All modules for which code is available
- ClearMap.Alignment.Annotation
- ClearMap.Alignment.Elastix
- ClearMap.Alignment.Resampling
- ClearMap.Alignment.Stitching.StitchingRigid
- ClearMap.Alignment.Stitching.StitchingWobbly
- ClearMap.Alignment.Stitching.Tracking
- ClearMap.Alignment.Stitching.layout_graph_utils
- ClearMap.Alignment.Stitching.plot_utils
- ClearMap.Alignment.Transformations.LinearTransformation
- ClearMap.Alignment.Transformations.ResamplingTransformation
- ClearMap.Alignment.Transformations.SlicingTransformation
- ClearMap.Alignment.Transformations.Transformation
- ClearMap.Alignment.orientation
- ClearMap.Alignment.utils
- ClearMap.Analysis.Curves.Extrapolation
- ClearMap.Analysis.Curves.Resampling
- ClearMap.Analysis.DimensionReduction
- ClearMap.Analysis.Graphs.Graph
- ClearMap.Analysis.Graphs.GraphGt
- ClearMap.Analysis.Graphs.GraphProcessing
- ClearMap.Analysis.Graphs.GraphRendering
- ClearMap.Analysis.Measurements.MeasureExpression
- ClearMap.Analysis.Measurements.MeasureRadius
- ClearMap.Analysis.Measurements.Voxelization
- ClearMap.Analysis.Measurements.maxima_detection
- ClearMap.Analysis.Measurements.shape_detection
- ClearMap.Analysis.Statistics.MultipleComparisonCorrection
- ClearMap.Analysis.Statistics.StatisticalTests
- ClearMap.Analysis.Statistics.data_frame_operations
- ClearMap.Analysis.Statistics.group_statistics
- ClearMap.Analysis.vasculature.annotation_utils
- 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.IO.CSV
- ClearMap.IO.FileList
- ClearMap.IO.FileUtils
- ClearMap.IO.GT
- ClearMap.IO.IO
- ClearMap.IO.MHD
- ClearMap.IO.MMP
- ClearMap.IO.NPY
- ClearMap.IO.NRRD
- ClearMap.IO.Slice
- ClearMap.IO.Source
- ClearMap.IO.TIF
- ClearMap.IO.Temporary
- ClearMap.IO.Workspace
- ClearMap.IO.elastix_config
- ClearMap.IO.metadata
- ClearMap.ImageProcessing.Binary.Filling
- ClearMap.ImageProcessing.Binary.FillingCode
- ClearMap.ImageProcessing.Binary.Smoothing
- ClearMap.ImageProcessing.Clipping.Clipping
- ClearMap.ImageProcessing.Clipping.ClippingCode
- ClearMap.ImageProcessing.Differentiation.Gradient
- ClearMap.ImageProcessing.Differentiation.Hessian
- ClearMap.ImageProcessing.Differentiation.HessianCode
- ClearMap.ImageProcessing.Experts.Axons
- ClearMap.ImageProcessing.Experts.Cells
- ClearMap.ImageProcessing.Experts.Vasculature
- ClearMap.ImageProcessing.Experts.utils
- ClearMap.ImageProcessing.Filter.FilterKernel
- 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.RankResample
- ClearMap.ImageProcessing.Filter.StructureElement
- ClearMap.ImageProcessing.Filter.Vector.Vector
- ClearMap.ImageProcessing.Filter.Vector.VectorCode
- ClearMap.ImageProcessing.Filter.Vector.VectorStructureElement
- ClearMap.ImageProcessing.GreyReconstruction
- ClearMap.ImageProcessing.IlluminationCorrection
- ClearMap.ImageProcessing.LightsheetCorrection
- ClearMap.ImageProcessing.LocalStatistics
- ClearMap.ImageProcessing.Skeletonization.PK12
- ClearMap.ImageProcessing.Skeletonization.SkeletonProcessing
- ClearMap.ImageProcessing.Skeletonization.Skeletonization
- ClearMap.ImageProcessing.Thresholding.Thresholding
- ClearMap.ImageProcessing.Thresholding.ThresholdingCode
- ClearMap.ImageProcessing.Topology.Topology2d
- ClearMap.ImageProcessing.Topology.Topology3d
- ClearMap.ImageProcessing.Tracing.Connect
- ClearMap.ImageProcessing.Tracing.Trace
- ClearMap.ImageProcessing.Tracing.TraceCode
- ClearMap.ParallelProcessing.Block
- ClearMap.ParallelProcessing.BlockProcessing
- 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.ParallelTraceback
- ClearMap.ParallelProcessing.ProcessWriter
- ClearMap.ParallelProcessing.SharedMemoryArray
- ClearMap.ParallelProcessing.SharedMemoryManager
- ClearMap.Scripts.align_new_api
- ClearMap.Scripts.cell_map_new_api
- ClearMap.Scripts.clearmap_utils
- ClearMap.Scripts.create_distance_file
- ClearMap.Scripts.generate_jsonl_file_ontology
- ClearMap.Settings
- ClearMap.Utils.Formatting
- ClearMap.Utils.HierarchicalDict
- ClearMap.Utils.Lazy
- ClearMap.Utils.RegularExpression
- ClearMap.Utils.Sound
- ClearMap.Utils.TagExpression
- ClearMap.Utils.Timer
- ClearMap.Utils.array_utils
- ClearMap.Utils.array_utils_cy
- ClearMap.Utils.exceptions
- ClearMap.Utils.install_utils
- ClearMap.Utils.path_utils
- ClearMap.Utils.utilities
- ClearMap.Visualization.Color.Color
- ClearMap.Visualization.Color.orientation_colormap
- ClearMap.Visualization.Matplotlib.PlotUtils
- ClearMap.Visualization.Mesh.IcoSphere
- ClearMap.Visualization.Qt.DataViewer
- ClearMap.Visualization.Qt.DataViewerAxon
- ClearMap.Visualization.Qt.Plot3d
- ClearMap.Visualization.Qt.data_viewer_luts
- ClearMap.Visualization.Qt.utils
- ClearMap.Visualization.Qt.widgets
- ClearMap.Visualization.Vispy.GraphVisual
- ClearMap.Visualization.Vispy.Plot3d
- ClearMap.Visualization.Vispy.PlotGraph3d
- ClearMap.Visualization.Vispy.VolumeVisual
- ClearMap.Visualization.Vispy.arbitrary_rotation_camera
- ClearMap.Visualization.atlas
- ClearMap.config.config_loader
- ClearMap.config.update_config
- 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.tabs
- ClearMap.gui.widget_monkeypatch_callbacks
- ClearMap.gui.widgets
- ClearMap.processors.batch_process
- ClearMap.processors.cell_map
- ClearMap.processors.generic_tab_processor
- ClearMap.processors.sample_preparation
- PyQt5.QtCore