Index _ | A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W | X | Y | Z _ _cfg_subtree (UiParameter attribute) _exp_dir (ExperimentController attribute) _factories (ExperimentController attribute) _status (StateManager attribute) _widget (ParamLink attribute) _workers (ExperimentController attribute) A a (PairKey property) abort_retry_popup() (in module ClearMap.gui.dialog_helpers) aborted (ProgressWatcher attribute) AboutDialog (class in ClearMap.gui.dialogs) AboutInfo (class in ClearMap.gui.about) abs_container_path() (InstanceContainerSpec method) abs_templates_path() (InstanceContainerSpec method) abspath() (in module ClearMap.IO.FileUtils) AbstractSource (class in ClearMap.IO.Source) accept() (RenameChannelsDialog method) (VerifyRenamingDialog method) accumulate() (PropertyAggregator method) action (RecoveryOption attribute) action() (ManageAssetsWidget method) activate() (Landmark method) add_asset() (ClearMapApp method) add_axes() (in module ClearMap.Visualization.Vispy.Plot3d) add_chain_id() (in module ClearMap.Analysis.graphs.graph_processing) add_channel() (CellMapParams method) (ColocalizationParams method) (EnvFileManager method) (RegistrationParams method) (SampleParameters method) (StitchingParams method) (TractMapParams method) (VesselParams method) add_channel_tab() (GenericTab method) add_channel_widget() (ExtendableTabWidget method) add_data() (Annotation method) add_dependency() (EnvFileManager method) add_disconnector() (ParamLink method) add_edge() (Graph method), [1] add_edge_property() (Graph method), [1] add_files() (FileDropListWidget method) add_filter_row() (GraphFilterList method) add_graph_filter() (VasculatureTab method) add_graph_filter_params() (VesselGraphParams method) add_graph_property() (Graph method) add_group() (BatchParameters method) (GroupsWidgetAdapter method) (PatternDialog method) add_item() (CheckableListWidget method) add_marker() (LandmarksSelectorDialog method) add_missing_combobox_items() (in module ClearMap.gui.gui_utils_base) add_perf_channel() (CellMapParams method) (VesselParams method) add_pip_dependency() (EnvFileManager method) add_pip_option() (EnvFileManager method) add_pipeline() (RegistrationProcessor method) add_regions() (OrthoViewer method) add_sub_type() (TypeSpec method) add_vertex() (Graph method), [1] add_vertex_property() (Graph method), [1] addAvailableItems() (TwoListSelection method) addConnections() (in module ClearMap.ImageProcessing.Tracing.Connect) addDilatedPathToMask() (in module ClearMap.ImageProcessing.Tracing.Connect) addItem() (FileDropListWidget method) addItems() (FileDropListWidget method) addPathToMask() (in module ClearMap.ImageProcessing.Tracing.Connect) addTabClicked (ExtendableTabWidget attribute) ADJUST (Step attribute) adjust_batch_groups_and_comparisons() (in module ClearMap.config.config_adjusters.group_adjusters) adjust_config() (ConfigCoordinator method) adjust_group_analysis_groups() (in module ClearMap.config.config_adjusters.group_adjusters) adjust_overlaps() (TiledLayout method) adjuster_safe() (in module ClearMap.pipeline_orchestrators.sample_info_management) AdjusterKind (class in ClearMap.config.config_adjusters.adjusters_api) AdjusterRunner (class in ClearMap.config.config_adjusters.engine) AdjusterScope (class in ClearMap.config.config_adjusters.type_hints) AdjusterSpec (class in ClearMap.config.config_adjusters.adjusters_api) AdjustmentContext (class in ClearMap.config.config_adjusters.type_hints) advanced_controls (UiParameter attribute) (UiParameterCollection attribute) advanced_controls_names (GenericTab attribute) (GroupAnalysisTab attribute) (RegistrationTab attribute) (StitchingTab attribute) (TractMapTab attribute) (VasculatureTab attribute) AffineTransformation (class in ClearMap.Alignment.Transformations.LinearTransformation) after (ChannelsChanged attribute) (UiChannelsChanged attribute) aggregate() (PropertyAggregator method) AggregatedValidationError align (BatchProcessingParams attribute) align() (in module ClearMap.Alignment.Elastix) (Layout method) (RegistrationProcessor method) align_2_sources() (in module ClearMap.Alignment.Stitching.stitching_rigid) align_2_sources_along_axis() (in module ClearMap.Alignment.Stitching.stitching_rigid) align_2_sources_along_axis_mip() (in module ClearMap.Alignment.Stitching.stitching_rigid) align_axis() (Layout method) align_channel() (RegistrationProcessor method) align_channel_rigid() (StitchingProcessor method) align_from_dict() (in module ClearMap.Alignment.Elastix) align_layout() (in module ClearMap.Alignment.Stitching.stitching_rigid) (in module ClearMap.Alignment.Stitching.stitching_wobbly) align_layout_axis() (in module ClearMap.Alignment.Stitching.stitching_rigid) align_layout_on_tiling() (in module ClearMap.Alignment.Stitching.stitching_rigid) align_layout_rigid_mip() (in module ClearMap.Alignment.Stitching.stitching_rigid) align_layout_rigid_mips() (in module ClearMap.Alignment.Stitching.stitching_rigid) align_on_tiling() (TiledLayout method) align_with (UiAlignWithChanged attribute) align_wobbly_axis() (in module ClearMap.Alignment.Stitching.stitching_wobbly) (WobblyAlignment method) ALIGNED (WobblyAlignment attribute) Alignment (class in ClearMap.Alignment.Stitching.stitching_rigid) alignment_from_tile_positions() (TiledLayout method) alignment_info() (WobblyLayoutPlotMixin method) alignment_reference (RunFacts attribute) alignment_reference_channel (SampleManager property) (SampleManagerProtocol property) AlignmentBase (class in ClearMap.Alignment.Stitching.stitching_rigid) AlignmentBasePlotMixin (class in ClearMap.Alignment.Stitching.stitching_plots) AlignmentPlotMixin (class in ClearMap.Alignment.Stitching.stitching_plots) alignments (Layout property) alignments_from_source_positions() (in module ClearMap.Alignment.Stitching.stitching_rigid) alignments_from_tile_position() (TiledLayout method) AlignmentTool (class in ClearMap.Alignment.landmarks_registration.engine) all_channels_defined() (PatternDialog method) all_colour (DataViewer property) all_instance_container_abs_paths() (ContainerSpecRegistry method) all_not_none() (in module ClearMap.Alignment.Resampling) all_pairs() (ComparisonsModel method) all_tiles_exist() (Workspace method) allow_entry_overwrite (BindPolicy attribute) allow_index_arrays (in module ClearMap.IO.Slice) ALLOWED_KINDS (PropertyAggregator attribute) alternative_names (ConfigAlternativesRegistry property) amend_ui() (ClearMapApp method) AnalysisGroupController (class in ClearMap.pipeline_orchestrators.experiment_controller) angle_between_vectors() (in module ClearMap.Analysis.vasculature.geometry_utils) annotate (VesselGraphParams attribute) annotate_edge_lengths() (in module ClearMap.Analysis.graphs.graph_processing) annotate_properties() (Graph method) AnnotatedGraph (class in ClearMap.Analysis.graphs.graph) annotation (AnnotatedGraph property) Annotation (class in ClearMap.Alignment.Annotation) annotation_to_distance_file() (in module ClearMap.Alignment.Annotation) annotators (RegistrationProcessor attribute) any_channel_property_changed() (in module ClearMap.config.change_detection) applies (StepSpec attribute) apply() (PropertyAggregator method) apply_channel_renames() (in module ClearMap.config.config_adjusters.policy) apply_local_function() (in module ClearMap.ImageProcessing.LocalStatistics) apply_lut() (in module ClearMap.ParallelProcessing.DataProcessing.ArrayProcessing) (in module ClearMap.ParallelProcessing.DataProcessing.ArrayProcessingCode) apply_lut_to_index() (in module ClearMap.ParallelProcessing.DataProcessing.ArrayProcessing) apply_lut_to_index_3d() (in module ClearMap.ParallelProcessing.DataProcessing.ArrayProcessingCode) apply_patch() (AnalysisGroupController method) apply_pipeline_to_config() (VesselBinarizationParams method) apply_prefs_and_close() (PreferenceUi method) APPLY_RENAMES (Step attribute) apply_smoothing() (in module ClearMap.ImageProcessing.Experts.Vasculature) apply_ui_patch (ExperimentController attribute) apply_ui_patch() (ExperimentController method) AppMode (class in ClearMap.pipeline_orchestrators.experiment_controller) ArbitraryRotationCamera (class in ClearMap.Visualization.Vispy.arbitrary_rotation_camera) arrange_plots() (in module ClearMap.Visualization.Qt.Plot3d) array (Layout property) (MiniBrain attribute) (Slice property) (Source property), [1], [2], [3], [4], [5], [6] (VirtualSource property), [1] array_along_axis() (Layout method) array_to_tif() (in module ClearMap.IO.TIF) array_wobbly() (WobblySource method) arteries_channel (VesselGraphProcessor property) arteries_min_noise_edges (ClassificationConfig attribute), [1] (VesselGraphParams attribute) ARTERY (VesselType attribute) artery_binary (VesselSignals attribute) artery_intensity (VesselSignals attribute) artery_intensity_min (ClassificationConfig attribute), [1] (VesselGraphParams attribute) artery_seed_threshold (ClassificationConfig attribute) artery_trace_radius (ClassificationConfig attribute), [1] artery_trace_radius_um (VesselGraphParams attribute) as_array() (Source method) as_buffer() (AbstractSource method) (Slice method) (Source method), [1], [2], [3], [4], [5], [6], [7] (VirtualSource method), [1] as_mask() (CombinedFilter method) (GraphFilter method) as_memmap() (Source method), [1], [2], [3] as_memory() (Source method) as_memory_block() (Block method) as_name (ImportTask attribute) as_real() (AbstractSource method) (Block method) (Layout method) (Slice method), [1] (Source method), [1], [2], [3], [4], [5], [6] (VirtualSource method), [1], [2], [3] as_source() (in module ClearMap.IO.IO) as_tuple() (CompoundKey method) (PairKey method) as_type() (in module ClearMap.Utils.Formatting) as_virtual() (AbstractSource method) (Block method) (Layout method) (Slice method), [1] (Source method), [1], [2], [3], [4], [5], [6], [7], [8], [9] (VirtualSource method) assert_all_images() (ManageAssetsWidget method) assert_cuda() (PytorchVersionManager static method) assert_input_shapes_match() (BinaryVesselProcessor method) assert_src_folder_set() (ClearMapApp method) asset_from_step_name() (BinaryVesselProcessorSteps method) (ProcessorSteps method) (VesselGraphProcessorSteps method) asset_names_to_assets() (SampleManager method) asset_types_to_assets() (ManageAssetsWidget method) AssetBase (class in ClearMap.IO.IO) AssetNotFoundError assets (DensityGroupAnalysisOrchestrator property) assets_to_binarize() (BinaryVesselProcessor method) assign_axes_from_combo() (Pattern method) assign_pressureBC() (in module ClearMap.Analysis.vasculature.flow.assign_p_bc) at_categories (PatternInverter attribute) atlas_align() (CellDetector method) atlas_base_name (AtlasParams property) (UiAtlasIdChanged attribute) atlas_folder (AtlasParams attribute) (in module ClearMap.Settings) atlas_id (AtlasParams attribute) AtlasParams (class in ClearMap.gui.params) attrs (ImportTask attribute) autofluorescence_is_tiled (SampleManager property) autolevel() (in module ClearMap.ImageProcessing.Filter.Rank) (in module ClearMap.ImageProcessing.Filter.Rank.PercentileCode) (in module ClearMap.ImageProcessing.Filter.Rank.Rank) (in module ClearMap.ImageProcessing.Filter.Rank.RankCode) autolevel_masked() (in module ClearMap.ImageProcessing.Filter.Rank.PercentileCode) (in module ClearMap.ImageProcessing.Filter.Rank.RankCode) autolevel_percentile() (in module ClearMap.ImageProcessing.Filter.Rank) (in module ClearMap.ImageProcessing.Filter.Rank.Percentile) avg_density_path() (GroupResultsAssets method) avg_streamlines_grid() (in module ClearMap.Analysis.vasculature.general_functions) axes_file (Source property) axes_list (Source property) axes_order (Source property), [1] (VirtualSource property) axes_to_tag_order() (Source method) axis (WobblySource property) axis_indices() (Graph method) B b (PairKey property) background_correction_diameter (ChannelCellMapParams attribute) background_level (RigidChannelStitchingParams attribute) background_pixels (RigidChannelStitchingParams attribute) backup_file() (in module ClearMap.Utils.utilities) base (Graph property) (in module ClearMap.ImageProcessing.Skeletonization.PK12) (Slice property) base() (in module ClearMap.IO.SMA) (in module ClearMap.ParallelProcessing.SharedMemoryArray) base_dir (ConfigCoordinator property) base_dir() (ConfigRepository method) base_lower (Slice property) base_position (Slice property) base_shape (Slice property) base_slicing (Slice property) base_upper (Slice property) BaseFilter (class in ClearMap.Analysis.graphs.graph_filters) BaseMetadataParser (class in ClearMap.IO.TIF) basename (TileRecord attribute) (TypeSpec property) batch_crop() (in module ClearMap.pipeline_orchestrators.batch_process) BatchParameters (class in ClearMap.gui.params) BatchProcessingParams (class in ClearMap.gui.params) BatchProcessingTab (class in ClearMap.gui.tabs) BatchProcessor (class in ClearMap.pipeline_orchestrators.batch_process) BatchTab (class in ClearMap.gui.tabs_interfaces) bbox_1d() (in module ClearMap.Analysis.colocalization.bbox) bbox_2d() (in module ClearMap.Analysis.colocalization.bbox) bbox_3d() (in module ClearMap.Analysis.colocalization.bbox) beep() (in module ClearMap.Utils.Sound) before (ChannelsChanged attribute) (UiChannelsChanged attribute) begin_hydration() (GuiController method) bilabel_bincount() (in module ClearMap.Analysis.colocalization.channel) binarization_clip_range (VesselBinarizationParams attribute) binarization_threshold (VesselBinarizationParams attribute) binarize (ChannelTractMapParams attribute) binarize() (BinaryVesselProcessor method) (in module ClearMap.ImageProcessing.Experts.Vasculature) (TractMapProcessor method) binarize_and_postprocess_channel() (VasculatureTab method) binarize_block() (in module ClearMap.ImageProcessing.Experts.Vasculature) binarize_channel() (BinaryVesselProcessor method) (TractMapTab method) binary (BinaryVesselProcessorSteps attribute) BINARY_NAMES (in module ClearMap.ImageProcessing.Experts.Vasculature) binary_shape (VesselGraphProcessor property) binary_statistics() (in module ClearMap.ImageProcessing.Experts.Vasculature) BINARY_STATUS (in module ClearMap.ImageProcessing.Experts.Vasculature) BinaryVesselProcessor (class in ClearMap.pipeline_orchestrators.tube_map) BinaryVesselProcessorSteps (class in ClearMap.pipeline_orchestrators.tube_map) bind_apply_patch() (UiParameter method) (UiParameterCollection method) bind_view_provider() (UiParameter method) (UiParameterCollection method) BindPolicy (class in ClearMap.config.config_adjusters.templates_resolver) blobwise_overlaps() (Channel method) Block (class in ClearMap.ParallelProcessing.Block) block_axes() (in module ClearMap.ParallelProcessing.BlockProcessing) block_ranges() (in module ClearMap.ParallelProcessing.DataProcessing.ArrayProcessing) block_re (TractMapProcessor attribute) block_sizes() (in module ClearMap.ParallelProcessing.BlockProcessing) block_sums() (in module ClearMap.ParallelProcessing.DataProcessing.ArrayProcessing) block_sums_1d() (in module ClearMap.ParallelProcessing.DataProcessing.ArrayProcessingCode) block_sums_2d() (in module ClearMap.ParallelProcessing.DataProcessing.ArrayProcessingCode) block_sums_3d() (in module ClearMap.ParallelProcessing.DataProcessing.ArrayProcessingCode) block_sums_3d_f() (in module ClearMap.ParallelProcessing.DataProcessing.ArrayProcessingCode) BlockProcessingParams (class in ClearMap.gui.params) BlockProcessingWidget (class in ClearMap.gui.widgets) blocks_shape (Block property) boot_new (ExperimentController attribute) boot_new() (ExperimentController method) boot_open (ExperimentController attribute) boot_open() (ExperimentController method) BootResult (class in ClearMap.config.early_boot) border_indices() (in module ClearMap.ImageProcessing.Binary.Filling) bottomhat() (in module ClearMap.ImageProcessing.Filter.Rank) (in module ClearMap.ImageProcessing.Filter.Rank.Rank) (in module ClearMap.ImageProcessing.Filter.Rank.RankCode) bottomhat_masked() (in module ClearMap.ImageProcessing.Filter.Rank.RankCode) bounding_box() (Channel method) boundingRect() (RedCross method) bridge_to_qt() (EventBus method) bring_to_front() (in module ClearMap.Visualization.Qt.Plot3d) brutal_rotate() (ITKImage method) buffer() (in module ClearMap.IO.IO) build (VesselGraphParams attribute) build_business_objects() (in module ClearMap.gui.app) build_graph() (VasculatureTab method) build_ln() (ElastixEntry method) build_params_dict() (AtlasParams method) (BatchParameters method) (BlockProcessingParams method) (ChannelCellMapParams method) (ChannelCellMapPerformanceParams method) (ChannelColocalizationParams method) (ChannelRegistrationParams method) (ChannelTractMapParams method) (GeneralChannelStitchingParams method) (NProcessesParams method) (PreferencesParams method) (RigidChannelStitchingParams method) (SampleChannelParameters method) (SharedRegistrationParams method) (SharedSampleParams method) (SharedVesselBinarizationParams method) (TractMapPerformanceParams method) (UiParameter method) (VesselBinarizationParams method) (VesselBinarizationPerformanceParams method) (VesselGraphParams method) (VesselGraphPerformanceParams method) (VesselVisualizationParams method) (WobblyChannelStitchingParams method) build_sample_manager() (in module ClearMap.pipeline_orchestrators.sample_info_management) build_schema_registry_from_dir() (in module ClearMap.config.validators.json_schema_utils) build_tree() (StructurePickerWidget static method) BusSubscriberMixin (class in ClearMap.Utils.event_bus) by_template_kind() (ContainerSpecRegistry method) bytes_to_human() (in module ClearMap.Utils.utilities) C can_convert() (SampleManager method) CancelableProcessPoolExecutor (class in ClearMap.Utils.utilities) CanceledProcessing candidate_ancestors_from_renames() (CompoundKey method) canonical() (CompoundKey method) (PairKey method) canonical_config_names (ConfigAlternativesRegistry property) canonical_global_config_names (ConfigAlternativesRegistry property) canonical_group_config_names (ConfigAlternativesRegistry property) canonical_pipeline_config_names (ConfigAlternativesRegistry property) canonical_str() (CompoundKey class method) CAPILLARY (VesselType attribute) cartesian_to_polar() (in module ClearMap.Analysis.vasculature.geometry_utils) cast_from_ui (ParamLink attribute) cast_max_from_ui() (ChannelCellMapParams method) cast_sentinel_from_ui() (VectorLink method) cast_sentinel_to_ui() (VectorLink method) cast_to_ui (ParamLink attribute) cell_filter_intensity (ChannelCellMapParams attribute) cell_filter_size (ChannelCellMapParams attribute) cell_map_entry_template() (ExperimentTemplatesResolver method) cell_map_perf_entry_template() (ExperimentTemplatesResolver method) cell_map_target_channels() (ExperimentTemplatesResolver method) CellCounterTab (class in ClearMap.gui.tabs) CellDetector (class in ClearMap.pipeline_orchestrators.cell_map) CellMapParams (class in ClearMap.gui.params) center() (Channel method) center_tile_position() (TiledLayout method) center_tile_source() (TiledLayout method) center_view() (in module ClearMap.Visualization.Vispy.Plot3d) centers() (Channel method) centers_df() (Channel method) centers_distances() (Channel method) cfg_converter() (in module ClearMap.config.convert_config_versions) cfg_coordinator (OrchestratorBase attribute), [1] (PipelineOrchestrator attribute) cfg_ensured (BootResult attribute) cfg_path (MachineConfig property) cfg_subtree (BatchParameters attribute) (BatchProcessingParams attribute) (BlockProcessingParams property) (ChannelCellMapParams property) (ChannelCellMapPerformanceParams property) (ChannelColocalizationParams property) (ChannelRegistrationParams property) (ChannelTractMapParams property) (ChannelUiParameter property) (GeneralChannelStitchingParams property) (GraphFilterParams property) (GroupAnalysisParams attribute) (NProcessesParams property) (PreferencesParams attribute) (RigidChannelStitchingParams property) (SampleChannelParameters property) (SampleParameters attribute) (SharedSampleParams attribute) (TractMapPerformanceParams attribute) (UiParameter property) (UiParameterCollection attribute) (VesselBinarizationParams property) (VesselBinarizationPerformanceParams property) (VesselGraphParams attribute) (VesselGraphPerformanceParams attribute) (WobblyChannelStitchingParams property) cfg_to_ui() (BatchParameters method) (GroupAnalysisParams method) (SampleChannelParameters method) (SampleParameters method) (UiParameter method) (UiParameterCollection method) (VesselBinarizationParams method) CfgChanged (class in ClearMap.Utils.events) change_max_projection() (DataViewer method) change_orientations_color() (DataViewer method) change_orientations_threshold() (DataViewer method) change_points_color() (DataViewer method) change_source_location() (Layout method) change_sources() (Layout method) change_vectors_color() (DataViewer method) change_vectors_threshold() (DataViewer method) changed_keys (CfgChanged attribute) channel (ChannelPipelineOrchestrator attribute) Channel (class in ClearMap.Analysis.colocalization.channel) channel (GroupOrchestratorBase attribute) (ManageAssetsWidget property) (PairKey attribute) (ProcessorSteps attribute) (TileRecord attribute) channel_cfg_view() (ChannelPipelineOrchestrator method) channel_count (Channel attribute) channel_data_type_changed() (in module ClearMap.config.change_detection) channel_index (UiRequestPlotAtlas attribute) (UiRequestPlotMiniBrain attribute) channel_is_compound() (in module ClearMap.gui.tabs_interfaces) channel_name (UiAlignWithChanged attribute) (UiCropChanged attribute) (UiLayoutChannelChanged attribute) (UiOrientationChanged attribute) (UiPrepareRawDataForClearMap attribute) (UiUseExistingLayoutChanged attribute) channel_names (Channel attribute) (ChannelSpec attribute) channel_number_to_name() (ChannelSpec class method) channel_params (ChannelsUiParameterCollection property) channel_path_changed() (in module ClearMap.config.change_detection) channel_snapshot() (ExperimentController method) channel_was_registered() (RegistrationProcessor method) channel_was_stitched_rigid() (StitchingProcessor method) ChannelCellMapParams (class in ClearMap.gui.params) ChannelCellMapPerformanceParams (class in ClearMap.gui.params) channelChanged (ExtendableTabWidget attribute) ChannelColocalizationParams (class in ClearMap.gui.params) ChannelDefaultsChanged (class in ClearMap.Utils.events) ChannelPatternSpec (class in ClearMap.IO.metadata) ChannelPipelineOrchestrator (class in ClearMap.pipeline_orchestrators.generic_orchestrators) ChannelRegistrationParams (class in ClearMap.gui.params) ChannelRenamed (class in ClearMap.Utils.events) channelRenamed (ExtendableTabWidget attribute) channels (ChannelsUiParameterCollection property) (CompoundChannelPipelineOrchestrator attribute) (RegistrationProcessor property) (SampleManager property) (SampleManagerProtocol property) (SharedSampleParams property) CHANNELS (TemplateKind attribute) channels_added_or_removed() (in module ClearMap.config.change_detection) CHANNELS_ASSETS_TYPES_CONFIG (in module ClearMap.IO.assets_constants) channels_to_binarize() (BinaryVesselProcessor method) channels_to_convert (SampleManager property) channels_to_detect (SampleManager property) (SampleManagerProtocol property) channels_to_register() (RegistrationProcessor method) channels_to_resample() (RegistrationProcessor method) channels_ui_name (CellCounterTab attribute) (ColocalizationTab attribute) (GenericTab attribute) (RegistrationTab attribute) (StitchingTab attribute) (TractMapTab attribute) (VasculatureTab attribute) channels_with_changed_property() (in module ClearMap.config.change_detection) ChannelsChanged (class in ClearMap.Utils.events) ChannelSpec (class in ClearMap.IO.assets_specs) ChannelsSnapshot (class in ClearMap.Utils.events) ChannelStitchingParams (class in ClearMap.gui.params) ChannelsUiParameterCollection (class in ClearMap.gui.params_interfaces) ChannelTractMapParams (class in ClearMap.gui.params) ChannelUiParameter (class in ClearMap.gui.params_interfaces) char_index() (Expression method) check_alignments_and_sources() (in module ClearMap.Alignment.Stitching.stitching_rigid) check_border() (in module ClearMap.ImageProcessing.Topology.Topology3d) check_chains() (in module ClearMap.Analysis.graphs.graph_processing) check_elastix_initialized() (in module ClearMap.Alignment.Elastix) check_enough_temp_space() (in module ClearMap.Utils.utilities) check_graph_is_reduce_compatible() (in module ClearMap.Analysis.graphs.graph_processing) check_has_all_tiles() (SampleManager method) check_ids_are_unique() (DensityGroupAnalysisOrchestrator method) check_item_at() (CheckableListWidget method) check_items() (CheckableListWidget method) check_protocol_coverage() (in module ClearMap.pipeline_orchestrators.sample_info_management) check_pytorch() (PytorchVersionManager static method) check_spaces() (in module ClearMap.Alignment.Elastix) check_state_changed (CheckableListWidget attribute) check_stopped() (in module ClearMap.Utils.utilities) check_success() (in module ClearMap.Alignment.Elastix) CheckableListWidget (class in ClearMap.gui.widgets) checkerboard_level_set() (in module ClearMap.ImageProcessing.Binary.morphsnake) CHECKSUM_ALGORITHMS (in module ClearMap.IO.assets_constants) ClassificationConfig (class in ClearMap.Analysis.graphs.vessel_classifier) ClassificationMetrics (class in ClearMap.Analysis.graphs.vessel_classifier) classify() (VesselClassifier method) clean (VesselGraphParams attribute) clean() (in module ClearMap.ParallelProcessing.SharedMemoryManager) clean_graph() (in module ClearMap.Analysis.graphs.graph_processing) (VesselGraphProcessor method) clean_open_branches() (in module ClearMap.ImageProcessing.Skeletonization.SkeletonProcessing) clean_path() (in module ClearMap.Utils.path_utils) cleanup() (in module ClearMap.Analysis.colocalization.channel) clear() (CheckableListWidget method) (TwoListSelection method) clear_atlas_caches() (in module ClearMap.Scripts.clearmap_utils) clear_cuda_cache() (in module ClearMap.Utils.utilities) clear_landmarks() (LandmarksSelectorDialog method) (RegistrationProcessor method) (RegistrationTab method) clear_layout() (in module ClearMap.gui.gui_utils_base) clear_plots() (ClearMapAppBase method) clear_renamed_channels() (SampleManager method) ClearMap module ClearMap.Alignment module ClearMap.Alignment.Annotation module ClearMap.Alignment.Elastix module ClearMap.Alignment.landmarks_registration module ClearMap.Alignment.landmarks_registration.engine module ClearMap.Alignment.landmarks_registration.registration_data module ClearMap.Alignment.orientation module ClearMap.Alignment.Resampling module ClearMap.Alignment.Stitching module ClearMap.Alignment.Stitching.layout_graph_utils module ClearMap.Alignment.Stitching.plot_utils module ClearMap.Alignment.Stitching.stitching_plots module ClearMap.Alignment.Stitching.stitching_rigid module ClearMap.Alignment.Stitching.stitching_wobbly module ClearMap.Alignment.Stitching.Tracking module ClearMap.Alignment.Transformation module ClearMap.Alignment.Transformations module ClearMap.Alignment.Transformations.LinearTransformation module ClearMap.Alignment.Transformations.ResamplingTransformation module ClearMap.Alignment.Transformations.SlicingTransformation module ClearMap.Alignment.Transformations.Transformation module ClearMap.Alignment.utils module ClearMap.Analysis module ClearMap.Analysis.colocalization module ClearMap.Analysis.colocalization.bbox module ClearMap.Analysis.colocalization.channel module ClearMap.Analysis.colocalization.parallelism module ClearMap.Analysis.Curves module ClearMap.Analysis.Curves.Extrapolation module ClearMap.Analysis.Curves.Resampling module ClearMap.Analysis.DimensionReduction module ClearMap.Analysis.graphs module ClearMap.Analysis.graphs.fast_graph_reduce module ClearMap.Analysis.graphs.graph module ClearMap.Analysis.graphs.graph_filters module ClearMap.Analysis.graphs.graph_gt module ClearMap.Analysis.graphs.graph_processing module ClearMap.Analysis.graphs.graph_rendering module ClearMap.Analysis.graphs.type_conversions module ClearMap.Analysis.graphs.utils module ClearMap.Analysis.graphs.vessel_classifier module ClearMap.Analysis.Measurements module ClearMap.Analysis.Measurements.maxima_detection module ClearMap.Analysis.Measurements.MeasureExpression module ClearMap.Analysis.Measurements.radius_measurements module ClearMap.Analysis.Measurements.shape_detection module ClearMap.Analysis.Measurements.Voxelization module ClearMap.Analysis.Statistics module ClearMap.Analysis.Statistics.data_frame_operations module ClearMap.Analysis.Statistics.group_assets module ClearMap.Analysis.Statistics.group_statistics module ClearMap.Analysis.Statistics.group_statistics_cumulatives module ClearMap.Analysis.Statistics.MultipleComparisonCorrection module ClearMap.Analysis.Statistics.StatisticalTests module ClearMap.Analysis.vasculature module ClearMap.Analysis.vasculature.annotation_utils module ClearMap.Analysis.vasculature.flow module ClearMap.Analysis.vasculature.flow.assign_p_bc module ClearMap.Analysis.vasculature.flow.linear_system module ClearMap.Analysis.vasculature.flow.units module ClearMap.Analysis.vasculature.general_functions module ClearMap.Analysis.vasculature.geometry_utils module ClearMap.Analysis.vasculature.graph_corrections module ClearMap.Analysis.vasculature.vasc_graph_utils module ClearMap.config module ClearMap.config.atlas module ClearMap.config.change_detection module ClearMap.config.compound_keys module ClearMap.config.config_adjusters module ClearMap.config.config_adjusters.adjusters_api module ClearMap.config.config_adjusters.dict_ops module ClearMap.config.config_adjusters.engine module ClearMap.config.config_adjusters.group_adjusters module ClearMap.config.config_adjusters.patch_ops module ClearMap.config.config_adjusters.policy module ClearMap.config.config_adjusters.policy_specs module ClearMap.config.config_adjusters.templates_resolver module ClearMap.config.config_adjusters.trace_logging module ClearMap.config.config_adjusters.type_hints module ClearMap.config.config_coordinator module ClearMap.config.config_handler module ClearMap.config.config_repository module ClearMap.config.convert_config_versions module ClearMap.config.defaults_provider module ClearMap.config.early_boot module ClearMap.config.update_config module ClearMap.config.utils module ClearMap.config.validators module ClearMap.config.validators._schema module ClearMap.config.validators._semantic module ClearMap.config.validators.json_schema_utils module ClearMap.gui module ClearMap.gui.about module ClearMap.gui.app module ClearMap.gui.creator module ClearMap.gui.creator.graphics_resources_rc module ClearMap.gui.creator.icons_rc module ClearMap.gui.dialog_helpers module ClearMap.gui.dialogs module ClearMap.gui.exception_handler module ClearMap.gui.gui_logging module ClearMap.gui.gui_utils_base module ClearMap.gui.gui_utils_images module ClearMap.gui.params module ClearMap.gui.params_interfaces module ClearMap.gui.params_mixins module ClearMap.gui.pipeline_model module ClearMap.gui.pipeline_widgets module ClearMap.gui.preferences module ClearMap.gui.pretty_imports module ClearMap.gui.pyuic_utils module ClearMap.gui.style module ClearMap.gui.tab_registry module ClearMap.gui.tabs module ClearMap.gui.tabs_interfaces module ClearMap.gui.widget_monkeypatch_callbacks module ClearMap.gui.widgets module ClearMap.ImageProcessing module ClearMap.ImageProcessing.Binary module ClearMap.ImageProcessing.Binary.Filling module ClearMap.ImageProcessing.Binary.FillingCode module ClearMap.ImageProcessing.Binary.morphsnake module ClearMap.ImageProcessing.Binary.Smoothing module ClearMap.ImageProcessing.Clipping module ClearMap.ImageProcessing.Clipping.Clipping module ClearMap.ImageProcessing.Clipping.ClippingCode module ClearMap.ImageProcessing.Differentiation module ClearMap.ImageProcessing.Differentiation.Gradient module ClearMap.ImageProcessing.Differentiation.Hessian module ClearMap.ImageProcessing.Differentiation.HessianCode module ClearMap.ImageProcessing.Experts module ClearMap.ImageProcessing.Experts.Cells module ClearMap.ImageProcessing.Experts.utils module ClearMap.ImageProcessing.Experts.Vasculature module ClearMap.ImageProcessing.Filter module ClearMap.ImageProcessing.Filter.FilterKernel module ClearMap.ImageProcessing.Filter.Rank module ClearMap.ImageProcessing.Filter.Rank.Bilateral module ClearMap.ImageProcessing.Filter.Rank.BilateralCode module ClearMap.ImageProcessing.Filter.Rank.Parametric module ClearMap.ImageProcessing.Filter.Rank.ParametricCode module ClearMap.ImageProcessing.Filter.Rank.Percentile module ClearMap.ImageProcessing.Filter.Rank.PercentileCode module ClearMap.ImageProcessing.Filter.Rank.Rank module ClearMap.ImageProcessing.Filter.Rank.RankCode module ClearMap.ImageProcessing.Filter.Rank.RankCoreCode module ClearMap.ImageProcessing.Filter.Rank.RankResample module ClearMap.ImageProcessing.Filter.StructureElement module ClearMap.ImageProcessing.grey_reconstruction module ClearMap.ImageProcessing.IlluminationCorrection module ClearMap.ImageProcessing.LightsheetCorrection module ClearMap.ImageProcessing.local_percentile_core module ClearMap.ImageProcessing.local_threshold_isodata module ClearMap.ImageProcessing.LocalStatistics module ClearMap.ImageProcessing.machine_learning module ClearMap.ImageProcessing.machine_learning.torch_utils module ClearMap.ImageProcessing.machine_learning.vertices_classification module ClearMap.ImageProcessing.machine_learning.vertices_classification.degree1_inference_utils module ClearMap.ImageProcessing.machine_learning.vessel_filling module ClearMap.ImageProcessing.machine_learning.vessel_filling.vessel_filling module ClearMap.ImageProcessing.machine_learning.vessel_filling.vessel_filling_network module ClearMap.ImageProcessing.Skeletonization module ClearMap.ImageProcessing.Skeletonization.PK12 module ClearMap.ImageProcessing.Skeletonization.Skeletonization module ClearMap.ImageProcessing.Skeletonization.SkeletonProcessing module ClearMap.ImageProcessing.Thresholding module ClearMap.ImageProcessing.Thresholding.Thresholding module ClearMap.ImageProcessing.Thresholding.ThresholdingCode module ClearMap.ImageProcessing.Topology module ClearMap.ImageProcessing.Topology.Topology2d module ClearMap.ImageProcessing.Topology.Topology3d module ClearMap.ImageProcessing.Tracing module ClearMap.ImageProcessing.Tracing.Connect module ClearMap.ImageProcessing.Tracing.Trace module ClearMap.ImageProcessing.Tracing.TraceCode module ClearMap.IO module ClearMap.IO.assets_constants module ClearMap.IO.assets_specs module ClearMap.IO.CSV module ClearMap.IO.elastix_config module ClearMap.IO.FileList module ClearMap.IO.FileUtils module ClearMap.IO.GT module ClearMap.IO.IO module ClearMap.IO.metadata module ClearMap.IO.MHD module ClearMap.IO.MMP module ClearMap.IO.NPY module ClearMap.IO.NRRD module ClearMap.IO.Slice module ClearMap.IO.SMA module ClearMap.IO.Source module ClearMap.IO.Temporary module ClearMap.IO.TIF module ClearMap.IO.Workspace module ClearMap.ParallelProcessing module ClearMap.ParallelProcessing.Block module ClearMap.ParallelProcessing.BlockProcessing module ClearMap.ParallelProcessing.DataProcessing module ClearMap.ParallelProcessing.DataProcessing.ArrayProcessing module ClearMap.ParallelProcessing.DataProcessing.ArrayProcessingCode module ClearMap.ParallelProcessing.DataProcessing.ConvolvePointList module ClearMap.ParallelProcessing.DataProcessing.ConvolvePointListCode module ClearMap.ParallelProcessing.DataProcessing.devolve_point_list_code module ClearMap.ParallelProcessing.DataProcessing.DevolvePointList module ClearMap.ParallelProcessing.DataProcessing.MeasurePointList module ClearMap.ParallelProcessing.DataProcessing.MeasurePointListCode module ClearMap.ParallelProcessing.DataProcessing.statistics module ClearMap.ParallelProcessing.ParallelTraceback module ClearMap.ParallelProcessing.ProcessWriter module ClearMap.ParallelProcessing.SharedMemoryArray module ClearMap.ParallelProcessing.SharedMemoryManager module ClearMap.pipeline_orchestrators module ClearMap.pipeline_orchestrators.batch_process module ClearMap.pipeline_orchestrators.cell_map module ClearMap.pipeline_orchestrators.colocalization module ClearMap.pipeline_orchestrators.degree1_inference_processor module ClearMap.pipeline_orchestrators.experiment_controller module ClearMap.pipeline_orchestrators.generic_orchestrators module ClearMap.pipeline_orchestrators.group_orchestrators module ClearMap.pipeline_orchestrators.registration_orchestrator module ClearMap.pipeline_orchestrators.sample_info_management module ClearMap.pipeline_orchestrators.stitching_orchestrator module ClearMap.pipeline_orchestrators.tract_map module ClearMap.pipeline_orchestrators.tube_map module ClearMap.pipeline_orchestrators.utils module ClearMap.Scripts module ClearMap.Scripts.align_new_api module ClearMap.Scripts.cell_map_new_api module ClearMap.Scripts.CellMap module ClearMap.Scripts.clearmap_utils module ClearMap.Scripts.create_distance_file module ClearMap.Scripts.generate_jsonl_file_ontology module ClearMap.Scripts.partial_gt_load_demo module ClearMap.Scripts.tract_map module ClearMap.Scripts.tube_map_new_api module ClearMap.Scripts.TubeMap module ClearMap.Settings module ClearMap.Utils module ClearMap.Utils.array_utils module ClearMap.Utils.array_utils_cy module ClearMap.Utils.event_bus module ClearMap.Utils.events module ClearMap.Utils.exceptions module ClearMap.Utils.Formatting module ClearMap.Utils.HierarchicalDict module ClearMap.Utils.install_utils module ClearMap.Utils.Lazy module ClearMap.Utils.path_utils module ClearMap.Utils.RegularExpression module ClearMap.Utils.Sound module ClearMap.Utils.tag_expression module ClearMap.Utils.Timer module ClearMap.Utils.utilities module ClearMap.Visualization module ClearMap.Visualization.Color module ClearMap.Visualization.Color.Color module ClearMap.Visualization.Color.orientation_colormap module ClearMap.Visualization.Matplotlib module ClearMap.Visualization.Matplotlib.PlotUtils module ClearMap.Visualization.Mesh module ClearMap.Visualization.Mesh.IcoSphere module ClearMap.Visualization.Plot3d module ClearMap.Visualization.Qt module ClearMap.Visualization.Qt.data_viewer_luts module ClearMap.Visualization.Qt.DataViewer module ClearMap.Visualization.Qt.Plot3d module ClearMap.Visualization.Qt.utils module ClearMap.Visualization.Qt.widgets module ClearMap.Visualization.Vispy module ClearMap.Visualization.Vispy.arbitrary_rotation_camera module ClearMap.Visualization.Vispy.graph_visual module ClearMap.Visualization.Vispy.Plot3d module ClearMap.Visualization.Vispy.plot_graph_3d module ClearMap.Visualization.Vispy.VolumeVisual module clearmap_path (in module ClearMap.Settings) ClearMapApp (class in ClearMap.gui.app) ClearMapAppBase (class in ClearMap.gui.app) ClearMapAssetError ClearMapConfigError ClearMapException ClearMapFileNotFoundError ClearMapIoException ClearMapMetadataParser (class in ClearMap.IO.TIF) ClearMapPermissionError ClearMapRuntimeError ClearMapValueError ClearMapVRamException ClearMapWorkspaceError ClickableFrame (class in ClearMap.gui.widgets) clicked (ClickableFrame attribute) clim (VolumeVisual property) clip() (in module ClearMap.ImageProcessing.Clipping) (in module ClearMap.ImageProcessing.Clipping.Clipping) (in module ClearMap.ImageProcessing.Clipping.ClippingCode) (in module ClearMap.ImageProcessing.Experts.Vasculature) clip_range (ChannelTractMapParams attribute) clipping_decimation_ratio (ChannelTractMapParams attribute) clipping_percents (ChannelTractMapParams attribute) clone_from() (ConfigCoordinator method) (ConfigRepository method) (ExperimentController method) close() (in module ClearMap.Visualization.Qt.Plot3d) (StructureSelector method) close_file() (Printer method) closest_center_distances() (Channel method) clp() (in module ClearMap.ImageProcessing.Filter.Rank.ParametricCode) clp_masked() (in module ClearMap.ImageProcessing.Filter.Rank.ParametricCode) cluster_components() (in module ClearMap.Alignment.Stitching.layout_graph_utils) cmap (VolumeVisual property) collapse_structures() (in module ClearMap.Analysis.Statistics.data_frame_operations) colocalization_channels (ColocalizationProcessor attribute) colocalization_compatible (ChannelCellMapParams attribute) colocalization_entry_template() (ExperimentTemplatesResolver method) colocalization_pair_keys() (SampleManager method) (SampleManagerProtocol method) colocalization_pairs() (SampleManager method) (SampleManagerProtocol method) ColocalizationParams (class in ClearMap.gui.params) ColocalizationProcessor (class in ClearMap.pipeline_orchestrators.colocalization) ColocalizationTab (class in ClearMap.gui.tabs) color (Landmark property) (StepSpec attribute) color() (in module ClearMap.Visualization.Color.Color) (Label method) color_axis (DataViewer property) color_last() (DataViewer method) color_map() (Annotation method) (in module ClearMap.Visualization.Color.Color) color_p_values() (in module ClearMap.Analysis.Statistics.group_statistics) ColorFormatter (class in ClearMap.Scripts.partial_gt_load_demo) colorize() (in module ClearMap.Utils.utilities) colormap() (in module ClearMap.Visualization.Color.Color) colors (LandmarksSelectorDialog property) colourise() (Printer method) combine() (VasculatureTab method) combine_arteries_and_veins() (in module ClearMap.Analysis.vasculature.vasc_graph_utils) combine_binary() (BinaryVesselProcessor method) combine_operator_name (GraphFilterParams property) combine_with() (GraphFilter method) combined (BinaryVesselProcessorSteps attribute) CombinedFilter (class in ClearMap.Analysis.graphs.graph_filters) combobox_getter() (in module ClearMap.gui.params_interfaces) combobox_setter() (in module ClearMap.gui.params_interfaces) comment (CondaPackage property) comments (SampleChannelParameters attribute) commit() (ConfigCoordinator method) (ConfigRepository method) common_parent() (Annotation method) compare() (Channel method) (in module ClearMap.Analysis.colocalization.parallelism) comparisons (GroupAnalysisParams property) ComparisonsModel (class in ClearMap.gui.widgets) ComparisonsWidgetAdapter (class in ClearMap.gui.widgets) competing_labels() (VesselType class method) competitor() (VesselType method) compile_validator() (in module ClearMap.config.validators.json_schema_utils) compound (InstanceContainerSpec attribute) compound_oriented (InstanceContainerSpec attribute) compound_prune_invalid_atoms (InstanceContainerSpec attribute) CompoundChannelPipelineOrchestrator (class in ClearMap.pipeline_orchestrators.generic_orchestrators) CompoundKey (class in ClearMap.config.compound_keys) compress() (SampleManager static method) compress_dtype() (in module ClearMap.Analysis.colocalization.channel) compute_blood_flow() (in module ClearMap.Analysis.vasculature.general_functions) compute_clip_range() (TractMapProcessor method) compute_clipping_range() (TractMapTab method) compute_colocalization() (ColocalizationProcessor method) compute_default_font_size() (ClearMapAppBase method) compute_filter_suffix() (VesselGraphParams method) compute_flow_f_schmid() (in module ClearMap.Analysis.vasculature.general_functions) compute_force() (in module ClearMap.ImageProcessing.Binary.morphsnake) compute_grid() (in module ClearMap.Analysis.vasculature.geometry_utils) (in module ClearMap.gui.gui_utils_base) compute_label_confidence() (in module ClearMap.Analysis.graphs.graph_processing) compute_layout() (ChannelStitchingParams method) (StitchingParams method) compute_means() (in module ClearMap.ImageProcessing.Binary.morphsnake) compute_p_values() (DensityGroupAnalysisOrchestrator method) compute_relevant_pipelines() (SampleManager method) compute_required_sections() (SampleManager method) (SampleManagerProtocol method) compute_sd_and_effect_size (GroupAnalysisParams attribute) compute_stats_tables() (DensityGroupAnalysisOrchestrator method) CondaPackage (class in ClearMap.Utils.install_utils) CondaParser (class in ClearMap.Utils.install_utils) conf_load_error_msg() (ClearMapApp method) config (ChannelPipelineOrchestrator property) (CompoundChannelPipelineOrchestrator property) (OrchestratorBase property) config_channels (SampleParameters property) config_exists() (ConfigCoordinator method) config_exists_any() (ConfigCoordinator method) config_handler (GroupTab attribute) config_name (BinaryVesselProcessor attribute) (CellDetector attribute) (ChannelPipelineOrchestrator attribute) (ColocalizationProcessor attribute) (CompoundChannelPipelineOrchestrator attribute) (OrchestratorBase attribute) (RegistrationProcessor attribute) (SampleManager attribute) (StitchingProcessor attribute) (TractMapProcessor attribute) (VesselGraphProcessor attribute) ConfigAlternativesRegistry (class in ClearMap.config.config_handler) ConfigCoordinator (class in ClearMap.config.config_coordinator) ConfigHandler (class in ClearMap.config.config_handler) ConfigNotFoundError configobj_to_dict() (in module ClearMap.config.utils) ConfigParsingError ConfigProxy (class in ClearMap.config.config_handler) ConfigRepository (class in ClearMap.config.config_repository) ConfigSpec (class in ClearMap.config.config_handler) ConfigValidator (class in ClearMap.config.validators) connect (ParamLink attribute), [1] connect() (AtlasParams method) (BatchParameters method) (ChannelCellMapParams method) (ChannelRegistrationParams method) (ChannelStitchingParams method) (GraphFilterParams method) (GroupPage method) (GroupsWidgetAdapter method) (SampleChannelParameters method) (UiParameter method) (WidgetOps method) connect_buttons() (LandmarksSelectorDialog method) (ManageAssetsWidget method) (PatternDialog method) (SamplePickerDialog method) (StructureSelector method) (WizardWidget method) connect_frame() (in module ClearMap.gui.params_interfaces) connect_group_name_changed() (GroupPage method) connect_simple_widgets() (UiParameter method) connect_sources() (in module ClearMap.Alignment.Stitching.layout_graph_utils) connect_whats_this_btn() (GenericTab method) connected() (in module ClearMap.Alignment.Stitching.stitching_rigid) (Layout method) connected_components() (in module ClearMap.Alignment.Stitching.stitching_rigid) (Layout method) CONNECTOR_H (LinearPipelineWidget attribute) connectPoint() (in module ClearMap.ImageProcessing.Tracing.Connect) consider (in module ClearMap.ImageProcessing.Skeletonization.PK12) consume_and_cleanup() (BinaryVesselProcessorSteps method) container_map() (InstanceContainerSpec method) container_path (InstanceContainerSpec attribute) ContainerRole (class in ClearMap.config.config_adjusters.policy_specs) ContainerSpecRegistry (class in ClearMap.config.config_adjusters.policy_specs) content_type (ChannelSpec attribute) contiguous_labels() (in module ClearMap.Analysis.colocalization.channel) contrast_limited_percentile() (in module ClearMap.ImageProcessing.Filter.Rank) (in module ClearMap.ImageProcessing.Filter.Rank.Parametric) convert() (in module ClearMap.config.convert_config_versions) (in module ClearMap.IO.FileList) (in module ClearMap.IO.IO) (SampleManager static method) convert_2_1_to_3_0() (in module ClearMap.config.convert_config_versions) convert_3_0_to_3_1() (in module ClearMap.config.convert_config_versions) convert_alignment_2_1_to_3_0() (in module ClearMap.config.convert_config_versions) convert_batch_3_0_to_3_1() (in module ClearMap.config.convert_config_versions) convert_cell_map_2_1_to_3_0() (in module ClearMap.config.convert_config_versions) convert_cell_map_3_0_to_3_1() (in module ClearMap.config.convert_config_versions) convert_cm2_to_cm2_1_fmt() (CellDetector method) convert_colocalization_3_0_to_3_1() (in module ClearMap.config.convert_config_versions) convert_files() (in module ClearMap.IO.IO) convert_group_analysis_3_0_to_3_1() (in module ClearMap.config.convert_config_versions) convert_label() (Annotation method) convert_machine_2_1_to_3_0() (in module ClearMap.config.convert_config_versions) convert_machine_3_0_to_3_1() (in module ClearMap.config.convert_config_versions) convert_property() (in module ClearMap.Analysis.graphs.graph_filters) convert_registration_3_0_to_3_1() (in module ClearMap.config.convert_config_versions) convert_sample_2_1_to_3_0() (in module ClearMap.config.convert_config_versions) convert_sample_3_0_to_3_1() (in module ClearMap.config.convert_config_versions) convert_stitching_3_0_to_3_1() (in module ClearMap.config.convert_config_versions) convert_tiles() (StitchingProcessor method) (StitchingTab method) convert_tiles_channel() (StitchingProcessor method) convert_to_cm_2_1() (in module ClearMap.pipeline_orchestrators.batch_process) convert_tract_map_3_0_to_3_1() (in module ClearMap.config.convert_config_versions) convert_vasculature_3_0_to_3_1() (in module ClearMap.config.convert_config_versions) convert_versions() (in module ClearMap.config.convert_config_versions) convolve_3d() (in module ClearMap.ParallelProcessing.DataProcessing.ConvolvePointList) convolve_3d_find_smaller_than() (in module ClearMap.ParallelProcessing.DataProcessing.ConvolvePointList) convolve_3d_indices() (in module ClearMap.ParallelProcessing.DataProcessing.ConvolvePointList) (in module ClearMap.ParallelProcessing.DataProcessing.ConvolvePointListCode) convolve_3d_indices_if_smaller_than() (in module ClearMap.ParallelProcessing.DataProcessing.ConvolvePointList) (in module ClearMap.ParallelProcessing.DataProcessing.ConvolvePointListCode) convolve_3d_indices_if_smaller_than_no_check() (in module ClearMap.ParallelProcessing.DataProcessing.ConvolvePointListCode) convolve_3d_indices_no_check() (in module ClearMap.ParallelProcessing.DataProcessing.ConvolvePointListCode) convolve_3d_points() (in module ClearMap.ParallelProcessing.DataProcessing.ConvolvePointList) (in module ClearMap.ParallelProcessing.DataProcessing.ConvolvePointListCode) convolve_3d_points_no_check() (in module ClearMap.ParallelProcessing.DataProcessing.ConvolvePointListCode) convolve_3d_xyz() (in module ClearMap.ParallelProcessing.DataProcessing.ConvolvePointList) (in module ClearMap.ParallelProcessing.DataProcessing.ConvolvePointListCode) convolve_3d_xyz_no_check() (in module ClearMap.ParallelProcessing.DataProcessing.ConvolvePointListCode) coordinate (WobblySource property) coordinate_from_local() (Region method) (WobblySource method) coordinate_to_local() (Region method) (WobblyAlignment method) (WobblySource method) coordinates (Scatter3D property) coordinates_to_edge_vectors() (in module ClearMap.Analysis.vasculature.general_functions) copy() (AlignmentBase method) (Graph method) (Region method) (Source method) (Verbose method) copy_file() (in module ClearMap.IO.FileUtils) copy_from_defaults() (ConfigCoordinator method) (ConfigRepository method) copy_or_stack() (StitchingProcessor method) copy_sources_and_alignments() (in module ClearMap.Alignment.Stitching.stitching_rigid) correct_graph() (in module ClearMap.Analysis.vasculature.graph_corrections) correct_illumination() (in module ClearMap.ImageProcessing.IlluminationCorrection) correct_lightsheet() (in module ClearMap.ImageProcessing.LightsheetCorrection) correct_lightsheet_divide() (in module ClearMap.ImageProcessing.LightsheetCorrection) correct_lightsheet_subdiv() (in module ClearMap.ImageProcessing.LightsheetCorrection) correct_p_values() (in module ClearMap.Analysis.Statistics.MultipleComparisonCorrection) correlate1d() (in module ClearMap.ParallelProcessing.DataProcessing.ArrayProcessing) correlate_1d() (in module ClearMap.ParallelProcessing.DataProcessing.ArrayProcessingCode) count_cells (BatchProcessingParams attribute) count_cells() (in module ClearMap.Analysis.Statistics.data_frame_operations) count_dones() (ProgressWatcher method) counter (Source attribute) counts (ClassificationMetrics attribute) cpu_vals_changed (PerfMonitor attribute) create() (in module ClearMap.IO.CSV) (in module ClearMap.IO.FileList) (in module ClearMap.IO.GT) (in module ClearMap.IO.IO) (in module ClearMap.IO.MHD) (in module ClearMap.IO.MMP) (in module ClearMap.IO.NPY) (in module ClearMap.IO.NRRD) (in module ClearMap.IO.TIF) (Workspace method) create_atlas_asset() (RegistrationProcessor method) CREATE_CHANNELS_RECONCILE (Step attribute) create_clearmap_widget() (in module ClearMap.gui.gui_utils_base) create_color_annotation() (Annotation method) create_debug() (Workspace method) create_directory() (in module ClearMap.IO.FileUtils) (Verbose method) create_label_table() (in module ClearMap.Alignment.utils) create_layout_from_ome() (StitchingProcessor method) create_missing_channels_from_view() (StitchingParams method) create_missing_file_msg() (ClearMapAppBase static method) CREATE_PIPELINE_SECTIONS (Step attribute) create_test_dataset() (CellDetector method) (TractMapProcessor method) create_tuning_sample() (PostProcessingTab method) (TractMapTab method) create_wizard() (BatchTab method) CRITICAL (Severity attribute) crop_dialog() (ManageAssetsWidget method) crop_x (ChannelCellMapParams attribute) (ChannelTractMapParams attribute) (HasSlicingFields attribute) (VesselVisualizationParams attribute) crop_x_max (OrthoviewerSlicingMixin property) crop_x_min (OrthoviewerSlicingMixin property) crop_y (ChannelCellMapParams attribute) (ChannelTractMapParams attribute) (HasSlicingFields attribute) (VesselVisualizationParams attribute) crop_y_max (OrthoviewerSlicingMixin property) crop_y_min (OrthoviewerSlicingMixin property) crop_z (ChannelCellMapParams attribute) (ChannelTractMapParams attribute) (HasSlicingFields attribute) (VesselVisualizationParams attribute) crop_z_max (OrthoviewerSlicingMixin property) crop_z_min (OrthoviewerSlicingMixin property) ctx_builder (InstanceContainerSpec attribute) ctype() (in module ClearMap.IO.SMA) (in module ClearMap.ParallelProcessing.SharedMemoryArray) cube() (in module ClearMap.ImageProcessing.Filter.StructureElement) cube_base_2() (in module ClearMap.ImageProcessing.Topology.Topology3d) cube_from_index() (in module ClearMap.ImageProcessing.Topology.Topology3d) cube_labeled() (in module ClearMap.ImageProcessing.Topology.Topology3d) cube_to_index() (in module ClearMap.ImageProcessing.Topology.Topology3d) cube_to_smoothing() (in module ClearMap.ImageProcessing.Binary.Smoothing) cuda_major (PytorchVersionManager property) cuda_version (PytorchVersionManager property) current_channel() (ExtendableTabWidget method) current_channels (ConfigCoordinator property) current_color (LandmarksSelectorDialog property) current_dtype (GraphFilterParams property) current_marker (LandmarksSelectorDialog property) current_slice_mask() (Scatter3D method) cy_reduce() (in module ClearMap.Analysis.graphs.fast_graph_reduce) D DARK_COLOR (StructurePickerWidget attribute) darker() (in module ClearMap.Visualization.Color.Color) DATA_CONTENT_TYPES (in module ClearMap.IO.assets_constants) data_type (ChannelPatternSpec attribute) (SampleChannelParameters attribute) data_type() (SampleManager method) (SampleManagerProtocol method) data_types (SampleManager property) DataFrameWidget (class in ClearMap.gui.widgets) DataViewer (class in ClearMap.Visualization.Qt.DataViewer) de_duplicate_path() (in module ClearMap.Utils.path_utils) debug (Workspace property) debug_mode() (PostProcessingTab method) decode() (VesselFillingNetwork method) decompress() (SampleManager static method) decompress_atlases() (in module ClearMap.Alignment.Annotation) deconvolve() (in module ClearMap.ImageProcessing.Experts.Vasculature) deep_fill_channel() (BinaryVesselProcessor method) deep_filled (BinaryVesselProcessorSteps attribute) deep_freeze() (in module ClearMap.Utils.utilities) deep_merge() (in module ClearMap.Utils.utilities) deep_merge_dicts() (in module ClearMap.config.update_config) deep_merge_missing() (in module ClearMap.config.config_adjusters.dict_ops) default (ParamLink attribute), [1] default_annotation_file (in module ClearMap.Alignment.Annotation) default_binarization_parameter (in module ClearMap.ImageProcessing.Experts.Vasculature) default_binarization_pipeline() (in module ClearMap.gui.pipeline_model) default_binarization_processing_parameter (in module ClearMap.ImageProcessing.Experts.Vasculature) default_blocks_per_process (in module ClearMap.ParallelProcessing.DataProcessing.ArrayProcessing) default_cell_detection_parameter (in module ClearMap.ImageProcessing.Experts.Cells) default_cell_detection_processing_parameter (in module ClearMap.ImageProcessing.Experts.Cells) default_cutoff (in module ClearMap.ParallelProcessing.DataProcessing.ArrayProcessing) default_distance_to_surface_file (in module ClearMap.Alignment.Annotation) default_extension (TypeSpec property) default_extra_label (in module ClearMap.Alignment.Annotation) default_flat_field_line_file_name (in module ClearMap.ImageProcessing.IlluminationCorrection) default_hemispheres_file (in module ClearMap.Alignment.Annotation) default_label_file (in module ClearMap.Alignment.Annotation) DEFAULT_N_DIMS (Graph attribute) default_overlap (in module ClearMap.ParallelProcessing.BlockProcessing) default_path_for() (ConfigRepository static method) default_postprocessing_parameter (in module ClearMap.ImageProcessing.Experts.Vasculature) default_postprocessing_processing_parameter (in module ClearMap.ImageProcessing.Experts.Vasculature) default_processes (in module ClearMap.ParallelProcessing.DataProcessing.ArrayProcessing) default_reference_file (in module ClearMap.Alignment.Annotation) DEFAULT_SCATTER_PARAMS (DataViewer attribute) default_size_max (in module ClearMap.ParallelProcessing.BlockProcessing) default_size_min (in module ClearMap.ParallelProcessing.BlockProcessing) default_tag_name() (in module ClearMap.Utils.tag_expression) default_tile_extension (SharedSampleParams attribute), [1] defaults (MachineConfig property) (TemplateResolverBase property) defaults_templates_path (InstanceContainerSpec attribute) DefaultsProvider (class in ClearMap.config.defaults_provider) define_auto_resolution() (in module ClearMap.IO.metadata) define_auto_stitching_params() (in module ClearMap.IO.metadata) define_edge_geometry_indices_graph() (Graph method) define_edge_property() (Graph method) define_graph_property() (Graph method) define_vertex_property() (Graph method) deform_1() (in module ClearMap.Visualization.Color.orientation_colormap) deform_xyz() (in module ClearMap.Visualization.Color.orientation_colormap) deformation_distance() (in module ClearMap.Alignment.Elastix) deformation_field() (in module ClearMap.Alignment.Elastix) DEGRADED (Severity attribute) degree1_verification() (in module ClearMap.pipeline_orchestrators.degree1_inference_processor) del_item_recursive() (in module ClearMap.Utils.utilities) delete (in module ClearMap.ImageProcessing.Skeletonization.PK12) delete() (ElastixPointFileManager method) delete_border() (in module ClearMap.ImageProcessing.Topology.Topology3d) delete_directory() (in module ClearMap.IO.FileUtils) delete_file() (in module ClearMap.IO.FileUtils) delete_item() (CheckableListWidget method) delete_resampled_files() (SampleManager method) delete_widget() (in module ClearMap.gui.gui_utils_base) density_files_are_comparable() (DensityGroupAnalysisOrchestrator method) density_orchestrator (AnalysisGroupController property) density_suffix (GroupAnalysisParams attribute) DensityGroupAnalysisOrchestrator (class in ClearMap.pipeline_orchestrators.group_orchestrators) depth (OrthoViewer property) description (StepSpec attribute) DeSepConv3d (class in ClearMap.ImageProcessing.machine_learning.vessel_filling.vessel_filling_network) desktop_entry_ok (BootResult attribute) detached (SampleInfoTab attribute) detect() (Expression method) (in module ClearMap.Utils.tag_expression) detect_cells (ChannelCellMapParams attribute) detect_cells() (CellCounterTab method) (in module ClearMap.ImageProcessing.Experts.Cells) detect_cells_block() (in module ClearMap.ImageProcessing.Experts.Cells) detect_config_type() (in module ClearMap.config.convert_config_versions) detect_label_conflicts() (in module ClearMap.Analysis.graphs.graph_processing) detect_local_minima() (in module ClearMap.Alignment.Stitching.stitching_wobbly) detect_maxima() (in module ClearMap.ImageProcessing.Experts.Cells) detect_shape() (in module ClearMap.Analysis.Measurements.shape_detection) detected (CellDetector property) detection_threshold (ChannelCellMapParams attribute) devolve() (in module ClearMap.ParallelProcessing.DataProcessing.DevolvePointList) devolve_uniform() (in module ClearMap.ParallelProcessing.DataProcessing.devolve_point_list_code) devolve_uniform_kernel() (in module ClearMap.ParallelProcessing.DataProcessing.devolve_point_list_code) devolve_weights() (in module ClearMap.ParallelProcessing.DataProcessing.devolve_point_list_code) devovle_weights_kernel() (in module ClearMap.ParallelProcessing.DataProcessing.devolve_point_list_code) df_path (CellDetector property) directed (Graph property), [1] directory (TypeSpec property) (Workspace property) directory_name() (in module ClearMap.IO.Workspace) (Workspace method) directory_type() (in module ClearMap.IO.Workspace) (Workspace method) directory_type_to_name (Workspace property) disable() (GenericTab method) disconnect_all() (ParamLink method) disconnect_widget_signal() (in module ClearMap.gui.gui_utils_base) discover_import_tasks() (in module ClearMap.gui.pretty_imports) disk() (in module ClearMap.ImageProcessing.Filter.StructureElement) displacement (Alignment property) displacement_at_coordinate() (WobblyAlignment method) displacements (WobblyAlignment property) display_about() (ClearMapApp method) display_atlas() (SampleInfoTab method) display_decimation_ratio (ChannelTractMapParams attribute) display_graph_chunk() (VasculatureTab method) display_graph_chunk_from_cfg() (VasculatureTab method) display_message (ImportTask property) distance_to_surface (VesselSignals attribute) distance_to_surface_min (ClassificationConfig attribute), [1] (VesselGraphParams attribute) distances() (in module ClearMap.Analysis.colocalization.channel) dock_resize_event() (in module ClearMap.gui.widget_monkeypatch_callbacks) dog_filter() (in module ClearMap.ImageProcessing.Experts.Cells) downsample() (in module ClearMap.ImageProcessing.machine_learning.vessel_filling.vessel_filling) dragEnterEvent() (FileDropListWidget method) dragMoveEvent() (FileDropListWidget method) drop_degree2_loops() (in module ClearMap.Analysis.graphs.graph_processing) dropEvent() (FileDropListWidget method) dtype (AbstractSource property) DTYPE (in module ClearMap.ImageProcessing.Experts.Vasculature) dtype (Layout property) (Slice property) (Source property), [1], [2], [3], [4], [5], [6], [7] (VectorLink property) (VirtualSource property) dtype() (in module ClearMap.IO.FileList) (in module ClearMap.IO.IO) (Tag method) dtype_range() (in module ClearMap.Utils.array_utils) dtype_to_gtype() (in module ClearMap.Analysis.graphs.type_conversions) dump() (ConfigHandler class method) E edge() (Graph method), [1] edge_annotation() (AnnotatedGraph method) (Graph method) edge_close_binary() (Graph method) edge_connectivity (PropertyAggregator property) edge_connectivity() (Graph method), [1] edge_coordinates() (GeometricGraph method) (Graph method) edge_coordinates_from_vertex_coordinates() (GeometricGraph method) edge_dilate_binary() (Graph method) edge_erode_binary() (Graph method) edge_filter_to_vertex_filter() (in module ClearMap.Analysis.vasculature.vasc_graph_utils) edge_geometry() (GeometricGraph method) (Graph method) edge_geometry_from_edge_property() (Graph method) edge_geometry_indices() (Graph method) edge_geometry_lengths() (Graph method) edge_geometry_properties (Graph property) edge_geometry_property() (Graph method) edge_geometry_property_name() (Graph method) edge_geometry_property_names (Graph property) edge_geometry_type (GeometricGraph property) (Graph property) edge_graph() (Graph method) edge_index() (Graph method) edge_indices() (Graph method) edge_iterator() (Graph method) edge_open_binary() (Graph method) edge_propagate() (Graph method) edge_properties (Graph property) edge_properties() (Graph method) edge_property() (Graph method), [1] edge_property_map() (Graph method) edge_property_map_from_python() (in module ClearMap.Analysis.graphs.type_conversions) edge_property_map_to_python() (in module ClearMap.Analysis.graphs.type_conversions) edge_radii() (GeometricGraph method) (Graph method) edge_radii_from_vertex_radii() (GeometricGraph method) edge_radii_um() (Graph method) edge_radii_voxels() (Graph method) edge_source_label() (Graph method) edge_target_label() (Graph method) edge_to_vertex_label() (Graph method) edge_to_vertex_label_or() (Graph method) edge_to_vertex_property() (in module ClearMap.Analysis.vasculature.vasc_graph_utils) edge_vectors() (GeometricGraph method) edges (Graph property), [1] edges_to_vertices() (in module ClearMap.Analysis.graphs.utils) edit() (in module ClearMap.IO.IO) (in module ClearMap.IO.MMP) edit_workspace_folders() (SampleInfoTab method) EditingFinishedFilter (class in ClearMap.gui.params_interfaces) effect_size (LoadedPValueResults attribute) effect_size_path() (GroupResultsAssets method) eigensystem() (in module ClearMap.ImageProcessing.Differentiation.HessianCode) eigenvalues() (in module ClearMap.ImageProcessing.Differentiation.HessianCode) elapsed_time() (Timer method) elastix_binary (in module ClearMap.Alignment.Elastix) elastix_lib (in module ClearMap.Alignment.Elastix) ElastixConfigPatcher (class in ClearMap.Alignment.Elastix) ElastixEntry (class in ClearMap.IO.elastix_config) ElastixParser (class in ClearMap.IO.elastix_config) ElastixPointFileManager (class in ClearMap.Alignment.landmarks_registration.engine) ElastixTransformation (class in ClearMap.Alignment.Elastix) element_strides (Slice property) (Source property), [1], [2], [3], [4], [5] (VirtualSource property) element_strides() (in module ClearMap.IO.IO) elevation (ArbitraryRotationCamera property) embedding() (in module ClearMap.Alignment.Stitching.stitching_rigid) (Layout method) empty() (in module ClearMap.IO.SMA) (in module ClearMap.ParallelProcessing.SharedMemoryArray) enable_mouse_clicks() (DataViewer method) enable_widgets() (WizardWidget static method) enabled (PipelineStep attribute) (Tracer attribute) enabled_steps (LinearPipeline property) encode() (VesselFillingNetwork method) end_hydration() (GuiController method) enhance_contrast() (in module ClearMap.ImageProcessing.Filter.Rank) (in module ClearMap.ImageProcessing.Filter.Rank.PercentileCode) (in module ClearMap.ImageProcessing.Filter.Rank.Rank) (in module ClearMap.ImageProcessing.Filter.Rank.RankCode) enhance_contrast_masked() (in module ClearMap.ImageProcessing.Filter.Rank.PercentileCode) (in module ClearMap.ImageProcessing.Filter.Rank.RankCode) enhance_contrast_percentile() (in module ClearMap.ImageProcessing.Filter.Rank) (in module ClearMap.ImageProcessing.Filter.Rank.Percentile) enrich_df() (Annotation method) ensure() (in module ClearMap.Utils.Formatting) ensure_channel_param() (SampleParameters method) ensure_compound_box_patched() (in module ClearMap.gui.widget_monkeypatch_callbacks) ensure_config_present() (ExperimentController method) ensure_inline_histogram() (in module ClearMap.gui.widgets) ensure_itk_warmed() (in module ClearMap.Alignment.landmarks_registration.registration_data) ensure_list() (VectorLink method) ensure_path_dict() (in module ClearMap.config.config_adjusters.dict_ops) ensure_present() (ConfigCoordinator method) (ConfigRepository method) ensure_qapp() (in module ClearMap.gui.gui_utils_base) ensure_required_static_blocks() (in module ClearMap.config.config_adjusters.policy) ENSURE_STATIC_BLOCKS (Step attribute) ensure_user_file() (DefaultsProvider method) entropy() (in module ClearMap.ImageProcessing.Filter.Rank) (in module ClearMap.ImageProcessing.Filter.Rank.Rank) (in module ClearMap.ImageProcessing.Filter.Rank.RankCode) entropy_masked() (in module ClearMap.ImageProcessing.Filter.Rank.RankCode) entry_point() (in module ClearMap.gui.app) entry_template() (ExperimentTemplatesResolver method) EnvFileManager (class in ClearMap.Utils.install_utils) equalize() (in module ClearMap.ImageProcessing.Experts.Cells) (in module ClearMap.ImageProcessing.Experts.Vasculature) (in module ClearMap.ImageProcessing.Filter.Rank) (in module ClearMap.ImageProcessing.Filter.Rank.Rank) (in module ClearMap.ImageProcessing.Filter.Rank.RankCode) equalize_masked() (in module ClearMap.ImageProcessing.Filter.Rank.RankCode) equals_disabled_value() (VectorLink method) escape_glob() (in module ClearMap.Utils.tag_expression) escapes (PatternInverter attribute) estimate_q_values() (in module ClearMap.Analysis.Statistics.MultipleComparisonCorrection) EventBus (class in ClearMap.Utils.event_bus) eventFilter() (DataViewer method) (EditingFinishedFilter method) ExceptionDialog (class in ClearMap.gui.exception_handler) excluded_roots() (ContainerSpecRegistry method) exec() (WizardWidget method) existing_steps (ProcessorSteps property) exists() (Source method) (Workspace method) exists_any() (ConfigRepository method) exp_controller (ExperimentTab property) exp_dir (ExperimentController property) (WorkspaceChanged attribute) expand() (ExperimentTemplatesResolver method) (in module ClearMap.Utils.HierarchicalDict) expand_edge_geometry() (GeometricGraph method) expand_graph() (in module ClearMap.Analysis.graphs.graph_processing) expand_graph_length() (in module ClearMap.Analysis.graphs.graph_processing) expand_vertex_filter() (Graph method) EXPERIMENT (AdjusterScope attribute) (AppMode attribute) (Scope attribute) ExperimentConfigConverter (class in ClearMap.config.convert_config_versions) ExperimentController (class in ClearMap.pipeline_orchestrators.experiment_controller) ExperimentTab (class in ClearMap.gui.tabs_interfaces) ExperimentTemplatesResolver (class in ClearMap.config.config_adjusters.templates_resolver) ExperimentUpgrade_2_1_to_3_0 (class in ClearMap.config.convert_config_versions) ExperimentUpgrade_3_0_to_3_1 (class in ClearMap.config.convert_config_versions) export_as_csv() (CellDetector method) export_collapsed_stats() (CellDetector method) export_df (ChannelTractMapParams attribute) export_df() (TractMapProcessor method) (TractMapTab method) export_name (ImportTask property) export_to_clearmap1_fmt() (CellDetector method) export_vertex_coordinates() (in module ClearMap.pipeline_orchestrators.degree1_inference_processor) export_vertex_properties() (Graph method) Expression (class in ClearMap.Utils.tag_expression) expression (Source property) (VirtualSource property) expression() (Workspace method) expression_to_glob() (in module ClearMap.Utils.RegularExpression) expression_to_pattern() (in module ClearMap.Utils.RegularExpression) extend_params_dict() (UiParameter method) ExtendableTabWidget (class in ClearMap.gui.widgets) extended_max() (in module ClearMap.Analysis.Measurements.maxima_detection) extension (ChannelPatternSpec attribute) (SampleChannelParameters attribute) extension() (Workspace method) extent (Region property) external_path (in module ClearMap.Settings) extract_annotated_region() (in module ClearMap.Analysis.vasculature.vasc_graph_utils) extract_changed_channel_names() (in module ClearMap.config.change_detection) extract_channel_number() (in module ClearMap.IO.metadata) extract_coordinates (ChannelTractMapParams attribute) extract_coordinates() (TractMapTab method) extract_neighbourhood() (in module ClearMap.ImageProcessing.Topology.Topology2d) (in module ClearMap.ImageProcessing.Topology.Topology3d) extractNeighbourhood() (in module ClearMap.ImageProcessing.Tracing.Connect) extrapolate_1d() (in module ClearMap.Analysis.Curves.Extrapolation) extrapolate_from_interpolator_1d() (in module ClearMap.Analysis.Curves.Extrapolation) F f_min() (in module ClearMap.Analysis.vasculature.geometry_utils) FATAL (Severity attribute) file_exists() (ClearMapAppBase method) file_extension() (in module ClearMap.IO.FileUtils) file_list (Source property) (VirtualSource property) file_list() (in module ClearMap.IO.IO) (Workspace method) file_list_to_df() (PatternFinder static method) file_name() (in module ClearMap.IO.Workspace) (Workspace method) file_type() (in module ClearMap.IO.Workspace) file_type_synonyms (Workspace property) file_type_to_directory_type (Workspace property) FileDropListWidget (class in ClearMap.gui.widgets) filename (ConfigProxy attribute) (in module ClearMap.ImageProcessing.Skeletonization.PK12) filename() (OrchestratorBase method) (Workspace method) filename_non_removable (in module ClearMap.ImageProcessing.Skeletonization.PK12) filename_to_module() (in module ClearMap.IO.IO) fileno() (Printer method) FilePath (class in ClearMap.Utils.utilities) fill() (in module ClearMap.ImageProcessing.Binary.Filling) (in module ClearMap.ImageProcessing.Binary.FillingCode) fill_channel() (BinaryVesselProcessor method) fill_combined (SharedVesselBinarizationParams attribute) FILL_MISSING_ONLY (ReconcileMode attribute) fill_vessels() (in module ClearMap.ImageProcessing.machine_learning.vessel_filling.vessel_filling) filled (BinaryVesselProcessorSteps attribute) filter_alignments() (in module ClearMap.Alignment.Stitching.stitching_rigid) filter_cells (ChannelCellMapParams attribute) filter_cells() (CellCounterTab method) (CellDetector method) (in module ClearMap.ImageProcessing.Experts.Cells) filter_df() (in module ClearMap.Analysis.Statistics.data_frame_operations) filter_graph_degrees() (in module ClearMap.Analysis.vasculature.vasc_graph_utils) filter_kernel() (in module ClearMap.ImageProcessing.Filter.FilterKernel) filter_kernel_2d() (in module ClearMap.ImageProcessing.Filter.FilterKernel) filter_kernel_3d() (in module ClearMap.ImageProcessing.Filter.FilterKernel) filter_table() (ColocalizationProcessor method) filter_type (GraphFilterParams property) filter_valid_vertices() (PatchDataset method) filtersChanged (GraphFilterList attribute) final (BinaryVesselProcessorSteps attribute) final_min_vein_radius (VesselGraphParams attribute) final_vein_radius (ClassificationConfig attribute) finalise() (Percentile method) (TwoPhaseReducer method) finalise_set_params() (GenericTab method) finalise_setup() (ColocalizationProcessor method) finalise_workers_setup() (GenericTab method) finalize_processing() (in module ClearMap.ParallelProcessing.DataProcessing.ArrayProcessing) find() (Annotation method) find_analysable_channels() (DensityGroupAnalysisOrchestrator method) find_available_density_suffixes() (DensityGroupAnalysisOrchestrator method) find_center_of_maxima() (in module ClearMap.Analysis.Measurements.maxima_detection) find_chains() (in module ClearMap.Analysis.graphs.graph_processing) find_child_by_name() (ClearMapAppBase method) find_degree2_branches() (in module ClearMap.Analysis.graphs.fast_graph_reduce) find_intensity() (in module ClearMap.Analysis.Measurements.shape_detection) find_maxima() (in module ClearMap.Analysis.Measurements.maxima_detection) find_parent_layout() (in module ClearMap.gui.gui_utils_base) find_size() (in module ClearMap.Analysis.Measurements.shape_detection) find_smaller_than_fraction() (in module ClearMap.ParallelProcessing.DataProcessing.MeasurePointList) (in module ClearMap.ParallelProcessing.DataProcessing.MeasurePointListCode) find_smaller_than_value() (in module ClearMap.ParallelProcessing.DataProcessing.MeasurePointList) (in module ClearMap.ParallelProcessing.DataProcessing.MeasurePointListCode) find_smaller_than_values() (in module ClearMap.ParallelProcessing.DataProcessing.MeasurePointList) (in module ClearMap.ParallelProcessing.DataProcessing.MeasurePointListCode) findEndpoints() (in module ClearMap.ImageProcessing.Tracing.Connect) finish() (ProgressWatcher method) finished (ProgressWatcher attribute) first_boot() (in module ClearMap.config.early_boot) first_edge() (Graph method) first_run (BootResult attribute) first_vertex() (Graph method) fit_for_pressureBC() (in module ClearMap.Analysis.vasculature.flow.assign_p_bc) fix_btn_boxes_text() (in module ClearMap.gui.widget_monkeypatch_callbacks) fix_btns_stylesheet() (ClearMapAppBase method) fix_df_column_names() (in module ClearMap.Analysis.Statistics.data_frame_operations) fix_isolated() (in module ClearMap.Alignment.Stitching.stitching_wobbly) (WobblySource method) fix_sizes() (ClearMapAppBase method) fix_stray_underscore() (ExperimentUpgrade_2_1_to_3_0 static method) fix_styles() (ClearMapAppBase method) fix_tooltips_stylesheet() (ClearMapAppBase method) fix_unaligned() (in module ClearMap.Alignment.Stitching.stitching_wobbly) (WobblyAlignment method) fix_widgets_backgrounds() (ClearMapAppBase method) FIXED (WobblyAlignment attribute) (WobblySource attribute) fixed_image (RegistrationData attribute) fixed_points (RegistrationData attribute) flags (Verbose attribute) flatfield_from_line() (in module ClearMap.ImageProcessing.IlluminationCorrection) flatfield_line_from_regression() (in module ClearMap.ImageProcessing.IlluminationCorrection) flatten() (in module ClearMap.Utils.HierarchicalDict) flatten_list() (in module ClearMap.config.config_handler) FlowList (class in ClearMap.config.config_handler) flush() (Printer method) fn (AdjusterSpec attribute) fold_sample_stats_dataframe() (in module ClearMap.Visualization.Matplotlib.PlotUtils) folder (UiBatchResultsFolderChanged attribute) font_size (PreferencesParams attribute) for_section() (ContainerSpecRegistry method) format() (ColorFormatter method) format_expression() (in module ClearMap.Utils.RegularExpression) format_long_nb() (in module ClearMap.gui.gui_utils_base) format_orientation() (in module ClearMap.Alignment.orientation) format_time() (Timer method) formatted_coords() (Landmark method) forward() (DeSepConv3d method) (Swin3DModel method) (VesselFillingNetwork method) fractions (ClassificationMetrics attribute) fragments_removed (ClassificationMetrics attribute) frame_getter() (in module ClearMap.gui.params_interfaces) frame_setter() (in module ClearMap.gui.params_interfaces) free() (in module ClearMap.ParallelProcessing.SharedMemoryManager) from_config() (ClassificationConfig class method) from_dict() (ChannelSpec class method) (Transformation class method) (TransformationBase class method) (TypeSpec class method) from_folder() (ConfigCoordinator class method) from_imports() (ImportTask class method) from_mixed_file_list() (PatternFinder class method) from_string() (CompoundKey class method) from_tuple() (CompoundKey class method) FULL (VesselGraphProcessor.RadiusLevel attribute) full_filename() (Verbose method) func (lazyattr attribute) G GeneralChannelStitchingParams (class in ClearMap.gui.params) generalized_radial_planar_orientation() (in module ClearMap.Analysis.vasculature.general_functions) generate_any() (PatternInverter method) generate_assert() (PatternInverter method) generate_assert_not() (PatternInverter method) generate_at() (PatternInverter method) generate_branch() (PatternInverter method) generate_color_squares() (in module ClearMap.Visualization.Color.orientation_colormap) generate_group() (PatternInverter method) generate_group_ref() (PatternInverter method) generate_in() (PatternInverter method) generate_literal() (PatternInverter method) generate_lookup_table() (in module ClearMap.ImageProcessing.Binary.Smoothing) (in module ClearMap.ImageProcessing.Skeletonization.PK12) generate_max_repeat() (PatternInverter method) generate_min_repeat() (PatternInverter method) generate_negate() (PatternInverter method) generate_not_literal() (PatternInverter method) generate_range() (PatternInverter method) generate_re() (PatternInverter method) generate_re_type() (PatternInverter method) generate_subpattern() (PatternInverter method) generate_summary_table() (in module ClearMap.Analysis.Statistics.group_statistics) GENERIC (ReconcileKind attribute) generic_instance_specs() (ContainerSpecRegistry method) GenericDialog (class in ClearMap.gui.tabs_interfaces) GenericTab (class in ClearMap.gui.tabs_interfaces) GenericUi (class in ClearMap.gui.tabs_interfaces) geometric_mean() (in module ClearMap.ImageProcessing.Filter.Rank) (in module ClearMap.ImageProcessing.Filter.Rank.Rank) (in module ClearMap.ImageProcessing.Filter.Rank.RankCode) geometric_mean_masked() (in module ClearMap.ImageProcessing.Filter.Rank.RankCode) GeometricGraph (class in ClearMap.Analysis.graphs.graph) geometry_settings_from (SampleChannelParameters attribute) get() (ChannelPipelineOrchestrator method) (ChannelsUiParameterCollection method) (CompoundChannelPipelineOrchestrator method) (DefaultsProvider method) (ElastixParser method) (in module ClearMap.ParallelProcessing.SharedMemoryManager) (in module ClearMap.Utils.HierarchicalDict) (MachineConfig method) (OrchestratorBase method) (RegistrationProcessor method) (UiParameter method) (WidgetOps method) get_3d_markers() (Scatter3D method) get_align_with() (RegistrationProcessor method) get_aligned_image() (RegistrationProcessor method) get_alignment_ref_channel_reg_cfg() (OrchestratorBase method) get_all_children_structures_ids() (in module ClearMap.Alignment.utils) (in module ClearMap.Scripts.generate_jsonl_file_ontology) get_all_paths() (BatchParameters method) (GroupsWidgetAdapter method) get_all_region_ids() (in module ClearMap.Alignment.utils) get_alternatives() (ConfigAlternativesRegistry method) get_analysable_channels() (GroupAnalysisTab method) get_args() (in module ClearMap.Scripts.create_distance_file) get_artery_vein_edge_coords_and_vectors() (in module ClearMap.Analysis.vasculature.general_functions) get_asset() (ProcessorSteps method) get_atlas_filepath() (in module ClearMap.Alignment.Annotation) get_atlas_files() (RegistrationProcessor method) get_atlas_paths() (Annotation method) get_best_match_cuda_version() (PytorchVersionManager method) get_caller_name() (in module ClearMap.Utils.exceptions) get_canonical_path() (ConfigHandler method) get_cells_df() (CellDetector method) (ColocalizationProcessor method) get_cfg() (ConfigHandler method) get_cfg_from_path() (ConfigHandler class method) get_cfg_path() (ConfigHandler method) get_cfg_reader_function() (in module ClearMap.config.config_handler) get_channel_indices() (Pattern method) get_channel_name() (RegistrationParams method) (SampleParameters method) get_channel_names() (PatternDialog method) get_channel_resolution() (SampleManager method) get_channel_sections() (ConfigAlternativesRegistry static method) get_channel_ui() (GenericTab method) get_channel_widget() (ExtendableTabWidget method) get_channels_by_condition() (SampleManager method) get_channels_by_pipeline() (SampleManager method) (SampleManagerProtocol method) get_channels_by_type() (SampleManager method) get_channels_names() (ExtendableTabWidget method) get_channels_to_run() (StitchingParams method) get_checked_items() (CheckableListWidget method) get_children() (Annotation method) get_clique_neighbours() (in module ClearMap.Analysis.graphs.graph_processing) get_clique_neighbours_set() (in module ClearMap.Analysis.graphs.graph_processing) get_color_ids() (in module ClearMap.Alignment.Stitching.layout_graph_utils) get_colored_p_vals() (in module ClearMap.Analysis.Statistics.group_statistics) get_colormap() (in module ClearMap.Visualization.Vispy.plot_graph_3d) get_colors_rgba() (Annotation method) get_colours() (Scatter3D method) get_columns() (Annotation method) get_conda_pkg_info() (CondaParser static method) get_config_view() (AnalysisGroupController method) (ConfigCoordinator method) (ExperimentController method) get_configobj_cfg() (in module ClearMap.config.config_handler) get_configs() (in module ClearMap.config.config_handler) (in module ClearMap.config.convert_config_versions) get_connected_components() (in module ClearMap.Alignment.Stitching.layout_graph_utils) get_conversion_steps() (in module ClearMap.config.convert_config_versions) get_coords() (CellDetector method) (DataViewer method) (LandmarksSelectorDialog method) get_cpu_percent() (PerfMonitor method) get_current_res() (in module ClearMap.gui.gui_utils_images) get_current_resolver() (in module ClearMap.config.config_adjusters.templates_resolver) get_default_cfg() (ConfigHandler class method) get_default_config() (DefaultsProvider method) get_default_model_path() (in module ClearMap.ImageProcessing.machine_learning.vertices_classification.degree1_inference_utils) get_default_path() (ConfigHandler class method) get_default_property_value() (GraphFilterParams method) get_defaults_provider() (in module ClearMap.config.defaults_provider) get_dict() (Annotation method) get_dict_children_to_parents() (Annotation method) get_dict_parents_to_children() (Annotation method) get_dictionary() (Annotation method) get_direct_children_structures_ids() (in module ClearMap.Alignment.utils) (in module ClearMap.Scripts.generate_jsonl_file_ontology) get_directory_dlg() (in module ClearMap.gui.dialog_helpers) get_distance_map_27() (in module ClearMap.Analysis.graphs.graph_processing) get_draw_params() (Scatter3D method) get_edge_vectors() (in module ClearMap.Analysis.vasculature.general_functions) get_edge_vectors_spherical() (in module ClearMap.Analysis.vasculature.general_functions) get_edges() (Graph method) get_edges_n_kinds() (in module ClearMap.Analysis.vasculature.vasc_graph_utils) get_elastix_version() (in module ClearMap.Alignment.Elastix) get_elx_asset() (RegistrationProcessor method) get_env_name() (EnvFileManager method) get_filter() (VesselGraphProcessor method) get_fixed_image() (RegistrationProcessor method) get_fixed_moving_channels() (RegistrationProcessor method) get_flattened_structure() (in module ClearMap.Alignment.utils) (in module ClearMap.Scripts.generate_jsonl_file_ontology) get_free_temp_space() (in module ClearMap.Utils.utilities) get_free_v_ram() (in module ClearMap.Utils.utilities) get_global_canonical_path() (ConfigHandler class method) get_global_path() (ConfigHandler class method) get_graph() (in module ClearMap.Alignment.Stitching.layout_graph_utils) get_hierarchical_dictionary() (Annotation method) get_img_to_register() (RegistrationProcessor method) get_indices_and_ranges() (PropertyAggregator method) get_info() (in module ClearMap.IO.IO) get_instance_keys_by_pipeline() (SampleManager method) get_inverse() (TransformationBase method) get_item() (CheckableListWidget method) get_item_recursive() (in module ClearMap.Utils.utilities) get_items_text() (FileDropListWidget method) get_json_cfg() (in module ClearMap.config.config_handler) get_last_output() (BinaryVesselProcessorSteps method) get_lateralised_volume_map() (Annotation method) get_left_elements() (TwoListSelection method) get_list() (Annotation method) get_local_canonical_path() (ConfigHandler method) get_map() (Annotation method) get_map_to_parent() (Annotation method) get_minimum_dtype() (in module ClearMap.Analysis.colocalization.channel) get_moving_channel() (RegistrationProcessor method) get_moving_image() (RegistrationProcessor method) get_n_blocks() (CellDetector method) get_n_detected_cells() (CellDetector method) get_n_filtered_cells() (CellDetector method) get_n_markers() (Scatter3D method) get_names_map() (Annotation method) get_nb_parallel_vessels() (in module ClearMap.Analysis.vasculature.general_functions) get_nb_radial_vessels() (in module ClearMap.Analysis.vasculature.general_functions) get_nested() (in module ClearMap.config.config_adjusters.dict_ops) get_new_cfg_writer() (ConfigHandler class method) get_new_channels() (RenameChannelsDialog method) get_new_color() (LandmarksSelectorDialog method) get_next_steps() (ProcessorSteps method) get_ok_n_ok_symbols() (in module ClearMap.Utils.utilities) get_ome_dict() (in module ClearMap.IO.metadata) get_or_init_sample_id() (ExperimentController method) get_orientation_from_normal_to_surface_global() (in module ClearMap.Analysis.vasculature.general_functions) get_orientation_from_normal_to_surface_local() (in module ClearMap.Analysis.vasculature.general_functions) get_original_sections() (ElastixConfigPatcher method) get_package_version() (EnvFileManager method) get_params_and_weights() (LandmarksWeightsPanel method) get_parent_id() (in module ClearMap.Scripts.generate_jsonl_file_ontology) (in module ClearMap.Visualization.Matplotlib.PlotUtils) get_parent_name() (in module ClearMap.Visualization.Matplotlib.PlotUtils) get_parent_structure() (in module ClearMap.Visualization.Matplotlib.PlotUtils) get_patched_cfg_from_path() (ConfigHandler class method) get_path() (OrchestratorBase method) get_paths() (BatchParameters method) (GroupsWidgetAdapter method) get_patterns() (PatternDialog method) get_percent_v_ram_use() (in module ClearMap.Utils.utilities) get_points() (AlignmentTool method) get_pos() (Scatter3D method) get_positions() (Workspace method) get_positions_from_tree() (in module ClearMap.Alignment.Stitching.layout_graph_utils) get_progress() (ProgressWatcher method) get_prop_from_aba_df() (in module ClearMap.Visualization.Matplotlib.PlotUtils) get_property_value() (GraphFilterParams method) get_pseudo_random_color() (in module ClearMap.gui.gui_utils_images) get_pytorch_cpu_info() (PytorchVersionManager method) get_pytorch_gpu_info() (PytorchVersionManager method) get_ram_percent() (PerfMonitor method) get_random_color() (in module ClearMap.gui.gui_utils_images) get_raw_metadata_dictionary() (Source method) get_reference_streamlines() (in module ClearMap.Analysis.vasculature.general_functions) get_region_volume() (in module ClearMap.Analysis.vasculature.annotation_utils) get_registration_sequence_channels() (CellDetector method) (RegistrationProcessor method) (TractMapProcessor method) (VesselGraphProcessor method) get_results() (PatternDialog method) get_right_elements() (TwoListSelection method) get_sample_manager() (AnalysisGroupController method) get_sample_manager_for() (GroupOrchestratorBase method) get_scaling() (ScalingTransformation method) get_selected_files() (VerifyRenamingDialog method) get_selected_steps_and_channels() (VesselParams method) get_source() (BinaryVesselProcessorSteps method) get_spec() (ConfigAlternativesRegistry method) get_stitchable_channels() (SampleManager method) get_stitching_order() (StitchingProcessor method) get_streamline_aec_path() (in module ClearMap.Analysis.vasculature.general_functions) get_streamline_agv_path() (in module ClearMap.Analysis.vasculature.general_functions) get_structure_colors() (in module ClearMap.Visualization.Matplotlib.PlotUtils) get_structure_path() (in module ClearMap.Alignment.utils) (in module ClearMap.Scripts.generate_jsonl_file_ontology) get_structure_sub_graph() (VesselGraphProcessor method) get_sub_graph() (in module ClearMap.Analysis.vasculature.vasc_graph_utils) get_sub_regions() (in module ClearMap.Analysis.vasculature.annotation_utils) get_sub_type() (TypeSpec method) get_symbol_sizes() (Scatter3D method) get_symbols() (Scatter3D method) get_tab_name() (GenericTab class method) get_tab_widget() (ClearMapApp method) get_template_method() (ExperimentTemplatesResolver method) get_thread_percent() (PerfMonitor method) get_tiles_list_from_sample_folder() (in module ClearMap.IO.metadata) get_toolkit_info() (PytorchVersionManager method) get_toolkit_versions() (PytorchVersionManager method) get_top_to_bottom_dist() (in module ClearMap.Analysis.vasculature.general_functions) get_transformations() (Transformation method) get_user_defaults_canonical_path() (ConfigHandler class method) get_value() (GroupsWidgetAdapter method) (in module ClearMap.IO.IO) get_vertex_coordinates() (in module ClearMap.Analysis.vasculature.vasc_graph_utils) get_vertices_n_kinds() (in module ClearMap.Analysis.vasculature.vasc_graph_utils) get_vessel_length() (in module ClearMap.Analysis.vasculature.vasc_graph_utils) get_view() (in module ClearMap.Visualization.Vispy.Plot3d) get_view_parameter() (in module ClearMap.Visualization.Vispy.Plot3d) get_voxelization_params() (CellDetector method) (ColocalizationProcessor method) get_weights() (LandmarksWeightsPanel method) get_widget() (in module ClearMap.gui.gui_utils_base) get_widgets() (PatternDialog method) get_wobbly_layout() (StitchingProcessor method) get_worker (ExperimentController attribute) get_worker() (AnalysisGroupController method) (ExperimentController method) (PostProcessingTab method) get_worker_for_sample() (GroupOrchestratorBase method) get_workers() (ExperimentController method) get_yml_cfg() (in module ClearMap.config.config_handler) getValue() (LandmarksWeightsPanel method) getXYAxes() (DataViewer method) glob() (Expression method) glob_pattern() (Expression method) (Tag method) glob_to_expression() (in module ClearMap.Utils.RegularExpression) GLOBAL (Scope attribute) global_cfg_converter() (in module ClearMap.config.convert_config_versions) global_score() (in module ClearMap.gui.tab_registry) go_to_orientation() (SampleInfoTab method) gp1 (PairKey attribute) gp1_avg (LoadedPValueResults attribute) gp1_imgs (LoadedPValueResults property) gp1_sd (LoadedPValueResults attribute) gp2 (PairKey attribute) gp2_avg (LoadedPValueResults attribute) gp2_imgs (LoadedPValueResults property) gp2_sd (LoadedPValueResults attribute) gp_stats_df_to_counts() (in module ClearMap.Visualization.Matplotlib.PlotUtils) gpu_info() (in module ClearMap.ImageProcessing.machine_learning.torch_utils) gpu_params() (in module ClearMap.Utils.utilities) gpu_util() (in module ClearMap.Utils.utilities) gpu_vals_changed (PerfMonitor attribute) gradient() (in module ClearMap.ImageProcessing.Differentiation) (in module ClearMap.ImageProcessing.Differentiation.Gradient) (in module ClearMap.ImageProcessing.Filter.Rank) (in module ClearMap.ImageProcessing.Filter.Rank.PercentileCode) (in module ClearMap.ImageProcessing.Filter.Rank.Rank) (in module ClearMap.ImageProcessing.Filter.Rank.RankCode) gradient_abs() (in module ClearMap.ImageProcessing.Differentiation) (in module ClearMap.ImageProcessing.Differentiation.Gradient) gradient_masked() (in module ClearMap.ImageProcessing.Filter.Rank.PercentileCode) (in module ClearMap.ImageProcessing.Filter.Rank.RankCode) gradient_percentile() (in module ClearMap.ImageProcessing.Filter.Rank) (in module ClearMap.ImageProcessing.Filter.Rank.Percentile) gradient_square() (in module ClearMap.ImageProcessing.Differentiation) (in module ClearMap.ImageProcessing.Differentiation.Gradient) Graph (class in ClearMap.Analysis.graphs.graph) (class in ClearMap.Analysis.graphs.graph_gt) graph (Source property) (VirtualSource property) graph_annotated (VesselGraphProcessor property) (VesselGraphProcessorSteps attribute) graph_by_name() (ClearMapAppBase method) graph_cleaned (VesselGraphProcessor property) (VesselGraphProcessorSteps attribute) graph_from_skeleton() (in module ClearMap.Analysis.graphs.graph_processing) graph_gt_to_igraph() (in module ClearMap.Analysis.vasculature.vasc_graph_utils) graph_properties (Graph property) graph_property() (Graph method) graph_property_map() (Graph method) graph_raw (VesselGraphProcessor property) (VesselGraphProcessorSteps attribute) graph_reduced (VesselGraphProcessor property) (VesselGraphProcessorSteps attribute) graph_step (VesselVisualizationParams attribute) graph_to_connected_components() (in module ClearMap.Alignment.Stitching.layout_graph_utils) graph_to_edge_coords_and_vectors() (in module ClearMap.Analysis.vasculature.general_functions) graph_to_skeleton() (in module ClearMap.Analysis.graphs.graph_processing) graph_traced (VesselGraphProcessor property) GraphFilter (class in ClearMap.Analysis.graphs.graph_filters) GraphFilterList (class in ClearMap.gui.widgets) GraphFilterParams (class in ClearMap.gui.params) GraphLineVisual (class in ClearMap.Visualization.Vispy.graph_visual) GraphMeshVisual (class in ClearMap.Visualization.Vispy.graph_visual) GraphSphereVisual (class in ClearMap.Visualization.Vispy.graph_visual) gray_image_to_rgb() (in module ClearMap.Visualization.Color.Color) grays_alpha() (in module ClearMap.Visualization.Vispy.Plot3d) GREEN (ColorFormatter attribute) grey_reconstruct() (in module ClearMap.ImageProcessing.grey_reconstruction) GROUP (AdjusterScope attribute) (AppMode attribute) (Scope attribute) group_base_dir (AdjustmentContext attribute) (AnalysisGroupController property) group_cfg_coordinator (AnalysisGroupController property) group_controller (GroupTab attribute) group_count() (GroupsWidgetAdapter method) group_counts() (in module ClearMap.Analysis.Statistics.data_frame_operations) group_dict() (in module ClearMap.Utils.RegularExpression) group_names (BatchParameters property) (ComparisonsModel attribute) (GroupsWidgetAdapter property) group_names() (in module ClearMap.Utils.RegularExpression) group_region_counts() (in module ClearMap.Analysis.Statistics.group_statistics) GroupAnalysisParams (class in ClearMap.gui.params) GroupAnalysisTab (class in ClearMap.gui.tabs) GroupOrchestratorBase (class in ClearMap.pipeline_orchestrators.generic_orchestrators) GroupPage (class in ClearMap.gui.widgets) GroupResultsAssets (class in ClearMap.Analysis.Statistics.group_assets) groups (AnalysisGroupController property) (BatchParameters attribute) (GroupOrchestratorBase property) (UiBatchGroupsChanged attribute) GroupStatsError GroupsWidgetAdapter (class in ClearMap.gui.widgets) GroupTab (class in ClearMap.gui.tabs_interfaces) GroupTemplatesResolver (class in ClearMap.config.config_adjusters.templates_resolver) gtype_from_source() (in module ClearMap.Analysis.graphs.type_conversions) GuiController (class in ClearMap.gui.app) H h_max (ChannelCellMapParams attribute) h_max_transform() (in module ClearMap.Analysis.Measurements.maxima_detection) handle_advanced_checked() (GenericTab method) handle_advanced_state_changed() (ChannelCellMapParams method) (UiParameterCollection method) handle_align_with_changed() (RegistrationTab method) handle_atlas_resolution_changed() (AtlasParams method) handle_channel_rename_request() (SampleParameters method) handle_colocalization_compatible_changed() (ChannelCellMapParams method) handle_deprecated_args() (in module ClearMap.Utils.utilities) handle_exception() (in module ClearMap.gui.exception_handler) handle_fig_fate() (in module ClearMap.Visualization.Matplotlib.PlotUtils) handle_gpu_vals_updated() (PerfMonitor method) handle_groups_changed() (GroupAnalysisTab method) handle_landmarks_weight_changed() (ChannelRegistrationParams method) handle_layout_channel_changed() (ChannelStitchingParams method) (StitchingParams method) handle_name_changed() (SampleChannelParameters method) handle_orientation_changed() (SampleChannelParameters method) handle_params_files_changed() (ChannelRegistrationParams method) handle_proc_changed() (PerfMonitor method) handle_property_name_changed() (GraphFilterParams method) handle_selection_changed() (ManageAssetsWidget method) handle_step_name_change() (ClearMapAppBase method) handle_sub_step_change() (ClearMapAppBase method) handle_tab_bar_click() (ExtendableTabWidget method) handle_tab_click() (ClearMapApp method) handle_tool_tab_changed() (CellCounterTab method) handle_use_existing_layout_changed() (ChannelStitchingParams method) handle_widget_changed() (UiParameter method) handleMouseClick() (DataViewer method) has_attrs (ImportTask property) has_colours (Scatter3D property) has_connect_function() (ParamLink method) has_edge_coordinates (Graph property) has_edge_geometry (GeometricGraph property) has_edge_geometry() (Graph method) has_edge_property() (Graph method) has_edge_radii (Graph property) has_edge_radii_um (Graph property) has_effect (LoadedPValueResults property) has_flag() (Verbose method) has_global_toggle (VectorLink property) has_graph_property() (Graph method) has_hemispheres (Scatter3D property) has_item_recursive() (in module ClearMap.Utils.utilities) has_npy() (SampleManager method) has_pipeline() (ChannelSpec method) has_sd (LoadedPValueResults property) has_tiles() (SampleManager method) has_vertex_coordinates (Graph property) has_vertex_property() (Graph method) has_vertex_radii (Graph property) HasSlicingFields (class in ClearMap.gui.params_mixins) head (Timer attribute) header_from_source() (in module ClearMap.IO.MHD) header_size() (in module ClearMap.IO.MMP) height (OrthoViewer property) (WobblySource property) hessian() (in module ClearMap.ImageProcessing.Differentiation) (in module ClearMap.ImageProcessing.Differentiation.Hessian) (in module ClearMap.ImageProcessing.Differentiation.HessianCode) hessian_eigensystem() (in module ClearMap.ImageProcessing.Differentiation) (in module ClearMap.ImageProcessing.Differentiation.Hessian) hessian_eigenvalues() (in module ClearMap.ImageProcessing.Differentiation) (in module ClearMap.ImageProcessing.Differentiation.Hessian) hex_to_rgb() (in module ClearMap.Visualization.Color.Color) hide_widgets() (WizardWidget static method) highlight_digits() (Pattern method) HighLowLUT (class in ClearMap.Visualization.Qt.data_viewer_luts) histogram() (in module ClearMap.ImageProcessing.Filter.Rank) (in module ClearMap.ImageProcessing.Filter.Rank.Rank) (in module ClearMap.ImageProcessing.Filter.Rank.RankCode) histogram_masked() (in module ClearMap.ImageProcessing.Filter.Rank.RankCode) html_to_ansi() (in module ClearMap.gui.gui_utils_base) html_to_plain_text() (in module ClearMap.gui.gui_utils_base) hydrating (ExperimentController property) (GuiController property) I icosphere() (in module ClearMap.Visualization.Mesh.IcoSphere) id (Label property) (Slice property) (Source property) identifier (Slice property) (Source property) identity_fn() (in module ClearMap.config.config_adjusters.type_hints) identity_op() (in module ClearMap.gui.params_interfaces) ids_to_acronyms() (Annotation method) ids_to_names() (Annotation method) idx_width_for_N() (in module ClearMap.Analysis.graphs.utils) ilastik_path (in module ClearMap.Settings) imageChanged() (LUTItem method) imagej_path (in module ClearMap.Settings) ImageJMetadataParser (class in ClearMap.IO.TIF) images (PlotPanel attribute) img_custom_attrs (OMEMetadataParser property) immediate_shutdown() (CancelableProcessPoolExecutor method) ImportTask (class in ClearMap.gui.pretty_imports) in_categories (PatternInverter attribute) IncompatibleSource increment() (ProgressWatcher method) increment_main_progress() (ProgressWatcher method) index (Block property) index() (Tag method) index_from_binary() (in module ClearMap.ImageProcessing.Topology.Topology3d) index_kernel() (in module ClearMap.ImageProcessing.Topology.Topology3d) index_label_correspondence (Channel property) index_neighbours() (in module ClearMap.ParallelProcessing.DataProcessing.ArrayProcessing) index_to_physical() (ITKImage method) index_to_physical_matrix (ITKImage property) index_to_physical_matrix() (in module ClearMap.Alignment.landmarks_registration.registration_data) index_to_physical_pair (ITKImage property) index_to_smoothing() (in module ClearMap.ImageProcessing.Binary.Smoothing) indices() (Expression method) infer_channel_index_from_name() (SampleManager method) infer_origin_from_caller() (in module ClearMap.Utils.utilities) infer_required_sections() (AnalysisGroupController method) info() (Block method) (Graph method) (Label method) (Source method) (Workspace method) init_sample_manager_and_processors() (in module ClearMap.pipeline_orchestrators.utils) inited (GenericTab attribute) initial_threshold (ClassificationConfig property) initialised (BatchTab property) initialize() (Annotation method) (in module ClearMap.IO.IO) initialize_buffer() (in module ClearMap.IO.IO) initialize_elastix() (in module ClearMap.Alignment.Elastix) initialize_lookup_table() (in module ClearMap.ImageProcessing.Binary.Smoothing) (in module ClearMap.ImageProcessing.Skeletonization.PK12) initialize_points_item() (DataViewer method) initialize_processing() (in module ClearMap.ParallelProcessing.DataProcessing.ArrayProcessing) initialize_sink() (in module ClearMap.ParallelProcessing.DataProcessing.ArrayProcessing) initialize_sinks() (in module ClearMap.ImageProcessing.Experts.utils) initialize_source() (in module ClearMap.ParallelProcessing.DataProcessing.ArrayProcessing) initialize_tree() (Annotation method) initialize_vectors_item() (DataViewer method) initialize_view() (in module ClearMap.Visualization.Vispy.Plot3d) initialized (in module ClearMap.Alignment.Elastix) initializeSources() (DataViewer method) inject_image_content_types() (in module ClearMap.config.validators.json_schema_utils) inject_sm_view() (in module ClearMap.config.config_adjusters.engine) input_dialog() (in module ClearMap.gui.dialog_helpers) insert() (in module ClearMap.ParallelProcessing.SharedMemoryManager) insert_group_names() (in module ClearMap.Utils.RegularExpression) inspect_align_layout() (in module ClearMap.Alignment.Stitching.stitching_wobbly) install_global_handler() (in module ClearMap.gui.exception_handler) instance_kind (Membership attribute) INSTANCE_OWNER (AdjusterKind attribute) instance_roots() (ContainerSpecRegistry method) INSTANCE_RUNTIME (ContainerRole attribute) InstanceContainerSpec (class in ClearMap.config.config_adjusters.policy_specs) InstancePolicy (class in ClearMap.config.config_adjusters.policy_specs) intensities_to_percentiles() (TractMapProcessor method) (TractMapTab method) interpolate_edge_geometry() (in module ClearMap.Analysis.graphs.graph_rendering) interpolate_vectors() (in module ClearMap.Analysis.vasculature.geometry_utils) INVALID (WobblyAlignment attribute) (WobblySource attribute) Invariants (ExperimentController attribute) inverse_transform() (in module ClearMap.Alignment.Elastix) invert() (in module ClearMap.gui.params_interfaces) invert_orientation() (in module ClearMap.Alignment.orientation) is_all_scalars() (in module ClearMap.config.config_handler) is_clearmap (Source property) is_colocalization_compatible (SampleManager property) (SampleManagerProtocol property) is_color() (DataViewer method) is_compatible() (Percentile method) (TwoPhaseReducer method) is_compound() (ChannelSpec method) is_compound_box() (in module ClearMap.gui.widget_monkeypatch_callbacks) is_csv() (in module ClearMap.IO.CSV) is_dark() (in module ClearMap.gui.gui_utils_images) is_default (RecoveryOption attribute) is_defined() (GraphFilter method) is_destructive (RecoveryOption attribute) is_directory() (in module ClearMap.IO.FileUtils) is_edge_geometry_consistent() (Graph method) is_expression() (Expression static method) (in module ClearMap.Utils.RegularExpression) (TypeSpec method) is_file() (in module ClearMap.IO.FileUtils) is_file_list() (in module ClearMap.IO.FileList) is_folder (TypeSpec property) is_global() (ConfigHandler static method) is_global_cfg() (ConfigAlternativesRegistry method) is_gp_stats_df() (in module ClearMap.Visualization.Matplotlib.PlotUtils) is_graph() (in module ClearMap.IO.GT) is_headless() (in module ClearMap.gui.gui_utils_base) is_in_range() (in module ClearMap.Utils.utilities) is_iterable() (in module ClearMap.Utils.utilities) is_legacy_cfg() (ConfigAlternativesRegistry method) is_list_box() (in module ClearMap.gui.widget_monkeypatch_callbacks) is_local() (ConfigHandler static method) is_local_file() (ConfigAlternativesRegistry method) is_memmap() (in module ClearMap.IO.MMP) is_mhd() (in module ClearMap.IO.MHD) is_nrrd() (in module ClearMap.IO.NRRD) is_numpy() (in module ClearMap.IO.NPY) is_optional_box() (in module ClearMap.gui.widget_monkeypatch_callbacks) is_persistable (Source property) is_relevant() (ParamLink method) is_set() (Landmark method) is_simple_attr() (UiParameter method) is_simple_channel() (ChannelSpec method) is_source() (in module ClearMap.IO.IO) is_tif() (in module ClearMap.IO.TIF) is_tiled() (SampleManager method) is_trivial() (in module ClearMap.IO.Slice) is_under() (in module ClearMap.config.config_adjusters.dict_ops) is_valid() (WobblySource method) is_valid_hex_color() (in module ClearMap.Visualization.Qt.widgets) is_valid_key_str() (CompoundKey class method) is_view (Graph property) is_view() (in module ClearMap.IO.Slice) is_writable (Source property) isChecked() (Landmark method) isodata_grid_sliding_xy() (in module ClearMap.ImageProcessing.local_threshold_isodata) ISOLATED (WobblySource attribute) items() (ChannelsUiParameterCollection method) itemsChanged (FileDropListWidget attribute) itemSelectionChanged (TwoListSelection attribute) iter_patch_items() (in module ClearMap.config.config_adjusters.patch_ops) iteration (Block property) iteration_info() (Block method) ITKImage (class in ClearMap.Alignment.landmarks_registration.registration_data) ix (TileRecord attribute) iy (TileRecord attribute) J join() (in module ClearMap.IO.FileUtils) (in module ClearMap.Utils.HierarchicalDict) join_neighbouring_degrees_1() (in module ClearMap.Analysis.vasculature.graph_corrections) K keep (in module ClearMap.ImageProcessing.Skeletonization.PK12) keep_changed (StepChip attribute) keep_intermediate (PipelineStep attribute) keep_intermediate_changed (LinearPipelineWidget attribute) keep_templates_out_of_working_config (BindPolicy attribute) key (ImportTask property) (TabActivationResult attribute) (UiTabActivated attribute) keys (ParamLink attribute), [1] keys() (ChannelsUiParameterCollection method) (Membership method) kind (AdjusterSpec attribute) (ReconcileStepSpec attribute) known_contexts (StateManager attribute) L Label (class in ClearMap.Alignment.Annotation) label (RecoveryOption attribute) (StepSpec attribute) label() (Tag method) (TractMapProcessor method) label_components() (Graph method) label_coordinates (ChannelTractMapParams attribute) label_coordinates() (TractMapTab method) label_index_correspondence (Channel property) label_points() (Annotation method) label_points_hemispheres() (Annotation method) label_points_wrapper() (in module ClearMap.pipeline_orchestrators.tract_map) label_re (TractMapProcessor attribute) label_representatives() (in module ClearMap.Analysis.Measurements.maxima_detection) label_temp() (in module ClearMap.ImageProcessing.Binary.FillingCode) label_to_color() (Annotation method) labeled_pixels_from_centers() (in module ClearMap.Analysis.Measurements.shape_detection) labels() (Channel method) lambda123() (in module ClearMap.ImageProcessing.Differentiation) (in module ClearMap.ImageProcessing.Differentiation.Hessian) (in module ClearMap.ImageProcessing.Differentiation.HessianCode) lambda123_threshold() (in module ClearMap.ImageProcessing.Differentiation.HessianCode) Landmark (class in ClearMap.gui.widgets) landmark_selector (RegistrationTab attribute) LandmarksSelectorDialog (class in ClearMap.gui.widgets) LandmarksWeightsPanel (class in ClearMap.gui.widgets) largest_component() (Graph method) last_real_tab_idx (ExtendableTabWidget property) last_step (ProcessorSteps property) launch_landmarks_dialog() (RegistrationTab method) launch_pattern_wizard() (SampleInfoTab method) launch_processor() (ExperimentController method) Layout (class in ClearMap.Alignment.Stitching.stitching_rigid) layout_along_axis_mip() (in module ClearMap.Alignment.Stitching.stitching_plots) layout_channel (GeneralChannelStitchingParams attribute) (UiLayoutChannelChanged attribute) layout_coloring() (in module ClearMap.Alignment.Stitching.stitching_plots) layout_from_region() (Layout method) LayoutPlotMixin (class in ClearMap.Alignment.Stitching.stitching_plots) layouts_along_axis_wobbly() (WobblyLayout method) lazy_mixin() (in module ClearMap.Utils.Lazy) lazyattr (class in ClearMap.Utils.Lazy) level (Label property) light_channelish_smells (SmellScanPolicy attribute) LIGHT_COLOR (StructurePickerWidget attribute) light_sheet_artifact_correction() (in module ClearMap.ImageProcessing.Filter.Rank) (in module ClearMap.ImageProcessing.Filter.Rank.Parametric) lighter() (in module ClearMap.Visualization.Color.Color) line_edit_getter() (in module ClearMap.gui.params_interfaces) LinearPipeline (class in ClearMap.gui.pipeline_model) LinearPipelineWidget (class in ClearMap.gui.pipeline_widgets) LinearSystem (class in ClearMap.Analysis.vasculature.flow.linear_system) link_dataviewers_cursors() (in module ClearMap.Visualization.Qt.utils) list_line_plot_3d() (in module ClearMap.Visualization.Vispy.Plot3d) list_plot_3d() (in module ClearMap.Visualization.Vispy.Plot3d) list_sections() (ConfigRepository method) list_valid_weighing_columns() (CellDetector method) list_widget_getter() (in module ClearMap.gui.params_interfaces) list_widget_setter() (in module ClearMap.gui.params_interfaces) load() (ConfigCoordinator method) (ConfigRepository method) (Graph class method) (Graph method) (in module ClearMap.Analysis.graphs.graph) (in module ClearMap.Analysis.graphs.graph_gt) (Layout method) (Workspace method) load_all() (ConfigCoordinator method) (ConfigRepository method) load_data() (in module ClearMap.ImageProcessing.machine_learning.vessel_filling.vessel_filling) load_graph() (in module ClearMap.Analysis.vasculature.general_functions) load_layout() (in module ClearMap.Alignment.Stitching.stitching_rigid) load_model() (in module ClearMap.ImageProcessing.machine_learning.vertices_classification.degree1_inference_utils) load_p_val_results() (GroupResultsAssets method) load_sample() (ClearMapApp method) load_yaml_schema() (in module ClearMap.config.validators.json_schema_utils) LoadedPValueResults (class in ClearMap.Analysis.Statistics.group_statistics) loader_functions (ConfigHandler attribute) loadUiType() (in module ClearMap.gui.pyuic_utils) local_histogram() (in module ClearMap.ImageProcessing.LocalStatistics) local_max() (in module ClearMap.Analysis.Measurements.maxima_detection) local_percentile() (in module ClearMap.ImageProcessing.LocalStatistics) local_report() (in module ClearMap.Analysis.colocalization.parallelism) local_report_body() (in module ClearMap.Analysis.colocalization.parallelism) local_slicing() (Region method) location (AbstractSource property) (Layout property) (Slice property) (Source property), [1], [2], [3], [4], [5], [6], [7] location() (in module ClearMap.IO.IO) location_to_module() (in module ClearMap.IO.IO) locked (PipelineStep attribute) log_progress() (ClearMapAppBase method) lower (Layout property) (Region property) (Slice property) lower_coordinate (WobblyAlignment property) lower_to_origin() (Layout method) lower_wobbly (WobblyLayout property) (WobblySource property) lsac() (in module ClearMap.ImageProcessing.Filter.Rank.ParametricCode) lsac_masked() (in module ClearMap.ImageProcessing.Filter.Rank.ParametricCode) LUT (class in ClearMap.Visualization.Qt.data_viewer_luts) lut (PlotPanel attribute) (PreferencesParams attribute) LUTItem (class in ClearMap.Visualization.Qt.data_viewer_luts) LUTWidget (class in ClearMap.Visualization.Qt.data_viewer_luts) M machine_cfg_path() (MachineConfig static method) machine_config (OrchestratorBase property) MachineConfig (class in ClearMap.config.early_boot) main() (in module ClearMap.gui.app) (in module ClearMap.pipeline_orchestrators.batch_process) (in module ClearMap.Scripts.cell_map_new_api) (in module ClearMap.Scripts.clearmap_utils) (in module ClearMap.Scripts.create_distance_file) (in module ClearMap.Scripts.tract_map) (in module ClearMap.Scripts.tube_map_new_api) main_max_changed (ProgressWatcher attribute) main_max_progress (ProgressWatcher property) main_progress_changed (ProgressWatcher attribute) main_step_name (ProgressWatcher property) main_step_name_changed (ProgressWatcher attribute) main_type (SubTypeSpec property) main_window (GenericUi attribute) make_abs() (in module ClearMap.Utils.utilities) make_cfg_coordinator_factory() (in module ClearMap.config.config_coordinator) make_colocalization_compatible() (CellCounterTab method) make_generic_3_0_to_3_1_converter() (in module ClearMap.config.convert_config_versions) make_group_stats_tables() (GroupAnalysisTab method) make_nested_progress_dialog() (in module ClearMap.gui.dialog_helpers) make_progress_dialog() (ClearMapAppBase method) make_simple_progress_dialog() (in module ClearMap.gui.dialog_helpers) make_splash() (in module ClearMap.gui.dialog_helpers) make_structure_acronyms_path_string() (in module ClearMap.Scripts.generate_jsonl_file_ontology) make_structure_ids_path_string() (in module ClearMap.Scripts.generate_jsonl_file_ontology) manage_assets() (ClearMapApp method) ManageAssetsWidget (class in ClearMap.gui.widgets) map_axes() (in module ClearMap.IO.TIF) map_volume (Annotation property) mark_inline_sequences() (in module ClearMap.config.config_handler) mask_to_coordinates() (TractMapProcessor method) masked_sizes() (Channel method) match() (in module ClearMap.Alignment.Stitching.Tracking) (in module ClearMap.ImageProcessing.Skeletonization.PK12) match_index() (in module ClearMap.ImageProcessing.Skeletonization.PK12) match_non_removable() (in module ClearMap.ImageProcessing.Skeletonization.PK12) match_pytorch_to_cuda() (PytorchVersionManager method) match_pytorch_to_toolkit() (PytorchVersionManager method) materialize_channel() (StitchingParams method) max_arteries_tracing_iterations (VesselGraphParams attribute) max_artery_trace_iter (ClassificationConfig attribute), [1] MAX_BIN (in module ClearMap.ImageProcessing.Experts.Vasculature) max_blobwise_overlap_rates() (Channel method) max_blobwise_overlaps() (Channel method) max_changed (ProgressWatcher attribute) max_intensity_projection() (in module ClearMap.Alignment.Stitching.stitching_rigid) max_level (Annotation property) max_particle_distance (ChannelColocalizationParams attribute) max_progress (ProgressWatcher property) max_projection (PlotPanel attribute) max_propagation_iter (ClassificationConfig property) max_shifts_x (RigidChannelStitchingParams attribute) (WobblyChannelStitchingParams attribute) max_shifts_y (RigidChannelStitchingParams attribute) (WobblyChannelStitchingParams attribute) max_shifts_z (RigidChannelStitchingParams attribute) (WobblyChannelStitchingParams attribute) max_value() (in module ClearMap.IO.IO) max_vein_trace_iter (ClassificationConfig attribute), [1] max_veins_tracing_iterations (VesselGraphParams attribute) maxima_shape (ChannelCellMapParams attribute) maximum() (in module ClearMap.ImageProcessing.Filter.Rank) (in module ClearMap.ImageProcessing.Filter.Rank.Rank) (in module ClearMap.ImageProcessing.Filter.Rank.RankCode) maximum_masked() (in module ClearMap.ImageProcessing.Filter.Rank.RankCode) mean() (in module ClearMap.ImageProcessing.Filter.Rank) (in module ClearMap.ImageProcessing.Filter.Rank.BilateralCode) (in module ClearMap.ImageProcessing.Filter.Rank.PercentileCode) (in module ClearMap.ImageProcessing.Filter.Rank.Rank) (in module ClearMap.ImageProcessing.Filter.Rank.RankCode) mean_bilateral() (in module ClearMap.ImageProcessing.Filter.Rank) (in module ClearMap.ImageProcessing.Filter.Rank.Bilateral) mean_masked() (in module ClearMap.ImageProcessing.Filter.Rank.BilateralCode) (in module ClearMap.ImageProcessing.Filter.Rank.PercentileCode) (in module ClearMap.ImageProcessing.Filter.Rank.RankCode) mean_percentile() (in module ClearMap.ImageProcessing.Filter.Rank) (in module ClearMap.ImageProcessing.Filter.Rank.Percentile) mean_scale() (in module ClearMap.ImageProcessing.Filter.Rank.BilateralCode) mean_scale_bilateral() (in module ClearMap.ImageProcessing.Filter.Rank) (in module ClearMap.ImageProcessing.Filter.Rank.Bilateral) mean_scale_masked() (in module ClearMap.ImageProcessing.Filter.Rank.BilateralCode) mean_vertex_coordinates() (in module ClearMap.Analysis.graphs.graph_processing) measure_expression() (in module ClearMap.Analysis.Measurements.MeasureExpression) measure_max() (in module ClearMap.ParallelProcessing.DataProcessing.MeasurePointList) (in module ClearMap.ParallelProcessing.DataProcessing.MeasurePointListCode) measure_mean() (in module ClearMap.ParallelProcessing.DataProcessing.MeasurePointList) (in module ClearMap.ParallelProcessing.DataProcessing.MeasurePointListCode) measure_min() (in module ClearMap.ParallelProcessing.DataProcessing.MeasurePointList) (in module ClearMap.ParallelProcessing.DataProcessing.MeasurePointListCode) measure_radius() (in module ClearMap.Analysis.Measurements.radius_measurements) measure_sum() (in module ClearMap.ParallelProcessing.DataProcessing.MeasurePointList) (in module ClearMap.ParallelProcessing.DataProcessing.MeasurePointListCode) MEASURED (WobblyAlignment attribute) median() (in module ClearMap.ImageProcessing.Filter.Rank) (in module ClearMap.ImageProcessing.Filter.Rank.Rank) (in module ClearMap.ImageProcessing.Filter.Rank.RankCode) median_masked() (in module ClearMap.ImageProcessing.Filter.Rank.RankCode) medoid_vertex_coordinates() (in module ClearMap.Analysis.graphs.graph_processing) Membership (class in ClearMap.config.config_adjusters.policy_specs) membership (InstanceContainerSpec attribute) memory() (in module ClearMap.IO.IO) merge_config() (in module ClearMap.config.update_config) merge_patches() (in module ClearMap.config.config_adjusters.patch_ops) merge_section_missing_only() (in module ClearMap.config.config_adjusters.dict_ops) mesh() (in module ClearMap.Analysis.graphs.graph_rendering) mesh_tube() (in module ClearMap.Analysis.graphs.graph_rendering) mesh_tube_from_coordinates_and_radii() (in module ClearMap.Analysis.graphs.graph_rendering) message (ImportTask attribute) (TabActivationResult attribute) metadata() (Source method), [1], [2] MetadataError method (VolumeVisual property) migrate_container_payload() (CompoundKey class method) migrate_payload (RenameStepSpec attribute) migrate_vasculature_performance_v3_0_to_v3_1() (in module ClearMap.config.convert_config_versions) migrate_vasculature_postprocessing_v3_0_to_v3_1() (in module ClearMap.config.convert_config_versions) migrate_vasculature_v3_0_to_v3_1() (in module ClearMap.config.convert_config_versions) min_artery_component_edges (ClassificationConfig attribute), [1] (VesselGraphParams attribute) min_component_edges (ClassificationConfig property) min_file_number (PatternDialog attribute) min_max (PlotPanel attribute) min_value() (in module ClearMap.IO.IO) min_vein_component_edges (ClassificationConfig attribute), [1] (VesselGraphParams attribute) mini_brains (RegistrationProcessor attribute) MiniBrain (class in ClearMap.pipeline_orchestrators.registration_orchestrator) minimum() (in module ClearMap.ImageProcessing.Filter.Rank) (in module ClearMap.ImageProcessing.Filter.Rank.Rank) (in module ClearMap.ImageProcessing.Filter.Rank.RankCode) minimum_masked() (in module ClearMap.ImageProcessing.Filter.Rank.RankCode) minimum_width (GenericTab attribute) minmax() (in module ClearMap.ImageProcessing.Filter.Rank) (in module ClearMap.ImageProcessing.Filter.Rank.Rank) (in module ClearMap.ImageProcessing.Filter.Rank.RankCode) minmax_masked() (in module ClearMap.ImageProcessing.Filter.Rank.RankCode) mip_axis() (Alignment method) missing_ok (ParamLink attribute) MISSING_OUTPUTS (RegistrationStatus attribute) MissingAssetError MissingChannelError MissingRequirementException modal() (in module ClearMap.ImageProcessing.Filter.Rank) (in module ClearMap.ImageProcessing.Filter.Rank.Rank) (in module ClearMap.ImageProcessing.Filter.Rank.RankCode) modal_masked() (in module ClearMap.ImageProcessing.Filter.Rank.RankCode) mode (ReconcileStepSpec attribute) (Source property), [1] modularity_measure() (in module ClearMap.Analysis.vasculature.vasc_graph_utils) module ClearMap ClearMap.Alignment ClearMap.Alignment.Annotation ClearMap.Alignment.Elastix ClearMap.Alignment.landmarks_registration ClearMap.Alignment.landmarks_registration.engine ClearMap.Alignment.landmarks_registration.registration_data ClearMap.Alignment.orientation ClearMap.Alignment.Resampling ClearMap.Alignment.Stitching ClearMap.Alignment.Stitching.layout_graph_utils ClearMap.Alignment.Stitching.plot_utils ClearMap.Alignment.Stitching.stitching_plots ClearMap.Alignment.Stitching.stitching_rigid ClearMap.Alignment.Stitching.stitching_wobbly ClearMap.Alignment.Stitching.Tracking ClearMap.Alignment.Transformation ClearMap.Alignment.Transformations ClearMap.Alignment.Transformations.LinearTransformation ClearMap.Alignment.Transformations.ResamplingTransformation ClearMap.Alignment.Transformations.SlicingTransformation ClearMap.Alignment.Transformations.Transformation ClearMap.Alignment.utils ClearMap.Analysis ClearMap.Analysis.colocalization ClearMap.Analysis.colocalization.bbox ClearMap.Analysis.colocalization.channel ClearMap.Analysis.colocalization.parallelism ClearMap.Analysis.Curves ClearMap.Analysis.Curves.Extrapolation ClearMap.Analysis.Curves.Resampling ClearMap.Analysis.DimensionReduction ClearMap.Analysis.graphs ClearMap.Analysis.graphs.fast_graph_reduce ClearMap.Analysis.graphs.graph ClearMap.Analysis.graphs.graph_filters ClearMap.Analysis.graphs.graph_gt ClearMap.Analysis.graphs.graph_processing ClearMap.Analysis.graphs.graph_rendering ClearMap.Analysis.graphs.type_conversions ClearMap.Analysis.graphs.utils ClearMap.Analysis.graphs.vessel_classifier ClearMap.Analysis.Measurements ClearMap.Analysis.Measurements.maxima_detection ClearMap.Analysis.Measurements.MeasureExpression ClearMap.Analysis.Measurements.radius_measurements ClearMap.Analysis.Measurements.shape_detection ClearMap.Analysis.Measurements.Voxelization ClearMap.Analysis.Statistics ClearMap.Analysis.Statistics.data_frame_operations ClearMap.Analysis.Statistics.group_assets ClearMap.Analysis.Statistics.group_statistics ClearMap.Analysis.Statistics.group_statistics_cumulatives ClearMap.Analysis.Statistics.MultipleComparisonCorrection ClearMap.Analysis.Statistics.StatisticalTests ClearMap.Analysis.vasculature ClearMap.Analysis.vasculature.annotation_utils ClearMap.Analysis.vasculature.flow ClearMap.Analysis.vasculature.flow.assign_p_bc ClearMap.Analysis.vasculature.flow.linear_system ClearMap.Analysis.vasculature.flow.units ClearMap.Analysis.vasculature.general_functions ClearMap.Analysis.vasculature.geometry_utils ClearMap.Analysis.vasculature.graph_corrections ClearMap.Analysis.vasculature.vasc_graph_utils ClearMap.config ClearMap.config.atlas ClearMap.config.change_detection ClearMap.config.compound_keys ClearMap.config.config_adjusters ClearMap.config.config_adjusters.adjusters_api ClearMap.config.config_adjusters.dict_ops ClearMap.config.config_adjusters.engine ClearMap.config.config_adjusters.group_adjusters ClearMap.config.config_adjusters.patch_ops ClearMap.config.config_adjusters.policy ClearMap.config.config_adjusters.policy_specs ClearMap.config.config_adjusters.templates_resolver ClearMap.config.config_adjusters.trace_logging ClearMap.config.config_adjusters.type_hints ClearMap.config.config_coordinator ClearMap.config.config_handler ClearMap.config.config_repository ClearMap.config.convert_config_versions ClearMap.config.defaults_provider ClearMap.config.early_boot ClearMap.config.update_config ClearMap.config.utils ClearMap.config.validators ClearMap.config.validators._schema ClearMap.config.validators._semantic ClearMap.config.validators.json_schema_utils ClearMap.gui ClearMap.gui.about ClearMap.gui.app ClearMap.gui.creator ClearMap.gui.creator.graphics_resources_rc ClearMap.gui.creator.icons_rc ClearMap.gui.dialog_helpers ClearMap.gui.dialogs ClearMap.gui.exception_handler ClearMap.gui.gui_logging ClearMap.gui.gui_utils_base ClearMap.gui.gui_utils_images ClearMap.gui.params ClearMap.gui.params_interfaces ClearMap.gui.params_mixins ClearMap.gui.pipeline_model ClearMap.gui.pipeline_widgets ClearMap.gui.preferences ClearMap.gui.pretty_imports ClearMap.gui.pyuic_utils ClearMap.gui.style ClearMap.gui.tab_registry ClearMap.gui.tabs ClearMap.gui.tabs_interfaces ClearMap.gui.widget_monkeypatch_callbacks ClearMap.gui.widgets ClearMap.ImageProcessing ClearMap.ImageProcessing.Binary ClearMap.ImageProcessing.Binary.Filling ClearMap.ImageProcessing.Binary.FillingCode ClearMap.ImageProcessing.Binary.morphsnake ClearMap.ImageProcessing.Binary.Smoothing ClearMap.ImageProcessing.Clipping ClearMap.ImageProcessing.Clipping.Clipping ClearMap.ImageProcessing.Clipping.ClippingCode ClearMap.ImageProcessing.Differentiation ClearMap.ImageProcessing.Differentiation.Gradient ClearMap.ImageProcessing.Differentiation.Hessian ClearMap.ImageProcessing.Differentiation.HessianCode ClearMap.ImageProcessing.Experts ClearMap.ImageProcessing.Experts.Cells ClearMap.ImageProcessing.Experts.utils ClearMap.ImageProcessing.Experts.Vasculature ClearMap.ImageProcessing.Filter ClearMap.ImageProcessing.Filter.FilterKernel ClearMap.ImageProcessing.Filter.Rank ClearMap.ImageProcessing.Filter.Rank.Bilateral ClearMap.ImageProcessing.Filter.Rank.BilateralCode ClearMap.ImageProcessing.Filter.Rank.Parametric ClearMap.ImageProcessing.Filter.Rank.ParametricCode ClearMap.ImageProcessing.Filter.Rank.Percentile ClearMap.ImageProcessing.Filter.Rank.PercentileCode ClearMap.ImageProcessing.Filter.Rank.Rank ClearMap.ImageProcessing.Filter.Rank.RankCode ClearMap.ImageProcessing.Filter.Rank.RankCoreCode ClearMap.ImageProcessing.Filter.Rank.RankResample ClearMap.ImageProcessing.Filter.StructureElement ClearMap.ImageProcessing.grey_reconstruction ClearMap.ImageProcessing.IlluminationCorrection ClearMap.ImageProcessing.LightsheetCorrection ClearMap.ImageProcessing.local_percentile_core ClearMap.ImageProcessing.local_threshold_isodata ClearMap.ImageProcessing.LocalStatistics ClearMap.ImageProcessing.machine_learning ClearMap.ImageProcessing.machine_learning.torch_utils ClearMap.ImageProcessing.machine_learning.vertices_classification ClearMap.ImageProcessing.machine_learning.vertices_classification.degree1_inference_utils ClearMap.ImageProcessing.machine_learning.vessel_filling ClearMap.ImageProcessing.machine_learning.vessel_filling.vessel_filling ClearMap.ImageProcessing.machine_learning.vessel_filling.vessel_filling_network ClearMap.ImageProcessing.Skeletonization ClearMap.ImageProcessing.Skeletonization.PK12 ClearMap.ImageProcessing.Skeletonization.Skeletonization ClearMap.ImageProcessing.Skeletonization.SkeletonProcessing ClearMap.ImageProcessing.Thresholding ClearMap.ImageProcessing.Thresholding.Thresholding ClearMap.ImageProcessing.Thresholding.ThresholdingCode ClearMap.ImageProcessing.Topology ClearMap.ImageProcessing.Topology.Topology2d ClearMap.ImageProcessing.Topology.Topology3d ClearMap.ImageProcessing.Tracing ClearMap.ImageProcessing.Tracing.Connect ClearMap.ImageProcessing.Tracing.Trace ClearMap.ImageProcessing.Tracing.TraceCode ClearMap.IO ClearMap.IO.assets_constants ClearMap.IO.assets_specs ClearMap.IO.CSV ClearMap.IO.elastix_config ClearMap.IO.FileList ClearMap.IO.FileUtils ClearMap.IO.GT ClearMap.IO.IO ClearMap.IO.metadata ClearMap.IO.MHD ClearMap.IO.MMP ClearMap.IO.NPY ClearMap.IO.NRRD ClearMap.IO.Slice ClearMap.IO.SMA ClearMap.IO.Source ClearMap.IO.Temporary ClearMap.IO.TIF ClearMap.IO.Workspace ClearMap.ParallelProcessing ClearMap.ParallelProcessing.Block ClearMap.ParallelProcessing.BlockProcessing ClearMap.ParallelProcessing.DataProcessing ClearMap.ParallelProcessing.DataProcessing.ArrayProcessing ClearMap.ParallelProcessing.DataProcessing.ArrayProcessingCode ClearMap.ParallelProcessing.DataProcessing.ConvolvePointList ClearMap.ParallelProcessing.DataProcessing.ConvolvePointListCode ClearMap.ParallelProcessing.DataProcessing.devolve_point_list_code ClearMap.ParallelProcessing.DataProcessing.DevolvePointList ClearMap.ParallelProcessing.DataProcessing.MeasurePointList ClearMap.ParallelProcessing.DataProcessing.MeasurePointListCode ClearMap.ParallelProcessing.DataProcessing.statistics ClearMap.ParallelProcessing.ParallelTraceback ClearMap.ParallelProcessing.ProcessWriter ClearMap.ParallelProcessing.SharedMemoryArray ClearMap.ParallelProcessing.SharedMemoryManager ClearMap.pipeline_orchestrators ClearMap.pipeline_orchestrators.batch_process ClearMap.pipeline_orchestrators.cell_map ClearMap.pipeline_orchestrators.colocalization ClearMap.pipeline_orchestrators.degree1_inference_processor ClearMap.pipeline_orchestrators.experiment_controller ClearMap.pipeline_orchestrators.generic_orchestrators ClearMap.pipeline_orchestrators.group_orchestrators ClearMap.pipeline_orchestrators.registration_orchestrator ClearMap.pipeline_orchestrators.sample_info_management ClearMap.pipeline_orchestrators.stitching_orchestrator ClearMap.pipeline_orchestrators.tract_map ClearMap.pipeline_orchestrators.tube_map ClearMap.pipeline_orchestrators.utils ClearMap.Scripts ClearMap.Scripts.align_new_api ClearMap.Scripts.cell_map_new_api ClearMap.Scripts.CellMap ClearMap.Scripts.clearmap_utils ClearMap.Scripts.create_distance_file ClearMap.Scripts.generate_jsonl_file_ontology ClearMap.Scripts.partial_gt_load_demo ClearMap.Scripts.tract_map ClearMap.Scripts.tube_map_new_api ClearMap.Scripts.TubeMap ClearMap.Settings ClearMap.Utils ClearMap.Utils.array_utils ClearMap.Utils.array_utils_cy ClearMap.Utils.event_bus ClearMap.Utils.events ClearMap.Utils.exceptions ClearMap.Utils.Formatting ClearMap.Utils.HierarchicalDict ClearMap.Utils.install_utils ClearMap.Utils.Lazy ClearMap.Utils.path_utils ClearMap.Utils.RegularExpression ClearMap.Utils.Sound ClearMap.Utils.tag_expression ClearMap.Utils.Timer ClearMap.Utils.utilities ClearMap.Visualization ClearMap.Visualization.Color ClearMap.Visualization.Color.Color ClearMap.Visualization.Color.orientation_colormap ClearMap.Visualization.Matplotlib ClearMap.Visualization.Matplotlib.PlotUtils ClearMap.Visualization.Mesh ClearMap.Visualization.Mesh.IcoSphere ClearMap.Visualization.Plot3d ClearMap.Visualization.Qt ClearMap.Visualization.Qt.data_viewer_luts ClearMap.Visualization.Qt.DataViewer ClearMap.Visualization.Qt.Plot3d ClearMap.Visualization.Qt.utils ClearMap.Visualization.Qt.widgets ClearMap.Visualization.Vispy ClearMap.Visualization.Vispy.arbitrary_rotation_camera ClearMap.Visualization.Vispy.graph_visual ClearMap.Visualization.Vispy.Plot3d ClearMap.Visualization.Vispy.plot_graph_3d ClearMap.Visualization.Vispy.VolumeVisual module (ImportTask attribute) module_only() (ImportTask class method) monkey_patch() (ClearMapAppBase method) morphological_chan_vese() (in module ClearMap.ImageProcessing.Binary.morphsnake) mosaic_shape() (Workspace method) mouse_clicked (DataViewer attribute) mousePressEvent() (ClickableFrame method) (StepChip method) move() (LinearPipeline method) moving_image (RegistrationData attribute) moving_points (RegistrationData attribute) multi_plot() (in module ClearMap.Visualization.Qt.Plot3d) multi_plot_from_panels() (in module ClearMap.Visualization.Qt.Plot3d) N n (CompoundKey property) n18 (in module ClearMap.ImageProcessing.Topology.Topology3d) n18_indices() (in module ClearMap.ImageProcessing.Topology.Topology3d) n26 (in module ClearMap.ImageProcessing.Topology.Topology3d) n26_indices() (in module ClearMap.ImageProcessing.Topology.Topology3d) n6 (in module ClearMap.ImageProcessing.Topology.Topology3d) n6_indices() (in module ClearMap.ImageProcessing.Topology.Topology3d) n_alignments (Layout property) n_cube_indices() (in module ClearMap.ImageProcessing.Topology.Topology3d) n_detected_cells (ChannelCellMapParams attribute) n_direct_contacts (ClassificationMetrics attribute) n_edges (ClassificationMetrics attribute) (Graph property), [1] n_filtered_cells (ChannelCellMapParams attribute) n_filters (VesselGraphParams property) n_groups (BatchParameters property) n_groups() (in module ClearMap.Utils.RegularExpression) n_image_groups (PatternDialog attribute) n_iterations (Block property) n_numbers (VectorLink property) n_proc_connector() (in module ClearMap.gui.params_interfaces) n_proc_getter() (in module ClearMap.gui.params_interfaces) n_proc_setter() (in module ClearMap.gui.params_interfaces) n_processes (BlockProcessingParams attribute) (BlockProcessingWidget property) (ChannelCellMapPerformanceParams attribute) (ChannelColocalizationParams attribute) (NProcessesParams attribute) (VesselBinarizationPerformanceParams attribute) n_registration_files (ChannelRegistrationParams property) n_registration_steps (RegistrationProcessor property) n_rigid_steps_to_run (StitchingProcessor property) n_seed_conflicts (ClassificationMetrics attribute) n_sources (Layout property) n_steps (VesselBinarizationParams property) n_structures (Annotation property) n_tags() (Expression method) n_vertices (Graph property), [1] n_wobbly_steps_to_run (StitchingProcessor property) name (AdjusterSpec attribute) (Alignment property) (Block property) (ChannelPatternSpec attribute) (ChannelSpec attribute) (ChannelUiParameter property) (CondaPackage property) (GenericUi attribute) (Graph property) (GroupPage property) (Label property) (Slice property) (Source property), [1] (StepSpec attribute) (Tag attribute) (TypeSpec property) (VirtualSource property) (WobblySource property) names (ChannelsSnapshot attribute) (ConfigSpec attribute) ndim (AlignmentBase property) (GeometricGraph property) (Graph property) (Layout property) (Region property) (Source property) ndim() (in module ClearMap.IO.FileList) (in module ClearMap.IO.IO) ndim_file (Source property) ndim_from_source() (in module ClearMap.Analysis.graphs.type_conversions) ndim_list (Source property) ndim_to_gtype() (in module ClearMap.Analysis.graphs.type_conversions) needs_channels (TabRequirements attribute) needs_registering() (SampleManager method) needs_workspace (TabRequirements attribute) neighbourhood_list() (in module ClearMap.ImageProcessing.Topology.Topology3d) neighbourhood_list_delete() (in module ClearMap.ImageProcessing.Topology.Topology3d) neighbourhood_opposing_directions() (in module ClearMap.ImageProcessing.Topology.Topology3d) neighbours (Block property) neighbours() (in module ClearMap.Analysis.graphs.graph_processing) (in module ClearMap.ParallelProcessing.DataProcessing.ArrayProcessing) (in module ClearMap.ParallelProcessing.DataProcessing.ArrayProcessingCode) network_binary_vessel_filling_filename (in module ClearMap.ImageProcessing.machine_learning.vessel_filling.vessel_filling) new (ChannelRenamed attribute) (UiChannelRenamed attribute) new_get_distutils_extension() (in module ClearMap.ImageProcessing.Thresholding.Thresholding) nice_contrast_limits() (ITKImage method) nilblack() (in module ClearMap.ImageProcessing.Filter.Rank) (in module ClearMap.ImageProcessing.Filter.Rank.Parametric) (in module ClearMap.ImageProcessing.Filter.Rank.ParametricCode) nilblack_masked() (in module ClearMap.ImageProcessing.Filter.Rank.ParametricCode) noise_filter() (in module ClearMap.ImageProcessing.Filter.Rank) (in module ClearMap.ImageProcessing.Filter.Rank.Rank) (in module ClearMap.ImageProcessing.Filter.Rank.RankCode) noise_filter_masked() (in module ClearMap.ImageProcessing.Filter.Rank.RankCode) NOMINIMA (WobblyAlignment attribute) non_removable (in module ClearMap.ImageProcessing.Skeletonization.PK12) normalise_cfg_name() (ConfigHandler static method) normalise_df_column_names() (in module ClearMap.Analysis.Statistics.data_frame_operations) normalise_dict() (in module ClearMap.config.config_adjusters.dict_ops) normalize_container_keys() (CompoundKey class method) normalize_df() (in module ClearMap.Analysis.Statistics.data_frame_operations) normalize_json_compat() (in module ClearMap.config.config_adjusters.dict_ops) NOSIGNAL (WobblyAlignment attribute) NOT_SELECTED (RegistrationStatus attribute) NotAnOmeFile notify_atlas_id_changed() (AtlasParams method) notify_selected() (GenericTab method) np_to_qpixmap() (in module ClearMap.gui.gui_utils_images) NProcessesParams (class in ClearMap.gui.params) NProcessesWidget (class in ClearMap.gui.widgets) NrrdError nucleus() (Channel method) number (ChannelSpec attribute) O object_name (ParamLink attribute), [1] offset (Slice property) (Source property), [1], [2], [3], [4] ok (TabActivationResult attribute) old (ChannelRenamed attribute) (UiChannelRenamed attribute) OMEMetadataParser (class in ClearMap.IO.TIF) on_channel_renamed() (ExperimentController method) on_channels_changed() (ExperimentController method) on_item_changed() (CheckableListWidget method) on_selected() (CellCounterTab method) (GenericTab method) (StitchingTab method) on_selection_changed() (TwoListSelection method) ones() (in module ClearMap.IO.SMA) (in module ClearMap.ParallelProcessing.SharedMemoryArray) onRangeChanged() (DataViewer method) open() (PreferenceUi method) open_ro() (in module ClearMap.IO.IO) (in module ClearMap.IO.MMP) operator_name_to_function() (in module ClearMap.Analysis.graphs.graph_filters) optimal_association_matrix() (in module ClearMap.Alignment.Stitching.Tracking) option_dialog() (in module ClearMap.gui.dialog_helpers) optional_text_link() (in module ClearMap.gui.params_interfaces) orbit() (ArbitraryRotationCamera method) OrchestratorBase (class in ClearMap.pipeline_orchestrators.generic_orchestrators) order (AbstractSource property) (AdjusterSpec attribute) (Label property) (Layout property) (Slice property) (Source property), [1], [2], [3], [4], [5] order() (in module ClearMap.ImageProcessing.Tracing.Connect) (in module ClearMap.IO.FileList) (in module ClearMap.IO.IO) (in module ClearMap.IO.NPY) ordered_for_reconcile() (ContainerSpecRegistry method) orient() (in module ClearMap.Alignment.orientation) orient_points() (in module ClearMap.Alignment.orientation) orient_resolution() (in module ClearMap.Alignment.orientation) orient_shape() (in module ClearMap.Alignment.orientation) orientation (SampleChannelParameters property) (UiOrientationChanged attribute) orientation_color() (in module ClearMap.Visualization.Color.orientation_colormap) orientation_color_cached() (in module ClearMap.Visualization.Color.orientation_colormap) orientation_colormap_cache() (in module ClearMap.Visualization.Color.orientation_colormap) orientation_to_boys() (in module ClearMap.Visualization.Color.Color) orientation_to_rgb() (in module ClearMap.Visualization.Color.Color) orientation_to_transposition() (in module ClearMap.Alignment.orientation) orientations() (in module ClearMap.ImageProcessing.Topology.Topology3d) OrientationTransformation (class in ClearMap.Alignment.Resampling) (class in ClearMap.Alignment.Transformations.ResamplingTransformation) oriented (CompoundKey property) (Membership attribute) origin (Region property) origin_wobbly (WobblyLayout property) original_resolution_from_shape() (in module ClearMap.Alignment.Resampling) original_shape_from_resolution() (in module ClearMap.Alignment.Resampling) original_std_err (Printer attribute) original_std_out (Printer attribute) OrthoViewer (class in ClearMap.gui.widgets) OrthoviewerSlicingMixin (class in ClearMap.gui.params_mixins) OTHER (AdjusterKind attribute) otsu() (in module ClearMap.ImageProcessing.Filter.Rank) (in module ClearMap.ImageProcessing.Filter.Rank.Rank) (in module ClearMap.ImageProcessing.Filter.Rank.RankCode) otsu_masked() (in module ClearMap.ImageProcessing.Filter.Rank.RankCode) overlap (BlockProcessingParams attribute) (BlockProcessingWidget property) (ChannelCellMapPerformanceParams attribute) Overlap (class in ClearMap.Alignment.Stitching.stitching_rigid) overlap (VesselBinarizationPerformanceParams attribute) overlap() (in module ClearMap.Alignment.Stitching.stitching_rigid) overlap_rates() (Channel method) overlay() (AlignmentBasePlotMixin method) (LayoutPlotMixin method) overlay_along_axis_mip() (in module ClearMap.Alignment.Stitching.stitching_plots) overlay_layout() (in module ClearMap.Alignment.Stitching.stitching_plots) overlay_layout_plane() (StitchingProcessor method) overlay_mip() (AlignmentBasePlotMixin method) overlay_mip_wobbly() (WobblyAlignmentPlotMixin method) overlay_overlap() (AlignmentBasePlotMixin method) overlay_sources() (in module ClearMap.Alignment.Stitching.stitching_plots) overlay_splash_message() (in module ClearMap.gui.app) overlay_wobbly() (WobblyAlignment method) owned_keys (AdjusterSpec attribute) owns_prefix() (InstanceContainerSpec method) P p_val_assets_exist() (GroupResultsAssets method) p_val_colors_path() (GroupResultsAssets method) p_vals (LoadedPValueResults attribute) padded_shape() (DataViewer method) page_index (UiRequestLandmarksDialog attribute) pages_mode (Source property) paint() (RedCross method) paintEvent() (StepChip method) PairKey (class in ClearMap.Analysis.Statistics.group_assets) (class in ClearMap.config.compound_keys) PAIRS (TemplateKind attribute) PAIRS_ORIENTED (ExperimentTemplatesResolver attribute) parallel_get_vessels_lengths() (in module ClearMap.Analysis.vasculature.vasc_graph_utils) parallel_traceback() (in module ClearMap.ParallelProcessing.ParallelTraceback) parallel_transform() (TractMapProcessor method) param_handler() (in module ClearMap.gui.params_interfaces) param_setter() (in module ClearMap.gui.params_interfaces) parametrize_assets() (RegistrationProcessor method) ParamLink (class in ClearMap.gui.params_interfaces) params (CellMapParams property) (ChannelStitchingParams property) (ColocalizationParams property) (GenericUi attribute) (RegistrationParams property) (SampleParameters property) (StitchingParams property) (TractMapParams property) (UiParameterCollection property) (VesselParams property) params_dict (UiParameter attribute) params_files (ChannelRegistrationParams property) params_set (GenericTab attribute) ParamsOrientationError parent_list() (Label method) parents() (Annotation method) parse() (BaseMetadataParser method) (ElastixEntry method) (ElastixParser method) (Expression method) (in module ClearMap.Utils.tag_expression) (Tag method) parse_channels_excitation() (BaseMetadataParser method) (OMEMetadataParser method) parse_date() (BaseMetadataParser method) parse_description() (BaseMetadataParser method) parse_flat_yaml() (in module ClearMap.config.utils) parse_img_res() (in module ClearMap.IO.metadata) parse_img_shape() (in module ClearMap.IO.metadata) parse_info_field() (ImageJMetadataParser method) parse_json() (StructurePickerWidget static method) parse_label() (ComparisonsModel method) parse_ome_info() (in module ClearMap.IO.metadata) parse_order() (BaseMetadataParser method) (ClearMapMetadataParser method) parse_overlap() (BaseMetadataParser method) (OMEMetadataParser method) parse_overlaps() (in module ClearMap.IO.metadata) parse_pixel_metadata() (BaseMetadataParser method) parse_resolution() (BaseMetadataParser method) (ClearMapMetadataParser method) (ImageJMetadataParser method) parse_sample_folders() (SamplePickerDialog method) parse_shape() (BaseMetadataParser method) parse_stitching() (BaseMetadataParser method) (OMEMetadataParser method) parse_tile_configuration() (BaseMetadataParser method) (OMEMetadataParser method) partial_load() (Graph class method) particle_diameter (ChannelColocalizationParams attribute) partners (ChannelDefaultsChanged attribute) parts (CompoundKey property) patch_adjuster() (in module ClearMap.config.config_adjusters.adjusters_api) patch_cfg() (in module ClearMap.config.config_handler) patch_channel() (ChannelPipelineOrchestrator method) (CompoundChannelPipelineOrchestrator method) (SampleManager method) patch_elastix_cfg_landmarks() (ElastixConfigPatcher method) patch_env() (in module ClearMap.Utils.install_utils) patch_env_var() (EnvFileManager method) patch_environment_package_line() (EnvFileManager method) patch_tmp() (MachineConfig method) patch_tool_boxes() (ClearMapAppBase method) patch_warnings_color() (ClearMapApp method) PatchConflictError PatchDataset (class in ClearMap.ImageProcessing.machine_learning.vertices_classification.degree1_inference_utils) path (AssetBase property) (SampleChannelParameters attribute) path() (ElastixPointFileManager method) (in module ClearMap.Settings) path_for() (ConfigCoordinator method) (ConfigRepository method) paths (GroupPage property) Pattern (class in ClearMap.IO.metadata) pattern_finder_min_n_files (PreferencesParams attribute) pattern_finders_from_base_dir() (in module ClearMap.IO.metadata) pattern_from_df() (PatternFinder static method) pattern_relpath (ChannelPatternSpec attribute) pattern_to_expression() (in module ClearMap.Utils.RegularExpression) PatternDialog (class in ClearMap.gui.widgets) PatternFinder (class in ClearMap.IO.metadata) PatternInverter (class in ClearMap.Utils.RegularExpression) patterns_finders (PatternDialog attribute) percent_thread (PerfMonitor attribute) Percentile (class in ClearMap.Analysis.graphs.graph_processing) percentile() (in module ClearMap.ImageProcessing.Filter.Rank) (in module ClearMap.ImageProcessing.Filter.Rank.Percentile) (in module ClearMap.ImageProcessing.Filter.Rank.PercentileCode) percentile2d_u16() (in module ClearMap.ImageProcessing.local_percentile_core) percentile2d_u16_window() (in module ClearMap.ImageProcessing.local_percentile_core) percentile2d_u16_window_grid() (in module ClearMap.ImageProcessing.local_percentile_core) percentile_masked() (in module ClearMap.ImageProcessing.Filter.Rank.PercentileCode) PERF (TemplateKind attribute) PerfMonitor (class in ClearMap.gui.widgets) perform_registration() (AlignmentTool method) permissive_min_vein_radius (VesselGraphParams attribute) permissive_vein_radius (ClassificationConfig attribute) phase (AdjusterSpec attribute) Phase (class in ClearMap.config.config_adjusters.adjusters_api) physical_to_index() (ITKImage method) pick_region() (VasculatureTab method) pickler() (in module ClearMap.Analysis.graphs.utils) pipeline (GroupAnalysisParams attribute) (LinearPipelineWidget property) (Membership attribute) (OrthoviewerSlicingMixin attribute) (VesselVisualizationParams attribute) pipeline_changed (LinearPipelineWidget attribute) pipeline_from_config() (VesselBinarizationParams method) pipeline_name (CellCounterTab attribute) (ColocalizationTab attribute) (PipelineTab attribute) (RegistrationTab attribute) (StitchingTab attribute) (TractMapTab attribute) (VasculatureTab attribute) pipeline_ready_channels (SampleManager property) pipeline_to_section_name() (ConfigAlternativesRegistry method) PipelineOrchestrator (class in ClearMap.pipeline_orchestrators.generic_orchestrators) PipelineStep (class in ClearMap.gui.pipeline_model) PipelineTab (class in ClearMap.gui.tabs_interfaces) pixels_metadata (BaseMetadataParser property) (ClearMapMetadataParser property) (ImageJMetadataParser property) (OMEMetadataParser property) pkg_to_v_string() (CondaParser static method) place() (Layout method) place_axis() (Layout method) place_layout() (in module ClearMap.Alignment.Stitching.stitching_rigid) (in module ClearMap.Alignment.Stitching.stitching_wobbly) place_layout_axis() (in module ClearMap.Alignment.Stitching.stitching_rigid) place_layout_rigid() (StitchingProcessor method) plane_axes (Scatter3D property) plane_base_2() (in module ClearMap.ImageProcessing.Topology.Topology2d) plane_from_index() (in module ClearMap.ImageProcessing.Topology.Topology2d) plane_label() (in module ClearMap.ImageProcessing.Topology.Topology2d) plane_to_index() (in module ClearMap.ImageProcessing.Topology.Topology2d) plot() (AlignmentBasePlotMixin method) (AlignmentPlotMixin method) (ColocalizationTab method) (in module ClearMap.Visualization.Qt.Plot3d) (LandmarksSelectorDialog method) (LayoutPlotMixin method) (Overlap method) (SampleManager static method) (Source method) (Workspace method) plot_3d() (in module ClearMap.Visualization.Vispy.Plot3d) plot_alignments() (in module ClearMap.Alignment.Stitching.stitching_plots) (LayoutPlotMixin method) plot_all_layouts() (in module ClearMap.Alignment.Stitching.plot_utils) plot_along_axis_mip() (in module ClearMap.Alignment.Stitching.stitching_plots) plot_atlas() (RegistrationProcessor method) plot_background_subtracted_img() (CellDetector method) plot_binarization_levels() (TractMapProcessor method) plot_binarization_result() (BinaryVesselProcessor method) plot_binarization_results() (VasculatureTab method) plot_binarization_thresholds() (TractMapTab method) plot_binary() (TractMapProcessor method) (TractMapTab method) plot_box() (in module ClearMap.Visualization.Vispy.Plot3d) plot_cell_filter_results() (CellCounterTab method) plot_cell_map_results() (CellCounterTab method) plot_cells_3d_scatter_w_atlas_colors() (CellDetector method) plot_channel_1 (SharedVesselBinarizationParams attribute) plot_channel_2 (SharedVesselBinarizationParams attribute) plot_combined() (BinaryVesselProcessor method) plot_curve() (in module ClearMap.Visualization.Matplotlib.PlotUtils) plot_debug_cropping_interface() (CellCounterTab method) (TractMapTab method) plot_density() (in module ClearMap.Visualization.Matplotlib.PlotUtils) plot_density_maps() (DensityGroupAnalysisOrchestrator method) (GroupAnalysisTab method) plot_detected_cells (ChannelCellMapParams attribute) plot_detection_results() (CellCounterTab method) plot_filtered_cells() (CellDetector method) plot_graph_chunk() (VesselGraphProcessor method) plot_graph_edge_geometry_property() (in module ClearMap.Visualization.Vispy.plot_graph_3d) plot_graph_edge_property() (in module ClearMap.Visualization.Vispy.plot_graph_3d) plot_graph_line() (in module ClearMap.Visualization.Vispy.plot_graph_3d) plot_graph_mesh() (in module ClearMap.Visualization.Vispy.plot_graph_3d) plot_graph_nodes() (in module ClearMap.Visualization.Vispy.plot_graph_3d) plot_graph_structure() (VasculatureTab method) (VesselGraphProcessor method) plot_graph_type_processing_chunk_slicer() (VasculatureTab method) plot_graph_vertex_property() (in module ClearMap.Visualization.Vispy.plot_graph_3d) plot_histograms() (GroupAnalysisTab method) plot_labeled_cells_scatter() (CellCounterTab method) plot_labeled_tracts_scatter() (TractMapTab method) plot_layout() (in module ClearMap.Alignment.Stitching.stitching_plots) (StitchingProcessor method) plot_mesh_3d() (in module ClearMap.Visualization.Vispy.Plot3d) plot_mini_brain() (SampleInfoTab method) plot_mip() (AlignmentBasePlotMixin method) plot_mip_wobbly() (WobblyAlignmentPlotMixin method) plot_nearest_neighbors() (ColocalizationProcessor method) plot_orthogonal_views() (OrthoViewer method) plot_overlap() (AlignmentBasePlotMixin method) plot_overlaps() (ColocalizationProcessor method) plot_overlay() (AlignmentBasePlotMixin method) plot_overlay_wobbly() (WobblyAlignmentPlotMixin method) plot_p_vals() (GroupAnalysisTab method) plot_p_value_maps() (DensityGroupAnalysisOrchestrator method) plot_regions() (in module ClearMap.Alignment.Stitching.stitching_plots) (LayoutPlotMixin method) plot_registration_results() (in module ClearMap.Scripts.align_new_api) (RegistrationProcessor method) (RegistrationTab method) plot_regular_polygon() (in module ClearMap.Visualization.Vispy.Plot3d) plot_results() (BinaryVesselProcessor method) plot_sample_stats_histogram() (in module ClearMap.Visualization.Matplotlib.PlotUtils) plot_scatter_markers() (DataViewer method) plot_slicer() (PostProcessingTab method) plot_sources() (in module ClearMap.Alignment.Stitching.stitching_plots) plot_step_1 (SharedVesselBinarizationParams attribute) plot_step_2 (SharedVesselBinarizationParams attribute) plot_stitching_results() (StitchingProcessor method) (StitchingTab method) plot_sub_df() (in module ClearMap.Visualization.Matplotlib.PlotUtils) plot_tract_map_results() (TractMapTab method) plot_tracts_3d_scatter_w_atlas_colors() (TractMapProcessor method) plot_tsne() (in module ClearMap.Analysis.DimensionReduction) plot_type (VesselVisualizationParams attribute) plot_vessel_filling_results() (BinaryVesselProcessor method) plot_volcano() (in module ClearMap.Visualization.Matplotlib.PlotUtils) plot_volcanoes() (GroupAnalysisTab method) plot_voxelization() (VasculatureTab method) (VesselGraphProcessor method) plot_voxelized_counts() (CellDetector method) (TractMapProcessor method) plot_voxelized_intensities() (CellDetector method) plot_when_finished (ChannelCellMapParams attribute) plot_wobble() (WobblyLayoutPlotMixin method) plotData() (in module ClearMap.ImageProcessing.Tracing.Connect) PlotGraphError PlotPanel (class in ClearMap.Visualization.Qt.Plot3d) plotTracingResult() (in module ClearMap.ImageProcessing.Tracing.Connect) policy (ReconcileStepSpec attribute) (TemplateResolverBase property) pop() (CellMapParams method) (in module ClearMap.ImageProcessing.Filter.Rank) (in module ClearMap.ImageProcessing.Filter.Rank.BilateralCode) (in module ClearMap.ImageProcessing.Filter.Rank.PercentileCode) (in module ClearMap.ImageProcessing.Filter.Rank.Rank) (in module ClearMap.ImageProcessing.Filter.Rank.RankCode) (UiParameterCollection method) (VesselParams method) pop_bilateral() (in module ClearMap.ImageProcessing.Filter.Rank) (in module ClearMap.ImageProcessing.Filter.Rank.Bilateral) pop_masked() (in module ClearMap.ImageProcessing.Filter.Rank.BilateralCode) (in module ClearMap.ImageProcessing.Filter.Rank.PercentileCode) (in module ClearMap.ImageProcessing.Filter.Rank.RankCode) pop_percentile() (in module ClearMap.ImageProcessing.Filter.Rank) (in module ClearMap.ImageProcessing.Filter.Rank.Percentile) populate_combobox() (in module ClearMap.gui.gui_utils_base) POPULATE_DEFAULTS_MATERIALIZE (Step attribute) popup() (ClearMapAppBase method) position (Layout property) (Region property) (Slice property), [1] position_at_coordinate() (WobblySource method) position_from_local() (Region method) position_to_local() (Region method) position_unsliced (Slice property) positions (WobblySource property) positions_from_optimization() (in module ClearMap.Alignment.Stitching.stitching_rigid) positions_from_tree() (in module ClearMap.Alignment.Stitching.stitching_rigid) post (AlignmentBase property) POST_COMMIT (Phase attribute) post_connect() (UiParameter method) (VesselBinarizationParams method) post_process() (VesselGraphProcessor method) post_process_binary_combined() (BinaryVesselProcessor method) post_process_cells() (CellCounterTab method) (CellDetector method) post_process_graph() (VasculatureTab method) POST_VALIDATE (Phase attribute) postprocess() (BinaryVesselProcessor method) (in module ClearMap.ImageProcessing.Experts.Vasculature) PostProcessingTab (class in ClearMap.gui.tabs_interfaces) pprint() (in module ClearMap.Utils.HierarchicalDict) pre (AlignmentBase property) PRE_COMMIT (Phase attribute) pre_process() (VesselGraphProcessor method) PRE_VALIDATE (Phase attribute) PreferencesParams (class in ClearMap.gui.params) PreferenceUi (class in ClearMap.gui.preferences) prefix (SampleManager property) prepare_all_channels_raw_data() (StitchingProcessor method) prepare_annotation_files() (Annotation static method) prepare_channel_raw_data() (SampleInfoTab method) prepare_for_substep() (ProgressWatcher method) prepare_normalization() (in module ClearMap.Alignment.Stitching.stitching_wobbly) prepare_temp() (in module ClearMap.ImageProcessing.Binary.FillingCode) prepare_watcher_for_substep() (PipelineOrchestrator method) prepend() (in module ClearMap.Utils.HierarchicalDict) PreProcessingTab (class in ClearMap.gui.tabs_interfaces) present_if (ParamLink attribute) preserve_existing (InstancePolicy attribute) preserve_existing_order (ReconcileStepSpec attribute) preview_cell_detection() (CellDetector method) preview_cell_filter() (CellCounterTab method) preview_stitching_dumb() (StitchingTab method) preview_stitching_smart() (StitchingTab method) print_array_shape() (in module ClearMap.ImageProcessing.machine_learning.vessel_filling.vessel_filling) print_cube() (in module ClearMap.ImageProcessing.Topology.Topology3d) print_elapsed_time() (Timer method) print_error_msg() (ClearMapAppBase method) print_graph_info() (in module ClearMap.Analysis.graphs.graph_processing) print_id() (StructurePickerWidget method) print_params() (in module ClearMap.ImageProcessing.Experts.utils) print_percent_degree() (in module ClearMap.Analysis.vasculature.graph_corrections) print_settings() (in module ClearMap.Alignment.Elastix) print_status_msg() (ClearMapAppBase method) print_warning_msg() (ClearMapAppBase method) Printer (class in ClearMap.gui.gui_logging) prioritize_top_keys() (in module ClearMap.config.config_handler) process (ProcessWriter attribute) process() (in module ClearMap.ParallelProcessing.BlockProcessing) process_block_block() (in module ClearMap.ParallelProcessing.BlockProcessing) process_block_source() (in module ClearMap.ParallelProcessing.BlockProcessing) process_folders() (BatchProcessor method) (in module ClearMap.pipeline_orchestrators.batch_process) process_sample() (in module ClearMap.pipeline_orchestrators.batch_process) processing_type (GenericTab attribute) (GroupTab attribute) (PipelineTab attribute) (PostProcessingTab attribute) (PreProcessingTab attribute) processor (GroupAnalysisTab property) ProcessorSteps (class in ClearMap.pipeline_orchestrators.generic_orchestrators) processSingleConnection() (in module ClearMap.ImageProcessing.Tracing.Connect) ProcessWriter (class in ClearMap.ParallelProcessing.ProcessWriter) progress_changed (ProgressWatcher attribute) progress_watcher (PipelineOrchestrator attribute), [1] (RegistrationProcessor attribute) ProgressWatcher (class in ClearMap.gui.widgets) project() (in module ClearMap.gui.gui_utils_images) project_converter() (in module ClearMap.config.convert_config_versions) project_mini_brain() (RegistrationProcessor method) projection_thickness (RigidChannelStitchingParams attribute) prompt_conversion() (StitchingTab method) prompt_dialog() (in module ClearMap.gui.dialog_helpers) prompt_experiment_folder() (ClearMapApp method) prompt_machine_params() (in module ClearMap.config.early_boot) prompt_params() (ManageAssetsWidget method) prompt_prepare_all_channels_raw_data() (SampleInfoTab method) prompt_tmp_folder() (MachineConfig method) propagate_labels() (in module ClearMap.Analysis.graphs.graph_processing) propagate_params() (SampleParameters method) propagated_counts (ClassificationMetrics attribute) propagation_floor (ClassificationConfig property) propagation_iterations (ClassificationMetrics attribute) property_name (GraphFilterParams property) property_names (PropertyAggregator property) PropertyAggregator (class in ClearMap.Analysis.graphs.graph_processing) prune_container_invalid_atoms() (CompoundKey class method) prune_edge_geometry() (Graph method) prune_obsolete_channels() (StitchingParams method) prune_removed (InstancePolicy attribute) pseudo_random_rgb_array() (in module ClearMap.gui.gui_utils_images) publish() (BusSubscriberMixin method) (EventBus method) publishes (AtlasParams attribute) (BatchParameters attribute) (ChannelRegistrationParams attribute) (ChannelsUiParameterCollection attribute) Publishes (class in ClearMap.Utils.event_bus) publishes (GeneralChannelStitchingParams attribute) (RegistrationParams attribute) (SampleChannelParameters attribute) (SampleParameters attribute) (StitchingParams attribute) (VesselGraphParams attribute) pullback_image (RegistrationData attribute) python_version (EnvFileManager property) pytorch_info (PytorchVersionManager property) PytorchVersionManager (class in ClearMap.Utils.install_utils) Q qCleanupResources() (in module ClearMap.gui.creator.graphics_resources_rc) (in module ClearMap.gui.creator.icons_rc) qInitResources() (in module ClearMap.gui.creator.graphics_resources_rc) (in module ClearMap.gui.creator.icons_rc) quality (Alignment property) quality_at_coordinate() (WobblyAlignment method) quickMinMax() (LUTItem method) quickPercentile() (LUT method) R R2() (in module ClearMap.ImageProcessing.Binary.Smoothing) radii (VesselSignals attribute) rand_cmap() (in module ClearMap.Visualization.Color.Color) random_channel() (in module ClearMap.Analysis.colocalization.channel) rank() (in module ClearMap.ImageProcessing.Filter.Rank.RankResample) ratios (OrthoviewerSlicingMixin property) re() (Expression method) (Tag method) read() (ElastixPointFileManager method) (in module ClearMap.IO.CSV) (in module ClearMap.IO.FileList) (in module ClearMap.IO.GT) (in module ClearMap.IO.IO) (in module ClearMap.IO.MHD) (in module ClearMap.IO.MMP) (in module ClearMap.IO.NPY) (in module ClearMap.IO.NRRD) (in module ClearMap.IO.TIF) (in module ClearMap.ParallelProcessing.DataProcessing.ArrayProcessing) (in module ClearMap.ParallelProcessing.DataProcessing.ArrayProcessingCode) (Source method), [1] (TransformationBase class method) (VirtualSource method) (Workspace method) read_cfg() (in module ClearMap.config.convert_config_versions) read_group() (in module ClearMap.Analysis.Statistics.group_statistics) read_points() (in module ClearMap.Alignment.Elastix) read_sample_version() (ExperimentController method) read_str() (in module ClearMap.Analysis.graphs.utils) realign() (in module ClearMap.pipeline_orchestrators.batch_process) rebuild() (ComparisonsWidgetAdapter method) reconcile (InstanceContainerSpec attribute) reconcile_channel_pages() (ExperimentTab method) reconcile_children_from_view() (StitchingParams method) reconcile_from_config() (SampleParameters method) reconcile_generic_instance_containers() (in module ClearMap.config.config_adjusters.policy) reconcile_instance_container() (in module ClearMap.config.config_adjusters.policy) reconcile_stitching_channels() (in module ClearMap.config.config_adjusters.policy) reconcile_stitching_channels_step() (in module ClearMap.config.config_adjusters.policy) reconcile_workers() (ExperimentController method) reconcile_workers_after_channel_change (ExperimentController attribute) reconcile_workers_after_channel_change() (ExperimentController method) ReconcileKind (class in ClearMap.config.config_adjusters.policy_specs) ReconcileMode (class in ClearMap.config.config_adjusters.policy_specs) ReconcileStepSpec (class in ClearMap.config.config_adjusters.policy_specs) reconstruct() (in module ClearMap.ImageProcessing.grey_reconstruction) record_final_counts() (ClassificationMetrics method) record_output() (BinaryVesselProcessorSteps method) record_seed_counts() (ClassificationMetrics method) RECOVERABLE (Severity attribute) recovery_options (ClearMapException property) (ClearMapVRamException property) (ClearMapWorkspaceError property) RecoveryOption (class in ClearMap.Utils.exceptions) recursive_patch_button_boxes() (in module ClearMap.gui.widget_monkeypatch_callbacks) recursive_patch_compound_boxes() (in module ClearMap.gui.widget_monkeypatch_callbacks) recursive_patch_widgets() (in module ClearMap.gui.widget_monkeypatch_callbacks) RedCross (class in ClearMap.Visualization.Qt.utils) reduce (VesselGraphParams attribute) reduce_edge_geometry() (GeometricGraph method) reduce_graph() (in module ClearMap.Analysis.graphs.graph_processing) (VesselGraphProcessor method) ref_channel_cfg (RegistrationProcessor property) reference_channel (OrthoviewerSlicingMixin attribute) reflect() (in module ClearMap.ImageProcessing.Topology.Topology3d) refresh() (DataViewer method) refresh_layout_channel_items() (GeneralChannelStitchingParams method) reg_params (RegistrationData attribute) Region (class in ClearMap.Alignment.Stitching.stitching_rigid) register() (in module ClearMap.Scripts.align_new_api) (VesselGraphProcessor method) (WidgetOps method) register_validator() (in module ClearMap.config.validators) register_worker_factory() (ExperimentController method) REGISTERED (RegistrationStatus attribute) registration_config (OrchestratorBase property) registration_entry_template() (ExperimentTemplatesResolver method) registration_params_files (RegistrationProcessor property) registration_processor (OrchestratorBase attribute), [1] (VesselGraphProcessor attribute) registration_status() (RegistrationProcessor method) registration_target_channels() (ExperimentTemplatesResolver method) RegistrationData (class in ClearMap.Alignment.landmarks_registration.registration_data) RegistrationParams (class in ClearMap.gui.params) RegistrationProcessor (class in ClearMap.pipeline_orchestrators.registration_orchestrator) RegistrationStatus (class in ClearMap.pipeline_orchestrators.registration_orchestrator) RegistrationStatusChanged (class in ClearMap.Utils.events) RegistrationTab (class in ClearMap.gui.tabs) rel_container_path() (InstanceContainerSpec method) rel_templates_path() (InstanceContainerSpec method) relative_overlap_threshold (ChannelColocalizationParams attribute) relative_step_size (VolumeVisual property) relative_string() (Pattern method) relevant_channels (ChannelsUiParameterCollection property) relevant_pipelines (SampleManager property) reload() (ConfigProxy method) reload_config() (OrchestratorBase method) reload_prefs() (ClearMapApp method) reload_processing_config() (VesselGraphProcessor static method) remap_array_ranges() (in module ClearMap.Utils.array_utils) remap_array_ranges_1_d() (in module ClearMap.Utils.array_utils_cy) remap_array_ranges_2_d() (in module ClearMap.Utils.array_utils_cy) remap_edge_geometry_properties() (Graph method) remove_auto_loops() (in module ClearMap.Analysis.vasculature.graph_corrections) remove_background() (in module ClearMap.ImageProcessing.Experts.Cells) remove_channel() (EnvFileManager method) (SampleInfoTab method) remove_channel_tab() (GenericTab method) remove_channel_widget() (ExtendableTabWidget method) remove_crust() (CellDetector method) remove_current_channel() (SampleInfoTab method) remove_current_group() (BatchParameters method) remove_current_page() (GroupsWidgetAdapter method) remove_dependencies() (EnvFileManager method) remove_dependency() (EnvFileManager method) remove_edge() (Graph method), [1] remove_edge_geometry() (Graph method) remove_edge_property() (Graph method), [1] remove_extra_keys() (in module ClearMap.config.update_config) remove_graph_property() (Graph method) remove_isolated_edges() (Graph method) remove_isolated_vertices() (Graph method) remove_marker() (LandmarksSelectorDialog method) remove_mutual_loops_gt() (in module ClearMap.Analysis.vasculature.graph_corrections) remove_next_steps_files() (ProcessorSteps method) remove_p_val_nans() (in module ClearMap.Analysis.Statistics.group_statistics) remove_selected() (FileDropListWidget method) remove_self_loops() (Graph method) remove_source() (Layout method) remove_spurious_branches() (in module ClearMap.Analysis.vasculature.graph_corrections) remove_surface() (in module ClearMap.Analysis.vasculature.vasc_graph_utils) remove_vertex() (Graph method), [1] remove_vertex_property() (Graph method), [1] rename (InstanceContainerSpec attribute) rename() (CompoundKey method) rename_channels_in_workspace() (SampleManager method) rename_container_keys() (CompoundKey class method) rename_key() (CompoundKey class method) rename_workers_channels() (ExperimentController method) RenameChannelsDialog (class in ClearMap.gui.dialogs) renamed_channels (SampleManager property) (SampleManagerProtocol property) renamed_items (RunFacts attribute) renamed_map (RunFacts attribute) RenameStepSpec (class in ClearMap.config.config_adjusters.policy_specs) reorder_shape() (in module ClearMap.IO.TIF) replace() (in module ClearMap.Utils.RegularExpression) REPLACE() (in module ClearMap.Utils.utilities) REPLACE_CONTAINER (ReconcileMode attribute) replace_source_location() (Layout method) replace_widget() (in module ClearMap.gui.gui_utils_base) represent_flow_list() (in module ClearMap.config.config_handler) representative_points (Channel property) request_add_channel() (SampleParameters method) require_dict() (in module ClearMap.config.config_adjusters.templates_resolver) requirements (GenericTab attribute) (PipelineTab attribute) requirements_fulfilled() (GenericTab class method) (PipelineTab class method) requires_assets() (in module ClearMap.Utils.utilities) requires_binary() (VesselGraphProcessor static method) requires_graph() (VesselGraphProcessor static method) requires_sample_manager (AdjusterSpec attribute) resample() (in module ClearMap.Alignment.Resampling) (in module ClearMap.Analysis.Curves.Resampling) (SampleManager static method) resample_1d() (in module ClearMap.Analysis.Curves.Resampling) resample_assets() (ManageAssetsWidget method) resample_channel() (RegistrationProcessor method) (RegistrationTab method) resample_dialog() (ManageAssetsWidget method) resample_factor() (in module ClearMap.Alignment.Resampling) (ResamplingTransformation method), [1] resample_for_registration() (RegistrationProcessor method) resample_information() (in module ClearMap.Alignment.Resampling) resample_inverse() (in module ClearMap.Alignment.Resampling) resample_kwargs() (ResamplingTransformation method), [1] resample_nd() (in module ClearMap.Analysis.Curves.Resampling) resample_points() (in module ClearMap.Alignment.Resampling) resample_points_inverse() (in module ClearMap.Alignment.Resampling) resample_resolution() (in module ClearMap.Alignment.Resampling) resample_resolution_from_shape() (in module ClearMap.Alignment.Resampling) resample_shape() (in module ClearMap.Alignment.Resampling) resample_shape_from_resolution() (in module ClearMap.Alignment.Resampling) resampled_shape (VesselGraphProcessor property) resampled_shape() (SampleManager method) ResamplingTransformation (class in ClearMap.Alignment.Resampling) (class in ClearMap.Alignment.Transformations.ResamplingTransformation) rescale_channel() (in module ClearMap.pipeline_orchestrators.batch_process) rescale_img() (in module ClearMap.pipeline_orchestrators.batch_process) rescale_size_and_spacing() (in module ClearMap.Alignment.Elastix) reserved_namespace_keys (SmellScanPolicy attribute) RESET (ColorFormatter attribute) reset() (ClearMapApp method) (ProgressWatcher method) (Timer method) reset_log_length() (ProgressWatcher method) reset_loggers() (ClearMapApp method) reset_working() (ConfigCoordinator method) resolution (SampleChannelParameters attribute) resolve() (WidgetOps method) resolve_keys() (InstanceContainerSpec method) resolve_path() (in module ClearMap.config.config_adjusters.dict_ops) resolve_renamed_channel() (ExperimentTemplatesResolver static method) resolve_write_path() (ConfigHandler class method) RESOURCE_TYPE_TO_FOLDER (in module ClearMap.IO.assets_constants) resources_path (in module ClearMap.ImageProcessing.machine_learning.vessel_filling.vessel_filling) (in module ClearMap.Settings) ResourceTypeToFolderDialog (class in ClearMap.gui.dialogs) restore_elastix_cfg_no_landmarks() (ElastixConfigPatcher method) restrict_to_template_keys (ReconcileStepSpec attribute) restrictive_min_vein_radius (VesselGraphParams attribute) restrictive_vein_radius (ClassificationConfig attribute), [1] result() (ResourceTypeToFolderDialog method) result_data_file() (in module ClearMap.Alignment.Elastix) result_mapping() (ResourceTypeToFolderDialog method) results_folder (BatchParameters attribute) (GroupOrchestratorBase property) rev (ConfigCoordinator property) reverse_scale_axis() (OrthoviewerSlicingMixin method) rgb_LUT() (in module ClearMap.Visualization.Color.Color) rgb_to_hex() (in module ClearMap.Visualization.Color.Color) rgb_to_LUT() (in module ClearMap.Visualization.Color.Color) RigidChannelStitchingParams (class in ClearMap.gui.params) role (InstanceContainerSpec attribute) rotate() (in module ClearMap.ImageProcessing.Topology.Topology3d) rotations (in module ClearMap.ImageProcessing.Skeletonization.PK12) rotations12() (in module ClearMap.ImageProcessing.Topology.Topology3d) rotations6() (in module ClearMap.ImageProcessing.Topology.Topology3d) rotations_edges() (in module ClearMap.ImageProcessing.Binary.Smoothing) rotations_faces() (in module ClearMap.ImageProcessing.Binary.Smoothing) rotations_node_faces() (in module ClearMap.ImageProcessing.Binary.Smoothing) rotations_nodes() (in module ClearMap.ImageProcessing.Binary.Smoothing) row_count() (GraphFilterList method) run (GeneralChannelStitchingParams property) run() (AdjusterRunner method) (BinaryVesselProcessor method) (ExperimentConfigConverter method) (GroupOrchestratorBase method) (PipelineOrchestrator method) (VesselGraphProcessor method) run_adjusters() (in module ClearMap.config.config_adjusters.engine) run_all() (VasculatureTab method) run_batch_process() (BatchProcessingTab method) run_binarization (VesselBinarizationParams attribute) run_binary_filling (VesselBinarizationParams attribute) run_cell_detection() (CellDetector method) run_cell_map() (CellCounterTab method) run_channel() (CellCounterTab method) (TractMapTab method) run_colocalization_for_pair() (ColocalizationTab method) run_deep_filling (VesselBinarizationParams attribute) run_df_plots() (GroupAnalysisTab method) run_facts() (ExperimentTemplatesResolver method) run_inference() (in module ClearMap.ImageProcessing.machine_learning.vertices_classification.degree1_inference_utils) run_label (AdjustmentContext attribute) run_p_vals() (GroupAnalysisTab method) run_pipeline() (TractMapProcessor method) run_plots() (DensityGroupAnalysisOrchestrator method) run_registration() (RegistrationTab method) run_semantic_checks() (in module ClearMap.config.validators._semantic) run_smoothing (VesselBinarizationParams attribute) run_staged_imports() (in module ClearMap.gui.pretty_imports) run_step() (in module ClearMap.ImageProcessing.Experts.utils) run_stitching() (StitchingTab method) run_tract_map() (TractMapTab method) run_tuning_cell_detection() (CellCounterTab method) run_tuning_tract_map() (TractMapTab method) run_vasculature (BatchProcessingParams attribute) RunFacts (class in ClearMap.config.config_adjusters.templates_resolver) RunnerConfig (class in ClearMap.config.config_adjusters.engine) runs_on_pycharm() (in module ClearMap.Utils.utilities) runs_on_spyder() (in module ClearMap.Utils.utilities) runs_on_ui() (in module ClearMap.Utils.utilities) S S3() (in module ClearMap.ImageProcessing.Binary.Smoothing) sample_channel_entry_template() (ExperimentTemplatesResolver method) sample_channels (RunFacts attribute) sample_id (SharedSampleParams attribute), [1] sample_manager (AdjustmentContext attribute) (ClearMapApp property) (ExperimentTab property) (PipelineOrchestrator attribute) (RegistrationProcessor attribute) (VesselGraphProcessor attribute) sample_params (ExperimentTab attribute) sample_path_exists() (ExperimentController method) SampleChannelParameters (class in ClearMap.gui.params) SampleInfoTab (class in ClearMap.gui.tabs) SampleManager (class in ClearMap.pipeline_orchestrators.sample_info_management) SampleManagerProtocol (class in ClearMap.config.config_adjusters.type_hints) SampleParameters (class in ClearMap.gui.params) SamplePickerDialog (class in ClearMap.gui.widgets) sanitize_df() (in module ClearMap.Analysis.Statistics.data_frame_operations) (in module ClearMap.Analysis.Statistics.group_statistics) sanitize_n_processes() (in module ClearMap.Utils.utilities) sanitize_neg_one() (UiParameter method) sanitize_nones() (UiParameter method) sanitize_path_read() (UiParameter method) sanitize_path_write() (UiParameter method) sanitize_runtime_template_roots() (in module ClearMap.config.config_adjusters.policy) sanity_warnings (ClassificationMetrics property) sauvola() (in module ClearMap.ImageProcessing.Filter.Rank) (in module ClearMap.ImageProcessing.Filter.Rank.Parametric) (in module ClearMap.ImageProcessing.Filter.Rank.ParametricCode) sauvola_masked() (in module ClearMap.ImageProcessing.Filter.Rank.ParametricCode) save() (Graph method), [1] (in module ClearMap.Analysis.graphs.graph) (in module ClearMap.Analysis.graphs.graph_gt) (in module ClearMap.Visualization.Vispy.Plot3d) (Layout method) (Workspace method) save_filtered_table() (ColocalizationProcessor method) (ColocalizationTab method) save_graph() (VesselGraphProcessor method) save_layout() (in module ClearMap.Alignment.Stitching.stitching_rigid) save_results() (PatternDialog method) save_screenshot() (DataViewer method) save_shape (ChannelCellMapParams attribute) save_stats() (VasculatureTab method) save_workspace() (SampleManager method) SCALAR_UM (VesselGraphProcessor.RadiusLevel attribute) scale_axis() (OrthoviewerSlicingMixin method) scale_coords() (DataViewer method) scale_landmarks() (ChannelRegistrationParams static method) scaling (MiniBrain attribute) scaling_factor() (in module ClearMap.Analysis.vasculature.flow.units) scaling_factor_du() (in module ClearMap.Analysis.vasculature.flow.units) ScalingTransformation (class in ClearMap.Alignment.Transformations.LinearTransformation) scan_config_smells() (in module ClearMap.config.config_adjusters.policy) scan_folder_for_experiments() (in module ClearMap.config.config_handler) scan_gt_properties() (Graph static method) scan_gt_props() (in module ClearMap.Analysis.graphs.utils) Scatter3D (class in ClearMap.Visualization.Qt.widgets) scope (AdjusterSpec attribute) (AdjustmentContext attribute) Scope (class in ClearMap.config.config_handler) scope (ConfigSpec attribute) scope_root (ParamLink attribute) SCOPES (Graph attribute) score_stats (ClassificationMetrics attribute) screen_geometry() (in module ClearMap.Visualization.Qt.utils) sd_density_path() (GroupResultsAssets method) seal_and_snapshot (ExperimentController attribute) seal_and_snapshot() (ExperimentController method) search_elx_bin() (in module ClearMap.Alignment.Elastix) search_elx_lib() (in module ClearMap.Alignment.Elastix) search_indices() (in module ClearMap.Analysis.Measurements.MeasureExpression) search_indices_rectangle() (in module ClearMap.Analysis.Measurements.radius_measurements) (in module ClearMap.Analysis.Measurements.Voxelization) search_indices_sphere() (in module ClearMap.Analysis.Measurements.radius_measurements) (in module ClearMap.Analysis.Measurements.Voxelization) section (InstanceContainerSpec attribute) section_missing_only_defaults() (TemplateResolverBase method) sections_from_keys() (in module ClearMap.config.config_adjusters.engine) SectionValidators (class in ClearMap.config.validators._schema) seed_counts (ClassificationMetrics attribute) seed_missing_from_defaults() (ConfigCoordinator method) seed_thresholds (ClassificationConfig property) select_tab() (ClearMapApp method) selected (ComparisonsModel attribute) selected_asset_types (ManageAssetsWidget property) selected_assets (ManageAssetsWidget property) selected_comparisons (GroupAnalysisParams property) selected_pairs() (ComparisonsWidgetAdapter method) sep (ComparisonsModel attribute) SEP (CompoundKey attribute) sep (CompoundKey property) SEP (PairKey attribute) serialize_label() (ComparisonsModel method) series (Source attribute) series_mode (Source property) set() (in module ClearMap.Utils.HierarchicalDict) (WidgetOps method) set_active_sections() (ConfigCoordinator method) set_advanced_controls_visibility() (GenericTab method) set_annotation_file() (Annotation method) set_artery_vein_if_missing() (in module ClearMap.Analysis.vasculature.vasc_graph_utils) set_axes_names() (Pattern method) set_axis_name() (Pattern method) set_background() (in module ClearMap.Visualization.Vispy.Plot3d) set_base_dir() (ConfigCoordinator method) (ConfigRepository method) set_channel_expression() (SampleManager method) set_channel_resolution() (SampleManager method) set_channel_tag_name() (Pattern method) set_channels_provider() (GroupAnalysisParams method) set_channels_to_run() (StitchingParams method) set_color_scheme() (DataViewer method) set_controller() (ExperimentTab method) (GroupTab method) set_coords() (RedCross method) set_current_channel_name() (ExtendableTabWidget method) set_current_coords() (LandmarksSelectorDialog method) set_current_resolver() (in module ClearMap.config.config_adjusters.templates_resolver) set_data() (Scatter3D method) (VolumeVisual method) set_defaults_provider() (ConfigCoordinator method) (in module ClearMap.config.defaults_provider) set_edge_annotation() (AnnotatedGraph method) (Graph method) set_edge_coordinates() (GeometricGraph method) (Graph method) set_edge_geometry() (GeometricGraph method) (Graph method) set_edge_geometry_edge_properties() (Graph method) set_edge_geometry_type() (Graph method) set_edge_geometry_vertex_properties() (Graph method) set_edge_property() (Graph method), [1] set_edge_property_map() (in module ClearMap.Analysis.graphs.type_conversions) set_edge_radii() (GeometricGraph method) (Graph method) set_elastix_library_path() (in module ClearMap.Alignment.Elastix) set_elastix_path() (in module ClearMap.Utils.install_utils) set_enabled() (RigidChannelStitchingParams method) (WobblyChannelStitchingParams method) set_experiment_dir() (ExperimentController method) set_file() (Printer method) set_font() (ClearMapAppBase method) set_font_size() (ClearMapAppBase method) set_geometry_settings_from_options() (SampleChannelParameters method) set_graph_property() (Graph method) set_group_base_dir() (AnalysisGroupController method) set_groups() (AnalysisGroupController method) set_high() (HighLowLUT method) set_invalid() (WobblySource method) set_isolated() (WobblySource method) set_item_checked() (CheckableListWidget method) set_item_recursive() (in module ClearMap.Utils.utilities) set_items() (CheckableListWidget method) (LandmarksWeightsPanel method) set_label_file() (Annotation method) set_light_to_camera() (in module ClearMap.Visualization.Vispy.Plot3d) set_low() (HighLowLUT method) set_main_progress() (ProgressWatcher method) set_metric_parameter_file() (in module ClearMap.Alignment.Elastix) set_mode() (GuiController method) set_next_registration_parameters() (AlignmentTool method) set_on_plot_group() (GroupAnalysisParams method) set_orientations() (DataViewer method) set_painting() (UiParameterCollection method) set_params() (ExperimentTab method) (GenericDialog method) (GenericTab method) (GenericUi method) (PreferenceUi method) set_patch_at_path() (in module ClearMap.config.config_adjusters.patch_ops) set_path_transform_files() (in module ClearMap.Alignment.Elastix) set_paths() (BatchParameters method) (GroupsWidgetAdapter method) set_pipeline() (AnalysisGroupController method) set_pipelines() (GroupAnalysisParams method) set_plotable_channels() (SharedVesselBinarizationParams method) set_points() (AlignmentTool method) (DataViewer method) set_poll_interval() (ProgressWatcher method) set_positions() (WobblyLayout method) set_progress() (ProgressWatcher method) set_progress_watcher() (AnalysisGroupController method) (GroupOrchestratorBase method) (PipelineOrchestrator method) set_renamed_channels() (SampleManager method) set_resource_type_to_folder() (SampleManager method) set_run_channel() (StitchingTab method) set_sample_id() (ExperimentController method) set_sections() (ConfigRepository method) set_source() (in module ClearMap.Visualization.Qt.Plot3d) set_source_positions() (Layout method) set_status_at_coordinate() (WobblyAlignment method) (WobblySource method) set_structure_id() (VesselVisualizationParams method) set_suffixes_provider() (GroupAnalysisParams method) set_tabs() (ClearMapApp method) set_tabs_progress_watchers() (ClearMapApp method) (ClearMapAppBase method) set_target_space() (OrthoviewerSlicingMixin method) set_thread_wrapper() (AnalysisGroupController method) (GroupOrchestratorBase method) set_transform_file_size_and_spacing() (in module ClearMap.Alignment.Elastix) set_type() (in module ClearMap.ImageProcessing.machine_learning.torch_utils) set_value() (GroupsWidgetAdapter method) set_vectors() (DataViewer method) set_vertex_annotation() (AnnotatedGraph method) (Graph method) set_vertex_coordinates() (GeometricGraph method) (Graph method) set_vertex_property() (Graph method), [1] set_vertex_property_map() (in module ClearMap.Analysis.graphs.type_conversions) set_vertex_radii() (GeometricGraph method) (Graph method) set_vertex_radius() (Graph method) set_view_parameter() (in module ClearMap.Visualization.Vispy.Plot3d) set_visible() (RigidChannelStitchingParams method) (WobblyChannelStitchingParams method) set_voxelization_radii() (CellDetector method) set_watcher_step() (PipelineOrchestrator method) set_weights() (LandmarksWeightsPanel method) set_workers_progress_watcher() (ExperimentController method) setMaximum() (NProcessesWidget method) setMinimum() (NProcessesWidget method) setMinMax() (DataViewer method) setRange() (NProcessesWidget method) setSelectedItems() (TwoListSelection method) setSliceAxis() (DataViewer method) setSource() (DataViewer method) setup() (BinaryVesselProcessor method) (CellDetector method) (ColocalizationProcessor method) (GenericTab method) (GenericUi method) (LandmarksSelectorDialog method) (ManageAssetsWidget method) (OrthoViewer method) (PatternDialog method) (PipelineOrchestrator method) (PreferenceUi method) (ProgressWatcher method) (RegistrationProcessor method) (SampleManager method) (SamplePickerDialog method) (StitchingProcessor method) (StructureSelector method) (TractMapProcessor method) (VesselGraphProcessor method) (WizardWidget method) setup_atlas() (RegistrationTab method) setup_atlases() (RegistrationProcessor method) setup_cell_param_histogram() (CellCounterTab method) setup_channel_operation() (BinaryVesselProcessor static method) setup_complete (GenericTab attribute) (OrchestratorBase attribute), [1] (RegistrationProcessor attribute) setup_except_hook() (Printer method) setup_icons() (ClearMapAppBase method) setup_if_needed() (OrchestratorBase method) (PipelineOrchestrator method) setup_loggers() (ClearMapApp method) setup_menus() (ClearMapApp method) setup_mini_brain() (in module ClearMap.pipeline_orchestrators.registration_orchestrator) setup_monitoring_bars() (ClearMapAppBase method) setup_plots() (ClearMapAppBase method) setup_preferences() (PreferenceUi method) setup_results_folder() (BatchTab method) setup_sample_manager() (ExperimentTab method) (PipelineTab method) setValue() (LandmarksWeightsPanel method) (NProcessesWidget method) severity (AggregatedValidationError attribute) (AssetNotFoundError attribute) Severity (class in ClearMap.Utils.exceptions) severity (ClearMapException attribute) (ClearMapFileNotFoundError attribute) (ClearMapPermissionError attribute) (ClearMapRuntimeError attribute) (ClearMapValueError attribute) (ClearMapVRamException attribute) (IncompatibleSource attribute) (MetadataError attribute) (MissingAssetError attribute) (MissingChannelError attribute) (MissingRequirementException attribute) (NotAnOmeFile attribute) (NrrdError attribute) (ParamsOrientationError attribute) (PatchConflictError attribute) (PlotGraphError attribute) (SmiError attribute) (SourceModuleNotFoundError attribute) shape (AbstractSource property) (GeometricGraph property) (Graph property) (Layout property) (OrthoViewer property) (Region property) (Slice property) (Source property), [1], [2], [3], [4], [5], [6], [7] (VirtualSource property), [1] shape() (in module ClearMap.IO.FileList) (in module ClearMap.IO.IO) shape_file (Source property) shape_file() (in module ClearMap.IO.FileList) shape_from_tif() (in module ClearMap.IO.TIF) shape_list (Source property) shape_list() (in module ClearMap.IO.FileList) shape_to_tif() (in module ClearMap.IO.TIF) shape_wobbly (WobblyLayout property) SharedRegistrationParams (class in ClearMap.gui.params) SharedSampleParams (class in ClearMap.gui.params) SharedVesselBinarizationParams (class in ClearMap.gui.params) shift (Alignment property) shift_coordinates() (TractMapProcessor method) shifts (WobblyAlignment property) shifts_from_minimization() (in module ClearMap.Alignment.Stitching.stitching_wobbly) shifts_from_tracing() (in module ClearMap.Alignment.Stitching.stitching_wobbly) show() (StructureSelector method) show_workspace_info() (ClearMapApp method) signal_process_finished() (ClearMapAppBase method) Signals (ExperimentController attribute) simplify_slicing() (in module ClearMap.IO.Slice) single_color_colormap() (in module ClearMap.Visualization.Vispy.Plot3d) sink (Tracer attribute) sink_slicing() (Layout method) size (Source property) size() (in module ClearMap.IO.IO) size_max (BlockProcessingParams attribute) (BlockProcessingWidget property) (ChannelCellMapPerformanceParams attribute) (VesselBinarizationPerformanceParams attribute) size_min (BlockProcessingParams attribute) (BlockProcessingWidget property) (ChannelCellMapPerformanceParams attribute) (VesselBinarizationPerformanceParams attribute) sizeHint() (LUTWidget method) sizes (Channel property) skeletonize (VesselGraphParams attribute) skeletonize() (in module ClearMap.ImageProcessing.Skeletonization.PK12) (in module ClearMap.ImageProcessing.Skeletonization.Skeletonization) (VesselGraphProcessor method) skeletonize_and_build_graph() (VesselGraphProcessor method) skeletonize_index() (in module ClearMap.ImageProcessing.Skeletonization.PK12) skip (RigidChannelStitchingParams attribute) (WobblyChannelStitchingParams attribute) skip_paths_for_missing_only_merge() (ContainerSpecRegistry method) skip_str() (in module ClearMap.Analysis.graphs.utils) skip_vec_scalar() (in module ClearMap.Analysis.graphs.utils) skip_vec_string() (in module ClearMap.Analysis.graphs.utils) Slice (class in ClearMap.Alignment.Stitching.stitching_rigid) (class in ClearMap.IO.Slice) slice_along_axis() (Layout method) (Source method) slice_along_axis_wobbly() (WobblyLayout method) slice_layout_along_axis() (in module ClearMap.Alignment.Stitching.stitching_rigid) slice_pixel_size (WobblyChannelStitchingParams attribute) slice_to_range() (in module ClearMap.IO.Slice) slice_tuples (OrthoviewerSlicingMixin property) slice_valid_range (WobblyChannelStitchingParams attribute) slice_x (SampleChannelParameters attribute) (UiCropChanged attribute) slice_y (SampleChannelParameters attribute) (UiCropChanged attribute) slice_z (SampleChannelParameters attribute) (UiCropChanged attribute) sliced_ndim() (in module ClearMap.IO.Slice) sliced_offset() (in module ClearMap.IO.Slice) sliced_order() (in module ClearMap.IO.Slice) sliced_reduction() (in module ClearMap.IO.Slice) sliced_shape() (in module ClearMap.IO.Slice) sliced_slicing() (in module ClearMap.IO.Slice) sliced_start() (in module ClearMap.IO.Slice) sliced_strides() (in module ClearMap.IO.Slice) slicing (OrthoviewerSlicingMixin property) (Slice property) SlicingTransformation (class in ClearMap.Alignment.Transformations.SlicingTransformation) sm (ExperimentTemplatesResolver property) SmellScanPolicy (class in ClearMap.config.config_adjusters.policy_specs) smi_query() (in module ClearMap.Utils.utilities) SmiError smooth_binary() (in module ClearMap.Alignment.Stitching.stitching_wobbly) smooth_by_configuration() (in module ClearMap.ImageProcessing.Binary.Smoothing) smooth_by_configuration_block() (in module ClearMap.ImageProcessing.Binary.Smoothing) smooth_by_configuration_filename (in module ClearMap.ImageProcessing.Binary.Smoothing) smooth_by_counting() (in module ClearMap.ImageProcessing.Binary.Smoothing) smooth_channel() (BinaryVesselProcessor method) smooth_displacements() (in module ClearMap.Alignment.Stitching.stitching_wobbly) (WobblyAlignment method) smooth_positions() (in module ClearMap.Alignment.Stitching.stitching_wobbly) (WobblySource method) smooth_window() (in module ClearMap.Alignment.Stitching.stitching_wobbly) smoothed (BinaryVesselProcessorSteps attribute) snake_to_title() (in module ClearMap.Utils.utilities) snapshot_to() (ConfigCoordinator method) solve() (LinearSystem method) sort_channels() (ColocalizationTab method) sort_connectivity_based_on_vertex_property() (in module ClearMap.Analysis.vasculature.general_functions) sort_sources_by_position() (Layout method) sort_sources_by_tile_position() (TiledLayout method) Source (class in ClearMap.Alignment.Stitching.stitching_rigid) (class in ClearMap.IO.CSV) (class in ClearMap.IO.FileList) (class in ClearMap.IO.GT) (class in ClearMap.IO.MHD) (class in ClearMap.IO.MMP) (class in ClearMap.IO.NPY) (class in ClearMap.IO.NRRD) (class in ClearMap.IO.Source) (class in ClearMap.IO.TIF) source (Membership attribute) (Slice property) (Source property) source() (in module ClearMap.IO.IO) (Workspace method) source_arrays() (Overlap method) source_from_tile_position() (TiledLayout method) source_index() (in module ClearMap.Alignment.Stitching.stitching_rigid) (Layout method) source_modules (in module ClearMap.IO.IO) SOURCE_OF_TRUTH (ContainerRole attribute) source_positions() (Layout method) source_slicings() (Overlap method) source_to_module() (in module ClearMap.IO.IO) source_to_tile_position() (TiledLayout method) SourceModuleNotFoundError SourceRegion (class in ClearMap.Alignment.Stitching.stitching_rigid) sources (AlignmentBase property) (Layout property) (Overlap property) sources_as_real() (Layout method) sources_as_virtual() (Layout method) sources_from_alignments() (in module ClearMap.Alignment.Stitching.stitching_rigid) space_axes (DataViewer property) spec_name (PipelineStep attribute) SPECIAL (ReconcileKind attribute) special_instance_specs() (ContainerSpecRegistry method) specs (ContainerSpecRegistry property) sphere() (in module ClearMap.ImageProcessing.Filter.StructureElement) split() (in module ClearMap.IO.FileUtils) split_channel() (PatternFinder class method) split_into_blocks() (in module ClearMap.ParallelProcessing.BlockProcessing) split_pattern (CondaPackage attribute) split_str() (CompoundKey class method) src_dir (ConfigHandler attribute) (ConfigHandler property) src_folder (ClearMapApp property) (SampleInfoTab property) (SharedSampleParams attribute) stack_columns() (StitchingProcessor method) stack_pixel_size (WobblyChannelStitchingParams attribute) stack_valid_range (WobblyChannelStitchingParams attribute) stack_voxelizations() (in module ClearMap.Analysis.Statistics.group_statistics) stacked_density_path() (GroupResultsAssets method) stage_x (TileRecord attribute) stage_y (TileRecord attribute) start() (GuiController method) (PerfMonitor method) (SlicingTransformation method) (Timer method) start_folder (PreferencesParams attribute) start_full_screen (MachineConfig property) (PreferencesParams attribute) start_polling() (ProgressWatcher method) stat_graph_properties() (in module ClearMap.Scripts.partial_gt_load_demo) StateManager (class in ClearMap.IO.assets_specs) STATIC_FILLER (AdjusterKind attribute) stats_imgs (LoadedPValueResults property) stats_table_path() (GroupResultsAssets method) status (StateManager property) (WobblySource property) status_at_coordinate() (WobblyAlignment method) (WobblySource method) status_to_description (WobblyAlignment attribute) (WobblySource attribute) status_to_description() (in module ClearMap.ImageProcessing.Experts.Vasculature) std() (in module ClearMap.ImageProcessing.Filter.Rank) (in module ClearMap.ImageProcessing.Filter.Rank.Rank) (in module ClearMap.ImageProcessing.Filter.Rank.RankCode) std_masked() (in module ClearMap.ImageProcessing.Filter.Rank.RankCode) step (AdjusterSpec attribute) Step (class in ClearMap.config.config_adjusters.adjusters_api) step() (SlicingTransformation method) step_exists() (GenericTab method) (ProcessorSteps method) step_id (PipelineStep attribute) StepChip (class in ClearMap.gui.pipeline_widgets) steps (BinaryVesselProcessorSteps property) (LinearPipeline attribute) (ProcessorSteps property) (VesselGraphProcessor attribute) StepSpec (class in ClearMap.config.config_adjusters.policy_specs) (class in ClearMap.gui.pipeline_model) stitch() (in module ClearMap.Scripts.align_new_api) (Layout method) (StitchingProcessor method) stitch_by_function() (in module ClearMap.Alignment.Stitching.stitching_rigid) stitch_by_function_with_weights() (in module ClearMap.Alignment.Stitching.stitching_rigid) stitch_by_interpolation() (in module ClearMap.Alignment.Stitching.stitching_rigid) stitch_by_interpolation_adjust_max() (in module ClearMap.Alignment.Stitching.stitching_rigid) stitch_by_max() (in module ClearMap.Alignment.Stitching.stitching_rigid) stitch_by_mean() (in module ClearMap.Alignment.Stitching.stitching_rigid) stitch_by_min() (in module ClearMap.Alignment.Stitching.stitching_rigid) stitch_channel_wobbly() (StitchingProcessor method) stitch_layout() (in module ClearMap.Alignment.Stitching.stitching_rigid) (in module ClearMap.Alignment.Stitching.stitching_wobbly) stitch_overlay() (StitchingProcessor method) stitch_weights() (in module ClearMap.Alignment.Stitching.stitching_rigid) stitchable_channels (SampleManager property) (SampleManagerProtocol property) stitched (BinaryVesselProcessorSteps attribute) stitched_shape() (SampleManager method) stitching_entry_template() (ExperimentTemplatesResolver method) stitching_target_channels() (ExperimentTemplatesResolver method) stitching_template_keys (ExperimentTemplatesResolver property) StitchingParams (class in ClearMap.gui.params) StitchingProcessor (class in ClearMap.pipeline_orchestrators.stitching_orchestrator) StitchingTab (class in ClearMap.gui.tabs) stop() (PerfMonitor method) (SlicingTransformation method) stop_polling() (ProgressWatcher method) stop_process() (PipelineOrchestrator method) stopped (PipelineOrchestrator attribute), [1] str_to_capitalize() (UiParameter method) str_to_lower() (UiParameter method) strides (Slice property) string() (Expression method) (Pattern method) (ProcessWriter method) (Tag method) string_from_index() (Expression method) (Tag method) strip_params() (ConfigHandler static method) strip_version_suffix() (ConfigHandler static method) strong_template_smells (SmellScanPolicy attribute) structure_element() (in module ClearMap.ImageProcessing.Filter.StructureElement) structure_element_offsets() (in module ClearMap.ImageProcessing.Filter.StructureElement) structure_specific_radius_filter() (in module ClearMap.Analysis.vasculature.general_functions) structure_tree_id (AtlasParams attribute) StructurePickerWidget (class in ClearMap.gui.widgets) StructureSelector (class in ClearMap.gui.widgets) sub_graph() (Graph method) sub_slice() (Graph method) sub_slice_edge_filter() (Graph method) sub_slice_vertex_filter() (Graph method) sub_step_name (ProgressWatcher property) sub_step_name_changed (ProgressWatcher attribute) subdir (ConfigSpec attribute) submit() (ConfigCoordinator method) submit_patch() (ConfigCoordinator method) subpatterns_to_groups() (in module ClearMap.Utils.RegularExpression) subplot_tiling() (in module ClearMap.Visualization.Matplotlib.PlotUtils) subscribe() (BusSubscriberMixin method) (EventBus method) substitute_deprecated_arg() (in module ClearMap.Utils.utilities) subtract_mean() (in module ClearMap.ImageProcessing.Filter.Rank) (in module ClearMap.ImageProcessing.Filter.Rank.PercentileCode) (in module ClearMap.ImageProcessing.Filter.Rank.Rank) (in module ClearMap.ImageProcessing.Filter.Rank.RankCode) subtract_mean_masked() (in module ClearMap.ImageProcessing.Filter.Rank.PercentileCode) (in module ClearMap.ImageProcessing.Filter.Rank.RankCode) subtract_mean_percentile() (in module ClearMap.ImageProcessing.Filter.Rank) (in module ClearMap.ImageProcessing.Filter.Rank.Percentile) SubTypeSpec (class in ClearMap.IO.assets_specs) success() (SuccessLogger method) SuccessLogger (class in ClearMap.Scripts.partial_gt_load_demo) suffix (PairKey attribute) suffix() (GraphFilterParams method) sum() (in module ClearMap.ImageProcessing.Filter.Rank.BilateralCode) (in module ClearMap.ImageProcessing.Filter.Rank.PercentileCode) (in module ClearMap.ImageProcessing.Filter.Rank.RankCode) sum_above() (in module ClearMap.ImageProcessing.Filter.Rank.PercentileCode) sum_above_masked() (in module ClearMap.ImageProcessing.Filter.Rank.PercentileCode) sum_above_percentile() (in module ClearMap.ImageProcessing.Filter.Rank) (in module ClearMap.ImageProcessing.Filter.Rank.Percentile) sum_bilateral() (in module ClearMap.ImageProcessing.Filter.Rank) (in module ClearMap.ImageProcessing.Filter.Rank.Bilateral) sum_masked() (in module ClearMap.ImageProcessing.Filter.Rank.BilateralCode) (in module ClearMap.ImageProcessing.Filter.Rank.PercentileCode) (in module ClearMap.ImageProcessing.Filter.Rank.RankCode) sum_percentile() (in module ClearMap.ImageProcessing.Filter.Rank) (in module ClearMap.ImageProcessing.Filter.Rank.Percentile) sum_realtive() (in module ClearMap.ImageProcessing.Filter.Rank.BilateralCode) sum_relaive_masked() (in module ClearMap.ImageProcessing.Filter.Rank.BilateralCode) sum_relative_bilateral() (in module ClearMap.ImageProcessing.Filter.Rank) (in module ClearMap.ImageProcessing.Filter.Rank.Bilateral) summarize_paths() (in module ClearMap.config.config_adjusters.trace_logging) summary() (ClassificationMetrics method) supported_exts (ConfigHandler attribute) surface_project() (in module ClearMap.gui.gui_utils_images) swap_old_channel() (in module ClearMap.pipeline_orchestrators.experiment_controller) swapped() (CompoundKey method) (PairKey method) Swin3DModel (class in ClearMap.ImageProcessing.machine_learning.vertices_classification.degree1_inference_utils) sync_cursors() (DataViewer method) synchronize() (in module ClearMap.Visualization.Qt.Plot3d) T t_test_region_counts() (in module ClearMap.Analysis.Statistics.group_statistics) t_test_voxelization() (in module ClearMap.Analysis.Statistics.group_statistics) tab (UiParameter attribute), [1] tab_idx (GenericTab attribute) TabActivationResult (class in ClearMap.Utils.events) TabRegistry (class in ClearMap.gui.tab_registry) TabRequirements (class in ClearMap.gui.tabs_interfaces) tabs (GuiController property) (TabsUpdated attribute) TabsUpdated (class in ClearMap.Utils.events) Tag (class in ClearMap.Utils.tag_expression) tag() (Expression method) (Tag method) tag_max() (Expression method) tag_min() (Expression method) tag_names() (Expression method) tag_range() (Expression method) tag_regexp (Expression attribute) tag_to_axes_order() (Source method) take_avg_streamlines() (in module ClearMap.Analysis.vasculature.general_functions) teardown() (UiParameter method) template_kind (InstanceContainerSpec attribute) template_roots() (ContainerSpecRegistry method) templateish_exact (SmellScanPolicy attribute) templateish_suffix (SmellScanPolicy attribute) TemplateKind (class in ClearMap.config.config_adjusters.policy_specs) TemplateResolverBase (class in ClearMap.config.config_adjusters.templates_resolver) temporary_filename() (in module ClearMap.IO.Temporary) tera_stitcher_path (in module ClearMap.Settings) test() (in module ClearMap.Analysis.Curves.Resampling) (in module ClearMap.Analysis.Measurements.MeasureExpression) (in module ClearMap.Analysis.Measurements.radius_measurements) (in module ClearMap.Analysis.vasculature.graph_corrections) (in module ClearMap.config.convert_config_versions) (in module ClearMap.IO.CSV) (in module ClearMap.IO.GT) (in module ClearMap.ParallelProcessing.DataProcessing.ConvolvePointList) (in module ClearMap.ParallelProcessing.DataProcessing.MeasurePointList) test_completed_cumulatives() (in module ClearMap.Analysis.Statistics.group_statistics_cumulatives) test_completed_inverted_cumulatives() (in module ClearMap.Analysis.Statistics.group_statistics_cumulatives) test_cramer_von_mises_2_sample() (in module ClearMap.Analysis.Statistics.StatisticalTests) test_data_path (in module ClearMap.Settings) test_path (in module ClearMap.Settings) text_updated (Printer attribute) three_d_plot_bg (PreferencesParams attribute) threshold (VolumeVisual property) threshold() (in module ClearMap.ImageProcessing.Filter.Rank) (in module ClearMap.ImageProcessing.Filter.Rank.PercentileCode) (in module ClearMap.ImageProcessing.Filter.Rank.Rank) (in module ClearMap.ImageProcessing.Filter.Rank.RankCode) (in module ClearMap.ImageProcessing.Thresholding.Thresholding) (in module ClearMap.ImageProcessing.Thresholding.ThresholdingCode) threshold_adaptive() (in module ClearMap.ImageProcessing.Experts.Vasculature) threshold_decay (ClassificationConfig property) threshold_isodata() (in module ClearMap.ImageProcessing.Experts.Vasculature) threshold_masked() (in module ClearMap.ImageProcessing.Filter.Rank.PercentileCode) (in module ClearMap.ImageProcessing.Filter.Rank.RankCode) threshold_percentile() (in module ClearMap.ImageProcessing.Filter.Rank) (in module ClearMap.ImageProcessing.Filter.Rank.Percentile) threshold_to_background() (in module ClearMap.ImageProcessing.Thresholding.ThresholdingCode) tif_shape (Source property) tif_to_clearmap_order() (in module ClearMap.IO.TIF) tile_dim (TiledLayout property) tile_extension (PatternDialog attribute) tile_position (Slice property) (Source property) tile_positions (TiledLayout property) tiled_layout() (in module ClearMap.Visualization.Qt.utils) TiledLayout (class in ClearMap.Alignment.Stitching.stitching_rigid) TileRecord (class in ClearMap.IO.TIF) time (Timer attribute) timed() (in module ClearMap.Utils.Timer) timeit() (in module ClearMap.Utils.Timer) Timer (class in ClearMap.Utils.Timer) title (PlotPanel attribute) title_to_snake() (in module ClearMap.Utils.utilities) titles (TabsUpdated attribute) tmp_dir (BootResult attribute) tmp_dtype (Percentile attribute) (TwoPhaseReducer attribute) TmpDebug (class in ClearMap.gui.gui_utils_base) to() (in module ClearMap.ImageProcessing.machine_learning.torch_utils) to_canonical() (ConfigAlternativesRegistry method) to_channel_config() (PatternFinder method) to_clearmap_order() (Source method) to_config_keys() (in module ClearMap.config.config_adjusters.adjusters_api) to_config_keys_tuples() (in module ClearMap.config.config_adjusters.adjusters_api) to_configobj() (in module ClearMap.config.config_handler) to_dict() (AffineTransformation method) (ChannelSpec method) (ElastixTransformation method) (OrientationTransformation method), [1] (ResamplingTransformation method), [1] (ScalingTransformation method) (SlicingTransformation method) (Transformation method) (TransformationBase method) (TypeSpec method) to_html() (AboutInfo method) to_json() (in module ClearMap.config.config_handler) to_yml() (in module ClearMap.config.config_handler) toggle() (LinearPipeline method) toggle_layer() (DataViewer method) toggled (StepChip attribute) toolkit_dep_to_version() (PytorchVersionManager method) toolkit_version_from_torch_pkg() (PytorchVersionManager method) tooltip (RecoveryOption attribute) tophat() (in module ClearMap.ImageProcessing.Filter.Rank) (in module ClearMap.ImageProcessing.Filter.Rank.Rank) (in module ClearMap.ImageProcessing.Filter.Rank.RankCode) tophat_masked() (in module ClearMap.ImageProcessing.Filter.Rank.RankCode) torch_build_to_cuda_version() (PytorchVersionManager method) trace (RunnerConfig attribute) trace() (in module ClearMap.ImageProcessing.Tracing.Trace) (in module ClearMap.ImageProcessing.Tracing.TraceCode) trace_edge_label() (in module ClearMap.Analysis.graphs.graph_processing) trace_paths (RunnerConfig attribute) trace_sink (RunnerConfig attribute) trace_to_mask() (in module ClearMap.ImageProcessing.Tracing.Trace) (in module ClearMap.ImageProcessing.Tracing.TraceCode) trace_vertex_label() (in module ClearMap.Analysis.graphs.graph_processing) tracePointToMask() (in module ClearMap.ImageProcessing.Tracing.Connect) tracePointToNeighbor() (in module ClearMap.ImageProcessing.Tracing.Connect) Tracer (class in ClearMap.config.config_adjusters.trace_logging) track_positions() (in module ClearMap.Alignment.Stitching.Tracking) tract_map_entry_template() (ExperimentTemplatesResolver method) tract_map_target_channels() (ExperimentTemplatesResolver method) TractMapParams (class in ClearMap.gui.params) TractMapPerformanceParams (class in ClearMap.gui.params) TractMapProcessor (class in ClearMap.pipeline_orchestrators.tract_map) TractMapTab (class in ClearMap.gui.tabs) train() (in module ClearMap.ImageProcessing.machine_learning.vessel_filling.vessel_filling) transform (VesselGraphParams attribute) transform() (in module ClearMap.Alignment.Elastix) transform_coordinates (ChannelTractMapParams attribute) transform_coordinates() (CellDetector method) (TractMapTab method) transform_data() (AffineTransformation method) (ElastixTransformation method) (OrientationTransformation method), [1] (ResamplingTransformation method), [1] (ScalingTransformation method) (SlicingTransformation method) (Transformation method) (TransformationBase method) transform_directory_and_file() (in module ClearMap.Alignment.Elastix) transform_file() (in module ClearMap.Alignment.Elastix) transform_file_size_and_spacing() (in module ClearMap.Alignment.Elastix) transform_params (RegistrationData attribute) transform_points() (AffineTransformation method) (ElastixTransformation method) (in module ClearMap.Alignment.Elastix) (OrientationTransformation method), [1] (ResamplingTransformation method), [1] (ScalingTransformation method) (SlicingTransformation method) (Transformation method) (TransformationBase method) transform_properties() (Graph method) transform_shape() (AffineTransformation method) (OrientationTransformation method), [1] (ResamplingTransformation method), [1] (ScalingTransformation method) (SlicingTransformation method) (Transformation method) (TransformationBase method) transform_slicing() (SlicingTransformation method) Transformation (class in ClearMap.Alignment.Transformations.Transformation) transformation() (TractMapProcessor static method) transformation_from_dict() (in module ClearMap.Alignment.Transformations.Transformation) TransformationBase (class in ClearMap.Alignment.Transformations.Transformation) transformix_binary (in module ClearMap.Alignment.Elastix) transpose_array() (in module ClearMap.IO.TIF) tree_id (UiAtlasStructureTreeIdChanged attribute) trigger_workspace_reset() (ClearMapApp method) trim_or_pad() (in module ClearMap.Utils.utilities) try_get_item_recursive() (in module ClearMap.Utils.utilities) try_load_points() (AlignmentTool method) tsne() (in module ClearMap.Analysis.DimensionReduction) ttype (AffineTransformation attribute) (ElastixTransformation attribute) (OrientationTransformation attribute), [1] (ScalingTransformation attribute) (SlicingTransformation attribute) (Tag attribute) (Transformation attribute) (TransformationBase attribute) ttype_to_dtype() (in module ClearMap.Utils.tag_expression) tubeness() (in module ClearMap.ImageProcessing.Differentiation) (in module ClearMap.ImageProcessing.Differentiation.Hessian) (in module ClearMap.ImageProcessing.Differentiation.HessianCode) tubeness_threshold() (in module ClearMap.ImageProcessing.Differentiation.HessianCode) tubify() (in module ClearMap.ImageProcessing.Experts.Vasculature) TwoListSelection (class in ClearMap.gui.widgets) TwoPhaseReducer (class in ClearMap.Analysis.graphs.graph_processing) type (ElastixEntry property) TypeSpec (class in ClearMap.IO.assets_specs) U U0() (in module ClearMap.ImageProcessing.Binary.Smoothing) U1() (in module ClearMap.ImageProcessing.Binary.Smoothing) U2() (in module ClearMap.ImageProcessing.Binary.Smoothing) u64() (in module ClearMap.Analysis.graphs.utils) u8() (in module ClearMap.Analysis.graphs.utils) ui (GenericUi attribute) ui_file_name (GenericUi attribute) ui_plot() (GenericTab static method) ui_task_progress() (in module ClearMap.gui.tabs) UiAlignWithChanged (class in ClearMap.Utils.events) UiAtlasIdChanged (class in ClearMap.Utils.events) UiAtlasStructureTreeIdChanged (class in ClearMap.Utils.events) UiBatchGroupsChanged (class in ClearMap.Utils.events) UiBatchResultsFolderChanged (class in ClearMap.Utils.events) UiChannelRenamed (class in ClearMap.Utils.events) UiChannelsChanged (class in ClearMap.Utils.events) UiCropChanged (class in ClearMap.Utils.events) UiLayoutChannelChanged (class in ClearMap.Utils.events) UiOrientationChanged (class in ClearMap.Utils.events) UiParameter (class in ClearMap.gui.params_interfaces) UiParameterCollection (class in ClearMap.gui.params_interfaces) UiPrepareRawDataForClearMap (class in ClearMap.Utils.events) UiRequestLandmarksDialog (class in ClearMap.Utils.events) UiRequestPlotAtlas (class in ClearMap.Utils.events) UiRequestPlotMiniBrain (class in ClearMap.Utils.events) UiRequestRefreshTabs (class in ClearMap.Utils.events) UiTabActivated (class in ClearMap.Utils.events) UiUseExistingLayoutChanged (class in ClearMap.Utils.events) UiVesselGraphFiltersChanged (class in ClearMap.Utils.events) UNALIGNED (WobblyAlignment attribute) unique_connect() (in module ClearMap.gui.gui_utils_base) UNLABELLED (VesselType attribute) unload_temporary_graphs() (VasculatureTab method) (VesselGraphProcessor method) unpack_slicing() (in module ClearMap.IO.Slice) unpacked_slicing (Slice property) unpickler() (in module ClearMap.Analysis.graphs.utils) unsubscribe_all() (BusSubscriberMixin method) UNTRACED (WobblyAlignment attribute) update() (LinearSystem method) (Workspace method) update_alignments_from_sources() (Layout method) update_atlas() (SampleInfoTab method) update_atlas_asset() (RegistrationProcessor method) update_atlas_resolution() (AtlasParams method) update_buttons_status() (TwoListSelection method) update_cell_number() (CellCounterTab method) update_cpu_bars() (ClearMapAppBase method) update_cpu_values() (PerfMonitor method) update_curve() (in module ClearMap.ImageProcessing.Binary.morphsnake) update_default_config() (in module ClearMap.config.update_config) update_file_suffix() (VasculatureTab method) update_gpu_bars() (ClearMapAppBase method) update_gpu_values() (PerfMonitor method) update_graph_properties() (in module ClearMap.ImageProcessing.machine_learning.vertices_classification.degree1_inference_utils) update_info() (BaseMetadataParser method) update_orientations() (DataViewer method) update_pbar() (in module ClearMap.gui.dialog_helpers) update_plotable_channels() (StitchingTab method) update_points() (DataViewer method) update_properties() (GraphFilterParams method) update_ranges() (OrthoViewer method) update_resample_params() (ManageAssetsWidget method) update_sources_from_alignments() (Layout method) update_vectors() (DataViewer method) update_watcher_main_progress() (PipelineOrchestrator method) update_watcher_progress() (PipelineOrchestrator method) update_workspace() (SampleManager method) updateImage() (DataViewer method) updateLabel() (DataViewer method) updateLabelFromMouseMove() (DataViewer method) updateRegionPercentile() (LUT method) updateRegionRange() (LUT method) updateSlice() (DataViewer method) updateSlicer() (DataViewer method) updateSourceRange() (DataViewer method) updateSourceSlice() (DataViewer method) upgrade_configs() (ExperimentController method) upper (Layout property) (Region property) (Slice property) upper_coordinate (WobblyAlignment property) upper_wobbly (WobblyLayout property) (WobblySource property) use_arteries (VesselGraphParams attribute) use_arteries_for_graph (VesselGraphProcessor property) use_default_radii() (GraphMeshVisual method) use_existing (UiUseExistingLayoutChanged attribute) use_existing_layout (GeneralChannelStitchingParams attribute) use_id_as_prefix (SharedSampleParams attribute), [1] use_landmarks_for (ChannelRegistrationParams property) use_npy (GeneralChannelStitchingParams attribute) use_npy() (SampleManager method) user_defaults_dir (ConfigHandler attribute) user_global_dir (ConfigHandler attribute) user_hint (AggregatedValidationError attribute) (ClearMapConfigError attribute) (ClearMapException attribute) (ClearMapPermissionError attribute) (ClearMapRuntimeError attribute) (ClearMapValueError attribute) (ClearMapVRamException attribute) (ClearMapWorkspaceError attribute) (ConfigParsingError attribute) (GroupStatsError attribute) (MetadataError attribute) (MissingAssetError property) (MissingChannelError attribute) (MissingRequirementException property) (NotAnOmeFile attribute) (NrrdError attribute) (ParamsOrientationError attribute) (PatchConflictError attribute) (PlotGraphError attribute) (SmiError attribute) (SourceModuleNotFoundError attribute) user_message (AggregatedValidationError property) (AssetNotFoundError property) (ClearMapException property) (ClearMapRuntimeError property) (ClearMapValueError property) (MetadataError property) (MissingAssetError property) (MissingRequirementException property) (ParamsOrientationError property) user_title (AggregatedValidationError attribute) (AssetNotFoundError attribute) (ClearMapAssetError attribute) (ClearMapConfigError attribute) (ClearMapException attribute) (ClearMapFileNotFoundError attribute) (ClearMapIoException attribute) (ClearMapPermissionError attribute) (ClearMapRuntimeError attribute) (ClearMapValueError attribute) (ClearMapVRamException attribute) (ClearMapWorkspaceError attribute) (ConfigNotFoundError attribute) (ConfigParsingError attribute) (GroupStatsError attribute) (IncompatibleSource attribute) (MetadataError attribute) (MissingAssetError attribute) (MissingChannelError attribute) (MissingRequirementException attribute) (NotAnOmeFile attribute) (NrrdError attribute) (ParamsOrientationError attribute) (PatchConflictError attribute) (PlotGraphError attribute) (SmiError attribute) (SourceModuleNotFoundError attribute) V valid (Block property) VALID (WobblyAlignment attribute) (WobblySource attribute) valid_tabs() (TabRegistry method) validate() (ConfigCoordinator method) validate_all() (in module ClearMap.config.validators) validate_arg() (in module ClearMap.Utils.utilities) validate_atoms() (CompoundKey method) validate_foreground() (in module ClearMap.Alignment.Stitching.stitching_wobbly) validate_orientation() (in module ClearMap.Utils.utilities) (SampleChannelParameters method) validate_parts() (CompoundKey method) validate_pattern() (PatternDialog method) validate_sections_with_jsonschema() (in module ClearMap.config.validators._schema) validator_for() (SectionValidators method) valids (WobblySource property) valids() (WobblyAlignment method) value() (NProcessesWidget method) (Tag method) valueChanged (NProcessesWidget attribute) valueChangedConnect() (LandmarksWeightsPanel method) values() (ChannelsUiParameterCollection method) (Expression method) vasculature_binarization_template() (ExperimentTemplatesResolver method) vasculature_perf_binarization_template() (ExperimentTemplatesResolver method) vasculature_target_channels() (ExperimentTemplatesResolver method) VasculatureTab (class in ClearMap.gui.tabs) VectorLink (class in ClearMap.gui.params_interfaces) VEIN (VesselType attribute) vein_binary (VesselSignals attribute) vein_intensity (VesselSignals attribute) vein_intensity_min (ClassificationConfig attribute), [1] (VesselGraphParams attribute) vein_intensity_range (ClassificationConfig attribute), [1] vein_intensity_range_on_arteries_channel (VesselGraphParams attribute) vein_seed_threshold (ClassificationConfig attribute) vein_trace_radius (ClassificationConfig attribute), [1] vein_trace_radius_um (VesselGraphParams attribute) veins_channel (VesselGraphProcessor property) Verbose (class in ClearMap.Alignment.Stitching.stitching_wobbly) verbose (OrchestratorBase property) verbose_has_flag() (in module ClearMap.Alignment.Stitching.stitching_wobbly) verbosity (MachineConfig property) (PreferencesParams attribute) verify_renaming() (ExperimentUpgrade_2_1_to_3_0 method) VerifyRenamingDialog (class in ClearMap.gui.dialogs) version (CondaPackage property) (UiParameterCollection property) version_guard() (in module ClearMap.config.convert_config_versions) vertex() (Graph method), [1] vertex_annotation() (AnnotatedGraph method) (Graph method) vertex_close_binary() (Graph method) vertex_coloring() (Graph method) vertex_coordinates() (GeometricGraph method) (Graph method) vertex_degree() (Graph method), [1] vertex_degrees (VesselVisualizationParams attribute) vertex_degrees() (Graph method), [1] vertex_dilate_binary() (Graph method) vertex_edges() (Graph method) vertex_edges_iterator() (Graph method) vertex_erode_binary() (Graph method) vertex_filter_to_edge_filter() (in module ClearMap.Analysis.vasculature.vasc_graph_utils) vertex_in_degree() (Graph method), [1] vertex_in_degrees() (Graph method), [1] vertex_in_edges() (Graph method) vertex_in_edges_iterator() (Graph method) vertex_in_neighbours() (Graph method) vertex_index() (Graph method) vertex_indices() (Graph method) vertex_iterator() (Graph method) vertex_neighbours() (Graph method) vertex_open_binary() (Graph method) vertex_out_degree() (Graph method), [1] vertex_out_degrees() (Graph method), [1] vertex_out_edges() (Graph method) vertex_out_edges_iterator() (Graph method) vertex_out_neighbours() (Graph method) vertex_propagate() (Graph method) vertex_properties (Graph property) vertex_properties() (Graph method) vertex_property() (Graph method), [1] vertex_property_map() (Graph method) vertex_property_map_from_python() (in module ClearMap.Analysis.graphs.type_conversions) vertex_property_map_to_python() (in module ClearMap.Analysis.graphs.type_conversions) vertex_radii() (GeometricGraph method) (Graph method) vertex_radii_units() (Graph method) vertex_radii_voxels() (Graph method) vertex_to_edge_label() (Graph method) vertex_to_edge_property() (in module ClearMap.Analysis.vasculature.vasc_graph_utils) vertices (Graph property), [1] vessel_filling_network() (in module ClearMap.ImageProcessing.machine_learning.vessel_filling.vessel_filling) VesselBinarizationParams (class in ClearMap.gui.params) VesselBinarizationPerformanceParams (class in ClearMap.gui.params) VesselClassifier (class in ClearMap.Analysis.graphs.vessel_classifier) VesselFillingNetwork (class in ClearMap.ImageProcessing.machine_learning.vessel_filling.vessel_filling_network) VesselGraphParams (class in ClearMap.gui.params) VesselGraphPerformanceParams (class in ClearMap.gui.params) VesselGraphProcessor (class in ClearMap.pipeline_orchestrators.tube_map) VesselGraphProcessor.RadiusLevel (class in ClearMap.pipeline_orchestrators.tube_map) VesselGraphProcessorSteps (class in ClearMap.pipeline_orchestrators.tube_map) VesselParams (class in ClearMap.gui.params) VesselSignals (class in ClearMap.Analysis.graphs.vessel_classifier) VesselType (class in ClearMap.Analysis.graphs.vessel_classifier) VesselVisualizationParams (class in ClearMap.gui.params) view (UiParameter property) (UiParameterCollection property) view() (ConfigCoordinator method) (Graph method) viewbox_mouse_event() (ArbitraryRotationCamera method) VirtualSource (class in ClearMap.IO.CSV) (class in ClearMap.IO.FileList) (class in ClearMap.IO.GT) (class in ClearMap.IO.MHD) (class in ClearMap.IO.MMP) (class in ClearMap.IO.NRRD) (class in ClearMap.IO.Source) (class in ClearMap.IO.TIF) visualize_graph_annotations() (VesselGraphProcessor method) VolumeVisual (class in ClearMap.Visualization.Vispy.VolumeVisual) voxel_number_overlap_threshold (ChannelColocalizationParams attribute) voxelization_radii (ChannelCellMapParams attribute) (ChannelTractMapParams attribute) voxelization_size (VesselVisualizationParams attribute) voxelization_weights (ChannelCellMapParams attribute) voxelize (ChannelCellMapParams attribute) (ChannelTractMapParams attribute) voxelize() (CellCounterTab method) (CellDetector method) (in module ClearMap.Analysis.Measurements.Voxelization) (TractMapProcessor method) (TractMapTab method) (VasculatureTab method) (VesselGraphProcessor method) voxelize_filtered_table() (ColocalizationProcessor method) (ColocalizationTab method) voxelize_folders() (in module ClearMap.pipeline_orchestrators.batch_process) voxelize_sample() (in module ClearMap.pipeline_orchestrators.batch_process) voxelize_unweighted() (ColocalizationProcessor method) VOXELS (VesselGraphProcessor.RadiusLevel attribute) W warn_config_smells() (in module ClearMap.config.config_adjusters.policy) warning_disclaimer() (Printer method) warning_popup() (in module ClearMap.gui.dialog_helpers) was_registered (RegistrationProcessor property) watched_keys (AdjusterSpec attribute) watershed_label() (in module ClearMap.Analysis.colocalization.channel) wavelength (SampleChannelParameters attribute) wdim (WobblySource property) weight (ImportTask attribute) weight_by_radius (VesselVisualizationParams attribute) weightAtChanged (LandmarksWeightsPanel attribute) weights_from_precentiles() (in module ClearMap.Analysis.Statistics.group_statistics_cumulatives) weightsChanged (LandmarksWeightsPanel attribute) where() (in module ClearMap.ParallelProcessing.DataProcessing.ArrayProcessing) where_1d() (in module ClearMap.ParallelProcessing.DataProcessing.ArrayProcessingCode) where_2d() (in module ClearMap.ParallelProcessing.DataProcessing.ArrayProcessingCode) where_3d() (in module ClearMap.ParallelProcessing.DataProcessing.ArrayProcessingCode) where_3d_f() (in module ClearMap.ParallelProcessing.DataProcessing.ArrayProcessingCode) where_re (TractMapProcessor attribute) whole_sample_changed() (in module ClearMap.config.change_detection) widget (GroupPage property) (ParamLink property) widget_class_name (GenericUi attribute) WidgetOps (class in ClearMap.gui.params_interfaces) width (OrthoViewer property) (Tag attribute) with_add_btn (GenericTab attribute) WizardWidget (class in ClearMap.gui.widgets) wobble (WobblySource property) wobble_at_coordinate() (WobblySource method) wobble_from_positions() (WobblySource method) WobblyAlignment (class in ClearMap.Alignment.Stitching.stitching_wobbly) WobblyAlignmentPlotMixin (class in ClearMap.Alignment.Stitching.stitching_plots) WobblyChannelStitchingParams (class in ClearMap.gui.params) WobblyLayout (class in ClearMap.Alignment.Stitching.stitching_wobbly) WobblyLayoutPlotMixin (class in ClearMap.Alignment.Stitching.stitching_plots) WobblySource (class in ClearMap.Alignment.Stitching.stitching_wobbly) worker (PreProcessingTab property) worker_is_ready() (ExperimentController method) workers_are_global (CellCounterTab attribute) (ColocalizationTab attribute) (PipelineTab attribute) (PreProcessingTab attribute) (TractMapTab attribute) (VasculatureTab attribute) Workspace (class in ClearMap.IO.Workspace) workspace (OrchestratorBase attribute), [1] (PipelineOrchestrator attribute) (ProcessorSteps attribute) (VesselGraphProcessor attribute) workspace_config_path (ConfigCoordinator property) WorkspaceChanged (class in ClearMap.Utils.events) wrap_in_thread() (ClearMapAppBase method) wrap_plot() (GenericTab method) wrap_step() (GenericTab method) write() (ConfigProxy method) (ElastixParser method) (ElastixPointFileManager method) (EnvFileManager method) (in module ClearMap.IO.CSV) (in module ClearMap.IO.FileList) (in module ClearMap.IO.GT) (in module ClearMap.IO.IO) (in module ClearMap.IO.MHD) (in module ClearMap.IO.MMP) (in module ClearMap.IO.NPY) (in module ClearMap.IO.NRRD) (in module ClearMap.IO.TIF) (in module ClearMap.ParallelProcessing.DataProcessing.ArrayProcessing) (in module ClearMap.ParallelProcessing.DataProcessing.ArrayProcessingCode) (in module ClearMap.Utils.HierarchicalDict) (Label method) (Printer method) (ProcessWriter method) (Source method), [1] (TransformationBase method) (VirtualSource method) (Workspace method) write_avg_density() (GroupResultsAssets method) write_color_palette() (Annotation method) write_coords() (LandmarksSelectorDialog method) write_effect_size() (GroupResultsAssets method) write_flat_yaml() (in module ClearMap.config.utils) write_header_from_source() (in module ClearMap.IO.MHD) write_LUT() (in module ClearMap.Visualization.Color.Color) write_p_val_colors() (GroupResultsAssets method) write_PAL() (in module ClearMap.Visualization.Color.Color) write_points() (in module ClearMap.Alignment.Elastix) write_registration_landmark_coords() (RegistrationTab method) write_sd_density() (GroupResultsAssets method) write_stats_table() (GroupResultsAssets method) write_vertex_table() (VesselGraphProcessor method) writer_functions (ConfigHandler attribute) wstype (Workspace property) X x_overlap (RigidChannelStitchingParams attribute) xyz_from_ndex() (in module ClearMap.ImageProcessing.Topology.Topology3d) xyz_to_index() (in module ClearMap.ImageProcessing.Topology.Topology3d) Y y_overlap (RigidChannelStitchingParams attribute) Z z_only() (SampleManager method) zero_to_one() (in module ClearMap.Visualization.Color.orientation_colormap) zeros() (in module ClearMap.IO.SMA) (in module ClearMap.ParallelProcessing.SharedMemoryArray) (in module ClearMap.ParallelProcessing.SharedMemoryManager) zeros_like() (in module ClearMap.IO.SMA) (in module ClearMap.ParallelProcessing.SharedMemoryArray)
