launch) server_command() (in module cellmap_flow.serving.launch) server_command_for() (in module cellmap_flow.serving.launch) server_config (cellmap_flow.dashboard.state.Session property) server_config_cached (cellmap_flow.dashboard.state.Session property) SERVER_CONFIG_DEFAULTS (in module cellmap_flow.jobs.settings) SERVER_CONFIG_KEYS (in module cellmap_flow.jobs.settings) SERVER_CONFIG_PATH (in module cellmap_flow.jobs.settings) server_cpus (cellmap_flow.jobs.site.SiteProfile attribute) SERVER_LOG_DIR (in module cellmap_flow.jobs.launch) server_started (cellmap_flow.finetune.session_loop.TrainingSession attribute) SERVER_URL_RE (in module cellmap_flow.finetune.markers) SERVER_URL_TEMPLATE_ENV (in module cellmap_flow.jobs.spec) ServerConfigUpdate (class in cellmap_flow.dashboard.requests) Session (class in cellmap_flow.dashboard.state) SESSION_DIR_RE (in module cellmap_flow.finetune.session.store) session_store() (in module cellmap_flow.dashboard.routes.finetune.common) session_volume() (cellmap_flow.finetune.session.store.SessionStore method) SessionStore (class in cellmap_flow.finetune.session.store) set() (cellmap_flow.process_chain.ProcessChain method) set_data() (in module cellmap_flow.dashboard.routes.index_page) set_pipeline() (cellmap_flow.dashboard.state.Session method) (cellmap_flow.globals.Flow method) set_user_prefs() (in module cellmap_flow.dashboard.routes.finetune.annotation_core) SetData (class in cellmap_flow.dashboard.requests) settings (cellmap_flow.dashboard.state.Session property) settings() (cellmap_flow.dashboard.requests.ModelNode method)

shader_controls (cellmap_flow.dashboard.state.Session attribute) shaders (cellmap_flow.dashboard.state.Session attribute) shape (cellmap_flow.dashboard.requests.BoundingBox attribute) (cellmap_flow.image_data_interface.ImageDataInterface attribute) (cellmap_flow.io.geometry.Box attribute) (cellmap_flow.io.metadata.ArrayMeta attribute) (cellmap_flow.io.resample.Resampling property) shape_voxels (cellmap_flow.finetune.data.reader.PatchReader attribute) shell (cellmap_flow.jobs.spec.JobSpec attribute) shell_join() (in module cellmap_flow.jobs.spec) shell_quote() (in module cellmap_flow.jobs.spec) SHIFT_TO_SIGNED (in module cellmap_flow.serving.probe) sigma (cellmap_flow.finetune.target_transforms.DistanceTargetTransform attribute) sigma_nm (cellmap_flow.finetune.target_transforms.IntervalTargetTransform attribute) sigmoid (cellmap_flow.models.configs.fly.FlyModelConfig attribute) (cellmap_flow.models.models_config.FlyModelConfig attribute) SigmoidPostprocessor (class in cellmap_flow.post.postprocessors) sign_weight (cellmap_flow.finetune.losses.IntervalLoss attribute) SIGNED_UNIT (in module cellmap_flow.serving.probe) SimpleBlockwiseMerger (built-in class) (class in cellmap_flow.post.postprocessors) singlescale_attrs() (in module cellmap_flow.io.ome) SiteProfile (class in cellmap_flow.jobs.site) size (cellmap_flow.norm.input_normalize.Dilate attribute) slack (cellmap_flow.finetune.losses.IntervalLoss attribute) slice_size (cellmap_flow.models.configs.cellpose.CellposeModelConfig attribute) (cellmap_flow.models.models_config.CellposeModelConfig attribute) slices (cellmap_flow.post.postprocessors.SimpleBlockwiseMerger attribute) slices_per_chunk (cellmap_flow.models.configs.bio.BioModelConfig attribute) (cellmap_flow.models.configs.cellpose.CellposeModelConfig attribute) (cellmap_flow.models.models_config.BioModelConfig attribute) (cellmap_flow.models.models_config.CellposeModelConfig attribute) SliceWise (class in cellmap_flow.finetune.trainable) slope_term() (cellmap_flow.finetune.losses.IntervalLoss method) slope_weight (cellmap_flow.finetune.losses.IntervalLoss attribute) slots (cellmap_flow.serving.chunkmirage_ops.DevicePostprocessOp attribute) (cellmap_flow.serving.chunkmirage_ops.InferenceOp attribute) smooth (cellmap_flow.finetune.losses.DiceLoss attribute) snap() (cellmap_flow.finetune.data.reader.PatchReader method) snap_integral() (in module cellmap_flow.io.metadata) snapshot_from_minio() (in module cellmap_flow.finetune.session.instance) soft_target_entropy() (in module cellmap_flow.finetune.losses) source (cellmap_flow.image_data_interface.ImageDataInterface attribute) (cellmap_flow.serving.chunkmirage_server.ChunkmirageServer attribute) source_shape (cellmap_flow.io.resample.Resampling attribute) source_voxel_size (cellmap_flow.io.resample.Resampling attribute) sparse_chunk_starts (cellmap_flow.finetune.data.sampler.PatchSampler attribute) sparse_foreground_rows (cellmap_flow.finetune.data.sampler.PatchSampler attribute) SPARSE_MSE_NOTE (in module cellmap_flow.dashboard.routes.finetune.common) spatial() (cellmap_flow.finetune.data.augment.Augmentation method) (cellmap_flow.io.metadata.ArrayMeta method) spatial_axes() (in module cellmap_flow.io.metadata) spatial_indices (cellmap_flow.io.metadata.ArrayMeta property) spatial_ndim (cellmap_flow.image_data_interface.LazyNormalization attribute) spawn_worker() (in module cellmap_flow.blockwise.blockwise_processor) spec (cellmap_flow.process_chain.ProcessChain property) split_container() (in module cellmap_flow.io.paths) split_dataset_url() (in module cellmap_flow.serving.protocol) split_view_objects() (in module cellmap_flow.dashboard.routes.finetune.view_labels) stage() (in module cellmap_flow.inference.timing) stage_dtype (cellmap_flow.serving.chunkmirage_ops.ServedModel attribute) STALE_AFTER_S (in module cellmap_flow.models.bioimage_catalog) start() (in module cellmap_flow.inference.timing) start_bbx_generator() (in module cellmap_flow.dashboard.routes.bbx_generator) start_hosts() (in module cellmap_flow.jobs.launch) start_iteration() (in module cellmap_flow.finetune.job_manager.state) start_periodic_sync() (in module cellmap_flow.finetune.session.sync) started_jobs() (in module cellmap_flow.jobs.launch) starting_jobs() (in module cellmap_flow.jobs.launch) startup_timeout_seconds (cellmap_flow.jobs.site.SiteProfile attribute) STARTUP_TIMEOUT_SECONDS (in module cellmap_flow.jobs.launch) state (cellmap_flow.finetune.session.minio.MinioServer attribute) static_dir (in module cellmap_flow.dashboard.app) status (cellmap_flow.cli.doctor.Result attribute) (cellmap_flow.finetune.job_manager.state.FinetuneJob attribute) (cellmap_flow.jobs.spec.Job attribute) STATUS_MARKER_RE (in module cellmap_flow.finetune.markers) statuses() (in module cellmap_flow.jobs.lsf) std (cellmap_flow.norm.input_normalize.ZScoreNormalizer attribute) step (cellmap_flow.serving.chunkmirage_ops.PostprocessOp attribute) stitch_threshold (cellmap_flow.dashboard.requests.CellposeSelection attribute) (cellmap_flow.models.configs.cellpose.CellposeModelConfig attribute) (cellmap_flow.models.models_config.CellposeModelConfig attribute) (cellmap_flow.post.postprocessors.CellposeMasksPostprocessor attribute) stop() (cellmap_flow.serving.chunkmirage_server.ChunkmirageServer method) stop_training_early() (in module cellmap_flow.dashboard.routes.finetune.training) store_geometry() (in module cellmap_flow.models.geometry_cache) strategy (cellmap_flow.finetune.lora_trainer.LoRAFinetuner attribute) strategy_for() (in module cellmap_flow.finetune.adaptation) stream_job_logs() (in module cellmap_flow.dashboard.routes.finetune.training) stream_logs() (in module cellmap_flow.dashboard.routes.logging_routes) submission_metadata() (in module cellmap_flow.finetune.job_manager.persistence) submit() (in module cellmap_flow.jobs.lsf) submit_blockwise_task() (in module cellmap_flow.dashboard.routes.blockwise) submit_bsub_job() (in module cellmap_flow.jobs.launch) submit_finetuning() (in module cellmap_flow.dashboard.routes.finetune.training) submit_finetuning_job() (cellmap_flow.finetune.job_manager.manager.FinetuneJobManager method) submit_models() (in module cellmap_flow.dashboard.routes.models) SubmitModels (class in cellmap_flow.dashboard.requests) suffix_format() (in module cellmap_flow.io.paths) suggest_affinity_chain() (in module cellmap_flow.serving.probe) suggest_input_norm() (in module cellmap_flow.serving.probe) suggest_postprocess_params() (in module cellmap_flow.serving.probe) SumModelMerger (class in cellmap_flow.models.model_merger) sync_all() (in module cellmap_flow.finetune.session.sync) sync_all_annotations_from_minio() (in module cellmap_flow.dashboard.finetune_utils) sync_annotation_volume_from_minio() (in module cellmap_flow.dashboard.finetune_utils) sync_annotations_manually() (in module cellmap_flow.dashboard.routes.finetune.overlay) SYNC_FAILURE_WARNING_INTERVAL (in module cellmap_flow.finetune.session.sync) sync_instance_correction() (in module cellmap_flow.dashboard.routes.finetune.instance_correction) SYNC_INTERVAL_S (in module cellmap_flow.jobs.synced_tee) SYNC_PERIOD_SECONDS (in module cellmap_flow.finetune.session.sync) sync_volume() (in module cellmap_flow.finetune.session.sync) sync_zarr_group_metadata() (in module cellmap_flow.finetune.session.sync) SYNCED_TEE (in module cellmap_flow.finetune.job_manager.submit)

T

T (in module cellmap_flow.io.store) tail() (in module cellmap_flow.jobs.spec) target_modules (cellmap_flow.finetune.adaptation.LoraStrategy attribute) target_transform (cellmap_flow.finetune.lora_trainer.LoRAFinetuner attribute) target_voxel_size (cellmap_flow.io.resample.Resampling attribute) TargetTransform (class in cellmap_flow.finetune.target_transforms) task_name (cellmap_flow.blockwise.blockwise_processor.CellMapFlowBlockwiseProcessor attribute) (cellmap_flow.dashboard.requests.BlockwiseSubmit attribute) tasks_dir() (cellmap_flow.dashboard.state.Session method) tb (cellmap_flow.finetune.lora_trainer.LoRAFinetuner attribute) tb_dir (cellmap_flow.finetune.lora_trainer.LoRAFinetuner attribute) tb_image_every (cellmap_flow.finetune.lora_trainer.LoRAFinetuner attribute) tb_position (cellmap_flow.finetune.session_loop.TrainingSession attribute) teacher() (cellmap_flow.finetune.adaptation.AdaptationStrategy method) (cellmap_flow.finetune.adaptation.FullStrategy method) (cellmap_flow.finetune.adaptation.LoraStrategy method) teacher_model (cellmap_flow.finetune.adaptation.AdaptationStrategy attribute) (cellmap_flow.finetune.adaptation.FullStrategy attribute) (cellmap_flow.finetune.adaptation.LoraStrategy attribute) (cellmap_flow.finetune.lora_trainer.LoRAFinetuner property) (cellmap_flow.finetune.session_loop.TrainingSession attribute) tee() (in module cellmap_flow.jobs.synced_tee) TEE_PYTHON (in module cellmap_flow.finetune.job_manager.submit) template_dir (in module cellmap_flow.dashboard.app) TERMINAL_STATUSES (in module cellmap_flow.finetune.job_manager.state) threshold (cellmap_flow.post.postprocessors.FillHolesPostprocessor attribute) (cellmap_flow.post.postprocessors.ThresholdPostprocessor attribute) ThresholdPostprocessor (built-in class) (class in cellmap_flow.post.postprocessors) TILE_OVERLAP (in module cellmap_flow.models.configs.cellpose) tile_size() (in module cellmap_flow.models.configs.cellpose) tiles_per_slice() (in module cellmap_flow.models.configs.cellpose) tmp_dir (cellmap_flow.dashboard.requests.BlockwiseSettings attribute) (cellmap_flow.dashboard.requests.BlockwiseTaskSettings attribute) (cellmap_flow.dashboard.state.Session attribute) to_dict() (cellmap_flow.finetune.job_manager.state.FinetuneJob method) (cellmap_flow.models.configs.base.Config method) (cellmap_flow.models.configs.base.ModelConfig method) (cellmap_flow.models.configs.bio.BioModelConfig method) (cellmap_flow.models.configs.cellmap.CellMapModelConfig method) (cellmap_flow.models.configs.cellpose.CellposeModelConfig method) (cellmap_flow.models.configs.dacapo.DaCapoModelConfig method) (cellmap_flow.models.configs.finetune.FinetuneModelConfig method) (cellmap_flow.models.configs.fly.FlyModelConfig method) (cellmap_flow.models.configs.huggingface.HuggingFaceModelConfig method) (cellmap_flow.models.configs.script.ScriptModelConfig method) (cellmap_flow.models.models_config.BioModelConfig method) (cellmap_flow.models.models_config.CellMapModelConfig method) (cellmap_flow.models.models_config.CellposeModelConfig method) (cellmap_flow.models.models_config.Config method) (cellmap_flow.models.models_config.DaCapoModelConfig method) (cellmap_flow.models.models_config.FinetuneModelConfig method) (cellmap_flow.models.models_config.FlyModelConfig method) (cellmap_flow.models.models_config.HuggingFaceModelConfig method) (cellmap_flow.models.models_config.ModelConfig method) (cellmap_flow.models.models_config.ScriptModelConfig method) (cellmap_flow.norm.input_normalize.SerializableInterface method) (PostProcessor method)

to_json() (cellmap_flow.models.resolve.Resolved method) to_json_data() (cellmap_flow.pipeline_spec.PipelineSpec method) to_model_info() (cellmap_flow.models.geometry.ModelGeometry method) to_ndarray_ts() (cellmap_flow.image_data_interface.ImageDataInterface method) (cellmap_flow.serving.chunkmirage_ops.BlockInput method) to_nm() (in module cellmap_flow.io.metadata) to_url_blob() (cellmap_flow.pipeline_spec.PipelineSpec method) token (cellmap_flow.viewer.raw.ScalePyramid property) TOKEN_FILE (in module cellmap_flow.serving.restart_token) TOKEN_HEADER (in module cellmap_flow.serving.restart_token) tokens_match() (in module cellmap_flow.serving.restart_token) total_epochs (cellmap_flow.finetune.job_manager.state.FinetuneJob attribute) track_progress (cellmap_flow.blockwise.blockwise_processor.CellMapFlowBlockwiseProcessor attribute) train() (cellmap_flow.finetune.lora_trainer.LoRAFinetuner method) train_mode() (cellmap_flow.finetune.adaptation.AdaptationStrategy method) (cellmap_flow.finetune.adaptation.FullStrategy method) (cellmap_flow.finetune.adaptation.LoraStrategy method) TRAIN_TILE (in module cellmap_flow.finetune.export_merged) trainable_model() (cellmap_flow.models.configs.base.ModelConfig method) (cellmap_flow.models.configs.bio.BioModelConfig method) (cellmap_flow.models.configs.cellpose.CellposeModelConfig method) (cellmap_flow.models.configs.finetune.FinetuneModelConfig method) (cellmap_flow.models.models_config.BioModelConfig method) (cellmap_flow.models.models_config.CellposeModelConfig method) (cellmap_flow.models.models_config.FinetuneModelConfig method) (cellmap_flow.models.models_config.ModelConfig method) trainable_model_types() (in module cellmap_flow.finetune.job_manager.submit) trainable_state() (cellmap_flow.finetune.adaptation.AdaptationStrategy method) (cellmap_flow.finetune.adaptation.FullStrategy method) (cellmap_flow.finetune.adaptation.LoraStrategy method) TRAINABLE_WEIGHT_FORMATS (in module cellmap_flow.models.configs.bio) trained_at() (in module cellmap_flow.models.bioimage_catalog) trained_at_geometry() (in module cellmap_flow.models.configs.finetune) trained_voxel_sizes() (in module cellmap_flow.finetune.run_outputs) TRAINED_VOXEL_SIZES_FILE (in module cellmap_flow.models.bioimage_catalog) trainer_outputs_from_log() (in module cellmap_flow.finetune.job_manager.tailer) TRAINING_DIVERGED (in module cellmap_flow.finetune.markers) TRAINING_ITERATION_COMPLETE (in module cellmap_flow.finetune.markers) training_patch_voxels() (cellmap_flow.models.configs.cellpose.CellposeModelConfig method) (cellmap_flow.models.models_config.CellposeModelConfig method) (in module cellmap_flow.finetune.data.loader) training_settings() (in module cellmap_flow.dashboard.routes.finetune.common) training_stats (cellmap_flow.finetune.lora_trainer.LoRAFinetuner attribute) TRAINING_TILE (in module cellmap_flow.models.configs.fly) TrainingSession (class in cellmap_flow.finetune.session_loop) TrainingSettings (class in cellmap_flow.dashboard.routes.finetune.common) translation (cellmap_flow.io.geometry.Grid attribute) (cellmap_flow.io.metadata.ArrayMeta attribute) ts (cellmap_flow.image_data_interface.ImageDataInterface property) (cellmap_flow.io.source.ArraySource property) ts_dataset (cellmap_flow.image_data_interface.LazyNormalization attribute) type (cellmap_flow.models.resolve.Resolved attribute), [1] (cellmap_flow.norm.input_normalize.EuclideanDistance attribute) type_default() (in module cellmap_flow.models.envs)

U

UNANSWERED_RETRY_SECONDS (in module cellmap_flow.dashboard.routes.finetune.view_labels) UNBOUNDED (in module cellmap_flow.serving.probe) UNDO_DEPTH (in module cellmap_flow.dashboard.routes.finetune.view_labels) undo_verdict() (in module cellmap_flow.review) undo_view_labels() (in module cellmap_flow.dashboard.routes.finetune.view_labels) unet_arguments() (in module cellmap_flow.models.configs.fly) UNIT (in module cellmap_flow.serving.probe) units (cellmap_flow.io.metadata.ArrayMeta attribute) unregister_cmd() (in module cellmap_flow.cli.main) unregister_plugin() (in module cellmap_flow.plugins) update() (cellmap_flow.dashboard.progress.Progress method) update_equivalences() (in module cellmap_flow.dashboard.routes.pipeline) update_metadata() (in module cellmap_flow.finetune.job_manager.persistence)

update_run_metadata() (in module cellmap_flow.finetune.cli) update_run_models() (in module cellmap_flow.dashboard.services.launch) update_server_config() (in module cellmap_flow.dashboard.routes.models) updates() (cellmap_flow.dashboard.requests.ServerConfigUpdate method) url_for() (cellmap_flow.finetune.session.minio.MinioServer method) URL_SCHEMES (in module cellmap_flow.io.store) 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.inference.runner.ModelRunner attribute) use_mixed_precision (cellmap_flow.finetune.lora_trainer.LoRAFinetuner attribute) USER_PREFS_FILE (in module cellmap_flow.dashboard.routes.finetune.common) uses_device (cellmap_flow.post.postprocessors.CellposeMasksPostprocessor attribute)

V

VALID_ENTRY_METHODS (in module cellmap_flow.review) valid_tile() (in module cellmap_flow.finetune.export_merged) VALID_VERDICTS (in module cellmap_flow.review) validate() (in module cellmap_flow.models.envs) validate_blockwise() (in module cellmap_flow.dashboard.routes.blockwise) validate_model_shapes (cellmap_flow.models.configs.base.ModelConfig attribute) (cellmap_flow.models.models_config.ModelConfig attribute) validate_pipeline_config() (in module cellmap_flow.dashboard.routes.pipeline) view (in module cellmap_flow.cli.aliases) view_box_nm() (in module cellmap_flow.dashboard.routes.finetune.good_regions) viewer (cellmap_flow.dashboard.state.Session attribute) viewer_position_and_scales() (in module cellmap_flow.dashboard.routes.finetune.common) viewer_url_for() (in module cellmap_flow.dashboard.routes.index_page) VIRTUAL_MANIFEST_FILENAME (in module cellmap_flow.finetune.session.manifest) VirtualPatchDataset (class in cellmap_flow.finetune.data) (class in cellmap_flow.finetune.data.dataset) volume_corner_nm() (in module cellmap_flow.finetune.session.volume) volume_layers (cellmap_flow.viewer.raw.ScalePyramid attribute) volume_record() (in module cellmap_flow.finetune.session.sync) volume_type (cellmap_flow.viewer.raw.ScalePyramid property)

volume_zarr_path (cellmap_flow.finetune.data.dataset.VirtualPatchDataset attribute) (cellmap_flow.finetune.data.reader.PatchReader attribute) (cellmap_flow.finetune.data.sampler.PatchSampler attribute) (cellmap_flow.finetune.data.VirtualPatchDataset attribute) VolumeGeometry (class in cellmap_flow.finetune.session.volume) volumes (cellmap_flow.finetune.session.minio.MinioServer attribute) volumes() (cellmap_flow.finetune.session.store.SessionStore method) voxel_size (cellmap_flow.dashboard.requests.BioimageSelection attribute) (cellmap_flow.dashboard.requests.CellposeSelection attribute) (cellmap_flow.dashboard.routes.model_resolve.ResolveModel attribute) (cellmap_flow.image_data_interface.ImageDataInterface attribute) (cellmap_flow.io.geometry.Grid attribute) (cellmap_flow.io.metadata.ArrayMeta attribute) (cellmap_flow.models.configs.bio.BioModelConfig attribute) (cellmap_flow.models.configs.cellpose.CellposeModelConfig attribute) (cellmap_flow.models.models_config.BioModelConfig attribute) (cellmap_flow.models.models_config.CellposeModelConfig attribute) voxel_size_nm (cellmap_flow.finetune.losses.IntervalLoss attribute) (cellmap_flow.finetune.target_transforms.IntervalTargetTransform attribute) voxels_inside_any_bbox() (in module cellmap_flow.finetune.session.manifest)

W

wait_for_host() (cellmap_flow.jobs.local.LocalJob method) (cellmap_flow.jobs.lsf.LSFJob method) (cellmap_flow.jobs.spec.Job method) wait_for_ready() (in module cellmap_flow.finetune.session.minio) wait_past() (cellmap_flow.dashboard.routes.review_routes.PickBoard method) WAITING_FOR_RESTART (cellmap_flow.finetune.job_manager.state.JobStatus attribute) (in module cellmap_flow.finetune.markers) walltime (cellmap_flow.blockwise.blockwise_processor.CellMapFlowBlockwiseProcessor attribute) (cellmap_flow.jobs.spec.JobSpec attribute) walltime_arg() (in module cellmap_flow.jobs.lsf) WARN (in module cellmap_flow.cli.doctor) weight_format (cellmap_flow.models.configs.bio.BioModelConfig attribute) (cellmap_flow.models.models_config.BioModelConfig attribute) WEIGHT_FORMATS (in module cellmap_flow.models.configs.bio) weights_changed() (cellmap_flow.serving.chunkmirage_ops.ServedModel method) (cellmap_flow.serving.chunkmirage_server.ChunkmirageServer method) weights_path (cellmap_flow.models.configs.finetune.FinetuneModelConfig attribute) (cellmap_flow.models.models_config.FinetuneModelConfig attribute)

weights_version (cellmap_flow.serving.chunkmirage_ops.ServedModel attribute) WholeNumber (in module cellmap_flow.dashboard.requests) with_access() (in module cellmap_flow.io.store) with_input_norms() (cellmap_flow.image_data_interface.ImageDataInterface method) worker_count() (in module cellmap_flow.finetune.session.sync) worker_cpus (cellmap_flow.jobs.site.SiteProfile attribute) workers (cellmap_flow.blockwise.blockwise_processor.CellMapFlowBlockwiseProcessor attribute) world_to_box() (cellmap_flow.io.geometry.Grid method) wrap_model_with_lora() (in module cellmap_flow.finetune.lora_wrapper) write_crop_into_volume() (in module cellmap_flow.finetune.session.volume) write_json_atomically() (in module cellmap_flow.finetune.json_files) write_manifest() (in module cellmap_flow.finetune.session.manifest) write_metadata() (in module cellmap_flow.finetune.job_manager.persistence) write_ready_file() (in module cellmap_flow.jobs.ready) write_restart_token() (in module cellmap_flow.serving.restart_token) write_serving_yaml() (in module cellmap_flow.finetune.run_outputs) write_shape (cellmap_flow.models.geometry.ModelGeometry attribute) write_volume_manifest() (in module cellmap_flow.dashboard.routes.finetune.common)

Y

yaml (cellmap_flow.dashboard.requests.LoadCrops attribute) (in module cellmap_flow.cli.aliases) YAML_ALIASES (in module cellmap_flow.models.registry) yaml_config (cellmap_flow.blockwise.blockwise_processor.CellMapFlowBlockwiseProcessor attribute) yaml_path (cellmap_flow.finetune.job_manager.tailer.Iterations attribute)

yaml_paths (cellmap_flow.dashboard.requests.BlockwisePrecheck attribute) (cellmap_flow.dashboard.requests.BlockwiseSubmit attribute) YAML_SIZE_LIMIT (in module cellmap_flow.finetune.crop_loader) YAML_SUFFIXES (in module cellmap_flow.finetune.crop_loader) YamlFileRefused

Z

ZARR_JSON (in module cellmap_flow.io.paths) zarray() (in module cellmap_flow.serving.virtual_zarr) zattrs() (in module cellmap_flow.serving.virtual_zarr) ZeroMeanUnitVariance (class in cellmap_flow.finetune.trainable)

ZOO_INDEX_URL (in module cellmap_flow.models.bioimage_catalog) ZOO_PAGE_URL (in module cellmap_flow.models.bioimage_catalog) ZooIndexError ZScoreNormalizer (class in cellmap_flow.norm.input_normalize)