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 A abort_retry_popup() (in module ClearMap.gui.dialogs) aborted (ProgressWatcher attribute) abspath() (in module ClearMap.IO.FileUtils) AbstractSource (class in ClearMap.IO.Source) add_axes() (in module ClearMap.Visualization.Vispy.Plot3d) add_data() (Annotation method) add_dependency() (EnvFileManager method) add_edge() (Graph method), [1] add_edge_property() (Graph method), [1] add_graph_property() (Graph method) add_group() (BatchParameters method) (PatternDialog method) add_marker() (LandmarksSelectorDialog method) add_regions() (OrthoViewer 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) addPathToMask() (in module ClearMap.ImageProcessing.Tracing.Connect) adjust_overlaps() (TiledLayout method) AffineTransformation (class in ClearMap.Alignment.Transformations.LinearTransformation) align (BatchProcessingParams property) align() (in module ClearMap.Alignment.Elastix) (Layout method) (PreProcessor method) align_2_sources() (in module ClearMap.Alignment.Stitching.StitchingRigid) align_2_sources_along_axis() (in module ClearMap.Alignment.Stitching.StitchingRigid) align_2_sources_along_axis_mip() (in module ClearMap.Alignment.Stitching.StitchingRigid) align_axis() (Layout method) align_layout() (in module ClearMap.Alignment.Stitching.StitchingRigid) (in module ClearMap.Alignment.Stitching.StitchingWobbly) align_layout_axis() (in module ClearMap.Alignment.Stitching.StitchingRigid) align_layout_on_tiling() (in module ClearMap.Alignment.Stitching.StitchingRigid) align_layout_rigid_mip() (in module ClearMap.Alignment.Stitching.StitchingRigid) align_layout_rigid_mips() (in module ClearMap.Alignment.Stitching.StitchingRigid) align_on_tiling() (TiledLayout method) align_wobbly_axis() (in module ClearMap.Alignment.Stitching.StitchingWobbly) (WobblyAlignment method) ALIGNED (WobblyAlignment attribute) aligned_autofluo_path (PreProcessor property) Alignment (class in ClearMap.Alignment.Stitching.StitchingRigid) alignment() (in module ClearMap.ImageProcessing.Filter.Vector.Vector) (in module ClearMap.ImageProcessing.Filter.Vector.VectorCode) alignment_from_tile_positions() (TiledLayout method) alignment_info() (WobblyLayout method) alignment_weighted() (in module ClearMap.ImageProcessing.Filter.Vector.VectorCode) AlignmentBase (class in ClearMap.Alignment.Stitching.StitchingRigid) AlignmentParams (class in ClearMap.gui.params) alignments (Layout property) alignments_from_source_positions() (in module ClearMap.Alignment.Stitching.StitchingRigid) alignments_from_tile_position() (TiledLayout method) AlignmentTab (class in ClearMap.gui.tabs) all_colour (DataViewer property) all_not_none() (in module ClearMap.Alignment.Resampling) all_stitching_params (AlignmentParams property) all_tiles_exist() (Workspace method) allow_index_arrays (in module ClearMap.IO.Slice) annotate (VesselGraphParams attribute) 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) 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_prefs_and_close() (PreferenceUi method) apply_smoothing() (in module ClearMap.ImageProcessing.Experts.Vasculature) ArbitraryRotationCamera (class in ClearMap.Visualization.Vispy.arbitrary_rotation_camera) arrange_plots() (in module ClearMap.Visualization.Qt.Plot3d) array (Layout property) (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_binarization_clip_range (VesselBinarizationParams attribute) arteries_binarization_threshold (VesselBinarizationParams property) arteries_min_radius (VesselGraphParams attribute) arteries_path (SampleParameters attribute), [1] arteries_resolution (SampleParameters attribute), [1] as_array() (Source method) as_buffer() (AbstractSource method) (Slice method) (Source method), [1], [2], [3], [4], [5], [6], [7] (VirtualSource method), [1], [2], [3], [4], [5] as_memmap() (Source method), [1], [2], [3] as_memory() (Source method) as_memory_block() (Block method) as_real() (AbstractSource method) (Block method) (Layout method) (Slice method), [1] (Source method), [1], [2], [3], [4], [5], [6], [7], [8] (VirtualSource method), [1], [2], [3], [4], [5], [6] as_source() (in module ClearMap.IO.IO) 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), [1], [2], [3], [4], [5], [6] assert_cuda() (PytorchVersionManager static method) AssetNotFoundError ASSETS_TYPES_CONFIG (in module ClearMap.IO.assets_constants) assign_pressureBC() (in module ClearMap.Analysis.vasculature.flow.assign_p_bc) at_categories (PatternInverter attribute) atlas_align() (CellDetector method) atlas_base_name (RegistrationParams property) atlas_folder (in module ClearMap.Settings) (RegistrationParams attribute) atlas_id (RegistrationParams property) atlas_id_changed (RegistrationParams attribute) atlas_resolution (RegistrationParams property) atlas_structure_tree_id_changed (RegistrationParams attribute) autofluo_path (SampleParameters attribute), [1] autofluorescence_is_tiled (PreProcessor property) autofluorescence_resolution (SampleParameters attribute), [1] 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) average_voxelization_groups() (in module ClearMap.Analysis.Statistics.group_statistics) 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 background_correction_diameter (CellMapParams property) background_level (RigidStitchingParams attribute) background_pixels (RigidStitchingParams 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_lower (Slice property) base_position (Slice property) base_shape (Slice property) base_slicing (Slice property) base_upper (Slice property) BaseMetadataParser (class in ClearMap.IO.TIF) batch_crop() (in module ClearMap.processors.batch_process) BatchParameters (class in ClearMap.gui.params) BatchProcessingParams (class in ClearMap.gui.params) BatchProcessingTab (class in ClearMap.gui.tabs) BatchProcessor (class in ClearMap.processors.batch_process) BatchTab (class in ClearMap.gui.tabs) beep() (in module ClearMap.Utils.Sound) binarize() (in module ClearMap.ImageProcessing.Experts.Vasculature) binarize_block() (in module ClearMap.ImageProcessing.Experts.Vasculature) binarize_channel() (VasculatureTab method) binary_fill_arteries (VesselBinarizationParams attribute) binary_fill_raw (VesselBinarizationParams attribute) BINARY_NAMES (in module ClearMap.ImageProcessing.Experts.Vasculature) binary_statistics() (in module ClearMap.ImageProcessing.Experts.Axons) (in module ClearMap.ImageProcessing.Experts.Vasculature) BINARY_STATUS (in module ClearMap.ImageProcessing.Experts.Vasculature) Block (class in ClearMap.ParallelProcessing.Block) block_axes() (in module ClearMap.ParallelProcessing.BlockProcessing) block_ranges() (in module ClearMap.ParallelProcessing.DataProcessing.ArrayProcessing) 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) blocks_shape (Block property) 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) boundingRect() (RedCross method) bring_to_front() (in module ClearMap.Visualization.Qt.Plot3d) buffer() (in module ClearMap.IO.IO) build (VesselGraphParams attribute) build_graph() (VasculatureTab method) build_ln() (ElastixEntry method) build_tree() (StructurePickerWidget static method) C c_order (Pattern property) c_rng (Pattern property) c_values (PatternFinder property) CancelableProcessPoolExecutor (class in ClearMap.Utils.utilities) CanceledProcessing cell_filter_intensity (CellMapParams property) cell_filter_size (CellMapParams attribute) CellCounterTab (class in ClearMap.gui.tabs) CellDetector (class in ClearMap.processors.cell_map) CellMapParams (class in ClearMap.gui.params) center_tile_position() (TiledLayout method) center_tile_source() (TiledLayout method) center_view() (in module ClearMap.Visualization.Vispy.Plot3d) cfg_to_ui() (BatchParameters method) (CellMapParams method) (GroupAnalysisParams method) (PreferencesParams method) (SampleParameters method) (UiParameter method) (UiParameterCollection method) change_max_projection() (DataViewer method), [1] change_orientations_color() (DataViewer method), [1] change_orientations_threshold() (DataViewer method), [1] change_points_color() (DataViewer method), [1] change_source_location() (Layout method) change_sources() (Layout method) change_vectors_color() (DataViewer method), [1] change_vectors_threshold() (DataViewer method), [1] channel_affine_file_path (RegistrationParams attribute) check_alignments_and_sources() (in module ClearMap.Alignment.Stitching.StitchingRigid) check_border() (in module ClearMap.ImageProcessing.Topology.Topology3d) check_elastix_initialized() (in module ClearMap.Alignment.Elastix) check_enough_temp_space() (in module ClearMap.Utils.utilities) check_has_all_tiles() (PreProcessor method) check_pytorch() (PytorchVersionManager static method) check_spaces() (in module ClearMap.Alignment.Elastix) CHECKSUM_ALGORITHMS (in module ClearMap.IO.assets_constants) chunk_size_max (PreferencesParams attribute) chunk_size_min (PreferencesParams attribute) chunk_size_overlap (PreferencesParams attribute) clean (VesselGraphParams attribute) clean() (in module ClearMap.ParallelProcessing.SharedMemoryManager) clean_graph() (in module ClearMap.Analysis.Graphs.GraphProcessing) clean_open_branches() (in module ClearMap.ImageProcessing.Skeletonization.SkeletonProcessing) clean_path() (in module ClearMap.config.config_loader) clear_atlas_caches() (in module ClearMap.Scripts.clearmap_utils) clear_landmarks() (AlignmentTab method) (PreProcessor method) clear_layout() (in module ClearMap.gui.gui_utils) ClearMap module ClearMap.Alignment module ClearMap.Alignment.Annotation module ClearMap.Alignment.Elastix 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.StitchingRigid module ClearMap.Alignment.Stitching.StitchingWobbly 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.Curves module ClearMap.Analysis.Curves.Extrapolation module ClearMap.Analysis.Curves.Resampling module ClearMap.Analysis.DimensionReduction module ClearMap.Analysis.Graphs module ClearMap.Analysis.Graphs.Graph module ClearMap.Analysis.Graphs.GraphGt module ClearMap.Analysis.Graphs.GraphProcessing module ClearMap.Analysis.Graphs.GraphRendering module ClearMap.Analysis.Measurements module ClearMap.Analysis.Measurements.maxima_detection module ClearMap.Analysis.Measurements.MeasureExpression module ClearMap.Analysis.Measurements.MeasureRadius 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_statistics 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.graph_corrections module ClearMap.Analysis.vasculature.vasc_graph_utils module ClearMap.config module ClearMap.config.atlas module ClearMap.config.config_loader module ClearMap.config.update_config module ClearMap.gui module ClearMap.gui.creator module ClearMap.gui.creator.graphics_resources_rc module ClearMap.gui.creator.icons_rc module ClearMap.gui.dialogs module ClearMap.gui.gui_logging module ClearMap.gui.gui_utils module ClearMap.gui.interfaces module ClearMap.gui.params module ClearMap.gui.params_interfaces module ClearMap.gui.preferences module ClearMap.gui.pyuic_utils module ClearMap.gui.style module ClearMap.gui.tabs 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.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.Axons 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.Orientation module ClearMap.ImageProcessing.Filter.Orientation.Orientation 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.Filter.Vector module ClearMap.ImageProcessing.Filter.Vector.Vector module ClearMap.ImageProcessing.Filter.Vector.VectorCode module ClearMap.ImageProcessing.Filter.Vector.VectorFilter module ClearMap.ImageProcessing.Filter.Vector.VectorStructureElement module ClearMap.ImageProcessing.GreyReconstruction module ClearMap.ImageProcessing.IlluminationCorrection module ClearMap.ImageProcessing.LightsheetCorrection module ClearMap.ImageProcessing.LocalStatistics module ClearMap.ImageProcessing.machine_learning module ClearMap.ImageProcessing.machine_learning.vessel_filling 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.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.DevolvePointList module ClearMap.ParallelProcessing.DataProcessing.DevolvePointListCode 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.processors module ClearMap.processors.batch_process module ClearMap.processors.cell_map module ClearMap.processors.generic_tab_processor module ClearMap.processors.sample_preparation 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.TubeMap module ClearMap.Settings module ClearMap.Utils module ClearMap.Utils.array_utils module ClearMap.Utils.array_utils_cy 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.TagExpression module ClearMap.Utils.Timer module ClearMap.Utils.utilities module ClearMap.Visualization module ClearMap.Visualization.atlas 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.DataViewerAxon 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.GraphVisual module ClearMap.Visualization.Vispy.Plot3d module ClearMap.Visualization.Vispy.PlotGraph3d module ClearMap.Visualization.Vispy.VolumeVisual module clearmap_path (in module ClearMap.Settings) clearmap_pattern (Pattern property) ClearMapAssetError ClearMapException ClearMapIoException ClearMapMetadataParser (class in ClearMap.IO.TIF) ClearMapVRamException ClearMapWorkspaceError 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.Axons) (in module ClearMap.ImageProcessing.Experts.Vasculature) close() (in module ClearMap.Visualization.Qt.Plot3d) (StructureSelector method) close_file() (Printer 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) color() (in module ClearMap.Visualization.Color.Color) (Label method) color_axis (DataViewer property) color_last() (DataViewer method) color_map() (in module ClearMap.Alignment.Annotation) (in module ClearMap.Visualization.Color.Color) color_p_values() (in module ClearMap.Analysis.Statistics.group_statistics) colorize() (in module ClearMap.Alignment.Annotation) (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) common_parent() (Annotation method) compare_groups() (in module ClearMap.Analysis.Statistics.group_statistics) comparisons (GroupAnalysisParams property) compute_grid() (in module ClearMap.gui.gui_utils) compute_p_vals() (GroupAnalysisProcessor method) CondaParser (class in ClearMap.Utils.install_utils) config (UiParameter property) config_path (UiParameter property) (UiParameterCollection property) ConfigLoader (class in ClearMap.config.config_loader) ConfigNotFoundError connect() (BatchParameters method) (CellMapParams method) (GeneralStitchingParams method) (RegistrationParams method) (RigidStitchingParams method) (SampleParameters method) (UiParameter method) (VesselBinarizationParams method) (VesselGraphParams method) (VesselVisualizationParams method) (WobblyStitchingParams method) connect_apply() (in module ClearMap.gui.widget_monkeypatch_callbacks) connect_buttons() (LandmarksSelectorDialog method) (PatternDialog method) (SamplePickerDialog method) (StructureSelector method) (WizardDialog method) connect_cancel() (in module ClearMap.gui.widget_monkeypatch_callbacks) connect_close() (in module ClearMap.gui.widget_monkeypatch_callbacks) connect_groups() (BatchParameters method) (GroupAnalysisParams method) connect_ok() (in module ClearMap.gui.widget_monkeypatch_callbacks) connect_open() (in module ClearMap.gui.widget_monkeypatch_callbacks) connect_save() (in module ClearMap.gui.widget_monkeypatch_callbacks) connect_simple_widgets() (UiParameter method) connect_sources() (in module ClearMap.Alignment.Stitching.layout_graph_utils) connect_text_changed() (in module ClearMap.gui.widget_monkeypatch_callbacks) connect_value_changed() (in module ClearMap.gui.widget_monkeypatch_callbacks) connect_whats_this() (GenericTab method) connected() (in module ClearMap.Alignment.Stitching.StitchingRigid) (Layout method) connected_components() (in module ClearMap.Alignment.Stitching.StitchingRigid) (Layout method) connectPoint() (in module ClearMap.ImageProcessing.Tracing.Connect) consider (in module ClearMap.ImageProcessing.Skeletonization.PK12) contrast_limited_percentile() (in module ClearMap.ImageProcessing.Filter.Rank) (in module ClearMap.ImageProcessing.Filter.Rank.Parametric) controls_enabled() (in module ClearMap.gui.widget_monkeypatch_callbacks) conversion_fmt (GeneralStitchingParams attribute) convert() (in module ClearMap.IO.FileList) (in module ClearMap.IO.IO) convert_array() (in module ClearMap.Alignment.Annotation) convert_arteries (GeneralStitchingParams attribute) convert_cm2_to_cm2_1_fmt() (CellDetector method) convert_files() (in module ClearMap.IO.IO) convert_label() (Annotation method) (in module ClearMap.Alignment.Annotation) convert_label_to_color() (in module ClearMap.Visualization.atlas) convert_output (GeneralStitchingParams property) convert_output() (AlignmentTab method) convert_raw (GeneralStitchingParams attribute) convert_stitched() (in module ClearMap.Scripts.align_new_api) convert_tiles() (AlignmentTab method) (PreProcessor method) convert_to_cm_2_1() (in module ClearMap.processors.batch_process) convert_to_image_format() (PreProcessor method) 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) copy() (AlignmentBase method) (Graph method) (Region method) (Source method) (Verbose method) copy_file() (in module ClearMap.IO.FileUtils) copy_sources_and_alignments() (in module ClearMap.Alignment.Stitching.StitchingRigid) 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 property) count_cells() (in module ClearMap.Analysis.Statistics.data_frame_operations) count_dones() (ProgressWatcher method) counter (Source 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_cell_detection_tuning_sample() (CellCounterTab method) create_clearmap_widget() (in module ClearMap.gui.gui_utils) create_color_annotation() (in module ClearMap.Visualization.atlas) create_debug() (Workspace method) create_directory() (in module ClearMap.IO.FileUtils) (Verbose method) create_label_table() (in module ClearMap.Alignment.utils) create_singleton() (in module ClearMap.Alignment.Annotation) create_test_dataset() (CellDetector method) create_wizard() (BatchTab method) crop_x_max (CellMapParams attribute) (VesselVisualizationParams attribute) crop_x_min (CellMapParams attribute) (VesselVisualizationParams attribute) crop_y_max (CellMapParams attribute) (VesselVisualizationParams attribute) crop_y_min (CellMapParams attribute) (VesselVisualizationParams attribute) crop_z_max (CellMapParams attribute) (VesselVisualizationParams attribute) crop_z_min (CellMapParams attribute) (VesselVisualizationParams 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_color (LandmarksSelectorDialog property) current_marker (LandmarksSelectorDialog property) current_slice_indices() (Scatter3D method) D DARK_COLOR (StructurePickerWidget attribute) darker() (in module ClearMap.Visualization.Color.Color) DATA_CONTENT_TYPES (in module ClearMap.IO.assets_constants) DataFrameWidget (class in ClearMap.gui.widgets) DataViewer (class in ClearMap.Visualization.Qt.DataViewer) (class in ClearMap.Visualization.Qt.DataViewerAxon) debug (Workspace property) decompress_atlases() (in module ClearMap.Alignment.Annotation) deconvolve() (in module ClearMap.ImageProcessing.Experts.Axons) (in module ClearMap.ImageProcessing.Experts.Vasculature) deep_merge_dicts() (in module ClearMap.config.update_config) default_annotation_file (in module ClearMap.Alignment.Annotation) default_binarization_parameter (in module ClearMap.ImageProcessing.Experts.Vasculature) 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_config (UiParameter property) default_cutoff (in module ClearMap.ParallelProcessing.DataProcessing.ArrayProcessing) default_dir (ConfigLoader attribute) default_distance_to_surface_file (in module ClearMap.Alignment.Annotation) 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_overlap (in module ClearMap.ParallelProcessing.BlockProcessing) 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), [1] default_size_max (in module ClearMap.ParallelProcessing.BlockProcessing) default_size_min (in module ClearMap.ParallelProcessing.BlockProcessing) default_tag_name() (in module ClearMap.Utils.TagExpression) define_auto_resolution() (in module ClearMap.IO.metadata) define_auto_stitching_params() (in module ClearMap.IO.metadata) 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) delete (in module ClearMap.ImageProcessing.Skeletonization.PK12) delete_border() (in module ClearMap.ImageProcessing.Topology.Topology3d) delete_directory() (in module ClearMap.IO.FileUtils) delete_file() (in module ClearMap.IO.FileUtils) delete_resampled_files() (PreProcessor method) density_files_are_comparable() (in module ClearMap.Analysis.Statistics.group_statistics) depth (OrthoViewer property) detect() (Expression method) (in module ClearMap.Utils.TagExpression) detect_cells (CellMapParams attribute) detect_cells() (CellCounterTab method) (in module ClearMap.ImageProcessing.Experts.Cells) detect_cells_block() (in module ClearMap.ImageProcessing.Experts.Cells) detect_local_minima() (in module ClearMap.Alignment.Stitching.StitchingWobbly) detect_maxima() (in module ClearMap.ImageProcessing.Experts.Cells) detect_shape() (in module ClearMap.Analysis.Measurements.shape_detection) detected (CellDetector property) detection_threshold (CellMapParams attribute) devolve() (in module ClearMap.ParallelProcessing.DataProcessing.DevolvePointList) devolve_uniform() (in module ClearMap.ParallelProcessing.DataProcessing.DevolvePointListCode) devolve_uniform_kernel() (in module ClearMap.ParallelProcessing.DataProcessing.DevolvePointListCode) devolve_weights() (in module ClearMap.ParallelProcessing.DataProcessing.DevolvePointListCode) devovle_weights_kernel() (in module ClearMap.ParallelProcessing.DataProcessing.DevolvePointListCode) df_path (CellDetector property) dir_to_sample_id() (in module ClearMap.Utils.path_utils) directed (Graph property), [1] directory (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) dirs_to_cells_dfs() (in module ClearMap.Analysis.Statistics.group_statistics) dirs_to_density_files() (in module ClearMap.Analysis.Statistics.group_statistics) disable() (GenericTab method) disable_controls() (in module ClearMap.gui.widget_monkeypatch_callbacks) disabled_to_minus_1() (in module ClearMap.gui.widget_monkeypatch_callbacks) disk() (in module ClearMap.ImageProcessing.Filter.StructureElement) displacement (Alignment property) displacement_at_coordinate() (WobblyAlignment method) displacements (WobblyAlignment property) display_atlas() (SampleTab method) display_auto_to_ref_landmarks_dialog() (AlignmentTab method) display_graph_chunk() (VasculatureTab method) display_graph_chunk_from_cfg() (VasculatureTab method) display_resampled_to_auto_landmarks_dialog() (AlignmentTab method) display_sample_id() (SampleTab method) display_use_id_as_prefix() (SampleTab method) display_whats_this() (GenericTab method) dock_resize_event() (in module ClearMap.gui.widget_monkeypatch_callbacks) dog_filter() (in module ClearMap.ImageProcessing.Experts.Cells) dtype (AbstractSource property) DTYPE (in module ClearMap.ImageProcessing.Experts.Vasculature) dtype (Layout property) (Slice property) (Source property), [1], [2], [3], [4], [5], [6], [7] (VirtualSource property) dtype() (in module ClearMap.IO.FileList) (in module ClearMap.IO.IO) (Tag method) dtype_to_gtype() (in module ClearMap.Analysis.Graphs.GraphGt) E edge() (Graph method), [1] edge_annotation() (AnnotatedGraph method) (Graph method) edge_close_binary() (Graph method) 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_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.GraphGt) edge_property_map_to_python() (in module ClearMap.Analysis.Graphs.GraphGt) edge_radii() (GeometricGraph method) (Graph method) edge_radii_from_vertex_radii() (GeometricGraph 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] 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) elastix_path (in module ClearMap.Settings) ElastixEntry (class in ClearMap.IO.elastix_config) ElastixParser (class in ClearMap.IO.elastix_config) 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.StitchingRigid) (Layout method) empty() (in module ClearMap.IO.SMA) (in module ClearMap.ParallelProcessing.SharedMemoryArray) enable_controls() (in module ClearMap.gui.widget_monkeypatch_callbacks) enable_mouse_clicks() (DataViewer method) enable_widgets() (WizardDialog static 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) 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) EnvFileManager (class in ClearMap.Utils.install_utils) equalize() (in module ClearMap.ImageProcessing.Experts.Axons) (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) escape_glob() (in module ClearMap.Utils.TagExpression) escapes (PatternInverter attribute) estimate_q_values() (in module ClearMap.Analysis.Statistics.MultipleComparisonCorrection) eventFilter() (DataViewer method), [1] exec() (WizardDialog method) existing_steps (ProcessorSteps property) exists() (Source method) (Workspace method) expand() (in module ClearMap.Utils.HierarchicalDict) expand_edge_geometry() (GeometricGraph method) expand_graph() (in module ClearMap.Analysis.Graphs.GraphProcessing) expand_graph_length() (in module ClearMap.Analysis.Graphs.GraphProcessing) expand_vertex_filter() (Graph method) export_as_csv() (CellDetector method) export_collapsed_stats() (CellDetector method) export_to_clearmap1_fmt() (CellDetector method) Expression (class in ClearMap.Utils.TagExpression) expression (Source property) (VirtualSource property) expression() (Workspace method) expression_to_glob() (in module ClearMap.Utils.RegularExpression) expression_to_pattern() (in module ClearMap.Utils.RegularExpression) extended_max() (in module ClearMap.Analysis.Measurements.maxima_detection) extension() (Workspace method) extent (Region property) external_path (in module ClearMap.Settings) extract_annotated_region() (in module ClearMap.Analysis.vasculature.vasc_graph_utils) 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 file_extension() (in module ClearMap.IO.FileUtils) file_list (Source property) (VirtualSource property) file_list() (in module ClearMap.IO.IO) (Workspace 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) filename (in module ClearMap.ImageProcessing.Skeletonization.PK12) filename() (PreProcessor 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_combined (VesselBinarizationParams attribute) fill_main_channel (VesselBinarizationParams attribute) fill_secondary_channel (VesselBinarizationParams attribute) filter_alignments() (in module ClearMap.Alignment.Stitching.StitchingRigid) filter_cells (CellMapParams 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) final_min_vein_radius (VesselGraphParams attribute) finalize_processing() (in module ClearMap.ParallelProcessing.DataProcessing.ArrayProcessing) find() (Annotation method) find_cells_df() (in module ClearMap.Utils.path_utils) find_center_of_maxima() (in module ClearMap.Analysis.Measurements.maxima_detection) find_density_file() (in module ClearMap.Utils.path_utils) find_file() (in module ClearMap.Utils.path_utils) find_intensity() (in module ClearMap.Analysis.Measurements.shape_detection) find_maxima() (in module ClearMap.Analysis.Measurements.maxima_detection) 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_edge() (Graph method) first_vertex() (Graph method) fit_for_pressureBC() (in module ClearMap.Analysis.vasculature.flow.assign_p_bc) fix_cfg_file() (AlignmentParams method) (SampleParameters method) (UiParameter method) (UiParameterCollection method) fix_config() (GenericTab method) fix_df_column_names() (in module ClearMap.Analysis.Statistics.data_frame_operations) fix_isolated() (in module ClearMap.Alignment.Stitching.StitchingWobbly) (WobblySource method) fix_unaligned() (in module ClearMap.Alignment.Stitching.StitchingWobbly) (WobblyAlignment method) FIXED (WobblyAlignment attribute) (WobblySource attribute) fixed_coords (LandmarksSelectorDialog property) 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_alternatives() (in module ClearMap.config.config_loader) flush() (Printer method) fold_sample_stats_dataframe() (in module ClearMap.Visualization.Matplotlib.PlotUtils) font_family (PreferencesParams property) font_size (PreferencesParams attribute) format_expression() (in module ClearMap.Utils.RegularExpression) format_long_nb_to_str() (in module ClearMap.gui.gui_utils) format_orientation() (in module ClearMap.Alignment.orientation) format_time() (Timer method) free() (in module ClearMap.ParallelProcessing.SharedMemoryManager) from_dict() (Transformation class method) (TransformationBase class method) from_mixed_tiff_lists() (PatternFinder class method) full_filename() (Verbose method) func (lazyattr attribute) G GeneralStitchingParams (class in ClearMap.gui.params) 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) GenericDialog (class in ClearMap.gui.interfaces) GenericTab (class in ClearMap.gui.interfaces) GenericUi (class in ClearMap.gui.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) get() (in module ClearMap.ParallelProcessing.SharedMemoryManager) (in module ClearMap.Utils.HierarchicalDict) get_all_children_structures_ids() (in module ClearMap.Alignment.utils) (in module ClearMap.Scripts.generate_jsonl_file_ontology) get_all_data() (Scatter3D method) get_all_paths() (BatchParameters method) get_all_structs() (in module ClearMap.Alignment.utils) get_alternatives() (in module ClearMap.config.config_loader) get_args() (in module ClearMap.Scripts.create_distance_file) get_atlas_files() (PreProcessor method) get_autofluo_pts_path() (PreProcessor method) get_base_dir() (in module ClearMap.IO.metadata) get_best_match_cuda_version() (PytorchVersionManager method) get_cells_df() (CellDetector method) get_cfg() (ConfigLoader method) get_cfg_from_path() (ConfigLoader static method) get_cfg_path() (ConfigLoader method) get_cfg_reader_function() (in module ClearMap.config.config_loader) get_chars_after_cluster_idx() (Pattern method) get_chars_before_cluster_idx() (Pattern method) get_check_box() (in module ClearMap.gui.widget_monkeypatch_callbacks) get_children() (Annotation method) get_color_ids() (in module ClearMap.Alignment.Stitching.layout_graph_utils) get_colored_p_vals() (in module ClearMap.Analysis.Statistics.group_statistics) get_colors_rgba() (Annotation method) get_colours() (Scatter3D method) get_conda_pkg_info() (CondaParser static method) get_configobj_cfg() (in module ClearMap.config.config_loader) get_configs() (in module ClearMap.config.config_loader) (PreProcessor method) get_connected_components() (in module ClearMap.Alignment.Stitching.layout_graph_utils) get_coords() (CellDetector method) (DataViewer method), [1] get_cpu_percent() (PerfMonitor method) get_current_res() (in module ClearMap.gui.gui_utils) get_default_path() (ConfigLoader static method) get_df_from_file_list() (PatternFinder static method) 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.dialogs) get_draw_params() (Scatter3D method) get_edges_n_kinds() (in module ClearMap.Analysis.vasculature.vasc_graph_utils) get_elastix_version() (in module ClearMap.Alignment.Elastix) get_env_name() (EnvFileManager method) get_file_path() (in module ClearMap.IO.metadata) get_flattened_structure() (in module ClearMap.Alignment.utils) (in module ClearMap.Scripts.generate_jsonl_file_ontology) get_formatted_pattern() (Pattern method) get_free_temp_space() (in module ClearMap.Utils.utilities) get_free_v_ram() (in module ClearMap.Utils.utilities) get_gp_ctrls() (BatchParameters method) get_graph() (in module ClearMap.Alignment.Stitching.layout_graph_utils) get_hierarchical_dictionary() (Annotation method) get_info() (in module ClearMap.IO.IO) get_inverse() (TransformationBase method) get_item_recursive() (in module ClearMap.Utils.utilities) get_json_cfg() (in module ClearMap.config.config_loader) get_lateralised_volume_map() (Annotation method) get_left_elements() (TwoListSelection method) get_list() (Annotation method) get_map() (Annotation method) get_map_to_parent() (Annotation 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() (in module ClearMap.Alignment.Annotation) get_new_color() (LandmarksSelectorDialog method) get_next_steps() (ProcessorSteps method) get_ome_dict() (in module ClearMap.IO.metadata) get_package_version() (EnvFileManager 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() (ConfigLoader static method) get_paths() (BatchParameters method) get_patterns() (PatternDialog method) get_percent_v_ram_use() (in module ClearMap.Utils.utilities) 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_pseudo_random_color() (in module ClearMap.gui.gui_utils) 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) get_raw_metadata_dictionary() (Source method) get_region_volume() (in module ClearMap.Analysis.vasculature.annotation_utils) get_right_elements() (TwoListSelection method) get_sample_id() (SampleTab method) get_scaling() (ScalingTransformation method) get_sorted_spin_boxes() (in module ClearMap.gui.widget_monkeypatch_callbacks) 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_sub_graph() (in module ClearMap.Analysis.vasculature.vasc_graph_utils) get_sub_regions() (in module ClearMap.Analysis.vasculature.annotation_utils) get_sub_tiff_list() (PatternFinder method) get_sub_tiff_paths() (PatternFinder method) get_symbol_sizes() (Scatter3D method) get_symbols() (Scatter3D method) get_text() (in module ClearMap.gui.widget_monkeypatch_callbacks) get_text_edit() (in module ClearMap.gui.widget_monkeypatch_callbacks) get_thread_percent() (PerfMonitor method) get_tiff_list() (PatternFinder class method) get_tiles_by_ext() (in module ClearMap.IO.metadata) get_tiles_list_from_sample_folder() (in module ClearMap.IO.metadata) get_toolkit_info() (PytorchVersionManager method) get_toolkit_versions() (PytorchVersionManager method) get_transformations() (Transformation method) get_value() (in module ClearMap.gui.widget_monkeypatch_callbacks) (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_volume_map() (in module ClearMap.Analysis.Statistics.group_statistics) get_voxelization_params() (CellDetector method) get_widgets() (PatternDialog method) get_wobbly_layout() (PreProcessor method) get_yml_cfg() (in module ClearMap.config.config_loader) getXYAxes() (DataViewer method), [1] glob() (Expression method) (Tag method) glob_to_expression() (in module ClearMap.Utils.RegularExpression) go_to_orientation() (SampleTab method) gp_add_folder_buttons (BatchParameters property) gp_group_name_ctrls (BatchParameters property) gp_list_widget (BatchParameters property) gp_remove_folder_buttons (BatchParameters property) gp_stats_df_to_counts() (in module ClearMap.Visualization.Matplotlib.PlotUtils) 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.GraphGt) graph (Source property) (VirtualSource property) graph_from_skeleton() (in module ClearMap.Analysis.Graphs.GraphProcessing) 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_step (VesselVisualizationParams attribute) graph_to_connected_components() (in module ClearMap.Alignment.Stitching.layout_graph_utils) graph_to_skeleton() (in module ClearMap.Analysis.Graphs.GraphProcessing) GraphLineVisual (class in ClearMap.Visualization.Vispy.GraphVisual) GraphMeshVisual (class in ClearMap.Visualization.Vispy.GraphVisual) gray_image_to_rgb() (in module ClearMap.Visualization.Color.Color) grays_alpha() (in module ClearMap.Visualization.Vispy.Plot3d) grey_reconstruct() (in module ClearMap.ImageProcessing.GreyReconstruction) group_cells_counts() (in module ClearMap.Analysis.Statistics.group_statistics) group_counts() (in module ClearMap.Analysis.Statistics.data_frame_operations) group_dict() (in module ClearMap.Utils.RegularExpression) group_names (BatchParameters property) group_names() (in module ClearMap.Utils.RegularExpression) GroupAnalysisParams (class in ClearMap.gui.params) GroupAnalysisProcessor (class in ClearMap.gui.tabs) GroupAnalysisTab (class in ClearMap.gui.tabs) groups (BatchParameters property) GroupStatsError gtype_from_source() (in module ClearMap.Analysis.Graphs.GraphGt) H h_max_transform() (in module ClearMap.Analysis.Measurements.maxima_detection) handle_add_src_folder_clicked() (BatchParameters method) handle_advanced_checked() (GenericTab method) handle_arteries_binarization_threshold_changed() (VesselBinarizationParams method) handle_atlas_id_changed() (RegistrationParams method) handle_atlas_resolution_changed() (RegistrationParams method) handle_background_correction_diameter_changed() (CellMapParams method) handle_convert_output_changed() (GeneralStitchingParams method) handle_deprecated_args() (in module ClearMap.Utils.utilities) handle_fig_fate() (in module ClearMap.Visualization.Matplotlib.PlotUtils) handle_filter_intensity_changed() (CellMapParams method) handle_gpu_vals_updated() (PerfMonitor method) handle_orientation_changed() (SampleParameters method) handle_proc_changed() (PerfMonitor method) handle_projection_thickness_changed() (RigidStitchingParams method) handle_raw_binarization_threshold_changed() (VesselBinarizationParams method) handle_raw_path_changed() (SampleParameters method) handle_remove_src_folder_clicked() (BatchParameters method) handle_results_folder_changed() (BatchParameters method) handle_sample_id_changed() (SampleParameters method) handle_structure_tree_id_changed() (RegistrationParams method) handle_tool_changed() (GroupAnalysisTab method) handle_tool_tab_changed() (CellCounterTab method) handle_widget_changed() (UiParameter method) handleMouseClick() (DataViewer method), [1] has_colours (Scatter3D property) has_edge_coordinates (Graph property) has_edge_geometry (GeometricGraph property) has_edge_geometry() (Graph method) has_edge_radii (Graph property) has_flag() (Verbose method) has_hemispheres (Scatter3D property) has_npy (PreProcessor property) has_prop() (in module ClearMap.gui.widget_monkeypatch_callbacks) has_tiles (PreProcessor property) has_vertex_coordinates (Graph property) has_vertex_radii (Graph property) 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() (WizardDialog static method) highlight_digits() (Pattern method) hightlighted_q_marks() (Pattern method) 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) html_to_plain_text() (in module ClearMap.gui.gui_utils) I icosphere() (in module ClearMap.Visualization.Mesh.IcoSphere) id (Label property) (Slice property) (Source property) identifier (Slice property) (Source property) ids_to_acronyms() (Annotation method) ids_to_names() (Annotation method) ilastik_path (in module ClearMap.Settings) imageChanged() (LUTItem method) imagej_path (in module ClearMap.Settings) ImageJMetadataParser (class in ClearMap.IO.TIF) immediate_shutdown() (CancelableProcessPoolExecutor method) 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_neighbours() (in module ClearMap.ParallelProcessing.DataProcessing.ArrayProcessing) index_to_smoothing() (in module ClearMap.ImageProcessing.Binary.Smoothing) indices() (Expression method) info() (Block method) (Graph method) (Label method) (Source method) (Workspace method) init_preprocessor() (in module ClearMap.processors.sample_preparation) init_ui() (GenericDialog method) (GenericTab method) (GenericUi method) initialised (BatchTab property) initialize() (Annotation method) (in module ClearMap.Alignment.Annotation) (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), [1] 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), [1] initialize_view() (in module ClearMap.Visualization.Vispy.Plot3d) initialized (in module ClearMap.Alignment.Elastix) initializeSources() (DataViewer method), [1] insert() (in module ClearMap.ParallelProcessing.SharedMemoryManager) insert_group_names() (in module ClearMap.Utils.RegularExpression) inspect_align_layout() (in module ClearMap.Alignment.Stitching.StitchingWobbly) interpolate_edge_geometry() (in module ClearMap.Analysis.Graphs.GraphRendering) INVALID (WobblyAlignment attribute) (WobblySource attribute) inverse_transform() (in module ClearMap.Alignment.Elastix) invert_orientation() (in module ClearMap.Alignment.orientation) is_checked() (UiParameter method) is_clearmap (Source property) is_color() (DataViewer method) is_csv() (in module ClearMap.IO.CSV) is_dark() (in module ClearMap.gui.gui_utils) is_density_file() (in module ClearMap.Utils.path_utils) is_directory() (in module ClearMap.IO.FileUtils) is_disableable() (in module ClearMap.gui.widget_monkeypatch_callbacks) is_edge_geometry_consistent() (Graph method) is_expression() (in module ClearMap.Utils.RegularExpression) is_feather() (in module ClearMap.Utils.path_utils) is_file() (in module ClearMap.IO.FileUtils) is_file_list() (in module ClearMap.IO.FileList) is_gp_stats_df() (in module ClearMap.Visualization.Matplotlib.PlotUtils) is_graph() (in module ClearMap.IO.GT) is_in_range() (in module ClearMap.Utils.utilities) is_iterable() (in module ClearMap.Utils.utilities) is_machine_file() (in module ClearMap.config.config_loader) 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_simple_attr() (UiParameter method) is_source() (in module ClearMap.IO.IO) is_tab_file() (in module ClearMap.config.config_loader) is_tif() (in module ClearMap.IO.TIF) is_tiled (PreProcessor property) is_trivial() (in module ClearMap.IO.Slice) is_valid() (WobblySource method) is_view (Graph property) is_view() (in module ClearMap.IO.Slice) ISOLATED (WobblySource attribute) iteration (Block property) iteration_info() (Block method) 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) L Label (class in ClearMap.Alignment.Annotation) label() (Tag method) label_components() (Graph method) label_points() (Annotation method) (in module ClearMap.Alignment.Annotation) label_temp() (in module ClearMap.ImageProcessing.Binary.FillingCode) label_to_color() (Annotation 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) LandmarksSelectorDialog (class in ClearMap.gui.widgets) largest_component() (Graph method) last_step (ProcessorSteps property) launch_pattern_wizard() (SampleTab method) Layout (class in ClearMap.Alignment.Stitching.StitchingRigid) layout_along_axis_mip() (in module ClearMap.Alignment.Stitching.StitchingRigid) layout_coloring() (in module ClearMap.Alignment.Stitching.StitchingRigid) layout_from_region() (Layout method) layouts_along_axis_wobbly() (WobblyLayout method) lazyattr (class in ClearMap.Utils.Lazy) level (Label property) 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) 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) load() (Graph method), [1] (in module ClearMap.Analysis.Graphs.Graph) (in module ClearMap.Analysis.Graphs.GraphGt) (Layout method) (Workspace method) load_config_to_gui() (GenericUi method) (SampleTab method) load_layout() (in module ClearMap.Alignment.Stitching.StitchingRigid) loader_functions (ConfigLoader 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_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) 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 (PreferencesParams property) LUTItem (class in ClearMap.Visualization.Qt.data_viewer_luts) LUTWidget (class in ClearMap.Visualization.Qt.data_viewer_luts) M main() (in module ClearMap.processors.batch_process) (in module ClearMap.processors.sample_preparation) (in module ClearMap.Scripts.cell_map_new_api) (in module ClearMap.Scripts.clearmap_utils) (in module ClearMap.Scripts.create_distance_file) 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) make_abs() (in module ClearMap.Utils.utilities) make_group_stats_tables() (GroupAnalysisTab method) make_nested_progress_dialog() (in module ClearMap.gui.dialogs) make_simple_progress_dialog() (in module ClearMap.gui.dialogs) make_splash() (in module ClearMap.gui.dialogs) 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) make_summary() (in module ClearMap.Analysis.Statistics.group_statistics) map_axes() (in module ClearMap.IO.TIF) map_volume (Annotation property) 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) max_arteries_tracing_iterations (VesselGraphParams attribute) MAX_BIN (in module ClearMap.ImageProcessing.Experts.Vasculature) max_changed (ProgressWatcher attribute) max_intensity_projection() (in module ClearMap.Alignment.Stitching.StitchingRigid) max_level (Annotation property) max_progress (ProgressWatcher property) max_shifts_x (RigidStitchingParams attribute) (WobblyStitchingParams attribute) max_shifts_y (RigidStitchingParams attribute) (WobblyStitchingParams attribute) max_shifts_z (RigidStitchingParams attribute) (WobblyStitchingParams attribute) max_value() (in module ClearMap.IO.IO) max_veins_tracing_iterations (VesselGraphParams attribute) maxima_shape (CellMapParams 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.GraphProcessing) 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.MeasureRadius) 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) memory() (in module ClearMap.IO.IO) merge_config() (in module ClearMap.config.update_config) mesh() (in module ClearMap.Analysis.Graphs.GraphRendering) mesh_tube() (in module ClearMap.Analysis.Graphs.GraphRendering) mesh_tube_from_coordinates_and_radii() (in module ClearMap.Analysis.Graphs.GraphRendering) metadata() (Source method), [1], [2] MetadataError method (VolumeVisual property) min_artery_size (VesselGraphParams attribute) min_value() (in module ClearMap.IO.IO) min_vein_size (VesselGraphParams attribute) 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) 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) minus_1_to_disabled() (in module ClearMap.gui.widget_monkeypatch_callbacks) mip_axis() (Alignment method) 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) modularity_measure() (in module ClearMap.Analysis.vasculature.vasc_graph_utils) module ClearMap ClearMap.Alignment ClearMap.Alignment.Annotation ClearMap.Alignment.Elastix ClearMap.Alignment.orientation ClearMap.Alignment.Resampling ClearMap.Alignment.Stitching ClearMap.Alignment.Stitching.layout_graph_utils ClearMap.Alignment.Stitching.plot_utils ClearMap.Alignment.Stitching.StitchingRigid ClearMap.Alignment.Stitching.StitchingWobbly 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.Curves ClearMap.Analysis.Curves.Extrapolation ClearMap.Analysis.Curves.Resampling ClearMap.Analysis.DimensionReduction ClearMap.Analysis.Graphs ClearMap.Analysis.Graphs.Graph ClearMap.Analysis.Graphs.GraphGt ClearMap.Analysis.Graphs.GraphProcessing ClearMap.Analysis.Graphs.GraphRendering ClearMap.Analysis.Measurements ClearMap.Analysis.Measurements.maxima_detection ClearMap.Analysis.Measurements.MeasureExpression ClearMap.Analysis.Measurements.MeasureRadius ClearMap.Analysis.Measurements.shape_detection ClearMap.Analysis.Measurements.Voxelization ClearMap.Analysis.Statistics ClearMap.Analysis.Statistics.data_frame_operations ClearMap.Analysis.Statistics.group_statistics 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.graph_corrections ClearMap.Analysis.vasculature.vasc_graph_utils ClearMap.config ClearMap.config.atlas ClearMap.config.config_loader ClearMap.config.update_config ClearMap.gui ClearMap.gui.creator ClearMap.gui.creator.graphics_resources_rc ClearMap.gui.creator.icons_rc ClearMap.gui.dialogs ClearMap.gui.gui_logging ClearMap.gui.gui_utils ClearMap.gui.interfaces ClearMap.gui.params ClearMap.gui.params_interfaces ClearMap.gui.preferences ClearMap.gui.pyuic_utils ClearMap.gui.style ClearMap.gui.tabs ClearMap.gui.widget_monkeypatch_callbacks ClearMap.gui.widgets ClearMap.ImageProcessing ClearMap.ImageProcessing.Binary ClearMap.ImageProcessing.Binary.Filling ClearMap.ImageProcessing.Binary.FillingCode 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.Axons ClearMap.ImageProcessing.Experts.Cells ClearMap.ImageProcessing.Experts.utils ClearMap.ImageProcessing.Experts.Vasculature ClearMap.ImageProcessing.Filter ClearMap.ImageProcessing.Filter.FilterKernel ClearMap.ImageProcessing.Filter.Orientation ClearMap.ImageProcessing.Filter.Orientation.Orientation 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.Filter.Vector ClearMap.ImageProcessing.Filter.Vector.Vector ClearMap.ImageProcessing.Filter.Vector.VectorCode ClearMap.ImageProcessing.Filter.Vector.VectorFilter ClearMap.ImageProcessing.Filter.Vector.VectorStructureElement ClearMap.ImageProcessing.GreyReconstruction ClearMap.ImageProcessing.IlluminationCorrection ClearMap.ImageProcessing.LightsheetCorrection ClearMap.ImageProcessing.LocalStatistics ClearMap.ImageProcessing.machine_learning ClearMap.ImageProcessing.machine_learning.vessel_filling 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.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.DevolvePointList ClearMap.ParallelProcessing.DataProcessing.DevolvePointListCode 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.processors ClearMap.processors.batch_process ClearMap.processors.cell_map ClearMap.processors.generic_tab_processor ClearMap.processors.sample_preparation 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.TubeMap ClearMap.Settings ClearMap.Utils ClearMap.Utils.array_utils ClearMap.Utils.array_utils_cy 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.TagExpression ClearMap.Utils.Timer ClearMap.Utils.utilities ClearMap.Visualization ClearMap.Visualization.atlas 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.DataViewerAxon ClearMap.Visualization.Qt.Plot3d ClearMap.Visualization.Qt.utils ClearMap.Visualization.Qt.widgets ClearMap.Visualization.Vispy ClearMap.Visualization.Vispy.arbitrary_rotation_camera ClearMap.Visualization.Vispy.GraphVisual ClearMap.Visualization.Vispy.Plot3d ClearMap.Visualization.Vispy.PlotGraph3d ClearMap.Visualization.Vispy.VolumeVisual mosaic_shape() (Workspace method) mouse_clicked (DataViewer attribute), [1] moving_coords (LandmarksSelectorDialog property) multi_plot() (in module ClearMap.Visualization.Qt.Plot3d) N 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_channels (PreProcessor property) n_channels_convert (PreProcessor property) n_cube_indices() (in module ClearMap.ImageProcessing.Topology.Topology3d) n_edges (Graph property), [1] n_groups (BatchParameters property) n_groups() (in module ClearMap.Utils.RegularExpression) n_iterations (Block property) n_processes_binarization (PreferencesParams property) n_processes_cell_detection (PreferencesParams property) n_processes_file_conv (PreferencesParams property) n_processes_resampling (PreferencesParams property) n_processes_stitching (PreferencesParams property) n_registration_steps (PreProcessor property) n_rigid_steps_to_run (PreProcessor property) n_sources (Layout property) n_steps (VesselBinarizationParams property) n_structures (Annotation property) n_vertices (Graph property), [1] n_wobbly_steps_to_run (PreProcessor property) name (Alignment property) (Block property) (Graph property) (Label property) (Slice property) (Source property), [1], [2], [3], [4], [5], [6], [7], [8], [9] (VirtualSource property), [1], [2], [3], [4], [5], [6] (WobblySource property) 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.GraphGt) ndim_list (Source property) ndim_to_gtype() (in module ClearMap.Analysis.Graphs.GraphGt) 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.ParallelProcessing.DataProcessing.ArrayProcessing) (in module ClearMap.ParallelProcessing.DataProcessing.ArrayProcessingCode) new_get_distutils_extension() (in module ClearMap.ImageProcessing.Thresholding.Thresholding) 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_df_column_names() (in module ClearMap.Analysis.Statistics.data_frame_operations) normalize_df() (in module ClearMap.Analysis.Statistics.data_frame_operations) NOSIGNAL (WobblyAlignment attribute) NotAnOmeFile np_to_qpixmap() (in module ClearMap.gui.gui_utils) NrrdError ntags() (Expression method) O offset (Slice property) (Source property), [1], [2], [3], [4] OMEMetadataParser (class in ClearMap.IO.TIF) ones() (in module ClearMap.IO.SMA) (in module ClearMap.ParallelProcessing.SharedMemoryArray) open() (PreferenceUi method) optimal_association_matrix() (in module ClearMap.Alignment.Stitching.Tracking) option_dialog() (in module ClearMap.gui.dialogs) orbit() (ArbitraryRotationCamera method) order (AbstractSource property) (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) 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 (SampleParameters attribute) (SampleParameters property) orientation() (in module ClearMap.ImageProcessing.Filter.Vector.Vector) (in module ClearMap.ImageProcessing.Filter.Vector.VectorCode) 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_ellipsoid() (in module ClearMap.ImageProcessing.Filter.Vector.Vector) (in module ClearMap.ImageProcessing.Filter.Vector.VectorCode) orientation_ellipsoid_weighted() (in module ClearMap.ImageProcessing.Filter.Vector.VectorCode) 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) orientation_weighted() (in module ClearMap.ImageProcessing.Filter.Vector.VectorCode) orientations() (in module ClearMap.ImageProcessing.Topology.Topology3d) OrientationTransformation (class in ClearMap.Alignment.Resampling) (class in ClearMap.Alignment.Transformations.ResamplingTransformation) 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) 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 (class in ClearMap.Alignment.Stitching.StitchingRigid) overlap() (in module ClearMap.Alignment.Stitching.StitchingRigid) overlay() (AlignmentBase method) (Layout method) overlay_along_axis_mip() (in module ClearMap.Alignment.Stitching.StitchingRigid) overlay_layout() (in module ClearMap.Alignment.Stitching.StitchingRigid) overlay_layout_plane() (PreProcessor method) overlay_mip() (AlignmentBase method) overlay_mip_wobbly() (WobblyAlignment method) overlay_overlap() (AlignmentBase method) overlay_sources() (in module ClearMap.Alignment.Stitching.StitchingRigid) overlay_wobbly() (WobblyAlignment method) P padded_shape() (DataViewer method) pages_mode (Source property) paint() (RedCross method) parallel_get_vessels_lengths() (in module ClearMap.Analysis.vasculature.vasc_graph_utils) parallel_traceback() (in module ClearMap.ParallelProcessing.ParallelTraceback) ParamLink (class in ClearMap.gui.params_interfaces) params (AlignmentParams property) (UiParameterCollection property) (VesselParams property) ParamsOrientationError parent_list() (Label method) parents() (Annotation method) parse() (BaseMetadataParser method) (ElastixEntry method) (ElastixParser method) (Expression method) (in module ClearMap.Utils.TagExpression) (Tag method) parse_date() (BaseMetadataParser method) parse_description() (BaseMetadataParser method) 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_order() (BaseMetadataParser method) (ClearMapMetadataParser method) parse_overlap() (BaseMetadataParser method) (OMEMetadataParser method) parse_overlaps() (in module ClearMap.IO.metadata) parse_pattern() (Pattern method) parse_pixel_metadata() (BaseMetadataParser method) parse_resolution() (BaseMetadataParser method) parse_sample_folders() (SamplePickerDialog method) parse_shape() (BaseMetadataParser method) parse_tile_configuration() (BaseMetadataParser method) (OMEMetadataParser method) patch_button_boxes() (GenericUi method) patch_cfg() (in module ClearMap.config.config_loader) patch_elastix_cfg_landmarks() (PreProcessor static method) patch_env() (in module ClearMap.Utils.install_utils) patch_env_var() (EnvFileManager method) patch_environment_package_line() (EnvFileManager method) patch_pipeline_name() (in module ClearMap.processors.batch_process) path (UiParameter property) path() (in module ClearMap.Settings) (ProcessorSteps method) path_from_step_name() (ProcessorSteps method) 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_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) percent_thread (PerfMonitor attribute) percentile() (in module ClearMap.ImageProcessing.Filter.Rank) (in module ClearMap.ImageProcessing.Filter.Rank.Percentile) (in module ClearMap.ImageProcessing.Filter.Rank.PercentileCode) percentile_masked() (in module ClearMap.ImageProcessing.Filter.Rank.PercentileCode) PerfMonitor (class in ClearMap.gui.widgets) permissive_min_vein_radius (VesselGraphParams attribute) pick_region() (VasculatureTab method) pickler() (in module ClearMap.Analysis.Graphs.GraphGt) pipeline_name (AlignmentParams property) pixels_metadata (BaseMetadataParser 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.StitchingRigid) (in module ClearMap.Alignment.Stitching.StitchingWobbly) place_layout_axis() (in module ClearMap.Alignment.Stitching.StitchingRigid) 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() (Alignment method) (AlignmentBase method) (in module ClearMap.Visualization.Qt.Plot3d) (Layout method) (Overlap method) (Source method) (Workspace method) plot_3d() (in module ClearMap.Visualization.Vispy.Plot3d) plot_alignments() (in module ClearMap.Alignment.Stitching.StitchingRigid) (Layout method) plot_all_layouts() (in module ClearMap.Alignment.Stitching.plot_utils) plot_along_axis_mip() (in module ClearMap.Alignment.Stitching.StitchingRigid) plot_atlas() (PreProcessor method) plot_background_subtracted_img() (CellDetector method) plot_binarization_results() (VasculatureTab method) plot_box() (in module ClearMap.Visualization.Vispy.Plot3d) plot_cell_filter_results() (CellCounterTab method) plot_cell_map_results() (CellCounterTab method) plot_cells() (CellDetector method) plot_cells_3d_scatter_w_atlas_colors() (CellDetector method) plot_cells_scatter_w_atlas_colors() (CellCounterTab method) plot_cells_scatter_w_atlas_colors_raw() (CellCounterTab method) plot_channel_1 (VesselBinarizationParams attribute) plot_channel_2 (VesselBinarizationParams attribute) plot_curve() (in module ClearMap.Visualization.Matplotlib.PlotUtils) plot_debug_cropping_interface() (CellCounterTab method) plot_density() (in module ClearMap.Visualization.Matplotlib.PlotUtils) plot_density_maps() (GroupAnalysisProcessor method) (GroupAnalysisTab method) plot_detected_cells (CellMapParams attribute) plot_detection_results() (CellCounterTab method) plot_filtered_cells() (CellDetector method) plot_graph_edge_property() (in module ClearMap.Visualization.Vispy.PlotGraph3d) plot_graph_line() (in module ClearMap.Visualization.Vispy.PlotGraph3d) plot_graph_mesh() (in module ClearMap.Visualization.Vispy.PlotGraph3d) plot_graph_structure() (VasculatureTab method) plot_graph_type_processing_chunk_slicer() (VasculatureTab method) plot_histograms() (GroupAnalysisTab method) plot_layout() (in module ClearMap.Alignment.Stitching.StitchingRigid) (PreProcessor method) plot_mesh_3d() (in module ClearMap.Visualization.Vispy.Plot3d) plot_mini_brain() (SampleTab method) plot_mip() (AlignmentBase method) plot_mip_wobbly() (WobblyAlignment method) plot_orthogonal_views() (OrthoViewer method) plot_overlap() (AlignmentBase method) plot_overlay() (AlignmentBase method) plot_overlay_wobbly() (WobblyAlignment method) plot_p_vals() (GroupAnalysisProcessor method) (GroupAnalysisTab method) plot_regions() (in module ClearMap.Alignment.Stitching.StitchingRigid) (Layout method) plot_registration_results() (in module ClearMap.Scripts.align_new_api) plot_registration_results_composite() (AlignmentTab method) plot_registration_results_composite_raw() (AlignmentTab method) plot_registration_results_side_by_side() (AlignmentTab method) plot_registration_results_side_by_side_raw() (AlignmentTab method) plot_regular_polygon() (in module ClearMap.Visualization.Vispy.Plot3d) 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.StitchingRigid) plot_step_1 (VesselBinarizationParams attribute) plot_step_2 (VesselBinarizationParams attribute) plot_stitching_results() (AlignmentTab method) (PreProcessor method) plot_sub_df() (in module ClearMap.Visualization.Matplotlib.PlotUtils) plot_tsne() (in module ClearMap.Analysis.DimensionReduction) plot_type (VesselVisualizationParams attribute) plot_volcano() (in module ClearMap.Visualization.Matplotlib.PlotUtils) plot_volcanoes() (GroupAnalysisTab method) plot_voxelization() (VasculatureTab method) plot_voxelized_counts() (CellDetector method) plot_voxelized_intensities() (CellDetector method) plot_when_finished (CellMapParams attribute) plot_wobble() (WobblyLayout method) plotData() (in module ClearMap.ImageProcessing.Tracing.Connect) PlotGraphError plotTracingResult() (in module ClearMap.ImageProcessing.Tracing.Connect) pop() (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) 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) 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.StitchingRigid) positions_from_tree() (in module ClearMap.Alignment.Stitching.StitchingRigid) post (AlignmentBase property) post_process_cells() (CellDetector method) post_process_graph() (VasculatureTab method) postprocess() (in module ClearMap.ImageProcessing.Experts.Vasculature) PostProcessingTab (class in ClearMap.gui.interfaces) pprint() (in module ClearMap.Utils.HierarchicalDict) pre (AlignmentBase property) PreferencesParams (class in ClearMap.gui.params) PreferenceUi (class in ClearMap.gui.preferences) prefix (PreProcessor property) prepare_annotation_files() (in module ClearMap.Alignment.Annotation) prepare_for_substep() (ProgressWatcher method) prepare_normalization() (in module ClearMap.Alignment.Stitching.StitchingWobbly) prepare_temp() (in module ClearMap.ImageProcessing.Binary.FillingCode) prepare_watcher_for_substep() (TabProcessor method) prepend() (in module ClearMap.Utils.HierarchicalDict) preprocess() (in module ClearMap.ImageProcessing.Experts.Axons) preprocess_block() (in module ClearMap.ImageProcessing.Experts.Axons) PreProcessor (class in ClearMap.processors.sample_preparation) preview_arteries (GeneralStitchingParams attribute) preview_cell_detection() (CellDetector method) preview_cell_filter() (CellCounterTab method) preview_raw (GeneralStitchingParams attribute) preview_stitching_dumb() (AlignmentTab method) preview_stitching_smart() (AlignmentTab method) print_cube() (in module ClearMap.ImageProcessing.Topology.Topology3d) print_elapsed_time() (Timer method) 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) Printer (class in ClearMap.gui.gui_logging) 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.processors.batch_process) process_sample() (in module ClearMap.processors.batch_process) ProcessorSteps (class in ClearMap.processors.generic_tab_processor) processSingleConnection() (in module ClearMap.ImageProcessing.Tracing.Connect) ProcessWriter (class in ClearMap.ParallelProcessing.ProcessWriter) progress_changed (ProgressWatcher attribute) ProgressWatcher (class in ClearMap.gui.widgets) project() (in module ClearMap.gui.gui_utils) projection_thickness (RigidStitchingParams property) prompt_dialog() (in module ClearMap.gui.dialogs) pseudo_random_rgb_array() (in module ClearMap.gui.gui_utils) 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) rand_cmap() (in module ClearMap.Visualization.Color.Color) rank() (in module ClearMap.ImageProcessing.Filter.Rank.RankResample) ratios (CellMapParams property) (VesselVisualizationParams property) raw_binarization_clip_range (VesselBinarizationParams attribute) raw_binarization_threshold (VesselBinarizationParams property) raw_path (SampleParameters attribute) (SampleParameters property) raw_resolution (SampleParameters attribute), [1] raw_stitched_shape (PreProcessor property) re() (Expression method) (Tag method) read() (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_configs() (GenericTab method) (UiParameter method) (UiParameterCollection method) read_group() (in module ClearMap.Analysis.Statistics.group_statistics) read_points() (in module ClearMap.Alignment.Elastix) realign() (in module ClearMap.processors.batch_process) reconstruct() (in module ClearMap.ImageProcessing.GreyReconstruction) RedCross (class in ClearMap.Visualization.Qt.utils) reduce (VesselGraphParams attribute) reduce_edge_geometry() (GeometricGraph method) reduce_graph() (in module ClearMap.Analysis.Graphs.GraphProcessing) ref_affine_file_path (RegistrationParams attribute) ref_bspline_file_path (RegistrationParams attribute) ref_pts_path (PreProcessor property) reflect() (in module ClearMap.ImageProcessing.Topology.Topology3d) refresh() (DataViewer method) Region (class in ClearMap.Alignment.Stitching.StitchingRigid) register() (in module ClearMap.Scripts.align_new_api) RegistrationParams (class in ClearMap.gui.params) relative_step_size (VolumeVisual property) reload() (UiParameter method) (UiParameterCollection 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) remove_auto_loops() (in module ClearMap.Analysis.vasculature.graph_corrections) remove_background() (in module ClearMap.ImageProcessing.Experts.Cells) remove_crust() (CellDetector 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_group() (BatchParameters 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_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] reorder_shape() (in module ClearMap.IO.TIF) replace() (in module ClearMap.Utils.RegularExpression) replace_source_location() (Layout method) requires_files() (in module ClearMap.Utils.utilities) resample() (in module ClearMap.Alignment.Resampling) (in module ClearMap.Analysis.Curves.Resampling) resample_1d() (in module ClearMap.Analysis.Curves.Resampling) resample_factor() (in module ClearMap.Alignment.Resampling) (ResamplingTransformation method), [1] resample_for_registration() (PreProcessor 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_pts_path (PreProcessor property) resampled_shape (PreProcessor property) ResamplingTransformation (class in ClearMap.Alignment.Resampling) (class in ClearMap.Alignment.Transformations.ResamplingTransformation) rescale_channel() (in module ClearMap.processors.batch_process) rescale_img() (in module ClearMap.processors.batch_process) rescale_size_and_spacing() (in module ClearMap.Alignment.Elastix) reset() (ProgressWatcher method) (Timer method) reset_log_length() (ProgressWatcher method) resize_edge_geometry() (Graph method) RESOURCE_TYPE_TO_FOLDER (in module ClearMap.IO.assets_constants) resources_path (in module ClearMap.Settings) restore_elastix_cfg_no_landmarks() (PreProcessor static method) restrictive_min_vein_radius (VesselGraphParams attribute) result_data_file() (in module ClearMap.Alignment.Elastix) results_folder (BatchParameters property) reverse_scale_axis() (CellMapParams method) (VesselVisualizationParams 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) RigidStitchingParams (class in ClearMap.gui.params) 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) run() (CellDetector method) (PreProcessor method) (TabProcessor method) run_all() (VasculatureTab method) run_arteries (GeneralStitchingParams attribute) run_arteries_binarization (VesselBinarizationParams attribute) run_batch_process() (BatchProcessingTab method) run_cell_detection() (CellDetector method) run_cell_map() (CellCounterTab method) run_p_vals() (GroupAnalysisTab method) run_plots() (GroupAnalysisProcessor method) (GroupAnalysisTab method) run_raw (GeneralStitchingParams attribute) run_raw_binarization (VesselBinarizationParams attribute) run_registration() (AlignmentTab method) run_step() (in module ClearMap.ImageProcessing.Experts.utils) run_stitching() (AlignmentTab method) run_tuning_cell_detection() (CellCounterTab method) run_vaculature (BatchProcessingParams property) 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_id (SampleParameters attribute) (SampleParameters property) SampleParameters (class in ClearMap.gui.params) SamplePickerDialog (class in ClearMap.gui.widgets) SampleTab (class in ClearMap.gui.tabs) sanitize_df() (in module ClearMap.Analysis.Statistics.data_frame_operations) (in module ClearMap.Analysis.Statistics.group_statistics) sanitize_neg_one() (UiParameter method) sanitize_nones() (UiParameter method) 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.GraphGt) (in module ClearMap.Visualization.Vispy.Plot3d) (Layout method) (Workspace method) save_cfg() (SampleTab method) save_layout() (in module ClearMap.Alignment.Stitching.StitchingRigid) save_results() (PatternDialog method) save_shape (CellMapParams attribute) save_stats() (VasculatureTab method) scale_axis() (CellMapParams method) (VesselVisualizationParams method) scale_coords() (DataViewer method), [1] 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) Scatter3D (class in ClearMap.Visualization.Qt.widgets) screen_geometry() (in module ClearMap.Visualization.Qt.utils) 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.MeasureRadius) (in module ClearMap.Analysis.Measurements.Voxelization) search_indices_sphere() (in module ClearMap.Analysis.Measurements.MeasureRadius) (in module ClearMap.Analysis.Measurements.Voxelization) selected_comparisons (GroupAnalysisParams property) series (Source attribute) series_mode (Source property) set() (in module ClearMap.Utils.HierarchicalDict) set_annotation_file() (in module ClearMap.Alignment.Annotation) set_artery_vein_if_missing() (in module ClearMap.Analysis.vasculature.vasc_graph_utils) set_background() (in module ClearMap.Visualization.Vispy.Plot3d) set_check_state() (UiParameter method) set_color_scheme() (DataViewer method), [1] set_configs() (PreProcessor method) set_coords() (RedCross method) set_data() (Scatter3D method) (VolumeVisual method) set_edge_annotation() (AnnotatedGraph method) (Graph method) set_edge_coordaintes() (Graph method) set_edge_coordinates() (GeometricGraph method) set_edge_geometry() (GeometricGraph method) (Graph method) set_edge_geometry_type() (Graph method) set_edge_property() (Graph method), [1] set_edge_property_map() (in module ClearMap.Analysis.Graphs.GraphGt) set_edge_radii() (GeometricGraph method) (Graph method) set_elastix_library_path() (in module ClearMap.Alignment.Elastix) set_file() (Printer method) set_fixed_coords() (LandmarksSelectorDialog method) set_graph_property() (Graph method) set_invalid() (WobblySource method) set_isolated() (WobblySource method) set_item_recursive() (in module ClearMap.Utils.utilities) set_label_file() (in module ClearMap.Alignment.Annotation) set_light_to_camera() (in module ClearMap.Visualization.Vispy.Plot3d) set_main_progress() (ProgressWatcher method) set_metric_parameter_file() (in module ClearMap.Alignment.Elastix) set_moving_coords() (LandmarksSelectorDialog method) set_orientations() (DataViewer method), [1] set_params() (AlignmentTab method) (BatchProcessingTab method) (CellCounterTab method) (GenericDialog method) (GenericTab method) (GenericUi method) (GroupAnalysisTab method) (PostProcessingTab method) (PreferenceUi method) (SampleTab method) (VasculatureTab method) set_path_transform_files() (in module ClearMap.Alignment.Elastix) set_paths() (BatchParameters method) set_points() (DataViewer method), [1] set_positions() (WobblyLayout method) set_progress() (ProgressWatcher method) set_progress_watcher() (AlignmentTab method) (CellCounterTab method) (GenericUi method) (TabProcessor method) (VasculatureTab 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_text() (in module ClearMap.gui.widget_monkeypatch_callbacks) set_transform_file_size_and_spacing() (in module ClearMap.Alignment.Elastix) set_value() (in module ClearMap.gui.widget_monkeypatch_callbacks) set_vectors() (DataViewer method), [1] set_vertex_annotation() (AnnotatedGraph method) (Graph method) set_vertex_coordinate() (Graph method) set_vertex_coordinates() (GeometricGraph method) (Graph method) set_vertex_property() (Graph method), [1] set_vertex_property_map() (in module ClearMap.Analysis.Graphs.GraphGt) set_vertex_radii() (GeometricGraph method) (Graph method) set_vertex_radius() (Graph method) set_view_parameter() (in module ClearMap.Visualization.Vispy.Plot3d) set_watcher_step() (TabProcessor method) setMinMax() (DataViewer method), [1] setSelectedItems() (TwoListSelection method) setSliceAxis() (DataViewer method), [1] setSource() (DataViewer method), [1] setup() (AlignmentTab method) (BatchProcessingTab method) (BatchTab method) (CellCounterTab method) (CellDetector method) (GroupAnalysisTab method) (LandmarksSelectorDialog method) (OrthoViewer method) (PatternDialog method) (PreferenceUi method) (PreProcessor method) (ProgressWatcher method) (SamplePickerDialog method) (SampleTab method) (StructureSelector method) (VasculatureTab method) (WizardDialog method) setup_atlas() (AlignmentTab method) setup_atlases() (PreProcessor method) setup_cell_detector() (CellCounterTab method) setup_cell_param_histogram() (CellCounterTab method) setup_mini_brain() (in module ClearMap.gui.widgets) setup_preferences() (PreferenceUi method) setup_preproc() (PostProcessingTab method) (VasculatureTab method) setup_results_folder() (BatchTab method) setup_vessel_processors() (VasculatureTab method) setup_workers() (AlignmentTab method) (CellCounterTab method) (GenericTab method) (GroupAnalysisTab method) (VasculatureTab method) 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) shape3d() (DataViewer method) 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) shift (Alignment property) shifts (WobblyAlignment property) shifts_from_minimization() (in module ClearMap.Alignment.Stitching.StitchingWobbly) shifts_from_tracing() (in module ClearMap.Alignment.Stitching.StitchingWobbly) show() (StructureSelector method) similarity() (in module ClearMap.ImageProcessing.Filter.Vector.Vector) (in module ClearMap.ImageProcessing.Filter.Vector.VectorCode) similarity_weighted() (in module ClearMap.ImageProcessing.Filter.Vector.VectorCode) simplify_slicing() (in module ClearMap.IO.Slice) single_color_colormap() (in module ClearMap.Visualization.Vispy.Plot3d) sink_slicing() (Layout method) size (Source property) size() (in module ClearMap.IO.IO) sizeHint() (LUTWidget method) skeletonize (VesselGraphParams attribute) skeletonize() (in module ClearMap.ImageProcessing.Skeletonization.PK12) (in module ClearMap.ImageProcessing.Skeletonization.Skeletonization) skeletonize_index() (in module ClearMap.ImageProcessing.Skeletonization.PK12) skip (RigidStitchingParams attribute) (WobblyStitchingParams attribute) skip_resampling (RegistrationParams attribute) Slice (class in ClearMap.Alignment.Stitching.StitchingRigid) (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.StitchingRigid) slice_pixel_size (WobblyStitchingParams attribute) slice_range (WobblyStitchingParams attribute) slice_to_range() (in module ClearMap.IO.Slice) slice_tuples (CellMapParams property) (VesselVisualizationParams property) slice_x (SampleParameters attribute), [1] slice_y (SampleParameters attribute), [1] slice_z (SampleParameters attribute), [1] 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 (CellMapParams property) (Slice property) (VesselVisualizationParams property) SlicingTransformation (class in ClearMap.Alignment.Transformations.SlicingTransformation) smi_query() (in module ClearMap.Utils.utilities) SmiError smooth_arteries (VesselBinarizationParams attribute) smooth_binary() (in module ClearMap.Alignment.Stitching.StitchingWobbly) 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_displacements() (in module ClearMap.Alignment.Stitching.StitchingWobbly) (WobblyAlignment method) smooth_positions() (in module ClearMap.Alignment.Stitching.StitchingWobbly) (WobblySource method) smooth_raw (VesselBinarizationParams attribute) smooth_window() (in module ClearMap.Alignment.Stitching.StitchingWobbly) solve() (LinearSystem method) sort_sources_by_position() (Layout method) sort_sources_by_tile_position() (TiledLayout method) Source (class in ClearMap.Alignment.Stitching.StitchingRigid) (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 (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.StitchingRigid) (Layout method) source_modules (in module ClearMap.IO.IO) 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.StitchingRigid) 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.StitchingRigid) sourceSlice() (DataViewer method) space_axes (DataViewer property) sphere() (in module ClearMap.ImageProcessing.Filter.StructureElement) split() (in module ClearMap.IO.FileUtils) split_axis() (PatternFinder class method) split_channel() (PatternFinder class method) split_into_blocks() (in module ClearMap.ParallelProcessing.BlockProcessing) src_folder (SampleTab property) stack_columns() (PreProcessor method) stack_tiles_to_columns() (in module ClearMap.IO.metadata) stack_voxelizations() (in module ClearMap.Analysis.Statistics.group_statistics) start() (PerfMonitor method) (SlicingTransformation method) (Timer method) start_folder (PreferencesParams attribute) start_full_screen (PreferencesParams attribute) status (WobblySource property) status_at_coordinate() (WobblyAlignment method) (WobblySource method) status_to_description (WobblyAlignment attribute) (WobblySource attribute) status_to_description() (in module ClearMap.ImageProcessing.Experts.Axons) (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() (SlicingTransformation method) step_exists() (GenericTab method) (ProcessorSteps method) steps (ProcessorSteps property) stitch() (in module ClearMap.Scripts.align_new_api) (Layout method) (PreProcessor method) stitch_and_plot_layout() (in module ClearMap.Alignment.Stitching.plot_utils) stitch_by_function() (in module ClearMap.Alignment.Stitching.StitchingRigid) stitch_by_function_with_weights() (in module ClearMap.Alignment.Stitching.StitchingRigid) stitch_by_interpolation() (in module ClearMap.Alignment.Stitching.StitchingRigid) stitch_by_interpolation_adjust_max() (in module ClearMap.Alignment.Stitching.StitchingRigid) stitch_by_max() (in module ClearMap.Alignment.Stitching.StitchingRigid) stitch_by_mean() (in module ClearMap.Alignment.Stitching.StitchingRigid) stitch_by_min() (in module ClearMap.Alignment.Stitching.StitchingRigid) stitch_layout() (in module ClearMap.Alignment.Stitching.StitchingRigid) (in module ClearMap.Alignment.Stitching.StitchingWobbly) stitch_overlay() (PreProcessor method) stitch_rigid() (PreProcessor method) stitch_weights() (in module ClearMap.Alignment.Stitching.StitchingRigid) stitch_wobbly() (PreProcessor method) stop() (PerfMonitor method) (SlicingTransformation method) stop_process() (TabProcessor method) strides (Slice property) string() (Expression method) (ProcessWriter method) (Tag method) string_from_index() (Expression method) (Tag method) structure_element() (in module ClearMap.ImageProcessing.Filter.StructureElement) structure_element_offsets() (in module ClearMap.ImageProcessing.Filter.StructureElement) structure_tree_id (RegistrationParams property) StructurePickerWidget (class in ClearMap.gui.widgets) StructureSelector (class in ClearMap.gui.widgets) sub_graph() (Graph method) sub_pattern_str() (PatternFinder 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) subpatterns_to_groups() (in module ClearMap.Utils.RegularExpression) subplot_tiling() (in module ClearMap.Visualization.Matplotlib.PlotUtils) 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) 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) supported_exts (ConfigLoader attribute) surface_project() (in module ClearMap.gui.gui_utils) sync_cursors() (DataViewer method), [1] 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) TabProcessor (class in ClearMap.processors.generic_tab_processor) Tag (class in ClearMap.Utils.TagExpression) tag() (Expression method) (Tag method) tag_names() (Expression method) tag_to_axes_order() (Source method) 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.MeasureRadius) (in module ClearMap.Analysis.vasculature.graph_corrections) (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) test_completed_inverted_cumulatives() (in module ClearMap.Analysis.Statistics.group_statistics) 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 property) 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.Axons) (in module ClearMap.ImageProcessing.Experts.Vasculature) threshold_isodata() (in module ClearMap.ImageProcessing.Experts.Axons) (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) tiff_list (PatternFinder property) tiff_paths (PatternFinder property) tile_dim (TiledLayout property) tile_extension (SampleParameters attribute), [1] tile_position (Slice property) (Source property) tile_positions (TiledLayout property) tiled_layout() (in module ClearMap.Visualization.Qt.utils) TiledLayout (class in ClearMap.Alignment.Stitching.StitchingRigid) time (Timer attribute) timeit() (in module ClearMap.Utils.Timer) Timer (class in ClearMap.Utils.Timer) title_to_snake() (in module ClearMap.Utils.utilities) TmpDebug (class in ClearMap.gui.gui_utils) to_clearmap_order() (Source method) to_dict() (AffineTransformation method) (ElastixTransformation method) (OrientationTransformation method), [1] (ResamplingTransformation method), [1] (ScalingTransformation method) (SlicingTransformation method) (Transformation method) (TransformationBase method) toggle_layer() (DataViewer method), [1] toolkit_dep_to_version() (PytorchVersionManager method) toolkit_version_from_torch_pkg() (PytorchVersionManager method) 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() (in module ClearMap.ImageProcessing.Tracing.Trace) (in module ClearMap.ImageProcessing.Tracing.TraceCode) trace_edge_label() (in module ClearMap.Analysis.Graphs.GraphProcessing) trace_to_mask() (in module ClearMap.ImageProcessing.Tracing.Trace) (in module ClearMap.ImageProcessing.Tracing.TraceCode) trace_vertex_label() (in module ClearMap.Analysis.Graphs.GraphProcessing) tracePointToMask() (in module ClearMap.ImageProcessing.Tracing.Connect) tracePointToNeighbor() (in module ClearMap.ImageProcessing.Tracing.Connect) track_positions() (in module ClearMap.Alignment.Stitching.Tracking) transform (VesselGraphParams attribute) transform() (in module ClearMap.Alignment.Elastix) transform_coordinates() (CellDetector 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_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_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) tsne() (in module ClearMap.Analysis.DimensionReduction) ttype (AffineTransformation attribute) (ElastixTransformation attribute) (OrientationTransformation attribute), [1] (ScalingTransformation attribute) (SlicingTransformation attribute) (Transformation attribute) (TransformationBase attribute) ttype_to_dtype() (in module ClearMap.Utils.TagExpression) 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.Axons) (in module ClearMap.ImageProcessing.Experts.Vasculature) TwoListSelection (class in ClearMap.gui.widgets) type (ElastixEntry property) U U0() (in module ClearMap.ImageProcessing.Binary.Smoothing) U1() (in module ClearMap.ImageProcessing.Binary.Smoothing) U2() (in module ClearMap.ImageProcessing.Binary.Smoothing) ui_to_cfg() (UiParameter method) (UiParameterCollection method) UiParameter (class in ClearMap.gui.params_interfaces) UiParameterCollection (class in ClearMap.gui.params_interfaces) UNALIGNED (WobblyAlignment attribute) unload_temporary_graphs() (VasculatureTab method) unpack_atlas() (PreProcessor method) unpack_slicing() (in module ClearMap.IO.Slice) unpacked_slicing (Slice property) unpickler() (in module ClearMap.Analysis.Graphs.GraphGt) UNTRACED (WobblyAlignment attribute) update() (LinearSystem method) (Workspace method) update_alignments_from_sources() (Layout method) update_buttons_status() (TwoListSelection method) update_cell_number() (CellCounterTab method) update_comparisons() (GroupAnalysisParams method) update_cpu_values() (PerfMonitor method) update_default_config() (in module ClearMap.config.update_config) update_gpu_values() (PerfMonitor method) update_info() (BaseMetadataParser method) update_orientations() (DataViewer method), [1] update_pbar() (in module ClearMap.gui.dialogs) update_points() (DataViewer method), [1] update_ranges() (OrthoViewer method) update_sources_from_alignments() (Layout method) update_vectors() (DataViewer method), [1] update_watcher_main_progress() (TabProcessor method) update_watcher_progress() (TabProcessor method) updateImage() (DataViewer method), [1] updateLabel() (DataViewer method), [1] updateLabelFromMouseMove() (DataViewer method), [1] updateRegionPercentile() (LUT method) updateRegionRange() (LUT method) updateSlice() (DataViewer method), [1] updateSlicer() (DataViewer method), [1] updateSourceRange() (DataViewer method), [1] updateSourceSlice() (DataViewer method), [1] upper (Layout property) (Region property) (Slice property) upper_coordinate (WobblyAlignment property) upper_wobbly (WobblyLayout property) (WobblySource property) use_arteries (VesselGraphParams attribute) use_default_radii() (GraphMeshVisual method) use_id_as_prefix (SampleParameters attribute), [1] use_npy (GeneralStitchingParams attribute) use_npy() (PreProcessor method) V valid (Block property) VALID (WobblyAlignment attribute) (WobblySource attribute) valid_range (WobblyStitchingParams attribute) validate_arg() (in module ClearMap.Utils.utilities) validate_foreground() (in module ClearMap.Alignment.Stitching.StitchingWobbly) validate_pattern() (PatternDialog method) valids (WobblySource property) valids() (WobblyAlignment method) value() (Tag method) values() (Expression method) VasculatureTab (class in ClearMap.gui.tabs) vectors_to_neighbours() (in module ClearMap.ImageProcessing.Filter.Vector.VectorStructureElement) vein_intensity_range_on_arteries_channel (VesselGraphParams attribute) Verbose (class in ClearMap.Alignment.Stitching.StitchingWobbly) verbose (TabProcessor property) verbose_has_flag() (in module ClearMap.Alignment.Stitching.StitchingWobbly) verbosity (PreferencesParams property) 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.GraphGt) vertex_property_map_to_python() (in module ClearMap.Analysis.Graphs.GraphGt) vertex_radii() (GeometricGraph method) (Graph method) vertex_to_edge_label() (Graph method) vertex_to_edge_property() (in module ClearMap.Analysis.vasculature.vasc_graph_utils) vertices (Graph property), [1] VesselBinarizationParams (class in ClearMap.gui.params) VesselGraphParams (class in ClearMap.gui.params) VesselParams (class in ClearMap.gui.params) VesselVisualizationParams (class in ClearMap.gui.params) view() (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) VolumeVisual (class in ClearMap.Visualization.Vispy.VolumeVisual) voxelization_radii (CellMapParams attribute) voxelization_size (VesselVisualizationParams attribute) voxelize (CellMapParams attribute) voxelize() (CellCounterTab method) (CellDetector method) (in module ClearMap.Analysis.Measurements.Voxelization) (VasculatureTab method) voxelize_folders() (in module ClearMap.processors.batch_process) voxelize_sample() (in module ClearMap.processors.batch_process) voxelize_unweighted() (CellDetector method) voxelize_weighted() (CellDetector method) W warning_popup() (in module ClearMap.gui.dialogs) was_registered (PreProcessor property) was_stitched_rigid (PreProcessor property) wdim (WobblySource property) weight_by_radius (VesselVisualizationParams attribute) weights_from_precentiles() (in module ClearMap.Analysis.Statistics.group_statistics) 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) width (OrthoViewer property) WizardDialog (class in ClearMap.gui.widgets) wobble (WobblySource property) wobble_at_coordinate() (WobblySource method) wobble_from_positions() (WobblySource method) WobblyAlignment (class in ClearMap.Alignment.Stitching.StitchingWobbly) WobblyLayout (class in ClearMap.Alignment.Stitching.StitchingWobbly) WobblySource (class in ClearMap.Alignment.Stitching.StitchingWobbly) WobblyStitchingParams (class in ClearMap.gui.params) Workspace (class in ClearMap.IO.Workspace) wrap_step() (GenericTab method) write() (ElastixParser 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_color_annotation() (in module ClearMap.Visualization.atlas) write_color_palette() (in module ClearMap.Visualization.atlas) write_config() (UiParameter method) (UiParameterCollection method) write_header_from_source() (in module ClearMap.IO.MHD) write_LUT() (in module ClearMap.Visualization.Color.Color) write_PAL() (in module ClearMap.Visualization.Color.Color) write_points() (in module ClearMap.Alignment.Elastix) write_registration_landmark_coords() (AlignmentTab method) wstype (Workspace property) X x_order (Pattern property) x_overlap (RigidStitchingParams attribute) x_rng (Pattern property) x_values (PatternFinder property) xyz_from_ndex() (in module ClearMap.ImageProcessing.Topology.Topology3d) xyz_to_index() (in module ClearMap.ImageProcessing.Topology.Topology3d) Y y_order (Pattern property) y_overlap (RigidStitchingParams attribute) y_rng (Pattern property) y_values (PatternFinder property) Z z_only() (PreProcessor method) z_order (Pattern property) z_rng (Pattern property) z_values (PatternFinder property) 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)
