Index

A

add_median_border() (in module clearex.preprocess.pad) allowed_failures (clearex.workflow.SlurmClusterConfig attribute) analysis_apply_to_all (clearex.workflow.WorkflowConfig attribute) analysis_chainable_output_component() (in module clearex.workflow) analysis_operation_for_output_component() (in module clearex.workflow) analysis_parameters (clearex.workflow.WorkflowConfig attribute) analysis_selected_experiment_path (clearex.workflow.WorkflowConfig attribute) analysis_targets (clearex.workflow.WorkflowConfig attribute) AnalysisDependencyError AnalysisExecutionProgressDialog (class in clearex.gui.app)

AnalysisExecutionWorker (class in clearex.gui.app) AnalysisInputDependencyIssue (class in clearex.workflow) AnalysisInputReference (class in clearex.workflow) AnalysisRunner (class in clearex.main) AnalysisSelectionDialog (class in clearex.gui.app) AnalysisTarget (class in clearex.workflow) annotate_frame_with_component_legend() (in module clearex.visualization.napari) attach_audit_log_manifest_to_latest_run() (in module clearex.io.provenance) axes (clearex.io.read.ImageInfo attribute) axis_labels_tczyx (clearex.visualization.pipeline.BuiltNapariScene attribute) (clearex.visualization.pipeline.NapariLayerPayload attribute)

B

background_correction() (in module clearex.segmentation.pointsource) BatchDataStoreMaterializationWorker (class in clearex.gui.app) blending (clearex.visualization.pipeline.ResolvedVolumeLayer attribute)

brief_descriptors_at_keypoints() (in module clearex.registration.tre) BuiltNapariScene (class in clearex.visualization.pipeline) bulk_transform_directory() (in module clearex.registration.common)

C

calculate_and_save_metrics() (clearex.registration.ImageRegistration method) calculate_metrics() (in module clearex.registration.common) cancel() (clearex.gui.app.AnalysisExecutionWorker method) cancelled (clearex.gui.app.AnalysisExecutionWorker attribute) capture_c_level_output() (in module clearex.io.log) channel_count (clearex.io.experiment.NavigateExperiment property) (clearex.visualization.pipeline.DisplayPyramidSummary attribute) channel_index (clearex.detect.pipeline.ParticleDetectionSummary attribute) channels (clearex.visualization.pipeline.ResolvedVolumeLayer attribute) chunk_id (clearex.registration.ChunkInfo attribute) ChunkedImageRegistration (class in clearex.registration) ChunkInfo (class in clearex.registration) chunks (clearex.workflow.WorkflowConfig attribute) chunks_processed (clearex.detect.pipeline.ParticleDetectionSummary attribute) chunks_ptczyx (clearex.workflow.ZarrSaveConfig attribute) chunks_tpczyx (clearex.io.experiment.MaterializedDataStore attribute) chunks_tpczyx() (clearex.workflow.ZarrSaveConfig method) claims() (clearex.io.read.Reader class method) clearex.context.environment module clearex.deconvolution.petakit module clearex.detect.particles module clearex.detect.pipeline module clearex.file_operations.dask module clearex.file_operations.tools module clearex.filter.filters module clearex.filter.kernels module clearex.fit.points module clearex.gui.app module clearex.io.cli module clearex.io.dask module clearex.io.experiment module clearex.io.log module clearex.io.provenance module clearex.io.read module clearex.main module clearex.plot.data module clearex.plot.images module

clearex.preprocess.pad module clearex.preprocess.scale module clearex.registration module clearex.registration.common module clearex.registration.linear module clearex.registration.nonlinear module clearex.registration.tre module clearex.segmentation.otsu module clearex.segmentation.pointsource module clearex.segmentation.regions module clearex.segmentation.tubes module clearex.stats.intensity module clearex.visualization.napari module clearex.visualization.pipeline module clearex.workflow module ClearExSetupDialog (class in clearex.gui.app) closeEvent() (clearex.gui.app.AnalysisSelectionDialog method) collect_analysis_input_references() (in module clearex.workflow) colormap (clearex.visualization.pipeline.ResolvedVolumeLayer attribute) compare_intensity() (in module clearex.stats.intensity) compile_movie (clearex.workflow.WorkflowConfig attribute) compiled_files (clearex.visualization.pipeline.CompileMovieSummary attribute) CompileMovieSummary (class in clearex.visualization.pipeline) component (clearex.detect.pipeline.ParticleDetectionSummary attribute) (clearex.visualization.pipeline.CompileMovieSummary attribute) (clearex.visualization.pipeline.DisplayPyramidSummary attribute) (clearex.visualization.pipeline.RenderMovieSummary attribute) (clearex.visualization.pipeline.ResolvedVolumeLayer attribute) (clearex.visualization.pipeline.VisualizationSummary attribute) config (clearex.workflow.LocalClusterRecommendation attribute) consumer_operation (clearex.workflow.AnalysisInputDependencyIssue attribute) (clearex.workflow.AnalysisInputReference attribute) contrast_limits_by_channel (clearex.visualization.pipeline.DisplayPyramidSummary attribute) cores (clearex.workflow.SlurmClusterConfig attribute) create_dask_client() (in module clearex.io.experiment) create_parser() (in module clearex.io.cli) create_viewer() (in module clearex.visualization.napari) crop (clearex.registration.ImageRegistration attribute) crop_data() (in module clearex.registration.common) crop_overlapping_datasets() (in module clearex.file_operations.tools) cv_tre_proxy() (in module clearex.registration.tre)

D

dashboard_address (clearex.workflow.SlurmClusterConfig attribute) dask_backend (clearex.workflow.WorkflowConfig attribute) dask_backend_from_dict() (in module clearex.workflow) dask_backend_to_dict() (in module clearex.workflow) DaskBackendConfig (class in clearex.workflow) DaskBackendConfigDialog (class in clearex.gui.app) data_image_info (clearex.io.experiment.MaterializedDataStore attribute) DataStoreMaterializationWorker (class in clearex.gui.app) death_timeout (clearex.workflow.SlurmClusterConfig attribute) deconvolution (clearex.workflow.WorkflowConfig attribute) default_analysis_operation_parameters() (in module clearex.workflow) default_analysis_store_path() (in module clearex.io.experiment) delete_filetype() (in module clearex.file_operations.tools) detect_particles() (in module clearex.detect.particles) detect_point_sources() (in module clearex.segmentation.pointsource) detected_cpu_count (clearex.workflow.LocalClusterRecommendation attribute) detected_gpu_count (clearex.workflow.LocalClusterRecommendation attribute)

detected_gpu_memory_bytes (clearex.workflow.LocalClusterRecommendation attribute) detected_memory_bytes (clearex.workflow.LocalClusterRecommendation attribute) detections (clearex.detect.pipeline.ParticleDetectionSummary attribute) difference_of_gaussian() (in module clearex.segmentation.otsu) display_logo() (in module clearex.io.cli) display_mode_fallback_reason (clearex.visualization.pipeline.PreparedVisualizationScene attribute) (clearex.visualization.pipeline.VisualizationSummary attribute) display_pyramid (clearex.workflow.WorkflowConfig attribute) DisplayPyramidSummary (class in clearex.visualization.pipeline) dog() (in module clearex.filter.filters) dog_cv2() (in module clearex.filter.filters) dragEnterEvent() (clearex.gui.app.ClearExSetupDialog method) dragMoveEvent() (clearex.gui.app.ClearExSetupDialog method) draw_bbox() (in module clearex.plot.images) draw_points() (in module clearex.plot.images) dropEvent() (clearex.gui.app.ClearExSetupDialog method) dtype (clearex.io.read.ImageInfo attribute)

E

eliminate_insignificant_point_sources() (in module clearex.detect.particles) estimated_chunk_bytes (clearex.workflow.LocalClusterRecommendation attribute) estimated_chunk_count (clearex.workflow.LocalClusterRecommendation attribute) estimated_dataset_bytes (clearex.workflow.LocalClusterRecommendation attribute) eventFilter() (clearex.gui.app.AnalysisSelectionDialog method) (clearex.gui.app.ClearExSetupDialog method) (clearex.gui.app.DaskBackendConfigDialog method) experiment (clearex.gui.app.ExperimentMetadataCacheEntry attribute) (clearex.gui.app.ExperimentStorePreparationRequest attribute) experiment_data_search_directories() (in module clearex.io.experiment) experiment_path (clearex.gui.app.ExperimentStorePreparationRequest attribute) (clearex.gui.app.ExperimentStorePreparationResult attribute) (clearex.workflow.AnalysisTarget attribute)

experiment_signature (clearex.gui.app.ExperimentMetadataCacheEntry attribute) ExperimentDataResolutionError ExperimentMetadataCacheEntry (class in clearex.gui.app) ExperimentStorePreparationRequest (class in clearex.gui.app) ExperimentStorePreparationResult (class in clearex.gui.app) export_affine_transform() (in module clearex.registration.common) export_tiff() (in module clearex.registration.common) exposure_ms (clearex.io.experiment.NavigateChannel attribute) extract_chunk() (clearex.registration.ChunkedImageRegistration method)

F

failed (clearex.gui.app.AnalysisExecutionWorker attribute) (clearex.gui.app.BatchDataStoreMaterializationWorker attribute) (clearex.gui.app.DataStoreMaterializationWorker attribute) field_name (clearex.workflow.AnalysisInputDependencyIssue attribute) (clearex.workflow.AnalysisInputReference attribute) file (clearex.workflow.WorkflowConfig attribute) file_type (clearex.io.experiment.NavigateExperiment attribute) find_experiment_data_candidates() (in module clearex.io.experiment) fit_line_profile() (in module clearex.fit.points) fit_transform_ransac() (in module clearex.registration.tre) fixed_image_path (clearex.registration.ImageRegistration attribute) fixed_mask (clearex.registration.ImageRegistration attribute) flatfield (clearex.workflow.WorkflowConfig attribute)

force_override (clearex.registration.ImageRegistration attribute) format_chunks() (in module clearex.workflow) format_dask_backend_summary() (in module clearex.workflow) format_local_cluster_recommendation_summary() (in module clearex.workflow) format_pyramid_levels() (in module clearex.workflow) format_spatial_calibration() (in module clearex.workflow) format_zarr_chunks_ptczyx() (in module clearex.workflow) format_zarr_pyramid_ptczyx() (in module clearex.workflow) fps (clearex.visualization.pipeline.CompileMovieSummary attribute) (clearex.visualization.pipeline.RenderMovieSummary attribute) frame_count (clearex.visualization.pipeline.RenderMovieSummary attribute) fusion (clearex.workflow.WorkflowConfig attribute) fwhm_to_sigma() (in module clearex.filter.filters)

G

gamma_otsu() (in module clearex.segmentation.otsu) gaussian_fit() (in module clearex.fit.points) gaussian_kernel() (in module clearex.filter.kernels) get_bounding_box() (in module clearex.segmentation.regions) get_dashboard_relay_manager() (in module clearex.gui.app) get_imaging_round() (in module clearex.io.cli)

get_installed_packages() (in module clearex.context.environment) get_moving_image_paths() (in module clearex.file_operations.tools) get_roi_indices() (in module clearex.file_operations.tools) get_variable_size() (in module clearex.file_operations.tools) get_viewer_perspective() (in module clearex.visualization.napari) GuiRunCallback (class in clearex.gui.app) GuiUnavailableError

H

has_analysis_selection() (clearex.workflow.WorkflowConfig method) has_canonical_data_component() (in module clearex.io.experiment)

has_complete_canonical_data_store() (in module clearex.io.experiment) HDF5Reader (class in clearex.io.read) histograms() (in module clearex.plot.data)

I

identify_minimal_bounding_box() (in module clearex.file_operations.tools) identify_robust_bounding_box() (in module clearex.file_operations.tools) idle_timeout (clearex.workflow.SlurmClusterConfig attribute) image_info (clearex.gui.app.ExperimentMetadataCacheEntry attribute) image_metadata (clearex.visualization.pipeline.NapariLayerPayload attribute) image_mode (clearex.io.experiment.NavigateExperiment attribute) ImageInfo (class in clearex.io.read) ImageOpener (class in clearex.io.read) ImageRegistration (class in clearex.registration) imaging_round (clearex.registration.ImageRegistration attribute) import_affine_transform() (in module clearex.registration.common)

import_tiff() (in module clearex.registration.common) infer_zyx_shape() (in module clearex.io.experiment) initialize_analysis_store() (in module clearex.io.experiment) initialize_logging() (in module clearex.io.log) initiate_logger() (in module clearex.io.log) inspect_affine_transform() (in module clearex.registration.linear) inspect_warp_transform() (in module clearex.registration.nonlinear) intensity_weighted_centroids() (in module clearex.detect.particles) interface (clearex.workflow.SlurmClusterConfig attribute) is_navigate_experiment_file() (in module clearex.io.experiment) is_selected (clearex.io.experiment.NavigateChannel attribute) is_zarr_store_path() (in module clearex.io.provenance)

J

job_extra_directives (clearex.workflow.SlurmClusterConfig attribute)

job_name (clearex.workflow.SlurmClusterConfig attribute)

K

keyframe_count (clearex.visualization.pipeline.VisualizationSummary attribute)

keyframe_manifest_path (clearex.visualization.pipeline.RenderMovieSummary attribute) (clearex.visualization.pipeline.VisualizationSummary attribute)

L

laser (clearex.io.experiment.NavigateChannel attribute) laser_index (clearex.io.experiment.NavigateChannel attribute) launch_gui() (in module clearex.gui.app) launch_mode (clearex.visualization.pipeline.VisualizationSummary attribute) layer_type (clearex.visualization.pipeline.ResolvedVolumeLayer attribute) linear_accuracy (clearex.registration.ImageRegistration attribute) linear_transform_path (clearex.registration.ChunkInfo attribute) load_latest_analysis_gui_state() (in module clearex.io.provenance) load_latest_completed_workflow_state() (in module clearex.io.provenance) load_navigate_experiment() (in module clearex.io.experiment)

load_navigate_experiment_source_image_info() (in module clearex.io.experiment) load_store_spatial_calibration() (in module clearex.io.experiment) load_tracks() (in module clearex.visualization.napari) load_variable_from_disk() (in module clearex.file_operations.tools) local_cluster (clearex.workflow.DaskBackendConfig attribute) local_directory (clearex.workflow.LocalClusterConfig attribute) (clearex.workflow.SlurmClusterConfig attribute) LocalClusterConfig (class in clearex.workflow) LocalClusterRecommendation (class in clearex.workflow) lut_strip_for_layer() (in module clearex.visualization.napari)

M

mail_user (clearex.workflow.SlurmClusterConfig attribute) main() (in module clearex.main) make_3d_structured_element() (in module clearex.filter.kernels) make_black_background_transparent() (in module clearex.visualization.napari) make_component_movie_frames() (in module clearex.visualization.napari) manifest_path (clearex.visualization.pipeline.BuiltNapariScene attribute) mask_zero_valued_data() (clearex.registration.ImageRegistration method) MaterializationProgressDialog (class in clearex.gui.app) materialize_experiment_data_store() (in module clearex.io.experiment) MaterializedDataStore (class in clearex.io.experiment) matlab_runtime_root (clearex.deconvolution.petakit.PetakitRuntimePaths attribute) mcc_master_launcher (clearex.deconvolution.petakit.PetakitRuntimePaths attribute) meijering_filter() (in module clearex.filter.filters) memory (clearex.workflow.SlurmClusterConfig attribute) memory_limit (clearex.workflow.LocalClusterConfig attribute) merge_bounding_boxes() (in module clearex.file_operations.tools) message (clearex.workflow.AnalysisInputDependencyIssue attribute) metadata (clearex.io.read.ImageInfo attribute) microscope_name (clearex.io.experiment.NavigateExperiment attribute) mip_export (clearex.workflow.WorkflowConfig attribute) mips() (in module clearex.plot.images) mode (clearex.workflow.DaskBackendConfig attribute) module clearex.context.environment clearex.deconvolution.petakit clearex.detect.particles clearex.detect.pipeline clearex.file_operations.dask clearex.file_operations.tools clearex.filter.filters clearex.filter.kernels clearex.fit.points clearex.gui.app clearex.io.cli clearex.io.dask clearex.io.experiment clearex.io.log clearex.io.provenance clearex.io.read clearex.main clearex.plot.data clearex.plot.images clearex.preprocess.pad clearex.preprocess.scale clearex.registration clearex.registration.common clearex.registration.linear clearex.registration.nonlinear clearex.registration.tre clearex.segmentation.otsu clearex.segmentation.pointsource clearex.segmentation.regions clearex.segmentation.tubes clearex.stats.intensity clearex.visualization.napari clearex.visualization.pipeline clearex.workflow

moving_image_path (clearex.registration.ImageRegistration attribute) moving_mask (clearex.registration.ImageRegistration attribute) multiposition_count (clearex.io.experiment.NavigateExperiment attribute) multiscale_policy (clearex.visualization.pipeline.ResolvedVolumeLayer attribute) multiscale_status (clearex.visualization.pipeline.ResolvedVolumeLayer attribute) mutual_nn_pairs() (in module clearex.registration.tre)

N

n_workers (clearex.workflow.LocalClusterConfig attribute) name (clearex.io.experiment.NavigateChannel attribute) (clearex.visualization.pipeline.ResolvedVolumeLayer attribute) napari_payload (clearex.visualization.pipeline.PreparedVisualizationScene attribute) NapariLayerPayload (class in clearex.visualization.pipeline) navigate_oblique_geometry (clearex.io.experiment.NavigateExperiment attribute) NavigateChannel (class in clearex.io.experiment) NavigateExperiment (class in clearex.io.experiment)

noise_normalized_otsu() (in module clearex.segmentation.otsu) nonlinear_accuracy (clearex.registration.ImageRegistration attribute) nonlinear_transform_path (clearex.registration.ChunkInfo attribute) normalize_analysis_operation_parameters() (in module clearex.workflow) normalize_analysis_targets() (in module clearex.workflow) normalize_spatial_calibration() (in module clearex.workflow) normalized_parameters (clearex.visualization.pipeline.PreparedVisualizationScene attribute) number_z_steps (clearex.io.experiment.NavigateExperiment attribute) NumpyReader (class in clearex.io.read)

O

opacity (clearex.visualization.pipeline.ResolvedVolumeLayer attribute) open() (clearex.io.read.HDF5Reader method) (clearex.io.read.ImageOpener method) (clearex.io.read.NumpyReader method) (clearex.io.read.Reader method) (clearex.io.read.TiffReader method) (clearex.io.read.ZarrReader method)

open_tiff_as_dask() (in module clearex.io.read) otsu() (in module clearex.segmentation.otsu) output_directory (clearex.visualization.pipeline.CompileMovieSummary attribute) (clearex.visualization.pipeline.RenderMovieSummary attribute) output_format (clearex.visualization.pipeline.CompileMovieSummary attribute) overlay_points_count (clearex.visualization.pipeline.VisualizationSummary attribute) override_directory (clearex.gui.app.ExperimentMetadataCacheEntry attribute)

P

ParallelChunkedImageRegistration (class in clearex.registration) parse_chunks() (in module clearex.workflow) parse_pyramid_levels() (in module clearex.workflow) parse_slurm_args() (in module clearex.io.cli) parse_spatial_calibration() (in module clearex.workflow) particle_detection (clearex.workflow.WorkflowConfig attribute) particle_registration_tre() (in module clearex.registration.tre) ParticleDetectionSummary (class in clearex.detect.pipeline) path (clearex.io.experiment.NavigateExperiment attribute) (clearex.io.read.ImageInfo attribute) persist_latest_analysis_gui_state() (in module clearex.io.provenance) persist_run_provenance() (in module clearex.io.provenance) petakit5d_root (clearex.deconvolution.petakit.PetakitRuntimePaths attribute) PetakitRuntimePaths (class in clearex.deconvolution.petakit) pixel_size (clearex.registration.ImageRegistration attribute) point_properties_by_position (clearex.visualization.pipeline.PreparedVisualizationScene attribute)

points_by_position (clearex.visualization.pipeline.PreparedVisualizationScene attribute) points_metadata (clearex.visualization.pipeline.NapariLayerPayload attribute) position_affines_tczyx (clearex.visualization.pipeline.PreparedVisualizationScene attribute) position_index (clearex.visualization.pipeline.VisualizationSummary attribute) prefer_dask (clearex.workflow.WorkflowConfig attribute) PreparedVisualizationScene (class in clearex.visualization.pipeline) preprocess() (in module clearex.detect.particles) primary_source_component (clearex.visualization.pipeline.BuiltNapariScene attribute) primary_source_components (clearex.visualization.pipeline.BuiltNapariScene attribute) processes (clearex.workflow.SlurmClusterConfig attribute) producer_operation (clearex.workflow.AnalysisInputDependencyIssue attribute) progress_changed (clearex.gui.app.AnalysisExecutionWorker attribute) (clearex.gui.app.BatchDataStoreMaterializationWorker attribute) (clearex.gui.app.DataStoreMaterializationWorker attribute) pyramid_ptczyx (clearex.workflow.ZarrSaveConfig attribute) pyramid_tpczyx() (clearex.workflow.ZarrSaveConfig method)

Q

queue (clearex.workflow.SlurmClusterConfig attribute)

R

raw (clearex.io.experiment.NavigateExperiment attribute) Reader (class in clearex.io.read) reason (clearex.workflow.AnalysisInputDependencyIssue attribute) recommend_local_cluster_config() (in module clearex.workflow) reference_position_index (clearex.visualization.pipeline.PreparedVisualizationScene attribute) register() (clearex.registration.ImageRegistration method) register_chunk() (clearex.registration.ChunkedImageRegistration method) register_image() (in module clearex.registration.linear) (in module clearex.registration.nonlinear) register_latest_output_reference() (in module clearex.io.provenance) register_round() (in module clearex.registration) registration (clearex.workflow.WorkflowConfig attribute) registration_errors() (in module clearex.registration.tre) reject() (clearex.gui.app.AnalysisSelectionDialog method) remove_close_blobs() (in module clearex.detect.particles) rename_tiff_to_tif() (in module clearex.io.read) render_component (clearex.visualization.pipeline.CompileMovieSummary attribute) render_manifest_path (clearex.visualization.pipeline.CompileMovieSummary attribute) (clearex.visualization.pipeline.RenderMovieSummary attribute) render_movie (clearex.workflow.WorkflowConfig attribute) rendered_level (clearex.visualization.pipeline.CompileMovieSummary attribute) rendered_levels (clearex.visualization.pipeline.RenderMovieSummary attribute) renderer (clearex.visualization.pipeline.VisualizationSummary attribute) renderer_info (clearex.visualization.pipeline.BuiltNapariScene attribute) rendering (clearex.visualization.pipeline.ResolvedVolumeLayer attribute)

RenderMovieSummary (class in clearex.visualization.pipeline) report_chunks() (in module clearex.file_operations.dask) representative_rgba_from_image_layer() (in module clearex.visualization.napari) representative_text_rgba_for_layer() (in module clearex.visualization.napari) requested_source (clearex.workflow.AnalysisInputDependencyIssue attribute) (clearex.workflow.AnalysisInputReference attribute) resize_data() (in module clearex.preprocess.scale) resolve_analysis_execution_sequence() (in module clearex.workflow) resolve_analysis_input_component() (in module clearex.workflow) resolve_data_store_path() (in module clearex.io.experiment) resolve_experiment_data_path() (in module clearex.io.experiment) resolve_petakit_runtime_paths() (in module clearex.deconvolution.petakit) resolved_component (clearex.workflow.AnalysisInputDependencyIssue attribute) ResolvedVolumeLayer (class in clearex.visualization.pipeline) reused_existing_levels (clearex.visualization.pipeline.DisplayPyramidSummary attribute) richardson_lucy() (in module clearex.deconvolution.petakit) run() (clearex.gui.app.AnalysisExecutionWorker method) (clearex.gui.app.BatchDataStoreMaterializationWorker method) (clearex.gui.app.DataStoreMaterializationWorker method) run_compile_movie_analysis() (in module clearex.visualization.pipeline) run_display_pyramid_analysis() (in module clearex.visualization.pipeline) run_particle_detection_analysis() (in module clearex.detect.pipeline) run_petakit_deconvolution() (in module clearex.deconvolution.petakit) run_render_movie_analysis() (in module clearex.visualization.pipeline) run_visualization_analysis() (in module clearex.visualization.pipeline) run_workflow_with_progress() (in module clearex.gui.app)

S

save_directory (clearex.io.experiment.NavigateExperiment attribute) (clearex.registration.ImageRegistration attribute) save_frame() (in module clearex.visualization.napari) save_particle_detections_to_store() (in module clearex.detect.pipeline) save_store_spatial_calibration() (in module clearex.io.experiment) save_variable_to_disk() (in module clearex.file_operations.tools) scale_tczyx (clearex.visualization.pipeline.BuiltNapariScene attribute) (clearex.visualization.pipeline.NapariLayerPayload attribute) scheduler_file (clearex.workflow.SlurmRunnerConfig attribute) scheduler_interface (clearex.workflow.SlurmClusterConfig attribute) second_derivative_gaussian_kernel() (in module clearex.filter.kernels) segment_tubular_structures() (in module clearex.segmentation.tubes) selected_analysis_operations() (in module clearex.workflow) selected_analysis_target() (clearex.workflow.WorkflowConfig method) selected_channels (clearex.io.experiment.NavigateExperiment attribute) selected_positions (clearex.visualization.pipeline.PreparedVisualizationScene attribute) (clearex.visualization.pipeline.VisualizationSummary attribute) serialized_volume_layers (clearex.visualization.pipeline.BuiltNapariScene attribute) set_dashboard_available() (clearex.gui.app.AnalysisExecutionProgressDialog method) set_origin_and_spacing() (in module clearex.registration.common) set_viewer_size_for_layer() (in module clearex.visualization.napari) shape (clearex.io.read.ImageInfo attribute) shear_transform (clearex.workflow.WorkflowConfig attribute) show_all_positions (clearex.visualization.pipeline.VisualizationSummary attribute) skipped_existing (clearex.gui.app.ExperimentStorePreparationResult attribute) slurm_cluster (clearex.workflow.DaskBackendConfig attribute) slurm_runner (clearex.workflow.DaskBackendConfig attribute) SlurmClusterConfig (class in clearex.workflow) SlurmRunnerConfig (class in clearex.workflow) sort_by_point_source_intensity() (in module clearex.detect.particles) source_component (clearex.io.experiment.MaterializedDataStore attribute) (clearex.visualization.pipeline.DisplayPyramidSummary attribute) (clearex.visualization.pipeline.PreparedVisualizationScene attribute) (clearex.visualization.pipeline.VisualizationSummary attribute)

source_components (clearex.visualization.pipeline.DisplayPyramidSummary attribute) (clearex.visualization.pipeline.PreparedVisualizationScene attribute) (clearex.visualization.pipeline.ResolvedVolumeLayer attribute) (clearex.visualization.pipeline.VisualizationSummary attribute) source_data_path (clearex.gui.app.ExperimentMetadataCacheEntry attribute) (clearex.gui.app.ExperimentStorePreparationRequest attribute) source_image_info (clearex.io.experiment.MaterializedDataStore attribute) source_path (clearex.io.experiment.MaterializedDataStore attribute) source_signature (clearex.gui.app.ExperimentMetadataCacheEntry attribute) spatial_calibration (clearex.visualization.pipeline.PreparedVisualizationScene attribute) (clearex.workflow.WorkflowConfig attribute) spatial_calibration_explicit (clearex.workflow.WorkflowConfig attribute) spatial_calibration_from_dict() (in module clearex.workflow) spatial_calibration_to_dict() (in module clearex.workflow) SpatialCalibrationConfig (class in clearex.workflow) SpatialCalibrationDialog (class in clearex.gui.app) spin_azimuth() (in module clearex.visualization.napari) stage_axis_map_by_world_axis() (clearex.workflow.SpatialCalibrationConfig method) stage_axis_map_zyx (clearex.workflow.SpatialCalibrationConfig attribute) store_latest_analysis_output() (in module clearex.io.provenance) store_path (clearex.gui.app.ExperimentStorePreparationResult attribute) (clearex.io.experiment.MaterializedDataStore attribute) (clearex.workflow.AnalysisTarget attribute) succeeded (clearex.gui.app.BatchDataStoreMaterializationWorker attribute) (clearex.gui.app.DataStoreMaterializationWorker attribute) SUFFIXES (clearex.io.read.HDF5Reader attribute) (clearex.io.read.NumpyReader attribute) (clearex.io.read.Reader attribute) (clearex.io.read.TiffReader attribute) (clearex.io.read.ZarrReader attribute) summarize_analysis_history() (in module clearex.io.provenance) summarize_image_info() (in module clearex.gui.app) summarize_navigate_bdv_n5_image_info() (in module clearex.io.experiment)

T

target_store (clearex.gui.app.ExperimentStorePreparationRequest attribute) theta_mode (clearex.workflow.SpatialCalibrationConfig attribute) threads_per_worker (clearex.workflow.LocalClusterConfig attribute) tiff_to_zarr() (in module clearex.file_operations.dask) TiffReader (class in clearex.io.read) timepoints (clearex.io.experiment.NavigateExperiment attribute)

to_metadata_dict() (clearex.io.experiment.NavigateExperiment method) to_tpczyx_chunks() (in module clearex.workflow) to_tpczyx_pyramid() (in module clearex.workflow) total_overlay_points (clearex.visualization.pipeline.PreparedVisualizationScene attribute) transform_image() (in module clearex.registration.common) (in module clearex.registration.linear) (in module clearex.registration.nonlinear)

U

update_progress() (clearex.gui.app.AnalysisExecutionProgressDialog method) (clearex.gui.app.MaterializationProgressDialog method)

update_viewer() (in module clearex.visualization.napari) usegment3d (clearex.workflow.WorkflowConfig attribute)

V

validate_analysis_input_references() (in module clearex.workflow) validate_petakit_runtime() (in module clearex.deconvolution.petakit) verify_provenance_chain() (in module clearex.io.provenance) viewer (clearex.visualization.pipeline.BuiltNapariScene attribute) viewer_ndisplay_effective (clearex.visualization.pipeline.PreparedVisualizationScene attribute) (clearex.visualization.pipeline.VisualizationSummary attribute) viewer_ndisplay_requested (clearex.visualization.pipeline.PreparedVisualizationScene attribute) (clearex.visualization.pipeline.VisualizationSummary attribute)

viewer_pid (clearex.visualization.pipeline.VisualizationSummary attribute) visible (clearex.visualization.pipeline.ResolvedVolumeLayer attribute) visualization (clearex.workflow.WorkflowConfig attribute) visualization_component (clearex.visualization.pipeline.RenderMovieSummary attribute) VisualizationSummary (class in clearex.visualization.pipeline) volume_export (clearex.workflow.WorkflowConfig attribute) volume_layers (clearex.visualization.pipeline.PreparedVisualizationScene attribute)

W

wait_for_workers (clearex.workflow.SlurmRunnerConfig attribute) walltime (clearex.workflow.SlurmClusterConfig attribute) workers (clearex.workflow.SlurmClusterConfig attribute)

WorkflowConfig (class in clearex.workflow) WorkflowExecutionCancelled write_zyx_block() (in module clearex.io.experiment)

X

x_end (clearex.registration.ChunkInfo attribute) x_end_ext (clearex.registration.ChunkInfo attribute) x_pixels (clearex.io.experiment.NavigateExperiment attribute)

x_start (clearex.registration.ChunkInfo attribute) x_start_ext (clearex.registration.ChunkInfo attribute) xy_from_rc() (in module clearex.registration.tre) xy_pixel_size_um (clearex.io.experiment.NavigateExperiment attribute)

Y

y_end (clearex.registration.ChunkInfo attribute) y_end_ext (clearex.registration.ChunkInfo attribute)

y_pixels (clearex.io.experiment.NavigateExperiment attribute) y_start (clearex.registration.ChunkInfo attribute) y_start_ext (clearex.registration.ChunkInfo attribute)

Z

z_end (clearex.registration.ChunkInfo attribute) z_end_ext (clearex.registration.ChunkInfo attribute) z_start (clearex.registration.ChunkInfo attribute) z_start_ext (clearex.registration.ChunkInfo attribute) z_step_um (clearex.io.experiment.NavigateExperiment attribute)

zarr_save (clearex.workflow.WorkflowConfig attribute) zarr_save_from_dict() (in module clearex.workflow) zarr_save_to_dict() (in module clearex.workflow) ZarrReader (class in clearex.io.read) ZarrSaveConfig (class in clearex.workflow) ZarrSaveConfigDialog (class in clearex.gui.app)