Python Module Index

a | c | g | i | p | s | u | v


	a
	`ClearMap.Alignment`
	`ClearMap.Alignment.Annotation`
	`ClearMap.Alignment.Elastix`
	`ClearMap.Alignment.landmarks_registration`
	`ClearMap.Alignment.landmarks_registration.engine`
	`ClearMap.Alignment.landmarks_registration.registration_data`
	`ClearMap.Alignment.orientation`
	`ClearMap.Alignment.Resampling`
	`ClearMap.Alignment.Stitching`
	`ClearMap.Alignment.Stitching.layout_graph_utils`
	`ClearMap.Alignment.Stitching.plot_utils`
	`ClearMap.Alignment.Stitching.stitching_plots`
	`ClearMap.Alignment.Stitching.stitching_rigid`
	`ClearMap.Alignment.Stitching.stitching_wobbly`
	`ClearMap.Alignment.Stitching.Tracking`
	`ClearMap.Alignment.Transformation`
	`ClearMap.Alignment.Transformations`
	`ClearMap.Alignment.Transformations.LinearTransformation`
	`ClearMap.Alignment.Transformations.ResamplingTransformation`
	`ClearMap.Alignment.Transformations.SlicingTransformation`
	`ClearMap.Alignment.Transformations.Transformation`
	`ClearMap.Alignment.utils`
	`ClearMap.Analysis`
	`ClearMap.Analysis.colocalization`
	`ClearMap.Analysis.colocalization.bbox`
	`ClearMap.Analysis.colocalization.channel`
	`ClearMap.Analysis.colocalization.parallelism`
	`ClearMap.Analysis.Curves`
	`ClearMap.Analysis.Curves.Extrapolation`
	`ClearMap.Analysis.Curves.Resampling`
	`ClearMap.Analysis.DimensionReduction`
	`ClearMap.Analysis.graphs`
	`ClearMap.Analysis.graphs.fast_graph_reduce`
	`ClearMap.Analysis.graphs.graph`
	`ClearMap.Analysis.graphs.graph_filters`
	`ClearMap.Analysis.graphs.graph_gt`
	`ClearMap.Analysis.graphs.graph_processing`
	`ClearMap.Analysis.graphs.graph_rendering`
	`ClearMap.Analysis.graphs.type_conversions`
	`ClearMap.Analysis.graphs.utils`
	`ClearMap.Analysis.graphs.vessel_classifier`
	`ClearMap.Analysis.Measurements`
	`ClearMap.Analysis.Measurements.maxima_detection`
	`ClearMap.Analysis.Measurements.MeasureExpression`
	`ClearMap.Analysis.Measurements.radius_measurements`
	`ClearMap.Analysis.Measurements.shape_detection`
	`ClearMap.Analysis.Measurements.Voxelization`
	`ClearMap.Analysis.Statistics`
	`ClearMap.Analysis.Statistics.data_frame_operations`
	`ClearMap.Analysis.Statistics.group_assets`
	`ClearMap.Analysis.Statistics.group_statistics`
	`ClearMap.Analysis.Statistics.group_statistics_cumulatives`
	`ClearMap.Analysis.Statistics.MultipleComparisonCorrection`
	`ClearMap.Analysis.Statistics.StatisticalTests`
	`ClearMap.Analysis.vasculature`
	`ClearMap.Analysis.vasculature.annotation_utils`
	`ClearMap.Analysis.vasculature.flow`
	`ClearMap.Analysis.vasculature.flow.assign_p_bc`
	`ClearMap.Analysis.vasculature.flow.linear_system`
	`ClearMap.Analysis.vasculature.flow.units`
	`ClearMap.Analysis.vasculature.general_functions`
	`ClearMap.Analysis.vasculature.geometry_utils`
	`ClearMap.Analysis.vasculature.graph_corrections`
	`ClearMap.Analysis.vasculature.vasc_graph_utils`

	c
	`ClearMap`
	`ClearMap.config`
	`ClearMap.config.atlas`
	`ClearMap.config.change_detection`
	`ClearMap.config.compound_keys`
	`ClearMap.config.config_adjusters`
	`ClearMap.config.config_adjusters.adjusters_api`
	`ClearMap.config.config_adjusters.dict_ops`
	`ClearMap.config.config_adjusters.engine`
	`ClearMap.config.config_adjusters.group_adjusters`
	`ClearMap.config.config_adjusters.patch_ops`
	`ClearMap.config.config_adjusters.policy`
	`ClearMap.config.config_adjusters.policy_specs`
	`ClearMap.config.config_adjusters.templates_resolver`
	`ClearMap.config.config_adjusters.trace_logging`
	`ClearMap.config.config_adjusters.type_hints`
	`ClearMap.config.config_coordinator`
	`ClearMap.config.config_handler`
	`ClearMap.config.config_repository`
	`ClearMap.config.convert_config_versions`
	`ClearMap.config.defaults_provider`
	`ClearMap.config.early_boot`
	`ClearMap.config.update_config`
	`ClearMap.config.utils`
	`ClearMap.config.validators`
	`ClearMap.config.validators._schema`
	`ClearMap.config.validators._semantic`
	`ClearMap.config.validators.json_schema_utils`

	g
	`ClearMap.gui`
	`ClearMap.gui.about`
	`ClearMap.gui.app`
	`ClearMap.gui.creator`
	`ClearMap.gui.creator.graphics_resources_rc`
	`ClearMap.gui.creator.icons_rc`
	`ClearMap.gui.dialog_helpers`
	`ClearMap.gui.dialogs`
	`ClearMap.gui.exception_handler`
	`ClearMap.gui.gui_logging`
	`ClearMap.gui.gui_utils_base`
	`ClearMap.gui.gui_utils_images`
	`ClearMap.gui.params`
	`ClearMap.gui.params_interfaces`
	`ClearMap.gui.params_mixins`
	`ClearMap.gui.pipeline_model`
	`ClearMap.gui.pipeline_widgets`
	`ClearMap.gui.preferences`
	`ClearMap.gui.pretty_imports`
	`ClearMap.gui.pyuic_utils`
	`ClearMap.gui.style`
	`ClearMap.gui.tab_registry`
	`ClearMap.gui.tabs`
	`ClearMap.gui.tabs_interfaces`
	`ClearMap.gui.widget_monkeypatch_callbacks`
	`ClearMap.gui.widgets`

	i
	`ClearMap.ImageProcessing`
	`ClearMap.ImageProcessing.Binary`
	`ClearMap.ImageProcessing.Binary.Filling`
	`ClearMap.ImageProcessing.Binary.FillingCode`
	`ClearMap.ImageProcessing.Binary.morphsnake`
	`ClearMap.ImageProcessing.Binary.Smoothing`
	`ClearMap.ImageProcessing.Clipping`
	`ClearMap.ImageProcessing.Clipping.Clipping`
	`ClearMap.ImageProcessing.Clipping.ClippingCode`
	`ClearMap.ImageProcessing.Differentiation`
	`ClearMap.ImageProcessing.Differentiation.Gradient`
	`ClearMap.ImageProcessing.Differentiation.Hessian`
	`ClearMap.ImageProcessing.Differentiation.HessianCode`
	`ClearMap.ImageProcessing.Experts`
	`ClearMap.ImageProcessing.Experts.Cells`
	`ClearMap.ImageProcessing.Experts.utils`
	`ClearMap.ImageProcessing.Experts.Vasculature`
	`ClearMap.ImageProcessing.Filter`
	`ClearMap.ImageProcessing.Filter.FilterKernel`
	`ClearMap.ImageProcessing.Filter.Rank`
	`ClearMap.ImageProcessing.Filter.Rank.Bilateral`
	`ClearMap.ImageProcessing.Filter.Rank.BilateralCode`
	`ClearMap.ImageProcessing.Filter.Rank.Parametric`
	`ClearMap.ImageProcessing.Filter.Rank.ParametricCode`
	`ClearMap.ImageProcessing.Filter.Rank.Percentile`
	`ClearMap.ImageProcessing.Filter.Rank.PercentileCode`
	`ClearMap.ImageProcessing.Filter.Rank.Rank`
	`ClearMap.ImageProcessing.Filter.Rank.RankCode`
	`ClearMap.ImageProcessing.Filter.Rank.RankCoreCode`
	`ClearMap.ImageProcessing.Filter.Rank.RankResample`
	`ClearMap.ImageProcessing.Filter.StructureElement`
	`ClearMap.ImageProcessing.grey_reconstruction`
	`ClearMap.ImageProcessing.IlluminationCorrection`
	`ClearMap.ImageProcessing.LightsheetCorrection`
	`ClearMap.ImageProcessing.local_percentile_core`
	`ClearMap.ImageProcessing.local_threshold_isodata`
	`ClearMap.ImageProcessing.LocalStatistics`
	`ClearMap.ImageProcessing.machine_learning`
	`ClearMap.ImageProcessing.machine_learning.torch_utils`
	`ClearMap.ImageProcessing.machine_learning.vertices_classification`
	`ClearMap.ImageProcessing.machine_learning.vertices_classification.degree1_inference_utils`
	`ClearMap.ImageProcessing.machine_learning.vessel_filling`
	`ClearMap.ImageProcessing.machine_learning.vessel_filling.vessel_filling`
	`ClearMap.ImageProcessing.machine_learning.vessel_filling.vessel_filling_network`
	`ClearMap.ImageProcessing.Skeletonization`
	`ClearMap.ImageProcessing.Skeletonization.PK12`
	`ClearMap.ImageProcessing.Skeletonization.Skeletonization`
	`ClearMap.ImageProcessing.Skeletonization.SkeletonProcessing`
	`ClearMap.ImageProcessing.Thresholding`
	`ClearMap.ImageProcessing.Thresholding.Thresholding`
	`ClearMap.ImageProcessing.Thresholding.ThresholdingCode`
	`ClearMap.ImageProcessing.Topology`
	`ClearMap.ImageProcessing.Topology.Topology2d`
	`ClearMap.ImageProcessing.Topology.Topology3d`
	`ClearMap.ImageProcessing.Tracing`
	`ClearMap.ImageProcessing.Tracing.Connect`
	`ClearMap.ImageProcessing.Tracing.Trace`
	`ClearMap.ImageProcessing.Tracing.TraceCode`
	`ClearMap.IO`
	`ClearMap.IO.assets_constants`
	`ClearMap.IO.assets_specs`
	`ClearMap.IO.CSV`
	`ClearMap.IO.elastix_config`
	`ClearMap.IO.FileList`
	`ClearMap.IO.FileUtils`
	`ClearMap.IO.GT`
	`ClearMap.IO.IO`
	`ClearMap.IO.metadata`
	`ClearMap.IO.MHD`
	`ClearMap.IO.MMP`
	`ClearMap.IO.NPY`
	`ClearMap.IO.NRRD`
	`ClearMap.IO.Slice`
	`ClearMap.IO.SMA`
	`ClearMap.IO.Source`
	`ClearMap.IO.Temporary`
	`ClearMap.IO.TIF`
	`ClearMap.IO.Workspace`

	p
	`ClearMap.ParallelProcessing`
	`ClearMap.ParallelProcessing.Block`
	`ClearMap.ParallelProcessing.BlockProcessing`
	`ClearMap.ParallelProcessing.DataProcessing`
	`ClearMap.ParallelProcessing.DataProcessing.ArrayProcessing`
	`ClearMap.ParallelProcessing.DataProcessing.ArrayProcessingCode`
	`ClearMap.ParallelProcessing.DataProcessing.ConvolvePointList`
	`ClearMap.ParallelProcessing.DataProcessing.ConvolvePointListCode`
	`ClearMap.ParallelProcessing.DataProcessing.devolve_point_list_code`
	`ClearMap.ParallelProcessing.DataProcessing.DevolvePointList`
	`ClearMap.ParallelProcessing.DataProcessing.MeasurePointList`
	`ClearMap.ParallelProcessing.DataProcessing.MeasurePointListCode`
	`ClearMap.ParallelProcessing.DataProcessing.statistics`
	`ClearMap.ParallelProcessing.ParallelTraceback`
	`ClearMap.ParallelProcessing.ProcessWriter`
	`ClearMap.ParallelProcessing.SharedMemoryArray`
	`ClearMap.ParallelProcessing.SharedMemoryManager`
	`ClearMap.pipeline_orchestrators`
	`ClearMap.pipeline_orchestrators.batch_process`
	`ClearMap.pipeline_orchestrators.cell_map`
	`ClearMap.pipeline_orchestrators.colocalization`
	`ClearMap.pipeline_orchestrators.degree1_inference_processor`
	`ClearMap.pipeline_orchestrators.experiment_controller`
	`ClearMap.pipeline_orchestrators.generic_orchestrators`
	`ClearMap.pipeline_orchestrators.group_orchestrators`
	`ClearMap.pipeline_orchestrators.registration_orchestrator`
	`ClearMap.pipeline_orchestrators.sample_info_management`
	`ClearMap.pipeline_orchestrators.stitching_orchestrator`
	`ClearMap.pipeline_orchestrators.tract_map`
	`ClearMap.pipeline_orchestrators.tube_map`
	`ClearMap.pipeline_orchestrators.utils`

	s
	`ClearMap.Scripts`
	`ClearMap.Scripts.align_new_api`
	`ClearMap.Scripts.cell_map_new_api`
	`ClearMap.Scripts.CellMap`
	`ClearMap.Scripts.clearmap_utils`
	`ClearMap.Scripts.create_distance_file`
	`ClearMap.Scripts.generate_jsonl_file_ontology`
	`ClearMap.Scripts.partial_gt_load_demo`
	`ClearMap.Scripts.tract_map`
	`ClearMap.Scripts.tube_map_new_api`
	`ClearMap.Scripts.TubeMap`
	`ClearMap.Settings`

	u
	`ClearMap.Utils`
	`ClearMap.Utils.array_utils`
	`ClearMap.Utils.array_utils_cy`
	`ClearMap.Utils.event_bus`
	`ClearMap.Utils.events`
	`ClearMap.Utils.exceptions`
	`ClearMap.Utils.Formatting`
	`ClearMap.Utils.HierarchicalDict`
	`ClearMap.Utils.install_utils`
	`ClearMap.Utils.Lazy`
	`ClearMap.Utils.path_utils`
	`ClearMap.Utils.RegularExpression`
	`ClearMap.Utils.Sound`
	`ClearMap.Utils.tag_expression`
	`ClearMap.Utils.Timer`
	`ClearMap.Utils.utilities`

	v
	`ClearMap.Visualization`
	`ClearMap.Visualization.Color`
	`ClearMap.Visualization.Color.Color`
	`ClearMap.Visualization.Color.orientation_colormap`
	`ClearMap.Visualization.Matplotlib`
	`ClearMap.Visualization.Matplotlib.PlotUtils`
	`ClearMap.Visualization.Mesh`
	`ClearMap.Visualization.Mesh.IcoSphere`
	`ClearMap.Visualization.Plot3d`
	`ClearMap.Visualization.Qt`
	`ClearMap.Visualization.Qt.data_viewer_luts`
	`ClearMap.Visualization.Qt.DataViewer`
	`ClearMap.Visualization.Qt.Plot3d`
	`ClearMap.Visualization.Qt.utils`
	`ClearMap.Visualization.Qt.widgets`
	`ClearMap.Visualization.Vispy`
	`ClearMap.Visualization.Vispy.arbitrary_rotation_camera`
	`ClearMap.Visualization.Vispy.graph_visual`
	`ClearMap.Visualization.Vispy.Plot3d`
	`ClearMap.Visualization.Vispy.plot_graph_3d`
	`ClearMap.Visualization.Vispy.VolumeVisual`