Index

_

__call__() (PostProcessor method)

_process() (PostProcessor method)

A

accept() (in module cellmap_flow.portable.ai_annotate_calls) accept_labels() (in module cellmap_flow.portable.ai_annotate) acknowledge (cellmap_flow.dashboard.requests.AIAnnotateSettings attribute) across() (in module cellmap_flow.finetune.data.reader) ACTION (in module cellmap_flow.dashboard.routes.finetune.ai_annotate) (in module cellmap_flow.dashboard.routes.finetune.restart_key) activation (cellmap_flow.norm.input_normalize.EuclideanDistance attribute) activation_evidence() (in module cellmap_flow.serving.probe) 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) add_training_flags() (in module cellmap_flow.finetune.cli) AddModel (class in cellmap_flow.dashboard.routes.model_resolve) affinities() (in module cellmap_flow.portable.label_it) affinity() (in module cellmap_flow.portable.targets) affinity_offsets() (in module cellmap_flow.portable.label_it) AffinityPostprocessor (built-in class) (class in cellmap_flow.post.postprocessors) AffinityTargetTransform (class in cellmap_flow.finetune.target_transforms) after_backward() (cellmap_flow.finetune.trainer.diagnostics.GradientFlow method) ai_annotate (cellmap_flow.dashboard.state.Session attribute) ai_annotate_accept() (in module cellmap_flow.dashboard.routes.finetune.ai_annotate) ai_annotate_config() (in module cellmap_flow.dashboard.routes.finetune.ai_annotate) ai_annotate_reject() (in module cellmap_flow.dashboard.routes.finetune.ai_annotate) ai_annotate_resend() (in module cellmap_flow.dashboard.routes.finetune.ai_annotate) ai_annotate_run() (in module cellmap_flow.dashboard.routes.finetune.ai_annotate) ai_annotate_settings() (in module cellmap_flow.dashboard.routes.finetune.ai_annotate) ai_annotate_status() (in module cellmap_flow.dashboard.routes.finetune.ai_annotate) AIAnnotateConfig (class in cellmap_flow.ai_annotate.config) AIAnnotateDecision (class in cellmap_flow.dashboard.requests) AIAnnotateError, [1] AIAnnotateResend (class in cellmap_flow.dashboard.requests) AIAnnotateRun (class in cellmap_flow.dashboard.requests) AIAnnotateSettings (class in cellmap_flow.dashboard.requests) aliases() (in module cellmap_flow.models.envs) aliases_file() (in module cellmap_flow.models.envs) ALIASES_FILE_ENV (in module cellmap_flow.models.envs) all_voxels (cellmap_flow.finetune.trainer.distillation.Distillation attribute) allowed_dataset_prefixes (cellmap_flow.ai_annotate.config.AIAnnotateConfig attribute) ALLOWED_FORMATS (in module cellmap_flow.ai_annotate.images) alpha (cellmap_flow.finetune.adaptation.LoraStrategy attribute) ALREADY_ASKED (in module cellmap_flow.dashboard.routes.finetune.restart_key) amp_dtype (cellmap_flow.finetune.trainer.recovery.Precision attribute) analyze_script() (in module cellmap_flow.plugins) anchor_boxes() (in module cellmap_flow.portable.regions) (in module cellmap_flow.portable.volume_calls) ANCHOR_SHARE (in module cellmap_flow.finetune.data.sampler) anchors_available (cellmap_flow.finetune.trainer.distillation.Distillation attribute) AndModelMerger (class in cellmap_flow.models.model_merger) anisotropy (cellmap_flow.models.configs.cellpose.CellposeModelConfig property) (cellmap_flow.models.models_config.CellposeModelConfig property) (cellmap_flow.norm.input_normalize.EuclideanDistance attribute)

annotate_id (cellmap_flow.dashboard.requests.AIAnnotateDecision attribute) (cellmap_flow.dashboard.requests.AIAnnotateResend attribute) ANNOTATE_ID_RE (in module cellmap_flow.ai_annotate.staging) annotated_chunks (cellmap_flow.finetune.data.sampler.PatchSampler attribute) annotation() (cellmap_flow.finetune.data.reader.PatchReader method) ANNOTATION_CODEC (in module cellmap_flow.finetune.session.volume) annotation_dtype() (in module cellmap_flow.portable.volume) 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) answered() (in module cellmap_flow.dashboard.routes.finetune.restart_key) app (cellmap_flow.serving.chunkmirage_server.ChunkmirageServer attribute) (in module cellmap_flow.cli.aliases) (in module cellmap_flow.dashboard.app) app_links() (in module cellmap_flow.portable.publish) 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.io.raw) 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) args (cellmap_flow.finetune.session_loop.TrainingSession attribute) ARGS_KEY (in module cellmap_flow.serving.protocol) argv (cellmap_flow.jobs.spec.JobSpec attribute) array (cellmap_flow.io.raw.RawInput attribute) (cellmap_flow.viewer.raw.LazyNormalization attribute) ARRAY_ATTRIBUTES (in module cellmap_flow.norm.safe_expression) ARRAY_METHODS (in module cellmap_flow.norm.safe_expression) as_bool() (in module cellmap_flow.portable.label_it) as_connectivity() (in module cellmap_flow.portable.label_it) as_dict() (cellmap_flow.jobs.settings.LauncherSettings method) as_given() (in module cellmap_flow.models.entry) as_logits() (in module cellmap_flow.finetune.losses) as_probabilities() (in module cellmap_flow.finetune.losses) augment (cellmap_flow.finetune.data.dataset.VirtualPatchDataset attribute) (cellmap_flow.finetune.data.VirtualPatchDataset attribute) (cellmap_flow.finetune.options.TrainingOptions 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() (cellmap_flow.finetune.trainer.recovery.Precision method) autocast_dtype (cellmap_flow.inference.runner.ModelRunner attribute) autodetect_output_type() (in module cellmap_flow.dashboard.routes.finetune.common) availability (cellmap_flow.schema.Route attribute) AVAILABILITY (in module cellmap_flow.schema) Availability (in module cellmap_flow.schema) available() (in module cellmap_flow.jobs.lsf) axes (cellmap_flow.serving.chunkmirage_server.ChunkmirageServer attribute) axes_names (cellmap_flow.models.configs.base.Config attribute) (cellmap_flow.models.models_config.Config attribute) AXIS_NAMES (in module cellmap_flow.portable.ai_annotate) axis_sources() (in module cellmap_flow.portable.carry)

B

Backend (class in cellmap_flow.ai_annotate.backends.base) background() (in module cellmap_flow.portable.fill_calls) balance_classes (cellmap_flow.finetune.losses.IntervalLoss attribute) (cellmap_flow.finetune.losses.MarginLoss attribute) (cellmap_flow.finetune.options.TrainingOptions attribute) (cellmap_flow.finetune.trainer.supervised.SupervisedLoss attribute) balanced_mean() (in module cellmap_flow.finetune.losses) BANNER (in module cellmap_flow.schema) 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.finetune.options.TrainingOptions attribute) (cellmap_flow.models.configs.cellpose.CellposeModelConfig attribute) (cellmap_flow.models.models_config.CellposeModelConfig attribute) BatchLoopWrapper (class in cellmap_flow.finetune.trainable) 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) best_device() (in module cellmap_flow.utils.device) best_loss (cellmap_flow.finetune.trainer.Finetuner attribute) (cellmap_flow.finetune.trainer.loop.Finetuner attribute) best_try() (in module cellmap_flow.portable.calls) (in module cellmap_flow.portable.rank) bg_ids (cellmap_flow.finetune.crop_loader.CropEntry attribute) bias (cellmap_flow.post.postprocessors.AffinityPostprocessor attribute) (cellmap_flow.post.postprocessors.DefaultPostprocessor attribute) BIAS_OPS (in module cellmap_flow.portable.activation) binary() (in module cellmap_flow.portable.targets) BinaryTargetTransform (class in cellmap_flow.finetune.target_transforms) bind_dashboard() (in module cellmap_flow.dashboard.app) bind_key() (in module cellmap_flow.viewer.keys) 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_model_entry() (in module cellmap_flow.dashboard.services.launch) BioimageSelection (class in cellmap_flow.dashboard.requests) BioModelConfig (class in cellmap_flow.models.configs.bio) (class in cellmap_flow.models.models_config) blank() (in module cellmap_flow.models.entry) 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_shapes() (in module cellmap_flow.portable.volume) 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) bounding_boxes (cellmap_flow.blockwise.blockwise_processor.CellMapFlowBlockwiseProcessor attribute) BoundingBox (class in cellmap_flow.blockwise.bounding_box) bounds_term() (cellmap_flow.finetune.losses.IntervalLoss method) box() (in module cellmap_flow.portable.fill_calls) box_voxels() (in module cellmap_flow.portable.fill) BroadcastBinaryTargetTransform (class in cellmap_flow.finetune.target_transforms) browser (cellmap_flow.norm.input_normalize.ChannelSelector attribute) (cellmap_flow.norm.input_normalize.LambdaNormalizer attribute) (cellmap_flow.norm.input_normalize.MinMaxNormalizer attribute) (cellmap_flow.norm.input_normalize.SerializableInterface attribute) (cellmap_flow.norm.input_normalize.ZScoreNormalizer attribute) (cellmap_flow.post.postprocessors.AffinityPostprocessor attribute) (cellmap_flow.post.postprocessors.ChannelSelection attribute) (cellmap_flow.post.postprocessors.DefaultPostprocessor attribute) (cellmap_flow.post.postprocessors.LabelPostprocessor attribute) (cellmap_flow.post.postprocessors.LambdaPostprocessor attribute) (cellmap_flow.post.postprocessors.MortonSegmentationRelabeling attribute) (cellmap_flow.post.postprocessors.SigmoidPostprocessor attribute) (cellmap_flow.post.postprocessors.SimpleBlockwiseMerger attribute) (cellmap_flow.post.postprocessors.ThresholdPostprocessor attribute) BROWSER_PARAMETERS (in module cellmap_flow.finetune.distill) BROWSER_SIDES (in module cellmap_flow.finetune.distill) 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_recolor_prompt() (in module cellmap_flow.ai_annotate.prompts) build_request() (in module cellmap_flow.ai_annotate.pipeline) 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_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) cached_bioimage_models() (in module cellmap_flow.models.bioimage_catalog) cached_huggingface_models() (in module cellmap_flow.models.hf_catalog) calculate_equivalences() (cellmap_flow.post.postprocessors.SimpleBlockwiseMerger method) calls_today() (in module cellmap_flow.ai_annotate.usage) 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) canonical() (in module cellmap_flow.portable.activation) carried_layer_json() (in module cellmap_flow.viewer.layers) carried_note() (in module cellmap_flow.portable.volume) carry() (in module cellmap_flow.portable.carry) carry_note() (in module cellmap_flow.portable.volume_calls) carry_onto_model() (in module cellmap_flow.dashboard.routes.finetune.annotation_core) carry_paint() (in module cellmap_flow.finetune.session.volume) (in module cellmap_flow.portable.calls) CATEGORIES (cellmap_flow.ai_annotate.backends.AIAnnotateError attribute) (cellmap_flow.ai_annotate.errors.AIAnnotateError attribute) (in module cellmap_flow.ai_annotate.errors) category (cellmap_flow.ai_annotate.backends.AIAnnotateError attribute) (cellmap_flow.ai_annotate.errors.AIAnnotateError attribute) 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.ai_annotate module cellmap_flow.ai_annotate.audit module cellmap_flow.ai_annotate.backends module cellmap_flow.ai_annotate.backends.base module cellmap_flow.ai_annotate.backends.fake module cellmap_flow.ai_annotate.backends.vertex_gemini module cellmap_flow.ai_annotate.config module cellmap_flow.ai_annotate.errors module cellmap_flow.ai_annotate.geometry module cellmap_flow.ai_annotate.images module cellmap_flow.ai_annotate.mask_extraction module cellmap_flow.ai_annotate.organelles module cellmap_flow.ai_annotate.pipeline module cellmap_flow.ai_annotate.prompts module cellmap_flow.ai_annotate.secrets module cellmap_flow.ai_annotate.staging module cellmap_flow.ai_annotate.usage module cellmap_flow.blockwise module cellmap_flow.blockwise.blockwise_processor module cellmap_flow.blockwise.bounding_box 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.ai_annotate 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.channel 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.publish module cellmap_flow.dashboard.routes.finetune.rank_routes module cellmap_flow.dashboard.routes.finetune.restart_key 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.distill module cellmap_flow.finetune.export_merged module cellmap_flow.finetune.export_web 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_wrapper module cellmap_flow.finetune.losses module cellmap_flow.finetune.markers module cellmap_flow.finetune.model_loading module cellmap_flow.finetune.options module cellmap_flow.finetune.rank 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.finetune.trainer module cellmap_flow.finetune.trainer.diagnostics module cellmap_flow.finetune.trainer.distillation module cellmap_flow.finetune.trainer.loop module cellmap_flow.finetune.trainer.recovery module cellmap_flow.finetune.trainer.supervised module cellmap_flow.finetune.trainer.tensorboard module cellmap_flow.globals module cellmap_flow.inference module cellmap_flow.inference.graph module cellmap_flow.inference.runner module cellmap_flow.inference.timing module cellmap_flow.inferencer module cellmap_flow.io module cellmap_flow.io.metadata module cellmap_flow.io.multiscale module cellmap_flow.io.paths module cellmap_flow.io.raw 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.onnx module cellmap_flow.models.configs.script module cellmap_flow.models.entry 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.portable module cellmap_flow.portable.activation module cellmap_flow.portable.ai_annotate module cellmap_flow.portable.ai_annotate_calls module cellmap_flow.portable.calls module cellmap_flow.portable.carry module cellmap_flow.portable.fill module cellmap_flow.portable.fill_calls module cellmap_flow.portable.label_it module cellmap_flow.portable.label_it_calls module cellmap_flow.portable.pasted module cellmap_flow.portable.publish module cellmap_flow.portable.publish_calls module cellmap_flow.portable.rank module cellmap_flow.portable.regions module cellmap_flow.portable.targets module cellmap_flow.portable.targets_calls module cellmap_flow.portable.volume module cellmap_flow.portable.volume_calls 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.schema 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.utils module cellmap_flow.utils.address module cellmap_flow.utils.bsub_utils module cellmap_flow.utils.device module cellmap_flow.utils.serialize_config module cellmap_flow.viewer module cellmap_flow.viewer.bootstrap module cellmap_flow.viewer.keys 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) CellMapModelConfig (class in cellmap_flow.models.configs.cellmap) (class in cellmap_flow.models.models_config) 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) center (cellmap_flow.viewer.raw.View attribute) chain() (cellmap_flow.io.raw.RawInput 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() (in module cellmap_flow.io.raw) CHANNEL_AXIS_NAMES (in module cellmap_flow.io) channel_choice() (in module cellmap_flow.dashboard.routes.finetune.common) 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) channel_pick_refusal() (in module cellmap_flow.dashboard.routes.finetune.annotation_core) channel_position() (in module cellmap_flow.viewer.layers) channel_refusal() (in module cellmap_flow.dashboard.routes.finetune.channel) channel_select() (in module cellmap_flow.io.raw) CHANNEL_STEP (in module cellmap_flow.portable.rank) channels (cellmap_flow.blockwise.blockwise_processor.CellMapFlowBlockwiseProcessor attribute) (cellmap_flow.models.configs.cellpose.CellposeModelConfig property) (cellmap_flow.models.configs.fly.FlyModelConfig attribute) (cellmap_flow.models.configs.onnx.OnnxModelConfig attribute) (cellmap_flow.models.models_config.CellposeModelConfig property) (cellmap_flow.models.models_config.FlyModelConfig attribute) (cellmap_flow.models.models_config.OnnxModelConfig 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) (in module cellmap_flow.schema) check_and_count() (in module cellmap_flow.ai_annotate.usage) check_block() (in module cellmap_flow.blockwise.blockwise_processor) check_cmd() (in module cellmap_flow.cli.envs_cli) check_dataset() (cellmap_flow.ai_annotate.config.AIAnnotateConfig method) check_equivalence() (in module cellmap_flow.finetune.export_merged) check_export() (in module cellmap_flow.finetune.job_manager.persistence) check_model() (cellmap_flow.ai_annotate.config.AIAnnotateConfig method) 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_NAME (in module cellmap_flow.finetune.distill) checkpoint_path (cellmap_flow.dashboard.requests.FinetuneSubmit attribute) (cellmap_flow.models.configs.fly.FlyModelConfig attribute) (cellmap_flow.models.models_config.FlyModelConfig attribute) choose_variant() (in module cellmap_flow.models.configs.onnx) 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.chunkmirage_ops) 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) chunk_voxels() (cellmap_flow.models.configs.cellpose.CellposeModelConfig method) (cellmap_flow.models.models_config.CellposeModelConfig method) ChunkmirageServer (class in cellmap_flow.serving.chunkmirage_server) chunks (cellmap_flow.portable.carry.Grid 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) (cellmap_flow.schema.StepSpec attribute) class_voxels (cellmap_flow.finetune.data.dataset.VirtualPatchDataset property) (cellmap_flow.finetune.data.sampler.PatchSampler attribute) (cellmap_flow.finetune.data.VirtualPatchDataset property) classify_output_range() (in module cellmap_flow.portable.label_it) 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.onnx.OnnxModelConfig 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.OnnxModelConfig 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) click_px (cellmap_flow.ai_annotate.backends.base.SegmentRequest attribute) (cellmap_flow.portable.ai_annotate.PlanePlan property) 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) CLIP_OPS (in module cellmap_flow.portable.activation) close() (cellmap_flow.dashboard.routes.review_routes.PickBoard method) (cellmap_flow.finetune.trainer.Finetuner method) (cellmap_flow.finetune.trainer.loop.Finetuner method) (cellmap_flow.finetune.trainer.tensorboard.TensorBoard method) closed (cellmap_flow.dashboard.routes.review_routes.PickBoard attribute) closeness() (in module cellmap_flow.finetune.distill) closest_raw_scale() (in module cellmap_flow.io.multiscale) CLOUD_PLATFORM_SCOPE (in module cellmap_flow.ai_annotate.secrets) coerce() (in module cellmap_flow.models.entry) coerce_value() (in module cellmap_flow.models.entry) color_name (cellmap_flow.ai_annotate.organelles.OrganelleProfile attribute) 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) components() (in module cellmap_flow.portable.label_it) CONCAT_OPS (in module cellmap_flow.portable.activation) 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) config_card() (cellmap_flow.finetune.trainer.tensorboard.TensorBoard method) CONFIG_ENV (in module cellmap_flow.ai_annotate.config) config_path() (in module cellmap_flow.ai_annotate.config) config_relative_paths (cellmap_flow.models.configs.base.ModelConfig attribute) (cellmap_flow.models.configs.onnx.OnnxModelConfig attribute) (cellmap_flow.models.models_config.ModelConfig attribute) (cellmap_flow.models.models_config.OnnxModelConfig attribute) ConfigError configs_by_name() (in module cellmap_flow.dashboard.services.launch) configure_logging() (in module cellmap_flow.logging_setup) connected_components (cellmap_flow.finetune.crop_loader.CropEntry attribute) connected_components() (in module cellmap_flow.portable.fill) (in module cellmap_flow.portable.label_it) CONNECTIVITIES (in module cellmap_flow.portable.label_it) connectivity (cellmap_flow.post.postprocessors.LabelPostprocessor attribute) CONSTANT_DOCS (in module cellmap_flow.schema) CONSTANT_OPS (in module cellmap_flow.portable.activation) constants() (in module cellmap_flow.schema) 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) control (cellmap_flow.finetune.session_loop.TrainingSession attribute) copy_chunks_parallel() (in module cellmap_flow.finetune.session.sync) corner_nm (cellmap_flow.finetune.data.reader.PatchReader attribute) (cellmap_flow.portable.carry.Grid 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) counts_up() (in module cellmap_flow.portable.fill) 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) credentials_file (cellmap_flow.ai_annotate.backends.vertex_gemini.VertexGeminiBackend attribute) crop (cellmap_flow.finetune.trainable.Crop attribute) Crop (class in cellmap_flow.finetune.trainable) crop_size_px (cellmap_flow.ai_annotate.config.AIAnnotateConfig attribute) 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.trainer.Finetuner attribute) (cellmap_flow.finetune.trainer.loop.Finetuner attribute) current_site() (in module cellmap_flow.jobs.site) CUTOFFS (in module cellmap_flow.finetune.rank) (in module cellmap_flow.portable.rank)

D

DACAPO_FRAMEWORKS (in module cellmap_flow.serving.probe) DaCapoModelConfig (class in cellmap_flow.models.configs.dacapo) (class in cellmap_flow.models.models_config) daily_call_limit (cellmap_flow.ai_annotate.config.AIAnnotateConfig attribute) dashboard() (in module cellmap_flow.cli.main) dashboard_url (cellmap_flow.dashboard.state.Session attribute) dataloader (cellmap_flow.finetune.trainer.Finetuner attribute) (cellmap_flow.finetune.trainer.loop.Finetuner 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_PARAM (in module cellmap_flow.portable.publish) 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) 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 (cellmap_flow.models.bioimage_catalog.VoxelSizeChoice attribute) declared_block_shape (cellmap_flow.models.geometry.ModelGeometry attribute) declared_default() (in module cellmap_flow.models.envs) declared_geometry() (cellmap_flow.models.configs.base.ModelConfig method) (cellmap_flow.models.configs.cellmap.CellMapModelConfig method) (cellmap_flow.models.configs.finetune.FinetuneModelConfig method) (cellmap_flow.models.configs.huggingface.HuggingFaceModelConfig method) (cellmap_flow.models.configs.onnx.OnnxModelConfig method) (cellmap_flow.models.models_config.CellMapModelConfig method) (cellmap_flow.models.models_config.FinetuneModelConfig method) (cellmap_flow.models.models_config.HuggingFaceModelConfig method) (cellmap_flow.models.models_config.ModelConfig method) (cellmap_flow.models.models_config.OnnxModelConfig method) declared_input_norm() (cellmap_flow.models.configs.base.ModelConfig method) (cellmap_flow.models.configs.cellmap.CellMapModelConfig method) (cellmap_flow.models.configs.huggingface.HuggingFaceModelConfig method) (cellmap_flow.models.configs.onnx.OnnxModelConfig method) (cellmap_flow.models.models_config.CellMapModelConfig method) (cellmap_flow.models.models_config.HuggingFaceModelConfig method) (cellmap_flow.models.models_config.ModelConfig method) (cellmap_flow.models.models_config.OnnxModelConfig method) 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_model_image() (in module cellmap_flow.ai_annotate.images) 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_CROP_SIZE_PX (in module cellmap_flow.ai_annotate.config) DEFAULT_DAILY_CALL_LIMIT (in module cellmap_flow.ai_annotate.config) 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.configs.onnx.OnnxModelConfig attribute) (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) (cellmap_flow.models.models_config.OnnxModelConfig 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_provider (cellmap_flow.ai_annotate.config.AIAnnotateConfig attribute) default_queues (cellmap_flow.jobs.site.SiteProfile property) DEFAULT_QUEUES (in module cellmap_flow.review_index) DEFAULT_REGION_SIZE_NM (in module cellmap_flow.portable.regions) default_size_nm() (in module cellmap_flow.portable.regions) DEFAULT_SLICES_PER_CHUNK (in module cellmap_flow.models.configs.bio) (in module cellmap_flow.models.configs.onnx) DEFAULT_TIMEOUT_S (in module cellmap_flow.ai_annotate.backends) (in module cellmap_flow.ai_annotate.config) DEFAULT_TIMEOUT_SECONDS (in module cellmap_flow.serving.client) DEFAULT_VARIANT (in module cellmap_flow.models.configs.onnx) DEFAULT_VERTEX_LOCATION (in module cellmap_flow.ai_annotate.backends) (in module cellmap_flow.ai_annotate.config) 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) deleted_in_viewer (cellmap_flow.dashboard.state.Session attribute) deleted_layers() (in module cellmap_flow.viewer.layers) 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) depth_axis (cellmap_flow.dashboard.requests.AIAnnotateRun attribute) (cellmap_flow.portable.ai_annotate.PlanePlan attribute) depth_axis_for_view() (in module cellmap_flow.ai_annotate.geometry)

depth_axis_from_layout() (in module cellmap_flow.ai_annotate.geometry) describe() (cellmap_flow.finetune.trainer.recovery.Precision method) (in module cellmap_flow.finetune.export_web) describe_first_batch() (in module cellmap_flow.finetune.trainer.diagnostics) describe_types() (in module cellmap_flow.models.registry) description (cellmap_flow.ai_annotate.organelles.OrganelleProfile attribute) deserialize_list() (in module cellmap_flow.norm.input_normalize) destination (cellmap_flow.dashboard.requests.AIAnnotateSettings attribute) destination() (cellmap_flow.ai_annotate.config.ProviderConfig method) 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 (cellmap_flow.dashboard.requests.HuggingFaceCredentials attribute) (cellmap_flow.finetune.session_loop.TrainingSession attribute) (cellmap_flow.finetune.trainer.Finetuner attribute) (cellmap_flow.finetune.trainer.loop.Finetuner attribute) (cellmap_flow.finetune.trainer.recovery.Precision attribute) (cellmap_flow.inference.runner.ModelRunner attribute) DEVICE_GRANT (in module cellmap_flow.dashboard.routes.finetune.publish) device_slots (cellmap_flow.inference.runner.ModelRunner attribute) DEVICE_URL (in module cellmap_flow.dashboard.routes.finetune.publish) 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) dir (cellmap_flow.finetune.trainer.tensorboard.TensorBoard attribute) disabled_reason() (in module cellmap_flow.ai_annotate.config) DISALLOWED_FUNCTIONS (in module cellmap_flow.plugins) DISALLOWED_IMPORTS (in module cellmap_flow.plugins) discard() (in module cellmap_flow.ai_annotate.staging) 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) display_dimensions (cellmap_flow.portable.ai_annotate.PlanePlan attribute) display_dimensions_for_view() (in module cellmap_flow.ai_annotate.geometry) (in module cellmap_flow.viewer) display_names() (in module cellmap_flow.portable.ai_annotate) distance() (in module cellmap_flow.portable.targets) distance_bounds() (cellmap_flow.finetune.target_transforms.IntervalTargetTransform method) (in module cellmap_flow.portable.targets) distance_sigma (cellmap_flow.finetune.options.TrainingOptions attribute) distance_watershed() (in module cellmap_flow.post.segment) DistanceTargetTransform (class in cellmap_flow.finetune.target_transforms) distill() (in module cellmap_flow.finetune.distill) distillation (cellmap_flow.finetune.trainer.Finetuner attribute) (cellmap_flow.finetune.trainer.loop.Finetuner attribute) Distillation (class in cellmap_flow.finetune.trainer.distillation) distillation_lambda (cellmap_flow.finetune.options.TrainingOptions attribute) (cellmap_flow.finetune.trainer.Finetuner property) (cellmap_flow.finetune.trainer.loop.Finetuner property) distillation_loss() (in module cellmap_flow.finetune.losses) distillation_scope (cellmap_flow.finetune.options.TrainingOptions attribute) do_3d (cellmap_flow.dashboard.requests.CellposeSelection attribute) (cellmap_flow.models.configs.cellpose.CellposeModelConfig attribute) (cellmap_flow.models.models_config.CellposeModelConfig attribute) DOCS (in module cellmap_flow.ai_annotate.config) DOCS_FILE (in module cellmap_flow.schema) download_export() (in module cellmap_flow.models.configs.huggingface) draw() (cellmap_flow.finetune.data.sampler.PatchSampler method) drop() (cellmap_flow.finetune.trainer.distillation.Distillation method) drop_config() (in module cellmap_flow.dashboard.services.launch) dropout (cellmap_flow.finetune.adaptation.LoraStrategy attribute) dtype (cellmap_flow.blockwise.blockwise_processor.CellMapFlowBlockwiseProcessor attribute) (cellmap_flow.norm.input_normalize.EuclideanDistance property) (cellmap_flow.norm.input_normalize.LambdaNormalizer property) (cellmap_flow.norm.input_normalize.MinMaxNormalizer property) (cellmap_flow.norm.input_normalize.SerializableInterface property) (cellmap_flow.norm.input_normalize.ZScoreNormalizer property) (cellmap_flow.post.postprocessors.AffinityPostprocessor property) (cellmap_flow.post.postprocessors.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) (cellmap_flow.viewer.raw.LazyNormalization property) (PostProcessor attribute) DTYPE_STRINGS (in module cellmap_flow.norm.safe_expression) dumps() (in module cellmap_flow.schema)

E

edges (cellmap_flow.dashboard.routes.pipeline.BuilderCanvas attribute) editable_prompt() (in module cellmap_flow.ai_annotate.prompts) 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_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) empty_tallies() (in module cellmap_flow.finetune.rank) (in module cellmap_flow.portable.rank) enabled (cellmap_flow.ai_annotate.config.AIAnnotateConfig attribute) (cellmap_flow.finetune.trainer.recovery.Precision attribute) encode_to_str() (in module cellmap_flow.serving.protocol) ENGINE (in module cellmap_flow.serving.chunkmirage_server) ensure_binding() (in module cellmap_flow.dashboard.routes.finetune.restart_key) 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_KEYS (in module cellmap_flow.models.registry) entry_voxel_size() (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 (cellmap_flow.finetune.trainer.tensorboard.TensorBoard attribute) epoch_bce_metrics() (cellmap_flow.finetune.trainer.supervised.SupervisedLoss method)

EPOCH_START_RE (in module cellmap_flow.finetune.markers) EPOCH_SUMMARY_RE (in module cellmap_flow.finetune.markers) EPOCHS (in module cellmap_flow.finetune.distill) 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.serving.chunkmirage_ops) EuclideanDistance (class in cellmap_flow.norm.input_normalize) EVENTS (in module cellmap_flow.ai_annotate.audit) EVERY_CHANNEL_TARGETS (in module cellmap_flow.dashboard.routes.finetune.common) existing_bounding_boxes (cellmap_flow.dashboard.requests.BbxGenerator attribute) exists_now() (in module cellmap_flow.jobs.spec) EXPIRED (in module cellmap_flow.dashboard.routes.finetune.publish) export() (cellmap_flow.finetune.adaptation.AdaptationStrategy method) (cellmap_flow.finetune.adaptation.FullStrategy method) (cellmap_flow.finetune.adaptation.LoraStrategy method) (in module cellmap_flow.finetune.export_web) export_config() (in module cellmap_flow.dashboard.routes.models) export_finetune_modes() (in module cellmap_flow.models.configs.cellmap) 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) EXPORT_POLL_SECONDS (in module cellmap_flow.dashboard.routes.finetune.publish) export_status() (in module cellmap_flow.finetune.export_web) EXPORTER (in module cellmap_flow.finetune.export_web) expression (cellmap_flow.norm.input_normalize.LambdaNormalizer attribute) (cellmap_flow.post.postprocessors.LambdaPostprocessor attribute) EXPRESSION_SAMPLES (in module cellmap_flow.serving.probe) 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) extract_mask() (in module cellmap_flow.ai_annotate.mask_extraction) (in module cellmap_flow.portable.ai_annotate)

F

face_erosion_iterations (cellmap_flow.post.postprocessors.SimpleBlockwiseMerger attribute) FACTS (in module cellmap_flow.models.hf_catalog) facts_of() (in module cellmap_flow.models.hf_catalog) 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) FakeBackend (class in cellmap_flow.ai_annotate.backends.fake) fall_back_to_fp32() (cellmap_flow.finetune.trainer.recovery.Precision method) fallback (cellmap_flow.finetune.job_manager.state.FinetuneJob attribute) fcntl (in module cellmap_flow.ai_annotate.usage) 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) field_of_view() (in module cellmap_flow.portable.label_it_calls) FIELD_OF_VIEW_MAX_VOXELS (in module cellmap_flow.portable.label_it) field_of_view_nm() (in module cellmap_flow.portable.label_it) file (cellmap_flow.models.configs.onnx.OnnxModelConfig attribute) (cellmap_flow.models.models_config.OnnxModelConfig attribute) fill_unpainted() (in module cellmap_flow.finetune.session.fill) FillHolesPostprocessor (class in cellmap_flow.post.postprocessors) filter() (cellmap_flow.ai_annotate.secrets.RedactingFilter method) 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_organelle_profile() (in module cellmap_flow.ai_annotate.organelles) 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.onnx.OnnxModelConfig 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.OnnxModelConfig 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_FORM_FIELDS (in module cellmap_flow.schema) 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.cellmap.CellMapModelConfig method) (cellmap_flow.models.configs.cellpose.CellposeModelConfig method) (cellmap_flow.models.configs.finetune.FinetuneModelConfig method) (cellmap_flow.models.configs.huggingface.HuggingFaceModelConfig 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.FinetuneModelConfig method) (cellmap_flow.models.models_config.HuggingFaceModelConfig 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) finetuned_network() (in module cellmap_flow.finetune.export_web) 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) FinetunePublish (class in cellmap_flow.dashboard.requests) Finetuner (class in cellmap_flow.finetune.trainer) (class in cellmap_flow.finetune.trainer.loop) 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) first_visit() (in module cellmap_flow.portable.carry) 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) flask_rules() (in module cellmap_flow.schema) Flow (class in cellmap_flow.globals) flow3d_smooth (cellmap_flow.models.configs.cellpose.CellposeModelConfig attribute) (cellmap_flow.models.models_config.CellposeModelConfig attribute) 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) FLOWS (in module cellmap_flow.dashboard.routes.finetune.rank_routes) FlowTargetTransform (class in cellmap_flow.finetune.instance_flows) flush() (cellmap_flow.finetune.trainer.tensorboard.TensorBoard method) FlyModelConfig (class in cellmap_flow.models.configs.fly) (class in cellmap_flow.models.models_config) folder (cellmap_flow.models.configs.onnx.OnnxModelConfig attribute) (cellmap_flow.models.models_config.OnnxModelConfig attribute) folder_facts() (in module cellmap_flow.models.hf_catalog) folder_name() (in module cellmap_flow.finetune.export_web) follow() (in module cellmap_flow.dashboard.routes.finetune.restart_key) follow_jobs() (in module cellmap_flow.dashboard.finetune_layers) for_dashboard() (cellmap_flow.serving.chunkmirage_ops.PostprocessOp method) for_session() (cellmap_flow.finetune.options.TrainingOptions method) foreground_mask() (in module cellmap_flow.portable.label_it) FOREGROUND_SHARE (in module cellmap_flow.finetune.data.sampler) forget (cellmap_flow.dashboard.requests.HuggingFaceCredentials attribute) forget_layer() (cellmap_flow.dashboard.state.Session method) FORMAT (in module cellmap_flow.serving.protocol) FORMATS (in module cellmap_flow.models.hf_catalog) forward() (cellmap_flow.finetune.instance_flows.FlowLoss 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.BatchLoopWrapper 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.SequentialWrapper method) (cellmap_flow.finetune.trainable.SliceWise method) (cellmap_flow.finetune.trainable.ZeroMeanUnitVariance method) FP32_REL_TOL (in module cellmap_flow.finetune.export_web) fresh_ids() (in module cellmap_flow.portable.fill) from_builder() (cellmap_flow.pipeline_spec.PipelineSpec class method) from_config() (cellmap_flow.models.geometry.ModelGeometry class method) from_dict() (cellmap_flow.portable.ai_annotate.PlanePlan class method) from_env() (cellmap_flow.inference.runner.DeviceSlots class method) from_json_data() (cellmap_flow.pipeline_spec.PipelineSpec class method) from_screen() (cellmap_flow.portable.ai_annotate.PlanePlan method) (in module cellmap_flow.portable.ai_annotate) 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) gather() (in module cellmap_flow.portable.label_it) 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) GENERATED_DIR (in module cellmap_flow.schema) GENERIC_FAILURE (in module cellmap_flow.dashboard.routes.finetune.ai_annotate) geometry (cellmap_flow.models.configs.base.ModelConfig property) (cellmap_flow.models.models_config.ModelConfig property) (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_backend() (in module cellmap_flow.ai_annotate.backends) 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.utils.address) get_huggingface_models() (in module cellmap_flow.dashboard.routes.models) 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_loaded_models() (in module cellmap_flow.dashboard.routes.models) 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_raw_channels() (in module cellmap_flow.dashboard.routes.pipeline) 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.trainer.Finetuner attribute) (cellmap_flow.finetune.trainer.loop.Finetuner 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) grad_abs_sum (cellmap_flow.finetune.trainer.diagnostics.GradientFlow attribute) grad_count (cellmap_flow.finetune.trainer.diagnostics.GradientFlow attribute) gradient_accumulation_steps (cellmap_flow.finetune.options.TrainingOptions attribute) (cellmap_flow.finetune.trainer.Finetuner attribute) (cellmap_flow.finetune.trainer.loop.Finetuner attribute) GradientFlow (class in cellmap_flow.finetune.trainer.diagnostics) gradients_finite() (cellmap_flow.finetune.trainer.recovery.Precision method) Grid (class in cellmap_flow.portable.carry) grid_change() (in module cellmap_flow.dashboard.routes.finetune.annotation_core) GRID_FIELDS (in module cellmap_flow.portable.volume) grid_origin (cellmap_flow.blockwise.blockwise_processor.CellMapFlowBlockwiseProcessor attribute) grid_text() (in module cellmap_flow.portable.volume)

H

half_precision (cellmap_flow.inference.runner.ModelRunner attribute) HALF_PRECISION_ENV (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) halve_batch() (in module cellmap_flow.finetune.trainer.recovery) has_channel (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) HELD_OUT_BLOCKS (in module cellmap_flow.finetune.distill) HELD_OUT_SEED (in module cellmap_flow.finetune.distill) HF_CACHE_DIR (in module cellmap_flow.models.hf_catalog) HF_CACHE_FILE (in module cellmap_flow.models.hf_catalog) HF_OAUTH_CLIENT_ID (in module cellmap_flow.portable.publish) HF_OAUTH_SCOPES (in module cellmap_flow.portable.publish) hold() (cellmap_flow.inference.runner.DeviceSlots method) holds_others (cellmap_flow.finetune.trainer.distillation.Distillation attribute)

host (cellmap_flow.jobs.spec.Job attribute) HOURS (in module cellmap_flow.finetune.distill) how (cellmap_flow.models.resolve.Resolved attribute), [1] http_status (cellmap_flow.ai_annotate.backends.AIAnnotateError attribute) (cellmap_flow.ai_annotate.errors.AIAnnotateError attribute) HUB (in module cellmap_flow.portable.publish) hub_refusal() (in module cellmap_flow.portable.publish) (in module cellmap_flow.portable.publish_calls) hub_repo (cellmap_flow.models.configs.onnx.OnnxModelConfig property) (cellmap_flow.models.models_config.OnnxModelConfig property) HUGGING_FACE_ORGS_NAME (in module cellmap_flow.models.hf_catalog) huggingface (cellmap_flow.dashboard.state.Session attribute) huggingface_account() (in module cellmap_flow.dashboard.routes.finetune.publish) huggingface_sign_in() (in module cellmap_flow.dashboard.routes.finetune.publish) HuggingFaceCredentials (class in cellmap_flow.dashboard.requests) 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.ai_annotate.config.ProviderConfig attribute) (cellmap_flow.dashboard.requests.BioimageSelection attribute) image (cellmap_flow.ai_annotate.backends.base.SegmentRequest attribute) image_every (cellmap_flow.finetune.trainer.tensorboard.TensorBoard attribute) image_shape (cellmap_flow.portable.ai_annotate.PlanePlan attribute) images() (cellmap_flow.finetune.trainer.tensorboard.TensorBoard method) include_dataset (cellmap_flow.dashboard.requests.FinetunePublish attribute) 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.serving.chunkmirage_server.ChunkmirageServer attribute) Inferencer (class in cellmap_flow.inferencer) inferencers (cellmap_flow.blockwise.blockwise_processor.CellMapFlowBlockwiseProcessor attribute) info() (cellmap_flow.viewer.raw.ScalePyramid method) initial (cellmap_flow.finetune.trainer.diagnostics.GradientFlow attribute) initial_state (cellmap_flow.finetune.session_loop.TrainingSession attribute) (cellmap_flow.finetune.trainer.Finetuner attribute) (cellmap_flow.finetune.trainer.loop.Finetuner 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_differences() (in module cellmap_flow.serving.probe) INPUT_NORM_KEY (in module cellmap_flow.serving.protocol) input_norm_set_by() (in module cellmap_flow.dashboard.routes.pipeline) input_norm_suggestion() (in module cellmap_flow.dashboard.routes.model_advice) input_normalizers() (in module cellmap_flow.finetune.data.reader) input_norms (cellmap_flow.dashboard.state.Session property) (cellmap_flow.io.raw.RawInput attribute) (cellmap_flow.process_chain.ProcessChain attribute) (cellmap_flow.serving.chunkmirage_ops.BlockInput attribute) input_path (cellmap_flow.blockwise.blockwise_processor.CellMapFlowBlockwiseProcessor attribute) INPUT_PNG (in module cellmap_flow.ai_annotate.staging) 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.configs.onnx.OnnxModelConfig attribute) (cellmap_flow.models.models_config.BioModelConfig attribute) (cellmap_flow.models.models_config.FlyModelConfig attribute) (cellmap_flow.models.models_config.OnnxModelConfig 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.configs.onnx.OnnxModelConfig attribute) (cellmap_flow.models.geometry.ModelGeometry attribute) (cellmap_flow.models.models_config.FinetuneModelConfig attribute) (cellmap_flow.models.models_config.FlyModelConfig attribute) (cellmap_flow.models.models_config.OnnxModelConfig attribute) (cellmap_flow.portable.ai_annotate.PlanePlan 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) INSTALL_HINT (in module cellmap_flow.ai_annotate.errors) install_log_redaction() (in module cellmap_flow.ai_annotate.secrets) instance_components() (in module cellmap_flow.finetune.instance_flows) INSTANCE_TARGETS (in module cellmap_flow.portable.volume) intensity() (cellmap_flow.finetune.data.augment.Augmentation method) interval() (in module cellmap_flow.portable.targets) 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_label_dtype() (in module cellmap_flow.io.raw) is_panel_cellpose() (in module cellmap_flow.dashboard.services.launch) is_path() (in module cellmap_flow.models.envs) is_peft_model() (in module cellmap_flow.finetune.adaptation) 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) 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 (cellmap_flow.finetune.export_web.WebExport 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)

job_parser() (in module cellmap_flow.finetune.export_web) JobControl (class in cellmap_flow.finetune.session_loop) 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) JSON2TS (in module cellmap_flow.schema)

K

key (cellmap_flow.ai_annotate.organelles.OrganelleProfile attribute) KEY (in module cellmap_flow.dashboard.routes.finetune.ai_annotate) (in module cellmap_flow.dashboard.routes.finetune.restart_key) KEYBINDING (in module cellmap_flow.dashboard.routes.finetune.ai_annotate) (in module cellmap_flow.dashboard.routes.finetune.restart_key) 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)

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) known_geometry() (in module cellmap_flow.models.geometry_cache) 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_key (cellmap_flow.dashboard.requests.AIAnnotateSettings attribute) LABEL_MAX_CHARS (in module cellmap_flow.dashboard.requests) label_name (cellmap_flow.dashboard.requests.AIAnnotateSettings attribute) label_smoothing (cellmap_flow.finetune.options.TrainingOptions attribute) (cellmap_flow.finetune.trainer.supervised.SupervisedLoss 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) labels_for_box() (in module cellmap_flow.portable.ai_annotate) 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_others_loss (cellmap_flow.finetune.trainer.Finetuner attribute) (cellmap_flow.finetune.trainer.loop.Finetuner attribute) last_supervised_loss (cellmap_flow.finetune.trainer.Finetuner attribute) (cellmap_flow.finetune.trainer.loop.Finetuner attribute) later() (in module cellmap_flow.viewer.keys) latest() (cellmap_flow.dashboard.routes.review_routes.PickBoard method) latest_loss (cellmap_flow.finetune.job_manager.state.FinetuneJob attribute) latest_loss_epoch (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) (in module cellmap_flow.serving.launch) 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) launching() (in module cellmap_flow.dashboard.services.launch) layer_blob() (cellmap_flow.dashboard.state.Session method) LAYER_BOOKKEEPING (in module cellmap_flow.dashboard.state) layer_ops() (in module cellmap_flow.serving.chunkmirage_ops) LazyNormalization (class in cellmap_flow.viewer.raw) learning_rate (cellmap_flow.finetune.options.TrainingOptions attribute) LEARNING_RATE (in module cellmap_flow.finetune.distill) learning_rate_factor() (in module cellmap_flow.finetune.trainer.loop) LEARNING_RATE_FLOOR (in module cellmap_flow.finetune.options) learning_rate_schedule (cellmap_flow.finetune.options.TrainingOptions attribute) level_shape (cellmap_flow.serving.chunkmirage_ops.BlockInput attribute) (cellmap_flow.serving.chunkmirage_ops.ServedModel attribute) lib_dir() (in module cellmap_flow.models.envs) LINEAR_OPS (in module cellmap_flow.portable.activation) 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_models() (in module cellmap_flow.cli.server_cli) list_plugins() (in module cellmap_flow.plugins) list_plugins_cmd() (in module cellmap_flow.cli.main) listed_geometry() (in module cellmap_flow.dashboard.routes.finetune.annotation_core) Listeners (class in cellmap_flow.finetune.job_manager.listener) LISTING_ORDER (in module cellmap_flow.post.postprocessors) load() (cellmap_flow.jobs.settings.LauncherSettings class method) (in module cellmap_flow.ai_annotate.staging) load_cached_geometry() (in module cellmap_flow.models.geometry_cache) load_checkpoint() (cellmap_flow.finetune.adaptation.AdaptationStrategy method) (cellmap_flow.finetune.trainer.Finetuner method) (cellmap_flow.finetune.trainer.loop.Finetuner method) load_config() (in module cellmap_flow.ai_annotate.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_google_credentials() (in module cellmap_flow.ai_annotate.secrets) 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) loaded_models() (in module cellmap_flow.dashboard.services.launch) LocalJob (class in cellmap_flow.jobs.local) location (cellmap_flow.ai_annotate.backends.vertex_gemini.VertexGeminiBackend attribute) log() (cellmap_flow.finetune.trainer.Finetuner static method) (cellmap_flow.finetune.trainer.loop.Finetuner static method) 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_epoch() (cellmap_flow.finetune.trainer.tensorboard.TensorBoard method) log_file (cellmap_flow.finetune.export_web.WebExport property) (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_ids (cellmap_flow.dashboard.state.Session attribute) log_level_option() (in module cellmap_flow.cli.common) LOG_LEVELS (in module cellmap_flow.cli.common) LOG_NAME (in module cellmap_flow.ai_annotate.audit) (in module cellmap_flow.finetune.export_web) log_path() (in module cellmap_flow.ai_annotate.audit) 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) log_step() (cellmap_flow.finetune.trainer.tensorboard.TensorBoard method) logger (in module cellmap_flow.ai_annotate.audit) (in module cellmap_flow.ai_annotate.backends.vertex_gemini) (in module cellmap_flow.ai_annotate.usage) (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.ai_annotate) (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.channel) (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.publish) (in module cellmap_flow.dashboard.routes.finetune.rank_routes) (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.distill) (in module cellmap_flow.finetune.export_merged) (in module cellmap_flow.finetune.export_web) (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_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.finetune.trainer.diagnostics) (in module cellmap_flow.finetune.trainer.distillation) (in module cellmap_flow.finetune.trainer.loop) (in module cellmap_flow.finetune.trainer.recovery) (in module cellmap_flow.finetune.trainer.supervised) (in module cellmap_flow.finetune.trainer.tensorboard) (in module cellmap_flow.inference.graph) (in module cellmap_flow.inference.runner) (in module cellmap_flow.inferencer) (in module cellmap_flow.io.metadata) (in module cellmap_flow.io.multiscale) (in module cellmap_flow.io.raw) (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.cellmap) (in module cellmap_flow.models.configs.cellpose) (in module cellmap_flow.models.configs.finetune) (in module cellmap_flow.models.configs.fly) (in module cellmap_flow.models.configs.huggingface) (in module cellmap_flow.models.configs.onnx) (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.serving.chunkmirage_ops) (in module cellmap_flow.serving.chunkmirage_server) (in module cellmap_flow.serving.client) (in module cellmap_flow.serving.launch) (in module cellmap_flow.serving.probe) (in module cellmap_flow.utils.address) (in module cellmap_flow.viewer.bootstrap) (in module cellmap_flow.viewer.keys) (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_alpha (cellmap_flow.finetune.options.TrainingOptions attribute) lora_copy (cellmap_flow.dashboard.requests.FinetunePublish attribute) lora_dropout (cellmap_flow.finetune.options.TrainingOptions attribute) lora_min_channels (cellmap_flow.finetune.options.TrainingOptions attribute) lora_r (cellmap_flow.finetune.options.TrainingOptions attribute) LoRAFinetuner (in module cellmap_flow.finetune.trainer) (in module cellmap_flow.finetune.trainer.loop) LoraStrategy (class in cellmap_flow.finetune.adaptation) loss_type (cellmap_flow.finetune.options.TrainingOptions attribute) (cellmap_flow.finetune.trainer.supervised.SupervisedLoss attribute) LOSS_TYPES (in module cellmap_flow.finetune.options) 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.distill) (in module cellmap_flow.finetune.export_merged) (in module cellmap_flow.finetune.export_web) (in module cellmap_flow.finetune.finetune_cli) (in module cellmap_flow.review_index) (in module cellmap_flow.schema) majority_vote_downsample() (in module cellmap_flow.finetune.session.volume) make_paint_volume() (in module cellmap_flow.dashboard.routes.finetune.annotation_core) make_s3_filesystem() (in module cellmap_flow.finetune.session.minio) make_server() (in module cellmap_flow.serving.engine) make_student() (in module cellmap_flow.finetune.distill) make_training_loader() (in module cellmap_flow.finetune.data) (in module cellmap_flow.finetune.data.loader) make_volume() (in module cellmap_flow.dashboard.routes.finetune.annotation_core) MANIFEST_FIELDS (in module cellmap_flow.finetune.options) MANIFEST_KEY (in module cellmap_flow.models.configs.onnx) MANIFEST_RETRY_SECONDS (in module cellmap_flow.models.configs.onnx) margin (cellmap_flow.finetune.losses.MarginLoss attribute) (cellmap_flow.finetune.options.TrainingOptions attribute) (cellmap_flow.finetune.trainer.supervised.SupervisedLoss attribute) MarginLoss (class in cellmap_flow.finetune.losses) mark_current_view_good() (in module cellmap_flow.dashboard.routes.finetune.good_regions) mark_region() (in module cellmap_flow.portable.volume_calls) markdown() (in module cellmap_flow.schema) mask (cellmap_flow.ai_annotate.backends.base.SegmentResult attribute) MASK_NPY (in module cellmap_flow.ai_annotate.staging) mask_to_write_shape() (in module cellmap_flow.portable.ai_annotate) mask_unannotated (cellmap_flow.finetune.options.TrainingOptions attribute) (cellmap_flow.finetune.trainer.supervised.SupervisedLoss attribute) masked_mean() (in module cellmap_flow.finetune.losses) MAX_ATTEMPTS (in module cellmap_flow.ai_annotate.backends.vertex_gemini) MAX_ENTRIES (in module cellmap_flow.models.geometry_cache) MAX_EXPONENT (in module cellmap_flow.norm.safe_expression) MAX_IMAGE_SIDE (in module cellmap_flow.portable.ai_annotate) MAX_LABEL (in module cellmap_flow.review_index) MAX_LENGTH (in module cellmap_flow.norm.safe_expression) MAX_PIXELS (in module cellmap_flow.ai_annotate.images) MAX_POSITIONAL (in module cellmap_flow.norm.safe_expression) MAX_PROMPT_CHARS (in module cellmap_flow.ai_annotate.prompts) MAX_REPLY_CHARS (in module cellmap_flow.ai_annotate.backends.vertex_gemini) max_slope (cellmap_flow.finetune.losses.IntervalLoss attribute) max_value (cellmap_flow.norm.input_normalize.MinMaxNormalizer attribute) MAX_VIEW_REACH (in module cellmap_flow.viewer.raw) 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) META_JSON (in module cellmap_flow.ai_annotate.staging) METADATA_FILE (in module cellmap_flow.finetune.job_manager.persistence) metadata_geometry() (in module cellmap_flow.models.configs.cellmap) metadata_input_norm() (in module cellmap_flow.serving.probe) 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) method (cellmap_flow.schema.Route attribute) 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_SECRET_LENGTH (in module cellmap_flow.ai_annotate.secrets) 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) mixed_precision (cellmap_flow.finetune.options.TrainingOptions attribute) mode (cellmap_flow.finetune.crop_loader.CropEntry attribute) (cellmap_flow.finetune.options.TrainingOptions attribute) model (cellmap_flow.ai_annotate.backends.base.SegmentResult attribute) (cellmap_flow.dashboard.requests.AIAnnotateSettings attribute) (cellmap_flow.dashboard.requests.CellposeSelection attribute) (cellmap_flow.finetune.session_loop.TrainingSession attribute) (cellmap_flow.finetune.trainable.BatchLoopWrapper attribute) (cellmap_flow.finetune.trainable.SequentialWrapper attribute) (cellmap_flow.finetune.trainer.diagnostics.GradientFlow attribute) (cellmap_flow.finetune.trainer.Finetuner attribute) (cellmap_flow.finetune.trainer.loop.Finetuner 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_card() (in module cellmap_flow.portable.publish) model_catalog (cellmap_flow.dashboard.state.Session attribute) 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.options.TrainingOptions 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_image (cellmap_flow.ai_annotate.backends.base.SegmentResult attribute) model_info() (cellmap_flow.serving.chunkmirage_server.ChunkmirageServer method) model_mask() (in module cellmap_flow.portable.ai_annotate) (in module cellmap_flow.portable.ai_annotate_calls) model_merger (cellmap_flow.blockwise.blockwise_processor.CellMapFlowBlockwiseProcessor attribute) model_metadata() (in module cellmap_flow.dashboard.routes.model_advice) 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_PARAM (in module cellmap_flow.portable.publish) MODEL_PNG (in module cellmap_flow.ai_annotate.staging) 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_target() (in module cellmap_flow.dashboard.routes.finetune.common) 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.ai_annotate.config.ProviderConfig attribute) (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) MODES (in module cellmap_flow.finetune.options) module cellmap_flow cellmap_flow.ai_annotate cellmap_flow.ai_annotate.audit cellmap_flow.ai_annotate.backends cellmap_flow.ai_annotate.backends.base cellmap_flow.ai_annotate.backends.fake cellmap_flow.ai_annotate.backends.vertex_gemini cellmap_flow.ai_annotate.config cellmap_flow.ai_annotate.errors cellmap_flow.ai_annotate.geometry cellmap_flow.ai_annotate.images cellmap_flow.ai_annotate.mask_extraction cellmap_flow.ai_annotate.organelles cellmap_flow.ai_annotate.pipeline cellmap_flow.ai_annotate.prompts cellmap_flow.ai_annotate.secrets cellmap_flow.ai_annotate.staging cellmap_flow.ai_annotate.usage cellmap_flow.blockwise cellmap_flow.blockwise.blockwise_processor cellmap_flow.blockwise.bounding_box 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.ai_annotate 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.channel 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.publish cellmap_flow.dashboard.routes.finetune.rank_routes cellmap_flow.dashboard.routes.finetune.restart_key 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.distill cellmap_flow.finetune.export_merged cellmap_flow.finetune.export_web 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_wrapper cellmap_flow.finetune.losses cellmap_flow.finetune.markers cellmap_flow.finetune.model_loading cellmap_flow.finetune.options cellmap_flow.finetune.rank 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.finetune.trainer cellmap_flow.finetune.trainer.diagnostics cellmap_flow.finetune.trainer.distillation cellmap_flow.finetune.trainer.loop cellmap_flow.finetune.trainer.recovery cellmap_flow.finetune.trainer.supervised cellmap_flow.finetune.trainer.tensorboard cellmap_flow.globals cellmap_flow.inference cellmap_flow.inference.graph cellmap_flow.inference.runner cellmap_flow.inference.timing cellmap_flow.inferencer cellmap_flow.io cellmap_flow.io.metadata cellmap_flow.io.multiscale cellmap_flow.io.paths cellmap_flow.io.raw 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.onnx cellmap_flow.models.configs.script cellmap_flow.models.entry 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.portable cellmap_flow.portable.activation cellmap_flow.portable.ai_annotate cellmap_flow.portable.ai_annotate_calls cellmap_flow.portable.calls cellmap_flow.portable.carry cellmap_flow.portable.fill cellmap_flow.portable.fill_calls cellmap_flow.portable.label_it cellmap_flow.portable.label_it_calls cellmap_flow.portable.pasted cellmap_flow.portable.publish cellmap_flow.portable.publish_calls cellmap_flow.portable.rank cellmap_flow.portable.regions cellmap_flow.portable.targets cellmap_flow.portable.targets_calls cellmap_flow.portable.volume cellmap_flow.portable.volume_calls cellmap_flow.post cellmap_flow.post.postprocessors cellmap_flow.post.segment cellmap_flow.process_chain cellmap_flow.review cellmap_flow.review_index cellmap_flow.schema 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.utils cellmap_flow.utils.address cellmap_flow.utils.bsub_utils cellmap_flow.utils.device cellmap_flow.utils.serialize_config cellmap_flow.viewer cellmap_flow.viewer.bootstrap cellmap_flow.viewer.keys cellmap_flow.viewer.layers cellmap_flow.viewer.raw

MODULE (in module cellmap_flow.finetune.distill) (in module cellmap_flow.finetune.export_web) module_command() (in module cellmap_flow.finetune.job_manager.submit) module_graph() (in module cellmap_flow.inference.graph) 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) move() (cellmap_flow.finetune.job_manager.submit.QueueFallback method) multiplier (cellmap_flow.post.postprocessors.DefaultPostprocessor attribute) mutex_watershed() (in module cellmap_flow.post.segment)

N

n (cellmap_flow.inference.runner.DeviceSlots attribute) name (cellmap_flow.ai_annotate.organelles.OrganelleProfile attribute) (cellmap_flow.cli.doctor.Result attribute) (cellmap_flow.dashboard.requests.PipelineNode attribute) (cellmap_flow.dashboard.requests.RemoveModel 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.onnx.OnnxModelConfig 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.OnnxModelConfig attribute) (cellmap_flow.models.models_config.ScriptModelConfig attribute) (cellmap_flow.models.resolve.Resolved attribute), [1] (cellmap_flow.schema.StepSpec attribute) (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) names() (in module cellmap_flow.models.entry) NANOMETER (in module cellmap_flow.io.metadata) NARROW_WINDOW (in module cellmap_flow.finetune.rank) (in module cellmap_flow.portable.rank) 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) nearest() (in module cellmap_flow.portable.ai_annotate) needed_postprocess() (in module cellmap_flow.portable.calls) (in module cellmap_flow.portable.rank) 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) network_parameters (cellmap_flow.finetune.job_manager.state.FinetuneJob attribute) NETWORK_PARAMETERS (in module cellmap_flow.finetune.markers) NETWORK_PARAMETERS_RE (in module cellmap_flow.finetune.markers) NEUROGLANCER_FORK_COMMIT (in module cellmap_flow.cli.doctor) NEUROGLANCER_FORK_INSTALL (in module cellmap_flow.cli.doctor) NEUROGLANCER_FORK_MARKER (in module cellmap_flow.cli.doctor)

NEUROGLANCER_SOURCE (in module cellmap_flow.portable.pasted) neuroglancer_source() (in module cellmap_flow.viewer.raw) NEUROGLANCER_TOP_ROW_PX (in module cellmap_flow.portable.label_it) neuroglancer_url (cellmap_flow.dashboard.state.Session attribute) new_annotate_id() (in module cellmap_flow.ai_annotate.staging) new_region() (in module cellmap_flow.portable.regions) 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.io.metadata) (in module cellmap_flow.models.configs.bio) NO_JOB (in module cellmap_flow.dashboard.routes.finetune.restart_key) NORM_FROM (in module cellmap_flow.dashboard.routes.finetune.rank_routes) norm_tries() (in module cellmap_flow.portable.calls) (in module cellmap_flow.portable.rank) normalise() (in module cellmap_flow.models.bioimage_catalog) normalise_artifact() (in module cellmap_flow.models.bioimage_catalog) normalize (cellmap_flow.io.raw.RawInput attribute) (cellmap_flow.viewer.raw.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) normalize_to_uint8() (in module cellmap_flow.portable.ai_annotate) 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) normalizers() (in module cellmap_flow.portable.rank) normalizes_input (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.models_config.BioModelConfig attribute) (cellmap_flow.models.models_config.CellposeModelConfig attribute) (cellmap_flow.models.models_config.FinetuneModelConfig property) (cellmap_flow.models.models_config.ModelConfig attribute) not_cubes (cellmap_flow.finetune.data.dataset.VirtualPatchDataset attribute) (cellmap_flow.finetune.data.VirtualPatchDataset attribute) NOT_RESTARTED (in module cellmap_flow.dashboard.routes.finetune.restart_key) NOT_SENT (in module cellmap_flow.dashboard.routes.finetune.ai_annotate) NOT_WAITING (in module cellmap_flow.dashboard.routes.finetune.restart_key) NotAnAnnotationVolume notes (cellmap_flow.models.resolve.Resolved attribute), [1] notify() (cellmap_flow.finetune.job_manager.listener.Listeners method) NotRemovable 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.finetune.options.TrainingOptions attribute) (cellmap_flow.finetune.trainer.Finetuner attribute) (cellmap_flow.finetune.trainer.loop.Finetuner attribute) num_previous_segments (cellmap_flow.post.postprocessors.AffinityPostprocessor attribute) (cellmap_flow.post.postprocessors.MortonSegmentationRelabeling attribute) num_workers (cellmap_flow.finetune.options.TrainingOptions attribute) number() (in module cellmap_flow.models.entry) numbers() (in module cellmap_flow.models.entry) 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.blockwise.bounding_box.BoundingBox attribute) offsets (cellmap_flow.finetune.options.TrainingOptions attribute) (cellmap_flow.finetune.target_transforms.AffinityTargetTransform attribute) OK (in module cellmap_flow.cli.doctor) on (cellmap_flow.finetune.trainer.distillation.Distillation property) (cellmap_flow.finetune.trainer.tensorboard.TensorBoard property) on_channel() (in module cellmap_flow.portable.rank) 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) ONLINE_TIMEOUT (in module cellmap_flow.models.resolve) ONNX_FILE_LIMIT (in module cellmap_flow.finetune.export_web) ONNX_REPO (in module cellmap_flow.models.resolve) OnnxModelConfig (class in cellmap_flow.models.configs.onnx) (class in cellmap_flow.models.models_config) op_listing() (in module cellmap_flow.norm.input_normalize) open_db() (in module cellmap_flow.review) open_labels() (in module cellmap_flow.finetune.session.volume) open_level() (in module cellmap_flow.io.metadata) open_raw() (in module cellmap_flow.io.raw) open_served_labels() (in module cellmap_flow.finetune.session.fill) optimize_model() (cellmap_flow.inference.runner.ModelRunner method) OPTIONAL_FIELDS (in module cellmap_flow.serving.client) options (cellmap_flow.ai_annotate.config.ProviderConfig attribute) (cellmap_flow.finetune.trainer.Finetuner attribute) (cellmap_flow.finetune.trainer.loop.Finetuner attribute) options() (cellmap_flow.dashboard.requests.FinetuneSubmit method) options_of() (in module cellmap_flow.finetune.cli) OrganelleProfile (class in cellmap_flow.ai_annotate.organelles) ORGANELLES (in module cellmap_flow.ai_annotate.organelles) origin (cellmap_flow.serving.chunkmirage_ops.ServedModel attribute) OrModelMerger (class in cellmap_flow.models.model_merger) OTHER_CHANNELS_WEIGHT (in module cellmap_flow.finetune.trainer.distillation) others_term() (cellmap_flow.finetune.trainer.distillation.Distillation method) output (cellmap_flow.dashboard.requests.CellposeSelection attribute) (cellmap_flow.jobs.lsf.JobIdMissingError attribute) (cellmap_flow.models.configs.cellpose.CellposeModelConfig attribute) (cellmap_flow.models.configs.onnx.OnnxModelConfig attribute) (cellmap_flow.models.models_config.CellposeModelConfig attribute) (cellmap_flow.models.models_config.OnnxModelConfig attribute) output_activation() (in module cellmap_flow.portable.activation) (in module cellmap_flow.portable.calls) output_channel_names() (in module cellmap_flow.serving.client) output_channels (cellmap_flow.models.geometry.ModelGeometry attribute) (cellmap_flow.serving.chunkmirage_ops.ServedModel attribute) OUTPUT_CHANNELS (in module cellmap_flow.models.configs.cellpose) OUTPUT_CHANNELS_3D (in module cellmap_flow.models.configs.cellpose) output_channels_is_dict (cellmap_flow.blockwise.blockwise_processor.CellMapFlowBlockwiseProcessor attribute) output_class (cellmap_flow.finetune.options.TrainingOptions attribute) (cellmap_flow.finetune.trainer.supervised.SupervisedLoss attribute) (cellmap_flow.inference.runner.ModelRunner attribute) output_class_from (cellmap_flow.inference.runner.ModelRunner attribute) output_class_of() (in module cellmap_flow.finetune.trainer.supervised) OUTPUT_CLASSES (in module cellmap_flow.finetune.options)

OUTPUT_CODEC (in module cellmap_flow.blockwise.blockwise_processor) OUTPUT_DESCRIPTIONS (in module cellmap_flow.finetune.export_web) output_dir (cellmap_flow.finetune.export_web.WebExport attribute) (cellmap_flow.finetune.job_manager.state.FinetuneJob attribute) (cellmap_flow.finetune.trainer.Finetuner attribute) (cellmap_flow.finetune.trainer.loop.Finetuner 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.serving.chunkmirage_ops.ServedModel attribute) output_dtype() (cellmap_flow.process_chain.ProcessChain method) output_graph() (cellmap_flow.models.configs.base.ModelConfig method) (cellmap_flow.models.configs.bio.BioModelConfig method) (cellmap_flow.models.configs.finetune.FinetuneModelConfig method) (cellmap_flow.models.configs.onnx.OnnxModelConfig method) (cellmap_flow.models.models_config.BioModelConfig method) (cellmap_flow.models.models_config.FinetuneModelConfig method) (cellmap_flow.models.models_config.ModelConfig method) (cellmap_flow.models.models_config.OnnxModelConfig 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_op (cellmap_flow.inference.runner.ModelRunner attribute) 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.configs.onnx.OnnxModelConfig attribute) (cellmap_flow.models.models_config.FlyModelConfig attribute) (cellmap_flow.models.models_config.OnnxModelConfig attribute) output_type (cellmap_flow.finetune.options.TrainingOptions attribute) OUTPUT_TYPES (in module cellmap_flow.finetune.options) 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.configs.onnx.OnnxModelConfig attribute) (cellmap_flow.models.geometry.ModelGeometry attribute) (cellmap_flow.models.models_config.FinetuneModelConfig attribute) (cellmap_flow.models.models_config.FlyModelConfig attribute) (cellmap_flow.models.models_config.OnnxModelConfig 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) outputs() (in module cellmap_flow.schema) overlay() (in module cellmap_flow.ai_annotate.staging) (in module cellmap_flow.portable.ai_annotate) OVERLAY_ALPHA (in module cellmap_flow.ai_annotate.staging) (in module cellmap_flow.portable.ai_annotate) overwrite (cellmap_flow.dashboard.requests.AIAnnotateDecision attribute)

P

package_logger (in module cellmap_flow.dashboard.app) paint() (in module cellmap_flow.portable.fill) paint_box() (in module cellmap_flow.finetune.session.fill) paint_depth_axes() (in module cellmap_flow.finetune.data.sampler) paint_edges() (in module cellmap_flow.finetune.rank) (in module cellmap_flow.portable.rank) PAINT_FIRST_CHUNK (in module cellmap_flow.portable.volume) paint_first_refusal() (in module cellmap_flow.dashboard.routes.finetune.annotation_core) PAINT_FIRST_TRAINING (in module cellmap_flow.portable.volume) paint_planes (cellmap_flow.finetune.data.sampler.PatchSampler attribute) painting_unavailable() (in module cellmap_flow.cli.doctor) panel_px() (in module cellmap_flow.portable.label_it) 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] (cellmap_flow.schema.StepSpec attribute) 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) parse_manifest() (in module cellmap_flow.models.configs.onnx) parts() (in module cellmap_flow.portable.carry) PASS_THROUGH_OPS (in module cellmap_flow.portable.activation) pasted_path() (in module cellmap_flow.portable.pasted) patch_refusal() (in module cellmap_flow.finetune.data.loader) patches_per_epoch (cellmap_flow.finetune.crop_loader.CropsConfig attribute) (cellmap_flow.finetune.data.dataset.VirtualPatchDataset attribute) (cellmap_flow.finetune.data.VirtualPatchDataset attribute) (cellmap_flow.finetune.options.TrainingOptions 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.models.configs.onnx.OnnxModelConfig attribute) (cellmap_flow.models.models_config.OnnxModelConfig attribute) (cellmap_flow.schema.Route 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) PENDING_S (in module cellmap_flow.dashboard.routes.finetune.restart_key) per_axis() (in module cellmap_flow.models.entry) 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) pixel_nm (cellmap_flow.viewer.raw.View attribute) 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) place() (in module cellmap_flow.portable.label_it_calls) PLACEHOLDER_DATA_PATHS (in module cellmap_flow.finetune.finetuned_model_templates) placement() (in module cellmap_flow.portable.label_it) plan() (in module cellmap_flow.portable.ai_annotate_calls) plan_paint_volume() (in module cellmap_flow.finetune.session.volume) (in module cellmap_flow.portable.volume) (in module cellmap_flow.portable.volume_calls) plan_plane() (in module cellmap_flow.ai_annotate.geometry) (in module cellmap_flow.portable.ai_annotate) plan_volume() (in module cellmap_flow.finetune.session.volume) (in module cellmap_flow.portable.volume) (in module cellmap_flow.portable.volume_calls) plane_axes (cellmap_flow.portable.ai_annotate.PlanePlan property) plane_image() (in module cellmap_flow.portable.ai_annotate) plane_name (cellmap_flow.portable.ai_annotate.PlanePlan property) PLANE_NAMES (in module cellmap_flow.finetune.data.sampler) (in module cellmap_flow.portable.ai_annotate) PlanePlan (class in cellmap_flow.portable.ai_annotate) PLUGINS_DIR (in module cellmap_flow.plugins) plugins_group() (in module cellmap_flow.cli.main) png_base64() (in module cellmap_flow.ai_annotate.images) point_latest_export() (in module cellmap_flow.finetune.run_outputs)

point_nm (cellmap_flow.dashboard.requests.AIAnnotateRun attribute) (cellmap_flow.portable.ai_annotate.PlanePlan 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) postprocess_config (cellmap_flow.process_chain.ProcessChain attribute) POSTPROCESS_KEY (in module cellmap_flow.serving.protocol) postprocess_set_by() (in module cellmap_flow.dashboard.routes.pipeline) 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) precision (cellmap_flow.finetune.trainer.distillation.Distillation attribute) (cellmap_flow.finetune.trainer.Finetuner attribute) (cellmap_flow.finetune.trainer.loop.Finetuner attribute) Precision (class in cellmap_flow.finetune.trainer.recovery) 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) (in module cellmap_flow.portable.ai_annotate_calls) 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) preview() (in module cellmap_flow.ai_annotate.staging) print_available_models() (in module cellmap_flow.models.registry) print_lora_parameters() (in module cellmap_flow.finetune.lora_wrapper) private (cellmap_flow.dashboard.requests.FinetunePublish attribute) probability() (in module cellmap_flow.portable.label_it) (in module cellmap_flow.portable.label_it_calls) probe_output_class() (in module cellmap_flow.finetune.trainer.supervised) probe_precision() (in module cellmap_flow.finetune.trainer.recovery) 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) project (cellmap_flow.ai_annotate.backends.vertex_gemini.VertexGeminiBackend attribute) prompt (cellmap_flow.ai_annotate.backends.base.SegmentRequest attribute) (cellmap_flow.dashboard.requests.AIAnnotateResend attribute) (cellmap_flow.dashboard.requests.AIAnnotateSettings attribute) PROMPT_MAX_CHARS (in module cellmap_flow.dashboard.requests) provider (cellmap_flow.dashboard.requests.AIAnnotateSettings attribute) provider() (cellmap_flow.ai_annotate.config.AIAnnotateConfig method) PROVIDER_OPTIONS (in module cellmap_flow.ai_annotate.config) ProviderConfig (class in cellmap_flow.ai_annotate.config) providers (cellmap_flow.ai_annotate.config.AIAnnotateConfig attribute) proxied_url() (in module cellmap_flow.finetune.session.minio) public() (cellmap_flow.ai_annotate.config.AIAnnotateConfig method) PUBLIC_APP (in module cellmap_flow.portable.publish) public_server_url() (in module cellmap_flow.jobs.spec) publication() (in module cellmap_flow.portable.publish_calls) publication_files() (in module cellmap_flow.portable.publish) publish_status() (in module cellmap_flow.dashboard.routes.finetune.publish) published_links() (in module cellmap_flow.portable.publish) (in module cellmap_flow.portable.publish_calls) published_manifest() (in module cellmap_flow.portable.publish) 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.dashboard.requests.ServerConfigUpdate attribute) (cellmap_flow.jobs.settings.LauncherSettings attribute) (cellmap_flow.jobs.spec.Job attribute) (cellmap_flow.jobs.spec.JobSpec attribute)

queue_list() (in module cellmap_flow.jobs.queues) QueueFallback (class in cellmap_flow.finetune.job_manager.submit) queues (cellmap_flow.finetune.job_manager.submit.QueueFallback attribute) Queues (in module cellmap_flow.dashboard.requests) 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) RANDOM_SHARE (in module cellmap_flow.finetune.distill) rank_add() (in module cellmap_flow.dashboard.routes.finetune.rank_routes) rank_added (cellmap_flow.dashboard.state.Session attribute) RANK_BLOCKS (in module cellmap_flow.finetune.rank) (in module cellmap_flow.portable.rank) rank_candidates() (in module cellmap_flow.dashboard.routes.finetune.rank_routes) rank_fits (cellmap_flow.dashboard.state.Session attribute) rank_input_norm() (in module cellmap_flow.dashboard.routes.finetune.rank_routes) RANK_PREFIX (in module cellmap_flow.review) rank_row() (in module cellmap_flow.portable.calls) rank_score() (in module cellmap_flow.dashboard.routes.finetune.rank_routes) (in module cellmap_flow.finetune.rank) (in module cellmap_flow.portable.calls) (in module cellmap_flow.portable.rank) RANK_SMOOTHING (in module cellmap_flow.finetune.rank) (in module cellmap_flow.portable.rank) rank_tally() (in module cellmap_flow.portable.calls) rank_use() (in module cellmap_flow.dashboard.routes.finetune.rank_routes) rate_words() (in module cellmap_flow.finetune.trainer.loop) ratio (cellmap_flow.serving.chunkmirage_ops.ServedModel attribute) raw (cellmap_flow.dashboard.state.Session attribute) raw() (cellmap_flow.finetune.data.reader.PatchReader method) raw_box() (in module cellmap_flow.ai_annotate.geometry) (in module cellmap_flow.portable.ai_annotate) RAW_CACHE_BYTES_DEFAULT (in module cellmap_flow.serving.chunkmirage_server) RAW_CACHE_BYTES_ENV (in module cellmap_flow.serving.chunkmirage_server) raw_channels() (in module cellmap_flow.io.raw) 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_dtype_and_range() (in module cellmap_flow.dashboard.routes.model_advice) raw_extent_nm() (in module cellmap_flow.ai_annotate.pipeline) raw_input (cellmap_flow.blockwise.blockwise_processor.CellMapFlowBlockwiseProcessor attribute) raw_layer() (in module cellmap_flow.viewer.layers) raw_level() (in module cellmap_flow.finetune.session.volume) raw_offset_nm (cellmap_flow.portable.ai_annotate.PlanePlan attribute) RAW_SAMPLE (in module cellmap_flow.dashboard.routes.finetune.rank_routes) RAW_SHADER (in module cellmap_flow.viewer.raw) raw_shape_nm (cellmap_flow.portable.ai_annotate.PlanePlan attribute) raw_voxel_sizes() (in module cellmap_flow.finetune.session.volume) RawInput (class in cellmap_flow.io.raw) read() (cellmap_flow.finetune.job_manager.tailer.LogTailer method) read_box() (in module cellmap_flow.portable.label_it) read_chunk() (cellmap_flow.serving.chunkmirage_server.ChunkmirageServer method) (in module cellmap_flow.finetune.session.manifest) read_graph() (in module cellmap_flow.models.configs.onnx) read_index() (cellmap_flow.io.raw.RawInput method) read_manifest() (in module cellmap_flow.finetune.session.manifest) (in module cellmap_flow.models.configs.onnx) read_metadata() (in module cellmap_flow.models.configs.onnx) read_offsets_from_script() (in module cellmap_flow.finetune.target_transforms) READ_ONLY (in module cellmap_flow.portable.publish) read_or_create_restart_token() (in module cellmap_flow.serving.restart_token) read_plane() (in module cellmap_flow.ai_annotate.pipeline) 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_root_attrs() (in module cellmap_flow.finetune.session.volume) 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) reader (cellmap_flow.finetune.data.dataset.VirtualPatchDataset attribute) (cellmap_flow.finetune.data.VirtualPatchDataset attribute) reads_input_itself() (cellmap_flow.models.configs.base.ModelConfig method) (cellmap_flow.models.configs.script.ScriptModelConfig method) (cellmap_flow.models.models_config.ModelConfig method) (cellmap_flow.models.models_config.ScriptModelConfig method) 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) (in module cellmap_flow.ai_annotate.audit) 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) redact() (in module cellmap_flow.ai_annotate.secrets) REDACTED (in module cellmap_flow.ai_annotate.secrets) RedactingFilter (class in cellmap_flow.ai_annotate.secrets) ref (cellmap_flow.dashboard.routes.model_resolve.ResolveModel attribute) ref_of() (in module cellmap_flow.portable.publish) 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) refund() (in module cellmap_flow.ai_annotate.usage) Refused REGENERATE (in module cellmap_flow.schema) region_box_nm() (in module cellmap_flow.portable.regions) region_boxes() (in module cellmap_flow.portable.volume_calls) region_centre_voxels() (in module cellmap_flow.portable.regions) region_size_nm() (in module cellmap_flow.portable.regions) 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_secret() (in module cellmap_flow.ai_annotate.secrets) register_volume() (cellmap_flow.finetune.session.store.SessionStore method) registry (cellmap_flow.serving.chunkmirage_server.ChunkmirageServer attribute) rehearsal_centres (cellmap_flow.finetune.data.sampler.PatchSampler attribute) rehearsal_fraction (cellmap_flow.finetune.data.sampler.PatchSampler attribute) (cellmap_flow.finetune.options.TrainingOptions 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.portable.fill) remap_labels() (in module cellmap_flow.finetune.crop_loader) remember (cellmap_flow.dashboard.requests.HuggingFaceCredentials attribute) remembered() (in module cellmap_flow.serving.launch) 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_loaded_model() (in module cellmap_flow.dashboard.routes.models) remove_manifest() (in module cellmap_flow.finetune.session.manifest) remove_model() (in module cellmap_flow.dashboard.services.launch) remove_small() (in module cellmap_flow.portable.label_it) REMOVED_IN (in module cellmap_flow.cli.common)

RemoveModel (class in cellmap_flow.dashboard.requests) rename_layer_in_viewer() (in module cellmap_flow.dashboard.routes.finetune.layers) replace_layer() (in module cellmap_flow.viewer.layers) replaced() (cellmap_flow.finetune.options.TrainingOptions method) repo (cellmap_flow.dashboard.requests.FinetunePublish attribute) (cellmap_flow.models.configs.huggingface.HuggingFaceModelConfig attribute) (cellmap_flow.models.configs.onnx.OnnxModelConfig attribute) (cellmap_flow.models.models_config.HuggingFaceModelConfig attribute) (cellmap_flow.models.models_config.OnnxModelConfig attribute) repo_facts() (in module cellmap_flow.models.hf_catalog) repo_refusal() (in module cellmap_flow.portable.publish) (in module cellmap_flow.portable.publish_calls) report() (cellmap_flow.finetune.data.augment.Augmentation method) (cellmap_flow.finetune.trainer.diagnostics.GradientFlow method) (in module cellmap_flow.cli.doctor) request (cellmap_flow.schema.Route attribute) request_image() (in module cellmap_flow.portable.ai_annotate_calls) REQUEST_MODELS (in module cellmap_flow.schema) request_models() (in module cellmap_flow.schema) request_restart() (cellmap_flow.finetune.session_loop.JobControl method) (in module cellmap_flow.finetune.job_manager.restart) request_stop() (cellmap_flow.finetune.session_loop.JobControl method) (in module cellmap_flow.finetune.job_manager.restart) requested_offset() (in module cellmap_flow.dashboard.routes.logging_routes) 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.io.raw) resample_option() (in module cellmap_flow.cli.common) reset() (cellmap_flow.finetune.adaptation.AdaptationStrategy method) (cellmap_flow.finetune.adaptation.FullStrategy method) (cellmap_flow.finetune.adaptation.LoraStrategy method) reset_epoch() (cellmap_flow.finetune.trainer.supervised.SupervisedLoss method) resize() (in module cellmap_flow.portable.ai_annotate) resolution_nm (cellmap_flow.portable.ai_annotate.PlanePlan attribute) resolve() (in module cellmap_flow.models.resolve) resolve_api_key() (in module cellmap_flow.ai_annotate.secrets) 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) resolve_organelle_profile() (in module cellmap_flow.ai_annotate.organelles) resolve_request() (in module cellmap_flow.dashboard.routes.model_resolve) 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_ALIASES (in module cellmap_flow.finetune.cli) restart_callback (cellmap_flow.serving.chunkmirage_server.ChunkmirageServer 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_key (cellmap_flow.dashboard.state.Session attribute) restart_params() (in module cellmap_flow.dashboard.routes.finetune.common) RESTART_STATUS (in module cellmap_flow.finetune.markers) restart_token (cellmap_flow.serving.chunkmirage_server.ChunkmirageServer attribute) RESTARTABLE_ARGS (in module cellmap_flow.finetune.cli) RESTARTING (in module cellmap_flow.dashboard.routes.finetune.restart_key) RESTARTING_TRAINING (in module cellmap_flow.finetune.markers) restore() (in module cellmap_flow.portable.fill) restore_box() (in module cellmap_flow.finetune.session.fill) Result (class in cellmap_flow.cli.doctor) result_file (cellmap_flow.finetune.export_web.WebExport property) RESULT_NAME (in module cellmap_flow.finetune.export_web) retire_annotation_volume() (in module cellmap_flow.dashboard.finetune_utils) retire_volume() (cellmap_flow.finetune.session.store.SessionStore method) (in module cellmap_flow.finetune.session.sync) RETRY_CODES (in module cellmap_flow.ai_annotate.backends.vertex_gemini) RETRY_STATUSES (in module cellmap_flow.ai_annotate.backends.vertex_gemini) RETRY_WAITS_S (in module cellmap_flow.ai_annotate.backends.vertex_gemini) 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.configs.onnx.OnnxModelConfig attribute) (cellmap_flow.models.models_config.HuggingFaceModelConfig attribute) (cellmap_flow.models.models_config.OnnxModelConfig attribute) rewrite() (in module cellmap_flow.portable.fill) rewrite_foreground() (in module cellmap_flow.finetune.session.fill) rewrite_minio_url_for_proxy() (in module cellmap_flow.dashboard.routes.finetune.common) rgb (cellmap_flow.ai_annotate.organelles.OrganelleProfile attribute) ROOT (in module cellmap_flow.schema) root_base_model_dict() (in module cellmap_flow.finetune.model_loading) Route (class in cellmap_flow.schema) routes() (in module cellmap_flow.schema) run() (cellmap_flow.blockwise.blockwise_processor.CellMapFlowBlockwiseProcessor method) (cellmap_flow.finetune.session_loop.TrainingSession method) (cellmap_flow.serving.chunkmirage_server.ChunkmirageServer method) (in module cellmap_flow.jobs.local) run_at_geometry() (in module cellmap_flow.models.geometry) run_checks() (in module cellmap_flow.cli.doctor) run_generic() (in module cellmap_flow.cli.infer) run_job() (in module cellmap_flow.finetune.export_web) run_metadata() (in module cellmap_flow.models.configs.fly) run_model() (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) run_voxel_size (cellmap_flow.models.configs.base.ModelConfig property) (cellmap_flow.models.models_config.ModelConfig property) RUN_VOXEL_SIZE_KEY (in module cellmap_flow.models.registry) run_voxel_sizes (cellmap_flow.dashboard.requests.SubmitModels attribute) run_voxel_sizes() (in module cellmap_flow.models.geometry) 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) runs_at() (in module cellmap_flow.models.configs.cellmap)

S

SAM_TILE_SIZE (in module cellmap_flow.models.configs.cellpose) same_grid() (in module cellmap_flow.portable.volume) same_steps() (in module cellmap_flow.portable.rank) same_value() (in module cellmap_flow.serving.probe) 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.portable.targets) save() (cellmap_flow.jobs.settings.LauncherSettings method) save_adapter() (cellmap_flow.finetune.trainer.Finetuner method) (cellmap_flow.finetune.trainer.loop.Finetuner method) save_checkpoint() (cellmap_flow.finetune.adaptation.AdaptationStrategy method) (cellmap_flow.finetune.trainer.Finetuner method) (cellmap_flow.finetune.trainer.loop.Finetuner 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) say() (in module cellmap_flow.viewer.keys) say_for() (in module cellmap_flow.viewer.keys) SCALAR_TENSOR_BYTES (in module cellmap_flow.models.configs.onnx) 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.onnx.OnnxModelConfig 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.OnnxModelConfig 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.trainer.recovery.Precision attribute) ScaleRange (class in cellmap_flow.finetune.trainable) schedule_steps (cellmap_flow.finetune.trainer.Finetuner property) (cellmap_flow.finetune.trainer.loop.Finetuner property) schedule_words() (in module cellmap_flow.finetune.trainer.loop) schema() (in module cellmap_flow.schema) SCHEMA_DRAFT (in module cellmap_flow.schema) SCHEMA_NAME (in module cellmap_flow.schema) score_row() (in module cellmap_flow.portable.rank) screen_axes() (in module cellmap_flow.portable.ai_annotate) screen_shape() (in module cellmap_flow.portable.ai_annotate) script_path (cellmap_flow.models.configs.script.ScriptModelConfig attribute) (cellmap_flow.models.models_config.ScriptModelConfig attribute) script_reads_input_itself() (in module cellmap_flow.models.configs.script) 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() (in module cellmap_flow.portable.fill_calls) (in module cellmap_flow.portable.label_it_calls) seed_channels() (in module cellmap_flow.portable.label_it) seed_instance_volume() (in module cellmap_flow.finetune.session.instance) seed_labels() (in module cellmap_flow.portable.fill) SEED_METHODS (in module cellmap_flow.portable.label_it) seed_methods() (in module cellmap_flow.dashboard.routes.finetune.view_labels) seed_options() (in module cellmap_flow.portable.label_it) (in module cellmap_flow.portable.label_it_calls) seed_plan() (in module cellmap_flow.portable.label_it_calls) seed_sources() (in module cellmap_flow.dashboard.routes.finetune.view_labels) seed_view_from_prediction() (in module cellmap_flow.dashboard.routes.finetune.view_labels) seen_nonzero (cellmap_flow.finetune.trainer.diagnostics.GradientFlow attribute) segment() (cellmap_flow.ai_annotate.backends.base.Backend method) (cellmap_flow.ai_annotate.backends.fake.FakeBackend method) (cellmap_flow.ai_annotate.backends.vertex_gemini.VertexGeminiBackend method) segment_prediction() (in module cellmap_flow.dashboard.routes.finetune.view_labels) segmentation_layer (cellmap_flow.dashboard.routes.review_routes.ReviewSession attribute) SegmentRequest (class in cellmap_flow.ai_annotate.backends.base) SegmentResult (class in cellmap_flow.ai_annotate.backends.base) select_channel (cellmap_flow.finetune.options.TrainingOptions attribute) (cellmap_flow.finetune.trainer.distillation.Distillation attribute) (cellmap_flow.finetune.trainer.Finetuner attribute) (cellmap_flow.finetune.trainer.loop.Finetuner attribute) selected() (cellmap_flow.viewer.raw.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.io.raw) selected_hf_models (cellmap_flow.dashboard.requests.SubmitModels attribute) selected_models (cellmap_flow.dashboard.requests.SubmitModels attribute) SELF_CONNECT_TIMEOUT (in module cellmap_flow.utils.address) SENTENCES (in module cellmap_flow.ai_annotate.prompts) separate_zarrs (cellmap_flow.blockwise.blockwise_processor.CellMapFlowBlockwiseProcessor attribute) seq (cellmap_flow.dashboard.routes.review_routes.PickBoard attribute) SequentialWrapper (class in cellmap_flow.finetune.trainable) 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_at_run_voxel_size() (in module cellmap_flow.dashboard.services.launch) served_dtype() (in module cellmap_flow.models.configs.bio) served_model() (in module cellmap_flow.serving.chunkmirage_ops) served_output_class() (in module cellmap_flow.dashboard.routes.finetune.common) ServedModel (class in cellmap_flow.serving.chunkmirage_ops) server_argv() (in module cellmap_flow.models.envs) (in module cellmap_flow.serving.launch) SERVER_COMMAND (in module cellmap_flow.jobs.launch) server_command() (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) SERVER_WAIT_SECONDS (in module cellmap_flow.dashboard.routes.finetune.rank_routes) ServerConfigUpdate (class in cellmap_flow.dashboard.requests) serving_entry() (in module cellmap_flow.finetune.export_web) Session (class in cellmap_flow.dashboard.state) SESSION_DIR_RE (in module cellmap_flow.finetune.session.store) session_raw_voxel_sizes() (in module cellmap_flow.dashboard.routes.finetune.annotation_core) 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_declared_input_norm() (in module cellmap_flow.dashboard.routes.pipeline) set_needed_postprocess() (in module cellmap_flow.dashboard.routes.pipeline) 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) settings_note() (in module cellmap_flow.dashboard.routes.finetune.common) SETUP_HOURS (in module cellmap_flow.finetune.distill) shader_controls (cellmap_flow.dashboard.state.Session attribute) shaders (cellmap_flow.dashboard.state.Session attribute) shape (cellmap_flow.blockwise.bounding_box.BoundingBox attribute) (cellmap_flow.blockwise.bounding_box.TaskBoundingBox attribute) (cellmap_flow.portable.carry.Grid attribute) 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) show_channel() (in module cellmap_flow.dashboard.routes.finetune.channel)

SHOW_S (in module cellmap_flow.dashboard.routes.finetune.restart_key) shown_channel() (cellmap_flow.dashboard.state.Session method) shown_channels (cellmap_flow.dashboard.state.Session attribute) shown_level() (in module cellmap_flow.portable.volume) (in module cellmap_flow.portable.volume_calls) SHOWN_LEVEL_SLACK (in module cellmap_flow.portable.volume) shown_voxel_size() (in module cellmap_flow.dashboard.routes.finetune.annotation_core) sigma (cellmap_flow.finetune.target_transforms.DistanceTargetTransform attribute) sigma_nm (cellmap_flow.finetune.target_transforms.IntervalTargetTransform attribute) sigma_nm() (in module cellmap_flow.portable.targets) sigma_voxels (cellmap_flow.finetune.target_transforms.IntervalTargetTransform attribute) sigmoid (cellmap_flow.models.configs.fly.FlyModelConfig attribute) (cellmap_flow.models.models_config.FlyModelConfig attribute) SIGMOID (in module cellmap_flow.portable.rank) SigmoidPostprocessor (class in cellmap_flow.post.postprocessors) SIGN_IN_FIRST (in module cellmap_flow.portable.publish) sign_weight (cellmap_flow.finetune.losses.IntervalLoss attribute) SIGNED_UNIT (in module cellmap_flow.portable.label_it) SIGNED_UNIT_OPS (in module cellmap_flow.portable.activation) SimpleBlockwiseMerger (built-in class) (class in cellmap_flow.post.postprocessors) since (cellmap_flow.finetune.job_manager.submit.QueueFallback attribute) SiteProfile (class in cellmap_flow.jobs.site) size (cellmap_flow.norm.input_normalize.Dilate attribute) sizes() (in module cellmap_flow.models.entry) slack (cellmap_flow.finetune.losses.IntervalLoss attribute) slice_axes() (in module cellmap_flow.finetune.data.reader) slice_planes (cellmap_flow.finetune.data.dataset.VirtualPatchDataset attribute) (cellmap_flow.finetune.data.VirtualPatchDataset attribute) slice_size (cellmap_flow.models.configs.cellpose.CellposeModelConfig attribute) (cellmap_flow.models.models_config.CellposeModelConfig attribute) slice_to_rgb() (in module cellmap_flow.ai_annotate.mask_extraction) 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.configs.onnx.OnnxModelConfig attribute) (cellmap_flow.models.models_config.BioModelConfig attribute) (cellmap_flow.models.models_config.CellposeModelConfig attribute) (cellmap_flow.models.models_config.OnnxModelConfig attribute) SliceWise (class in cellmap_flow.finetune.trainable) slope_term() (cellmap_flow.finetune.losses.IntervalLoss method) slope_weight (cellmap_flow.finetune.losses.IntervalLoss attribute) (cellmap_flow.finetune.options.TrainingOptions attribute) slots (cellmap_flow.serving.chunkmirage_ops.DevicePostprocessOp attribute) (cellmap_flow.serving.chunkmirage_ops.InferenceOp attribute) SLOW_DOWN_SECONDS (in module cellmap_flow.dashboard.routes.finetune.publish) small_copy (cellmap_flow.dashboard.requests.FinetunePublish attribute) small_manifest() (in module cellmap_flow.portable.publish) SMALL_SUFFIX (in module cellmap_flow.portable.publish) smooth (cellmap_flow.finetune.losses.DiceLoss attribute) snap() (cellmap_flow.finetune.data.reader.PatchReader method) snap_integral() (in module cellmap_flow.io.metadata) (in module cellmap_flow.portable.ai_annotate) snapshot_from_minio() (in module cellmap_flow.finetune.session.instance) soft_target_entropy() (in module cellmap_flow.finetune.losses) source (cellmap_flow.models.bioimage_catalog.VoxelSizeChoice attribute) (cellmap_flow.serving.chunkmirage_server.ChunkmirageServer attribute) SOURCE_BOUND_LAYER_KEYS (in module cellmap_flow.viewer.layers) SOURCES (in module cellmap_flow.dashboard.services.launch) sparse_chunk_starts (cellmap_flow.finetune.data.sampler.PatchSampler attribute) sparse_depth (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) spatial_axes() (in module cellmap_flow.io.raw) spatial_shape() (in module cellmap_flow.io.raw) spawn_worker() (in module cellmap_flow.blockwise.blockwise_processor) spec (cellmap_flow.process_chain.ProcessChain property) split() (in module cellmap_flow.models.entry) (in module cellmap_flow.portable.fill_calls) split_dataset_url() (in module cellmap_flow.serving.protocol) split_view_objects() (in module cellmap_flow.dashboard.routes.finetune.view_labels) spread() (in module cellmap_flow.finetune.rank) (in module cellmap_flow.portable.rank) stage() (in module cellmap_flow.ai_annotate.staging) (in module cellmap_flow.inference.timing) (in module cellmap_flow.portable.ai_annotate_calls) stage_dtype (cellmap_flow.serving.chunkmirage_ops.ServedModel attribute) STAGE_LABELS (in module cellmap_flow.dashboard.routes.finetune.ai_annotate) staging_dir() (in module cellmap_flow.ai_annotate.staging) STAGING_DIRNAME (in module cellmap_flow.ai_annotate.staging) 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_distill() (in module cellmap_flow.finetune.distill) start_error() (in module cellmap_flow.dashboard.services.launch) start_export() (in module cellmap_flow.finetune.export_web) start_hosts() (in module cellmap_flow.jobs.launch) start_input_norm() (in module cellmap_flow.dashboard.routes.pipeline) start_iteration() (in module cellmap_flow.finetune.job_manager.state) start_job() (in module cellmap_flow.finetune.export_web) start_periodic_sync() (in module cellmap_flow.finetune.session.sync) start_postprocess (cellmap_flow.dashboard.state.Session attribute) start_publish() (in module cellmap_flow.dashboard.routes.finetune.publish) START_WAIT_SECONDS (in module cellmap_flow.dashboard.routes.finetune.rank_routes) 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_KEY (in module cellmap_flow.dashboard.routes.finetune.ai_annotate) (in module cellmap_flow.dashboard.routes.finetune.restart_key) 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.finetune.trainer.tensorboard.TensorBoard attribute) (cellmap_flow.serving.chunkmirage_ops.PostprocessOp attribute) step_bce_metrics (cellmap_flow.finetune.trainer.supervised.SupervisedLoss attribute) step_interval_terms (cellmap_flow.finetune.trainer.supervised.SupervisedLoss attribute) steps() (in module cellmap_flow.schema) STEPS_PER_EPOCH (in module cellmap_flow.finetune.distill) StepSpec (class in cellmap_flow.schema) 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_callback (cellmap_flow.serving.chunkmirage_server.ChunkmirageServer attribute) stop_requested (cellmap_flow.finetune.trainer.Finetuner attribute) (cellmap_flow.finetune.trainer.loop.Finetuner attribute) stop_training_early() (cellmap_flow.finetune.job_manager.manager.FinetuneJobManager method) (in module cellmap_flow.dashboard.routes.finetune.training) store_geometry() (in module cellmap_flow.models.geometry_cache) stored_voxel_size() (in module cellmap_flow.finetune.data.dataset) strategy (cellmap_flow.finetune.trainer.distillation.Distillation attribute) (cellmap_flow.finetune.trainer.Finetuner attribute) (cellmap_flow.finetune.trainer.loop.Finetuner 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 (cellmap_flow.finetune.job_manager.submit.QueueFallback attribute) 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) 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) SUPERSEDED_DIRNAME (in module cellmap_flow.finetune.session.store) supervised (cellmap_flow.finetune.trainer.Finetuner attribute) (cellmap_flow.finetune.trainer.loop.Finetuner attribute) SupervisedLoss (class in cellmap_flow.finetune.trainer.supervised) survive_oom() (in module cellmap_flow.finetune.trainer.recovery) 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

tail() (in module cellmap_flow.jobs.spec) take_restart() (cellmap_flow.finetune.session_loop.JobControl method) take_stop() (cellmap_flow.finetune.session_loop.JobControl method) TAKEN (in module cellmap_flow.dashboard.routes.finetune.restart_key) taken() (in module cellmap_flow.dashboard.routes.finetune.restart_key) takes_probabilities (cellmap_flow.finetune.trainer.supervised.SupervisedLoss attribute) tally() (cellmap_flow.finetune.trainer.supervised.SupervisedLoss method) (in module cellmap_flow.finetune.rank) (in module cellmap_flow.portable.rank) target_modules (cellmap_flow.finetune.adaptation.LoraStrategy attribute) target_rgb (cellmap_flow.ai_annotate.backends.base.SegmentRequest attribute) target_transform (cellmap_flow.finetune.trainer.supervised.SupervisedLoss attribute) targets() (cellmap_flow.finetune.trainer.supervised.SupervisedLoss method) (in module cellmap_flow.portable.targets_calls) TargetTransform (class in cellmap_flow.finetune.target_transforms) task_name (cellmap_flow.blockwise.blockwise_processor.CellMapFlowBlockwiseProcessor attribute) (cellmap_flow.dashboard.requests.BlockwiseSubmit attribute) TaskBoundingBox (class in cellmap_flow.blockwise.bounding_box) tasks_dir() (cellmap_flow.dashboard.state.Session method) tb (cellmap_flow.finetune.trainer.Finetuner attribute) (cellmap_flow.finetune.trainer.loop.Finetuner 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.session_loop.TrainingSession attribute) (cellmap_flow.finetune.trainer.distillation.Distillation property) (cellmap_flow.finetune.trainer.Finetuner property) (cellmap_flow.finetune.trainer.loop.Finetuner property) teacher_needed (cellmap_flow.finetune.trainer.distillation.Distillation property) teacher_prediction() (cellmap_flow.finetune.trainer.distillation.Distillation method) TEACHER_SHARE (in module cellmap_flow.finetune.distill) 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) tensorboard (cellmap_flow.finetune.options.TrainingOptions attribute) TensorBoard (class in cellmap_flow.finetune.trainer.tensorboard) term() (cellmap_flow.finetune.trainer.distillation.Distillation method) TERMINAL_STATUSES (in module cellmap_flow.finetune.job_manager.state) this_machine_ip() (in module cellmap_flow.utils.address) threshold (cellmap_flow.post.postprocessors.FillHolesPostprocessor attribute) (cellmap_flow.post.postprocessors.ThresholdPostprocessor attribute) THRESHOLD (in module cellmap_flow.portable.rank) 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) tiles_per_volume() (in module cellmap_flow.models.configs.cellpose) timeout_s (cellmap_flow.ai_annotate.backends.vertex_gemini.VertexGeminiBackend attribute) 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.onnx.OnnxModelConfig 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.OnnxModelConfig method) (cellmap_flow.models.models_config.ScriptModelConfig method) (cellmap_flow.norm.input_normalize.SerializableInterface method) (cellmap_flow.portable.ai_annotate.PlanePlan 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.io.raw.RawInput method) (cellmap_flow.serving.chunkmirage_ops.BlockInput method) to_screen() (cellmap_flow.portable.ai_annotate.PlanePlan method) (in module cellmap_flow.portable.ai_annotate) to_url_blob() (cellmap_flow.pipeline_spec.PipelineSpec method) token (cellmap_flow.dashboard.requests.HuggingFaceCredentials attribute) (cellmap_flow.viewer.raw.ScalePyramid property) TOKEN_FILE (in module cellmap_flow.serving.restart_token) TOKEN_HEADER (in module cellmap_flow.serving.restart_token) TOKEN_REFUSED (in module cellmap_flow.portable.publish) TOKEN_URL (in module cellmap_flow.dashboard.routes.finetune.publish) 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.trainer.Finetuner method) (cellmap_flow.finetune.trainer.loop.Finetuner 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 (cellmap_flow.models.bioimage_catalog.VoxelSizeChoice attribute) trained_at() (in module cellmap_flow.models.bioimage_catalog) trained_at_geometry() (in module cellmap_flow.models.geometry) trained_volume_name() (in module cellmap_flow.finetune.session.manifest) 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_block() (in module cellmap_flow.finetune.export_web) TRAINING_DIVERGED (in module cellmap_flow.finetune.markers) training_flags() (in module cellmap_flow.finetune.cli) TRAINING_ITERATION_COMPLETE (in module cellmap_flow.finetune.markers) training_job_of() (in module cellmap_flow.dashboard.finetune_layers) training_manifest() (in module cellmap_flow.finetune.export_web) 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_refusal() (in module cellmap_flow.portable.volume) (in module cellmap_flow.portable.volume_calls) training_stats (cellmap_flow.finetune.trainer.Finetuner attribute) (cellmap_flow.finetune.trainer.loop.Finetuner attribute) TRAINING_TILE (in module cellmap_flow.models.configs.fly) TrainingOptions (class in cellmap_flow.finetune.options) TrainingSession (class in cellmap_flow.finetune.session_loop) trains_one_channel() (in module cellmap_flow.dashboard.routes.finetune.common) translation (cellmap_flow.serving.chunkmirage_ops.BlockInput attribute) (cellmap_flow.serving.chunkmirage_ops.ServedModel attribute) TS_NAME (in module cellmap_flow.schema) type (cellmap_flow.ai_annotate.config.ProviderConfig attribute) (cellmap_flow.dashboard.requests.CreateModelConfig attribute) (cellmap_flow.models.resolve.Resolved attribute), [1] (cellmap_flow.norm.input_normalize.EuclideanDistance attribute) type_default() (in module cellmap_flow.models.envs) type_name() (cellmap_flow.dashboard.requests.CreateModelConfig method) typescript() (in module cellmap_flow.schema)

U

UNANSWERED_RETRY_SECONDS (in module cellmap_flow.dashboard.routes.finetune.view_labels) UNBOUNDED (in module cellmap_flow.portable.label_it) undo() (in module cellmap_flow.portable.fill_calls) 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.portable.label_it) UNIT_OPS (in module cellmap_flow.portable.activation) UNREACHABLE (in module cellmap_flow.dashboard.routes.finetune.publish) 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_root_attrs() (in module cellmap_flow.finetune.session.volume) 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) usage (cellmap_flow.ai_annotate.backends.base.SegmentResult attribute) usage_path() (in module cellmap_flow.ai_annotate.usage) use_bce (cellmap_flow.finetune.trainer.supervised.SupervisedLoss attribute) use_exact (cellmap_flow.post.postprocessors.AffinityPostprocessor attribute) (cellmap_flow.post.postprocessors.MortonSegmentationRelabeling attribute) (cellmap_flow.post.postprocessors.SimpleBlockwiseMerger attribute) use_flow (cellmap_flow.finetune.trainer.supervised.SupervisedLoss attribute) use_half_prediction (cellmap_flow.inference.runner.ModelRunner attribute) use_interval (cellmap_flow.finetune.trainer.supervised.SupervisedLoss attribute) use_mse (cellmap_flow.finetune.trainer.supervised.SupervisedLoss attribute) user_message (cellmap_flow.ai_annotate.backends.AIAnnotateError attribute) (cellmap_flow.ai_annotate.errors.AIAnnotateError 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) variant (cellmap_flow.models.configs.onnx.OnnxModelConfig attribute) (cellmap_flow.models.models_config.OnnxModelConfig attribute) VARIANTS (in module cellmap_flow.models.configs.onnx) VARIANTS_HELP (in module cellmap_flow.finetune.export_web) VertexGeminiBackend (class in cellmap_flow.ai_annotate.backends.vertex_gemini) View (class in cellmap_flow.viewer.raw) view (in module cellmap_flow.cli.aliases) view_box_nm() (in module cellmap_flow.dashboard.routes.finetune.good_regions) VIEW_HALF_WIDTH_PX (in module cellmap_flow.viewer.raw) view_of() (in module cellmap_flow.viewer.raw) viewer (cellmap_flow.dashboard.state.Session attribute) VIEWER_AXES (in module cellmap_flow.viewer) viewer_position_and_scales() (in module cellmap_flow.dashboard.routes.finetune.common) viewer_space() (in module cellmap_flow.viewer.bootstrap) viewer_url() (in module cellmap_flow.viewer.bootstrap) 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.portable.fill) (in module cellmap_flow.portable.volume)

volume_grid() (in module cellmap_flow.dashboard.routes.finetune.annotation_core) 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_NEEDS (in module cellmap_flow.dashboard.routes.finetune.rank_routes) voxel_nm (cellmap_flow.portable.carry.Grid attribute) voxel_size (cellmap_flow.dashboard.requests.BioimageSelection attribute) (cellmap_flow.dashboard.requests.CellposeSelection attribute) (cellmap_flow.dashboard.requests.CreateVolume attribute) (cellmap_flow.dashboard.routes.model_resolve.ResolveModel attribute) (cellmap_flow.models.bioimage_catalog.VoxelSizeChoice 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) (cellmap_flow.serving.chunkmirage_ops.BlockInput attribute) voxel_size() (in module cellmap_flow.models.entry) 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) VoxelSizeChoice (class in cellmap_flow.models.bioimage_catalog)

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 (in module cellmap_flow.finetune.export_web) walltime_arg() (in module cellmap_flow.jobs.lsf) WARN (in module cellmap_flow.cli.doctor) warn_if_single_class() (in module cellmap_flow.finetune.trainer.diagnostics) watch_layer_deletes() (in module cellmap_flow.dashboard.services.launch) WEB_MODELS_REPO (in module cellmap_flow.models.hf_catalog) WebExport (class in cellmap_flow.finetune.export_web) weight (cellmap_flow.finetune.trainer.distillation.Distillation attribute) WEIGHT_ENDINGS (in module cellmap_flow.models.hf_catalog) weight_facts() (in module cellmap_flow.models.hf_catalog) 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)

WHOLE_VOXEL_TOLERANCE (in module cellmap_flow.portable.volume) whole_voxels() (in module cellmap_flow.portable.volume) WholeNumber (in module cellmap_flow.dashboard.requests) WINDOW_MARGIN (in module cellmap_flow.finetune.rank) (in module cellmap_flow.portable.rank) windowed() (in module cellmap_flow.finetune.rank) (in module cellmap_flow.portable.calls) (in module cellmap_flow.portable.rank) with_input_norms() (cellmap_flow.io.raw.RawInput method) with_requests() (in module cellmap_flow.dashboard.routes.finetune.restart_key) worker_cpus (cellmap_flow.jobs.site.SiteProfile attribute) workers (cellmap_flow.blockwise.blockwise_processor.CellMapFlowBlockwiseProcessor attribute) WORKERS (in module cellmap_flow.finetune.distill) wrap_model_with_lora() (in module cellmap_flow.finetune.lora_wrapper) write_crop_into_volume() (in module cellmap_flow.finetune.session.volume) write_hi (cellmap_flow.portable.ai_annotate.PlanePlan attribute) write_json_atomically() (in module cellmap_flow.finetune.json_files) write_lo (cellmap_flow.portable.ai_annotate.PlanePlan attribute) 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) (cellmap_flow.portable.ai_annotate.PlanePlan property) write_volume_manifest() (in module cellmap_flow.dashboard.routes.finetune.common) writer (cellmap_flow.finetune.trainer.tensorboard.TensorBoard attribute)

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

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)