Method Index

This page provides an index of all methods available in the SNT API.

Total methods: 1426 across 75 classes.

A

• Frangi.accept - No description available

• Tubeness.accept - No description available

• SNT.accessToValidImageData - No description available

• AllenCompartment.acronym - No description available

• InsectBrainCompartment.acronym - No description available

• InteractiveTracerCanvas.action - No description available

• PathManagerUI.action - No description available

• SNTChart.action - No description available

• SNTUI.action - No description available

• TracerCanvas.action - No description available

• SNTChart.actionPerformed - Shows a bivariate histogram (two-dimensional histogram) from two DescriptiveStatistics objects. The number of bins is…

• Fill.add - Adds a node to the filled structure.

• InteractiveTracerCanvas.add - No description available

• Path.add - No description available

• PathManagerUI.add - Runs a menu command with options.

• SNTChart.add - No description available

• SNTTable.add - No description available

• SNTUI.add - Updates the status bar.

• TracerCanvas.add - No description available

• Tree.add - Adds a new Path to this Tree.

• Viewer2D.add - Appends a tree to the viewer rendered after the specified measurement.

• Viewer3D.add - Script friendly method to add a supported object (Tree, OBJMesh, AbstractDrawable, etc.) to this viewer. Note that…

• SNTTable.addAll - No description available

• SNTChart.addAncestorListener - No description available

• SNTChart.addChartMouseListener - No description available

• MultiViewer3D.addColorBarLegend - No description available

• SNTChart.addColorBarLegend - Adds a color bar legend (LUT ramp).

• Viewer2D.addColorBarLegend - Adds a color bar legend (LUT ramp) to the viewer. Does nothing if no measurement mapping occurred successfully. Note…

• Viewer3D.addColorBarLegend - Adds a color bar legend (LUT ramp).

• SNTTable.addColumn - No description available

• InteractiveTracerCanvas.addComponentListener - No description available

• PathManagerUI.addComponentListener - No description available

• SNTChart.addComponentListener - No description available

• SNTUI.addComponentListener - No description available

• TracerCanvas.addComponentListener - No description available

• PathManagerUI.addContainerListener - No description available

• SNTChart.addContainerListener - No description available

• SNTUI.addContainerListener - No description available

• SNT.addFillerThread - No description available

• SNTTable.addFirst - Sets a SciJava context to this table.

• InteractiveTracerCanvas.addFocusListener - No description available

• PathManagerUI.addFocusListener - No description available

• SNTChart.addFocusListener - No description available

• SNTUI.addFocusListener - No description available

• TracerCanvas.addFocusListener - No description available

• SNTTable.addGenericColumn - No description available

• GroupedTreeStatistics.addGroup - Adds a comparison group to the analysis queue.

• InteractiveTracerCanvas.addHierarchyBoundsListener - No description available

• PathManagerUI.addHierarchyBoundsListener - No description available

• SNTChart.addHierarchyBoundsListener - No description available

• SNTUI.addHierarchyBoundsListener - No description available

• TracerCanvas.addHierarchyBoundsListener - No description available

• InteractiveTracerCanvas.addHierarchyListener - No description available

• PathManagerUI.addHierarchyListener - No description available

• SNTChart.addHierarchyListener - No description available

• SNTUI.addHierarchyListener - No description available

• TracerCanvas.addHierarchyListener - No description available

• NodeProfiler.addInput - No description available

• PathProfiler.addInput - No description available

• WekaModelLoader.addInput - No description available

• InteractiveTracerCanvas.addInputMethodListener - No description available

• PathManagerUI.addInputMethodListener - No description available

• SNTChart.addInputMethodListener - No description available

• SNTUI.addInputMethodListener - No description available

• TracerCanvas.addInputMethodListener - No description available

• InteractiveTracerCanvas.addKeyListener - No description available

• PathManagerUI.addKeyListener - No description available

• SNTChart.addKeyListener - No description available

• SNTUI.addKeyListener - No description available

• TracerCanvas.addKeyListener - No description available

• Viewer3D.addLabel - Adds an annotation label to the scene.

• SNTTable.addLast - No description available

• SNT.addListener - No description available

• Viewer3D.addMesh - Loads a Wavefront .OBJ file. Should be called before_ displaying the scene, otherwise, if the scene is already visible,…

• InteractiveTracerCanvas.addMouseListener - No description available

• PathManagerUI.addMouseListener - No description available

• SNTChart.addMouseListener - No description available

• SNTUI.addMouseListener - No description available

• TracerCanvas.addMouseListener - No description available

• InteractiveTracerCanvas.addMouseMotionListener - No description available

• PathManagerUI.addMouseMotionListener - No description available

• SNTChart.addMouseMotionListener - No description available

• SNTUI.addMouseMotionListener - No description available

• TracerCanvas.addMouseMotionListener - No description available

• InteractiveTracerCanvas.addMouseWheelListener - No description available

• PathManagerUI.addMouseWheelListener - No description available

• SNTChart.addMouseWheelListener - No description available

• SNTUI.addMouseWheelListener - No description available

• TracerCanvas.addMouseWheelListener - No description available

• FillerThread.addNode - No description available

• Path.addNode - Appends a node to this Path.

• SearchThread.addNode - No description available

• TracerThread.addNode - No description available

• Viewer2D.addNodes - No description available

• InteractiveTracerCanvas.addNotify - No description available

• PathManagerUI.addNotify - No description available

• SNTChart.addNotify - No description available

• SNTUI.addNotify - No description available

• TracerCanvas.addNotify - No description available

• NodeProfiler.addOutput - No description available

• PathProfiler.addOutput - No description available

• WekaModelLoader.addOutput - No description available

• SNTChart.addOverlay - No description available

• PathAndFillManager.addPath - No description available

• PathAndFillManager.addPathAndFillListener - Adds a PathAndFillListener. This is used by the interface to have changes in the path manager reported so that they can…

• Path.addPointDouble - No description available

• SNTChart.addPolygon - No description available

• Viewer2D.addPolygon - No description available

• BiSearch.addProgressListener - No description available

• FillerThread.addProgressListener - No description available

• SearchThread.addProgressListener - No description available

• TracerThread.addProgressListener - No description available

• InteractiveTracerCanvas.addPropertyChangeListener - No description available

• PathManagerUI.addPropertyChangeListener - No description available

• SNTChart.addPropertyChangeListener - No description available

• SNTUI.addPropertyChangeListener - No description available

• TracerCanvas.addPropertyChangeListener - No description available

• PathAndFillManager.addTree - Adds a Tree. If an image is currently being traced, it is assumed it is large enough to contain the tree.

• SciViewSNT.addTree - Adds a tree to the associated SciView instance. A new SciView instance is automatically instantiated if…

• Viewer3D.addTree - Adds a tree to this viewer. Note that calling updateView() may be required to ensure that the current View’s bounding…

• PathAndFillManager.addTrees - Adds a collection of Trees.

• SNTChart.addVetoableChangeListener - No description available

• PathManagerUI.addWindowFocusListener - No description available

• SNTUI.addWindowFocusListener - No description available

• PathManagerUI.addWindowListener - No description available

• SNTUI.addWindowListener - No description available

• PathManagerUI.addWindowStateListener - No description available

• SNTUI.addWindowStateListener - No description available

• AllenCompartment.aliases - No description available

• InsectBrainCompartment.aliases - No description available

• PathAndFillManager.allPointsIterator - No description available

• Frangi.andThen - No description available

• Tubeness.andThen - No description available

• SNTChart.annotate - Adds a subtitle to the chart.

• SNTChart.annotateCategory - Annotates the specified category (Category plots only).

• Viewer3D.annotateLine - Adds a line annotation to this viewer.

• Viewer3D.annotateMidPlane - No description available

• Viewer3D.annotatePlane - No description available

• SNTChart.annotatePoint - Highlights a point in a histogram/XY plot by drawing a labeled arrow at the specified location.

• Viewer3D.annotatePoint - Adds a highlighting point annotation to this viewer.

• Viewer3D.annotatePoints - Adds a scatter (point cloud) annotation to this viewer.

• Viewer3D.annotateSurface - Computes a convex hull from a collection of points and adds it to the scene as an annotation.

• SNTChart.annotateXline - Annotates the specified X-value (XY plots and histograms).

• SNTChart.annotateYline - Annotates the specified Y-value (XY plots and histograms).

• GroupedTreeStatistics.anovaPValue - Computes the one-way ANOVA P-value for all the groups being analyzed. It is assumed that data fulfills basic…

• PathAndFillManager.anySelected - Checks whether at least one Path is currently selected in the UI.

• BoundingBox.append - Computes the bounding box of the specified point cloud and appends it to this bounding box, resizing it as needed.

• SNTTable.appendColumn - No description available

• SNTTable.appendColumns - No description available

• SNTTable.appendRow - No description available

• SNTTable.appendRows - No description available

• SNTTable.appendToLastRow - Appends a value to the last row in the specified column. If the table is empty, a new row is created first. The value…

• Tree.applyCanvasOffset - Specifies the offset to be used when rendering this Tree in a TracerCanvas. Path coordinates remain unaltered.

• InteractiveTracerCanvas.applyComponentOrientation - No description available

• PathManagerUI.applyComponentOrientation - No description available

• SNTChart.applyComponentOrientation - No description available

• SNTUI.applyComponentOrientation - No description available

• TracerCanvas.applyComponentOrientation - No description available

• PathManagerUI.applyDefaultTags - Applies a default (built-in) tag to selected Path(s).

• PathFitter.applyFit - Sets the fallback strategy for radii at locations in which fitting failed

• Tree.applyProperties - Applies properties from another Tree to this Tree.

• PathManagerUI.applyResourceBundle - No description available

• SNTUI.applyResourceBundle - No description available

• PathManagerUI.applySelectionFilter - Selects paths matching a morphometric criteria.

• PathFitter.applySettings - No description available

• SNTChart.applyStyle - No description available

• PathManagerUI.applyTag - Applies a custom tag/ color to selected Path(s).

• InteractiveTracerCanvas.areFocusTraversalKeysSet - No description available

• PathManagerUI.areFocusTraversalKeysSet - No description available

• SNTChart.areFocusTraversalKeysSet - Saves this chart.

• SNTUI.areFocusTraversalKeysSet - No description available

• TracerCanvas.areFocusTraversalKeysSet - No description available

• DefaultSearchNode.asPath - No description available

• DefaultSearchNode.asPathReversed - No description available

• NodeStatistics.assignBranches - Associates the nodes being analyzed to the branches of the specified tree

• Tree.assignImage - Assigns spatial calibration from a Dataset to this Tree.

• PathAndFillManager.assignSpatialSettings - No description available

• Viewer3D.assignUniqueColors - No description available

• Tree.assignValue - Assigns a numeric property to this Tree.

• PathProfiler.assignValues - Retrieves pixel intensities at each node of the Path storing them as Path values

• SNTService.assignValues - Assigns pixel intensities at each Path node, storing them as Path values. Assigned intensities are those of the channel…

• SNT.autoTrace - Automatically traces a path from a point A to a point B. See autoTrace(List, PointInImage) for details.

B

• RootAngleAnalyzer.balancingFactor - Returns the balancing factor, computed from centripetalBias().

• ConvexHull2D.boundarySize - No description available

• ConvexHull3D.boundarySize - No description available

• InteractiveTracerCanvas.bounds - No description available

• PathManagerUI.bounds - No description available

• SNTChart.bounds - No description available

• SNTUI.bounds - No description available

• TracerCanvas.bounds - No description available

C

• PathFitter.call - Takes the signal from the image specified in the constructor to fit cross-section circles around the nodes of input…

• ConvexHullAnalyzer.cancel - No description available

• MultiTreeStatistics.cancel - Main method for testing and demonstration purposes. Creates a MultiTreeStatistics instance using demo data and displays…

• NodeProfiler.cancel - No description available

• PathProfiler.cancel - No description available

• PathStatistics.cancel - Measures specified metrics for each individual path and creates a detailed table. This method generates a comprehensive…

• TreeStatistics.cancel - Sets the table for this TreeStatistics instance.

• WekaModelLoader.cancel - No description available

• SNT.cancelPath - Cancels the temporary path.

• SNT.cancelSearch - No description available

• SNT.cancelTemporary - No description available

• SNT.captureView - Retrieves a WYSIWYG ‘snapshot’ of a tracing canvas without voxel data.

• RootAngleAnalyzer.centripetalBias - Returns the strength of the centripetal bias, also known as κ. κ is defined as the concentration of the von Mises fit…

• SNTUI.changeState - Changes this UI to a new state. Does nothing if newState is the current UI state

• SNT.changeUIState - No description available

• PathAndFillManager.characters - No description available

• SNTChart.chartChanged - No description available

• SNTChart.chartProgress - No description available

• PointInImage.chebyshevDxTo - No description available

• SWCPoint.chebyshevDxTo - No description available

• PointInImage.chebyshevXYdxTo - No description available

• SWCPoint.chebyshevXYdxTo - No description available

• PointInImage.chebyshevZdxTo - No description available

• SWCPoint.chebyshevZdxTo - No description available

• InteractiveTracerCanvas.checkImage - No description available

• PathManagerUI.checkImage - No description available

• SNTChart.checkImage - No description available

• SNTUI.checkImage - No description available

• TracerCanvas.checkImage - No description available

• PathAndFillManager.clear - Deletes all paths and fills.

• SNTTable.clear - No description available

• PathManagerUI.clearSelection - Clears the current path selection.

• BoundingBox.clone - Creates a copy of this BoundingBox.

• Path.clone - Creates a copy of this Path with optional inclusion of immediate children. This method creates a clone of this path and…

• PointInImage.clone - Creates a copy of this PointInImage. This method creates a copy of the point including all properties such as…

• SNTTable.clone - No description available

• SWCPoint.clone - No description available

• Tree.clone - Creates a deep copy of this Tree. This method creates a complete copy of the tree including all paths and their…

• SNT.closeAndResetAllPanes - No description available

• AllenCompartment.color - No description available

• InsectBrainCompartment.color - No description available

• SNTColor.color - Retrieves the AWT color

• Annotation3D.colorCode - No description available

• Viewer3D.colorCode - Runs TreeColorMapper on the specified Tree.

• BoundingBox.combine - Combines this bounding box with another one. It is assumed both boxes share the same voxel spacing/Calibration.

• DefaultSearchNode.compareTo - No description available

• Path.compareTo - No description available

• SNTService.compareTo - No description available

• SWCPoint.compareTo - No description available

• BoundingBox.compute - Computes a new positioning so that this box encloses the specified point cloud.

• ConvexHull2D.compute - No description available

• ConvexHull3D.compute - No description available

• Frangi.compute - No description available

• Tubeness.compute - No description available

• SNT.confirmTemporary - No description available

• BoundingBox.contains - No description available

• InteractiveTracerCanvas.contains - No description available

• Path.contains - Checks if this path contains the specified point within the given tolerance.

• PathManagerUI.contains - No description available

• SNTTable.contains - No description available

• SNTUI.contains - No description available

• TracerCanvas.contains - No description available

• BoundingBox.contains2D - No description available

• SNTTable.containsAll - No description available

• ConvexHullAnalyzer.context - No description available

• MultiTreeStatistics.context - No description available

• NodeProfiler.context - No description available

• PathProfiler.context - No description available

• PathStatistics.context - No description available

• SNTService.context - No description available

• TreeStatistics.context - No description available

• WekaModelLoader.context - No description available

• FillConverter.convert - Map values between the input and output at fill voxel positions.

• FillConverter.convertBinary - Set 1 at fill voxel positions.

• FillConverter.convertDistance - Map the node distance measure to fill voxel positions. This corresponds to the g-score of a node assigned during the…

• FillConverter.convertLabels - Map the fill component label to fill voxel positions. The concrete IntegerType should be chosen based on the…

• PathManagerUI.countComponents - No description available

• SNTUI.countComponents - Gets the current UI state.

• InteractiveTracerCanvas.createBufferStrategy - No description available

• PathManagerUI.createBufferStrategy - No description available

• SNTUI.createBufferStrategy - No description available

• TracerCanvas.createBufferStrategy - No description available

• SNT.createCanvas - No description available

• InteractiveTracerCanvas.createImage - No description available

• PathManagerUI.createImage - No description available

• SNTUI.createImage - No description available

• TracerCanvas.createImage - No description available

• FillerThread.createNewNode - No description available

• SearchThread.createNewNode - No description available

• TracerThread.createNewNode - No description available

• SNTTable.createOrUpdateDisplay - Creates a new display or updates an existing one. If no display exists, creates a new table display window. If a…

• Path.createPath - Returns a new Path with this Path’s attributes (e.g. spatial scale), but no nodes.

• InteractiveTracerCanvas.createVolatileImage - No description available

• PathManagerUI.createVolatileImage - No description available

• SNTUI.createVolatileImage - No description available

• TracerCanvas.createVolatileImage - No description available

• InteractiveTracerCanvas.cursorOverImage - No description available

• TracerCanvas.cursorOverImage - No description available

D

• PathAndFillManager.declaration - No description available

• PathAndFillManager.deletePath - Deletes a path.

• PathAndFillManager.deletePaths - Delete paths by position.

• InteractiveTracerCanvas.deliverEvent - No description available

• PathManagerUI.deliverEvent - No description available

• SNTUI.deliverEvent - No description available

• TracerCanvas.deliverEvent - No description available

• SNTService.demoImage - Returns one of the demo images bundled with SNT image associated with the demo (fractal) tree.

• SNTService.demoTree - Returns a demo tree.

• SNTService.demoTrees - Returns a collection of four demo reconstructions (dendrites from pyramidal cells from the MouseLight database). NB:…

• BoundingBox.depth - No description available

• Path.detachFromParent - Detaches this path from its parent, converting it into an independent primary path. Removes the parent-child…

• InteractiveTracerCanvas.disable - No description available

• PathManagerUI.disable - No description available

• SNTUI.disable - No description available

• TracerCanvas.disable - No description available

• InteractiveTracerCanvas.disableEvents - No description available

• TracerCanvas.disableEvents - No description available

• SNT.disableEventsAllPanes - Description copied from interface: PaneOwner

• InteractiveTracerCanvas.disablePopupMenu - No description available

• TracerCanvas.disablePopupMenu - No description available

• SNT.disableZoomAllPanes - No description available

• InteractiveTracerCanvas.dispatchEvent - No description available

• PathManagerUI.dispatchEvent - No description available

• SNTUI.dispatchEvent - No description available

• TracerCanvas.dispatchEvent - No description available

• MultiTreeStatistics.dispose - Description copied from class: TreeStatistics

• PathAndFillManager.dispose - No description available

• PathManagerUI.dispose - No description available

• PathStatistics.dispose - No description available

• SNTService.dispose - Quits SNT. Does nothing if SNT is currently not running.

• SNTUI.dispose - No description available

• StrahlerAnalyzer.dispose - Clears internal caches and mappings to free memory.

• TreeStatistics.dispose - Clears internal caches and mappings to free memory.

• Viewer3D.dispose - Closes and releases all the resources used by this viewer.

• PointInImage.distanceSquaredTo - No description available

• SWCPoint.distanceSquaredTo - No description available

• PointInImage.distanceTo - No description available

• SWCPoint.distanceTo - No description available

• InteractiveTracerCanvas.doLayout - No description available

• PathManagerUI.doLayout - No description available

• SNTUI.doLayout - No description available

• TracerCanvas.doLayout - No description available

• Path.downsample - Downsamples this path (in-place) by reducing the number of nodes while preserving its overall shape. This method…

• Tree.downsample - Downsamples the tree, i.e., reduces the density of its nodes by increasing internode spacing. Note that 1) upsampling…

• PathAndFillManager.downsampleAll - Downsamples alls path using Ramer–Douglas–Peucker simplification. Downsampling occurs only between branch points and…

• Path.drawPathAsPoints - No description available

• ConvexHullAnalyzer.dump - No description available

• Viewer3D.duplicate - Creates a duplicate of this viewer containing only visible objects. This method creates a new Viewer3D instance and…

E

• SNT.editModeAllowed - Assesses if activation of ‘Edit Mode’ is possible.

• InteractiveTracerCanvas.enable - No description available

• SNTUI.enable - No description available

• TracerCanvas.enable - No description available

• SNT.enableAstar - Toggles the A* search algorithm (enabled by default)

• SNT.enableAutoActivation - No description available

• SNT.enableAutoSelectionOfFinishedPath - No description available

• SNT.enableSecondaryLayerTracing - No description available

• SNT.enableSnapCursor - Enables SNT’s XYZ snap cursor feature. Does nothing if no image data is available or currently loaded image is binary

• NeuroMorphoLoader.enableSourceVersion - Enables or disables the use of source version URLs.

• PathAndFillManager.endDocument - No description available

• PathAndFillManager.endElement - No description available

• PathAndFillManager.endPrefixMapping - Sets whether this PathAndFillManager instance should run headless.

• SNTTable.ensureCapacity - No description available

• PathAndFillManager.error - No description available

• SNTUI.error - No description available

• PointInImage.euclideanDxTo - No description available

• SWCPoint.euclideanDxTo - No description available

• PathAndFillManager.exportAllPathsAsSWC - Exports all as Paths as SWC file(s). Multiple files are created if multiple Trees exist.

• PathAndFillManager.exportFillsAsCSV - Export fills as CSV.

• PathAndFillManager.exportToCSV - Output some potentially useful information about all the Paths managed by this instance as a CSV (comma separated…

• PathAndFillManager.exportTree - No description available

F

• PathAndFillManager.fatalError - No description available

• SNTTable.fillEmptyCells - Fills all empty cells in the table with the specified value. Iterates through all cells in the table and replaces null…

• NodeStatistics.filter - Filters the current pool of nodes matching a measurement-based criterion.

• SNTUI.findComponentAt - No description available

• Path.findJunctionIndices - Returns the indices of nodes which are indicated to be a join, either in this Path object, or any other that starts or…

• Path.findJunctions - Returns the nodes which are indicated to be a join (junction/branch point), either in this Path object, or any other…

• PathProfiler.findMaxima - Finds the maxima in the profile of the specified path. A maxima (peak) will only be considered if protruding more than…

• PathProfiler.findMinima - Finds the minima in the profile of the specified path. A maxima (peak) will only be considered if protruding less than…

• SNT.findPointInStack - No description available

• SNT.findPointInStackPrecise - No description available

• SNT.finished - No description available

• InteractiveTracerCanvas.firePropertyChange - No description available

• TracerCanvas.firePropertyChange - No description available

• Path.firstNode - Returns the first node of this path.

• InteractiveTracerCanvas.fitToWindow - No description available

• TracerCanvas.fitToWindow - No description available

• SNT.flushSecondaryData - No description available

• SNTTable.forEach - No description available

• Viewer3D.freeze - Does not allow scene to be interactive. Only static orthogonal views allowed.

G

• SNTTable.geColumnHeaders - No description available

• SNTTable.geColumnStats - No description available

• SNTTable.geRowStats - No description available

• ConvexHullAnalyzer.get - Gets the value of a specific convex hull metric. Retrieves the computed value for the specified metric name. The metric…

• NodeStatistics.get - Gets the list of nodes associated with the specified compartment (neuropil label).

• SNTTable.get - No description available

• Tree.get - Returns the Path at the specified position.

• InteractiveTracerCanvas.getAccessibleContext - No description available

• TracerCanvas.getAccessibleContext - No description available

• InteractiveTracerCanvas.getAlignmentX - No description available

• TracerCanvas.getAlignmentX - No description available

• InteractiveTracerCanvas.getAlignmentY - No description available

• TracerCanvas.getAlignmentY - No description available

• ConvexHullAnalyzer.getAnalysis - Gets all computed convex hull analysis metrics. Returns a map containing all the computed convex hull metrics and their…

• RootAngleAnalyzer.getAnalysis - No description available

• AllenCompartment.getAncestor - Gets the nth ancestor of this compartment.

• InsectBrainCompartment.getAncestor - No description available

• AllenCompartment.getAncestors - Gets the ancestor ontologies of this compartment as a flat (non-hierarchical) list.

• Path.getAngle - Computes the angle between the specified node and its two flanking neighbors. With B being the specified node, A its…

• RootAngleAnalyzer.getAngles - No description available

• NodeStatistics.getAnnotatedFrequencies - Retrieves the count frequencies across brain compartment.

• NodeStatistics.getAnnotatedFrequenciesByHemisphere - No description available

• NodeStatistics.getAnnotatedFrequencyHistogram - Retrieves the histogram of count frequencies across brain areas of the specified ontology level across the specified…

• NodeStatistics.getAnnotatedHistogram - Retrieves the histogram of count frequencies across brain areas of the specified ontology level.

• MultiTreeStatistics.getAnnotatedLength - Description copied from class: TreeStatistics

• PathStatistics.getAnnotatedLength - No description available

• TreeStatistics.getAnnotatedLength - Retrieves the amount of cable length present on each brain compartment innervated by the analyzed neuron.

• MultiTreeStatistics.getAnnotatedLengthHistogram - No description available

• PathStatistics.getAnnotatedLengthHistogram - No description available

• TreeStatistics.getAnnotatedLengthHistogram - Retrieves the histogram of cable length frequencies across brain areas of the specified ontology level across the…

• MultiTreeStatistics.getAnnotatedLengthsByHemisphere - Description copied from class: TreeStatistics

• PathStatistics.getAnnotatedLengthsByHemisphere - No description available

• TreeStatistics.getAnnotatedLengthsByHemisphere - Retrieves the amount of cable length present on each brain compartment innervated by the analyzed neuron in the two…

• NodeStatistics.getAnnotatedNodes - Splits the nodes being analyzed into groups sharing the same brain annotation.

• PointInImage.getAnnotation - No description available

• SNTPoint.getAnnotation - No description available

• SWCPoint.getAnnotation - No description available

• Viewer3D.getAnnotation - Gets the annotation associated with the specified label.

• InsectBrainLoader.getAnnotations - Gets the brain compartment annotations for this neuron.

• MultiTreeStatistics.getAnnotations - Description copied from class: TreeStatistics

• PathStatistics.getAnnotations - No description available

• TreeStatistics.getAnnotations - Retrieves the brain compartments (neuropil labels) associated with the Tree being measured innervated by the analyzed…

• Viewer3D.getAnnotations - Returns all annotations added to this viewer.

• InteractiveTracerCanvas.getAnnotationsColor - No description available

• TracerCanvas.getAnnotationsColor - No description available

• Path.getApproximatedSurface - Returns an estimated surface area of this path, treating each inter-node segment as a frustum.

• Tree.getApproximatedSurface - Retrieves an approximate estimate of Tree’s surface are by approximating the surface area of each path, and summing to…

• Path.getApproximatedVolume - Returns an estimated volume of this path. The most accurate volume of each path segment would be the volume of a convex…

• Tree.getApproximatedVolume - Retrieves an approximate estimate of Tree’s volume by approximating the volume of each path, and summing to total. The…

• Frangi.getArity - No description available

• Tubeness.getArity - No description available

• Tree.getAssignedValue - Retrieves the numeric property assigned to this Tree.

• MultiTreeColorMapper.getAvailableLuts - No description available

• NodeColorMapper.getAvailableLuts - Gets the available LUTs.

• TreeColorMapper.getAvailableLuts - Gets the available LUTs.

• Viewer2D.getAvailableLuts - No description available

• SNT.getAverageSeparation - No description available

• StrahlerAnalyzer.getAvgBifurcationRatio - No description available

• MultiTreeStatistics.getAvgBranchLength - No description available

• PathStatistics.getAvgBranchLength - Gets the total length of terminal branches. Calculates the sum of lengths of all terminal branches as defined by…

• TreeStatistics.getAvgBranchLength - Gets average length for all the branches of the analyzed tree.

• MultiTreeStatistics.getAvgContraction - No description available

• PathStatistics.getAvgContraction - No description available

• TreeStatistics.getAvgContraction - Gets average contraction for all the branches of the analyzed tree.

• StrahlerAnalyzer.getAvgContractions - No description available

• StrahlerAnalyzer.getAvgExtensionAngle - Gets the average relative extension angle for branches of a specific Strahler order.

• StrahlerAnalyzer.getAvgExtensionAngles - Gets a map of average relative extension angles for all Strahler orders.

• MultiTreeStatistics.getAvgFractalDimension - No description available

• PathStatistics.getAvgFractalDimension - No description available

• TreeStatistics.getAvgFractalDimension - Gets the average fractal dimension of the analyzed tree. Note that branches with less than 5 points are ignored during…

• MultiTreeStatistics.getAvgFragmentation - No description available

• PathStatistics.getAvgFragmentation - No description available

• TreeStatistics.getAvgFragmentation - Gets the average no. of nodes (fragmentation) for all the branches of the analyzed tree.

• StrahlerAnalyzer.getAvgFragmentations - No description available

• MultiTreeStatistics.getAvgPartitionAsymmetry - No description available

• PathStatistics.getAvgPartitionAsymmetry - No description available

• TreeStatistics.getAvgPartitionAsymmetry - Gets the average partition asymmetry of the analyzed tree. Note that branch points with more than 2 children are…

• MultiTreeStatistics.getAvgRemoteBifAngle - No description available

• PathStatistics.getAvgRemoteBifAngle - No description available

• TreeStatistics.getAvgRemoteBifAngle - Gets the average remote bifurcation angle of the analyzed tree. Note that branch points with more than 2 children are…

• Tree.getBPs - Gets the branch points (junctions) of the graph. This is simply an alias for DirectedWeightedGraph.getBPs().

• InteractiveTracerCanvas.getBackground - No description available

• TracerCanvas.getBackground - No description available

• PersistenceAnalyzer.getBarcode has examples - Gets the persistence barcode for the specified filter function. The barcode is a simplified representation of the…

• Annotation3D.getBarycentre - Returns the center of this annotation bounding box.

• InteractiveTracerCanvas.getBaseline - No description available

• TracerCanvas.getBaseline - No description available

• StrahlerAnalyzer.getBifurcationRatios - No description available

• ConvexHullAnalyzer.getBoundarySize - Gets the boundary size (perimeter for 2D hulls or surface area for 3D hulls) of the convex hull.

• PathAndFillManager.getBoundingBox - Returns the BoundingBox enclosing all nodes of all existing Paths.

• Tree.getBoundingBox - Gets the bounding box associated with this tree.

• GroupedTreeStatistics.getBoxPlot - Assembles a Box and Whisker Plot for the specified feature.

• MultiTreeStatistics.getBoxPlot - No description available

• ConvexHullAnalyzer.getBoxivity - Gets the boxivity of the convex hull, which measures how box-like the convex hull is. Values closer to 1 indicate a…

• StrahlerAnalyzer.getBranchCounts - No description available

• Path.getBranchPoint - Gets the branch point (junction) where this path starts, i.e., connects to its parent path.

• StrahlerAnalyzer.getBranchPointCounts - No description available

• Path.getBranchPointIndex - Gets the index of the branch point in the parent path.

• MultiTreeStatistics.getBranchPoints - Description copied from class: TreeStatistics

• Path.getBranchPoints - This is a version of findJunctions() ensuring that a junction node is only retrieved once even if multiple child paths…

• PathStatistics.getBranchPoints - No description available

• TreeStatistics.getBranchPoints - Gets the position of all the branch points in the analyzed tree associated with the specified annotation.

• MultiTreeStatistics.getBranches - Description copied from class: TreeStatistics

• PathStatistics.getBranches - Gets all the paths being analyzed as branches. In PathStatistics, all paths are considered as branches since each path…

• StrahlerAnalyzer.getBranches - No description available

• TreeStatistics.getBranches - Gets all the branches in the analyzed tree. A branch is defined as the Path composed of all the nodes between two…

• MultiTreeStatistics.getCableLength - Description copied from class: TreeStatistics

• PathStatistics.getCableLength - No description available

• TreeStatistics.getCableLength - Gets the cable length associated with the specified compartment (neuropil label).

• MultiTreeStatistics.getCableLengthNorm - No description available

• PathStatistics.getCableLengthNorm - No description available

• TreeStatistics.getCableLengthNorm - Gets the cable length associated with the specified compartment (neuropil label) as a ratio of total length.

• BoundingBox.getCalibration - Creates a Calibration object using information from this BoundingBox

• Path.getCalibration - Gets the spatial calibration of this Path.

• ConvexHullAnalyzer.getCancelReason - No description available

• MultiTreeStatistics.getCancelReason - No description available

• NodeProfiler.getCancelReason - No description available

• PathProfiler.getCancelReason - No description available

• PathStatistics.getCancelReason - No description available

• TreeStatistics.getCancelReason - No description available

• WekaModelLoader.getCancelReason - No description available

• Path.getCanvasOffset - Returns the translation offset used to render this Path in a TracerCanvas.

• BoundingBox.getCentroid - No description available

• ConvexHullAnalyzer.getCentroid - No description available

• Path.getChannel - Gets the hyperstack channel associated with this Path.

• SNT.getChannel - No description available

• Viewer2D.getChart - Gets the current viewer as a SNTChart object

• AllenCompartment.getChildren - Gets the child ontologies of this compartment as a flat (non-hierarchical) list.

• Path.getChildren - Gets the list of child paths that branch from this path. Returns the collection of paths that have this path as their…

• Annotation3D.getColor - No description available

• MultiTreeColorMapper.getColor - No description available

• NodeColorMapper.getColor - No description available

• Path.getColor - Gets the color of this Path

• SWCPoint.getColor - Gets the color of this point.

• Tree.getColor - Gets the color assigned to this Tree.

• TreeColorMapper.getColor - No description available

• Viewer2D.getColor - No description available

• MultiTreeColorMapper.getColorRGB - No description available

• NodeColorMapper.getColorRGB - No description available

• Path.getColorRGB - Gets the color of this Path

• TreeColorMapper.getColorRGB - No description available

• Viewer2D.getColorRGB - No description available

• MultiTreeColorMapper.getColorTable - No description available

• NodeColorMapper.getColorTable - Description copied from class: ColorMapper

• TreeColorMapper.getColorTable - No description available

• Viewer2D.getColorTable - No description available

• SNTTable.getColumnCount - No description available

• SNTTable.getColumnHeader - No description available

• SNTTable.getColumnIndex - No description available

• ConvexHullAnalyzer.getCompactness - No description available

• ConvexHullAnalyzer.getContext - No description available

• MultiTreeStatistics.getContext - No description available

• NodeProfiler.getContext - No description available

• PathProfiler.getContext - No description available

• PathStatistics.getContext - No description available

• SNT.getContext - No description available

• SNTService.getContext - No description available

• TreeStatistics.getContext - No description available

• WekaModelLoader.getContext - No description available

• Path.getContraction - Returns the ratio between the “Euclidean distance” of this path and its length. The Euclidean distance of this path is…

• MultiTreeStatistics.getConvexAnalyzer - No description available

• PathStatistics.getConvexAnalyzer - No description available

• TreeStatistics.getConvexAnalyzer - Gets the ConvexHullAnalyzer instance associated with this TreeStatistics instance.

• Tree.getConvexHull - Retrieves the convex hull of this tree.

• MultiTreeStatistics.getConvexHullMetric - No description available

• PathStatistics.getConvexHullMetric - No description available

• TreeStatistics.getConvexHullMetric - Convenience method to obtain a single-value metric from ConvexHullAnalyzer

• PointInImage.getCoordinateOnAxis - Gets the coordinate along the specified axis.

• SNTPoint.getCoordinateOnAxis - No description available

• SWCPoint.getCoordinateOnAxis - No description available

• PathAndFillManager.getCorrespondences - For each point in this PathAndFillManager, find the corresponding point on the other one. If there’s no corresponding…

• SNT.getCostType - No description available

• RootAngleAnalyzer.getCramerVonMisesStatistic - Computes the Cramér-von Mises statistic between computed root angles and fitted von Mises distribution. A value of 0…

• SNT.getCurrentPath - No description available

• MouseLightLoader.getDOI - Gets the DOI for this neuron.

• SNT.getDataset - No description available

• NodeProfiler.getDelegateObject - No description available

• PathProfiler.getDelegateObject - No description available

• WekaModelLoader.getDelegateObject - No description available

• RootAngleAnalyzer.getDensityPlot - No description available

• MultiTreeStatistics.getDepth - No description available

• PathStatistics.getDepth - No description available

• SNT.getDepth - No description available

• TreeStatistics.getDepth - Returns the depth of the BoundingBox box of the tree being measured

• NodeStatistics.getDescriptiveStatistics - Computes the DescriptiveStatistics for the specified measurement.

• RootAngleAnalyzer.getDescriptiveStatistics - No description available

• MultiTreeStatistics.getDescriptiveStats - Description copied from class: TreeStatistics

• PathStatistics.getDescriptiveStats - No description available

• TreeStatistics.getDescriptiveStats - Computes the DescriptiveStatistics for the specified measurement.

• BoundingBox.getDiagonal - Gets the box diagonal

• PersistenceAnalyzer.getDiagram has examples - Gets the persistence diagram for the specified filter function. The persistence diagram is the core output of the…

• PersistenceAnalyzer.getDiagramNodes has examples - Gets the tree nodes associated with each point in the persistence diagram. This method returns the actual SWCPoint…

• BoundingBox.getDimensions - Gets this BoundingBox dimensions.

• FillerThread.getDistanceAtPoint - No description available

• SNT.getDrawDiameters - No description available

• Annotation3D.getDrawable - Returns the AbstractDrawable associated with this annotation.

• ConvexHullAnalyzer.getEccentricity - No description available

• Path.getEditableNodeIndex - Gets the position of the node tagged as ‘editable’, if any.

• ConvexHullAnalyzer.getElongation - Gets the elongation of the convex hull, which measures how elongated the convex hull is. Higher values indicate more…

• PathResult.getErrorMessage - No description available

• Fill.getEstimatedMeanRadius - Returns the estimated mean radius of the fill, assuming a cylindric shape

• FillerThread.getExitReason - No description available

• SearchThread.getExitReason - No description available

• TracerThread.getExitReason - No description available

• Path.getExtensionAngle3D - Returns a single angle representing the 3D extension direction. This is the angle between the path’s direction vector…

• Path.getExtensionAngleFromHorizontal - Returns the angle between the path’s 3D direction and the horizontal axis.

• Path.getExtensionAngleFromVertical - Returns the angle between the path’s 3D direction and the vertical axis.

• Path.getExtensionAngleXY - Returns the overall extension angle of this path in the XY plane. The angle is obtained from the slope of a linear…

• Path.getExtensionAngleXZ - Returns the overall extension angle of this path in the XZ plane. The angle is obtained from the slope of a linear…

• Path.getExtensionAngleZY - Returns the overall extension angle of this path in the ZY plane. The angle is obtained from the slope of a linear…

• StrahlerAnalyzer.getExtensionAngles - Gets a map of relative extension angles for all branches in each Strahler order.

• Path.getExtensionAngles3D - Returns the complete 3D orientation of this path’s extension direction as spherical coordinates using…

• Path.getExtensionDirection3D - Returns the 3D extension direction vector of this path using linear regression. The vector represents the overall…

• BiSearchNode.getF - No description available

• BiSearchNode.getFFromGoal - No description available

• BiSearchNode.getFFromStart - No description available

• FillerThread.getFill - No description available

• SNT.getFilledBinaryImp - No description available

• SNT.getFilledDistanceImp - No description available

• SNT.getFilledImp - No description available

• SNT.getFilledLabelImp - No description available

• FillConverter.getFillerStack - Merges the input FillerThreads into a single SearchImageStack. When a filled voxel position is present in multiple…

• SNT.getFilterType - No description available

• SNTTable.getFirst - No description available

• Path.getFitted - Gets the fitted version (‘flavor’) of this Path.

• GroupedTreeStatistics.getFlowPlot - Assembles a Flow plot (aka Sankey diagram) for the specified feature.

• MultiTreeStatistics.getFlowPlot - Description copied from class: TreeStatistics

• PathStatistics.getFlowPlot - No description available

• TreeStatistics.getFlowPlot - Assembles a Flow plot (aka Sankey diagram) for the specified feature.

• MultiTreeStatistics.getFractalDimension - No description available

• Path.getFractalDimension - Gets the fractal dimension of this path.

• PathStatistics.getFractalDimension - No description available

• TreeStatistics.getFractalDimension - Gets the fractal dimension of each branch in the analyzed tree. Note that branches with less than 5 points are ignored.

• Path.getFrame - Gets the hyperstack frame position associated with this Path.

• SNT.getFrame - No description available

• Viewer3D.getFrame - Gets the frame containing this viewer, optionally controlling its visibility. Returns the AWT Frame that contains this…

• BiSearchNode.getG - No description available

• BiSearchNode.getGFromGoal - No description available

• BiSearchNode.getGFromStart - No description available

• StrahlerAnalyzer.getGraph - No description available

• Tree.getGraph - Assembles a DirectedGraph from this Tree.

• SkeletonConverter.getGraphs - Generates a list of `DirectedWeightedGraph`s from the skeleton image. Each graph corresponds to one connected component…

• MultiTreeStatistics.getGroup - Gets the collection of Trees being analyzed.

• GroupedTreeStatistics.getGroupStats - Gets the group statistics.

• GroupedTreeStatistics.getGroups - Gets the group identifiers currently queued for analysis.

• DefaultSearchNode.getHandle - No description available

• BiSearchNode.getHeapHandle - No description available

• BiSearchNode.getHeapHandleFromGoal - No description available

• BiSearchNode.getHeapHandleFromStart - No description available

• MultiTreeStatistics.getHeight - No description available

• PathStatistics.getHeight - No description available

• SNT.getHeight - No description available

• TreeStatistics.getHeight - Returns the height of the BoundingBox box of the tree being measured

• PointInImage.getHemisphere - No description available

• SNTPoint.getHemisphere - No description available

• SWCPoint.getHemisphere - No description available

• SNT.getHeuristicType - No description available

• StrahlerAnalyzer.getHighestBranchOrder - No description available

• MultiTreeStatistics.getHighestPathOrder - No description available

• PathStatistics.getHighestPathOrder - Gets the number of branches (paths) being analyzed. Returns the total count of paths in this PathStatistics instance.

• TreeStatistics.getHighestPathOrder - Gets the highest path order of the analyzed tree

• GroupedTreeStatistics.getHistogram - Gets the relative frequencies histogram for a univariate measurement. The number of bins is determined using the…

• MultiTreeStatistics.getHistogram - Description copied from class: TreeStatistics

• NodeStatistics.getHistogram - Gets the relative frequencies histogram for a univariate measurement. The number of bins is determined using the…

• PathStatistics.getHistogram - No description available

• RootAngleAnalyzer.getHistogram - No description available

• TreeStatistics.getHistogram - Retrieves the histogram of relative frequencies histogram for a univariate measurement. The number of bins is…

• ConvexHullAnalyzer.getHull - Gets the convex hull object being analyzed. The hull is initialized if needed.

• MouseLightLoader.getID - Gets the neuron ID for this loader.

• Viewer3D.getID - Returns this Viewer’s id.

• SNTService.getIdentifier - No description available

• SNT.getImagePlus - Gets the Image associated with a view pane.

• Tree.getImpContainer - Gets an empty image capable of holding the skeletonized version of this tree.

• Frangi.getIndependentInstance - No description available

• Tubeness.getIndependentInstance - No description available

• NodeProfiler.getInfo - No description available

• PathProfiler.getInfo - No description available

• SNTService.getInfo - No description available

• WekaModelLoader.getInfo - No description available

• MultiTreeStatistics.getInnerBranches - Description copied from class: TreeStatistics

• PathStatistics.getInnerBranches - Gets the inner branches from the analyzed paths. In PathStatistics, inner branches are equivalent to primary branches.

• TreeStatistics.getInnerBranches - Retrieves the branches of highest Strahler order in the Tree. This typically correspond to the most ‘internal’ branches…

• MultiTreeStatistics.getInnerLength - No description available

• PathStatistics.getInnerLength - Gets the total length of inner branches. In PathStatistics, this returns the same value as getPrimaryLength().

• TreeStatistics.getInnerLength - Gets the cable length of inner branches

• NodeProfiler.getInput - No description available

• PathProfiler.getInput - No description available

• WekaModelLoader.getInput - No description available

• NodeProfiler.getInputs - No description available

• PathProfiler.getInputs - No description available

• WekaModelLoader.getInputs - No description available

• SNTService.getInstance - Returns a reference to the active SNT instance.

• Viewer2D.getJFreeChart - Gets the current viewer as a JFreeChart object

• MouseLightLoader.getJSON - Gets all the data associated with this reconstruction as a JSON object.

• Annotation3D.getLabel - Gets the annotation label

• Tree.getLabel - Returns the identifying label of this tree. When importing files, the label typically defaults to the imported filename,

• PersistenceAnalyzer.getLandscape - Gets the persistence landscape as a vectorized representation. Persistence landscapes transform persistence diagrams…

• SNTTable.getLast - No description available

• StrahlerAnalyzer.getLengths - No description available

• ShollAnalyzer.getLinearStats - Gets the LinearProfileStats associated with this analyzer. By default, it is set to determine the polynomial of…

• SNT.getLoadedData - No description available

• SNT.getLoadedDataAsImp - Retrieves the pixel data of the main image currently loaded in memory as an ImagePlus object. Returned image is always…

• PathAndFillManager.getLoadedFills - No description available

• SNT.getLoadedIterable - No description available

• SNTService.getLocation - No description available

• Viewer3D.getManagerPanel - Returns a reference to ‘RV Controls’ panel.

• ShollAnalyzer.getMaximaRadii - No description available

• AllenCompartment.getMesh - No description available

• ConvexHull3D.getMesh - No description available

• InsectBrainCompartment.getMesh - No description available

• Viewer3D.getMesh - Gets the mesh associated with the specified label.

• InsectBrainLoader.getMeshes - Gets the 3D meshes associated with this neuron’s brain compartments.

• Viewer3D.getMeshes - Returns all meshes added to this viewer.

• Fill.getMetric - No description available

• MultiTreeStatistics.getMetric - No description available

• PathStatistics.getMetric - Gets a specific metric value for an individual path. This method provides direct access to morphometric properties of…

• TreeStatistics.getMetric - Computes the specified metric.

• MultiTreeColorMapper.getMinMax - No description available

• NodeColorMapper.getMinMax - Description copied from class: ColorMapper

• TreeColorMapper.getMinMax - No description available

• Viewer2D.getMinMax - No description available

• MultiTreeColorMapper.getMultiViewer - Description copied from class: TreeColorMapper

• TreeColorMapper.getMultiViewer - Assembles a Multi-pane viewer using all the Trees mapped so far.

• Viewer2D.getMultiViewer - No description available

• GroupedTreeStatistics.getN - Gets the number of Trees in a specified group.

• TreeStatistics.getNBranchPoints - Gets the number of branch points in the analyzed tree associated with the specified annotation.

• MultiTreeColorMapper.getNaNColor - No description available

• NodeColorMapper.getNaNColor - No description available

• TreeColorMapper.getNaNColor - No description available

• Viewer2D.getNaNColor - No description available

• InsectBrainLoader.getNeuronInfo - No description available

• SWCPoint.getNextPoints - Returns the list holding the subsequent nodes in the reconstructed structure after this one.

• Fill.getNodeList - Returns the list of nodes in the filled structure.

• MouseLightLoader.getNodes - Script-friendly method to extract the nodes of a cellular compartment.

• NodeColorMapper.getNodes - Gets the collection of nodes being mapped.

• Tree.getNodes - Gets all the nodes (path points) forming this tree.

• BiSearch.getNodesAsImage - No description available

• FillerThread.getNodesAsImage - No description available

• FillerThread.getNodesAsImageFromGoal - No description available

• SearchThread.getNodesAsImageFromGoal - No description available

• TracerThread.getNodesAsImageFromGoal - No description available

• FillerThread.getNodesAsImageFromStart - No description available

• SearchThread.getNodesAsImageFromStart - No description available

• TracerThread.getNodesAsImageFromStart - No description available

• Tree.getNodesAsSWCPoints - No description available

• NodeColorMapper.getNodesByColor - No description available

• Tree.getNodesCount - Gets the total number of nodes across all paths in this Tree.

• ShollAnalyzer.getNormStats - Gets the NormalizedProfileStats associated with this analyzer. By default it is set to determine the regression…

• PathResult.getNumberOfPoints - No description available

• AllenCompartment.getOntologyDepth - Gets the ontology depth of this compartment.

• InsectBrainCompartment.getOntologyDepth - No description available

• SNTService.getOrCreateSciViewSNT - No description available

• NodeProfiler.getOutput - No description available

• PathProfiler.getOutput - No description available

• WekaModelLoader.getOutput - No description available

• NodeProfiler.getOutputs - No description available

• PathProfiler.getOutputs - No description available

• WekaModelLoader.getOutputs - No description available

• AllenCompartment.getParent - Gets the parent of this compartment.

• InsectBrainCompartment.getParent - No description available

• PathAndFillManager.getPath - Returns the Path at the specified position in the PathAndFillManager list.

• PathFitter.getPath - No description available

• PathResult.getPath - No description available

• PointInImage.getPath - Returns the Path associated with this node (if any)

• SWCPoint.getPath - No description available

• SNTService.getPathAndFillManager - Returns the PathAndFillManager associated with the current SNT instance.

• PathAndFillManager.getPathFromID - Returns the Path with the specified id.

• PathAndFillManager.getPathFromName - Returns the Path with the specified name.

• PathAndFillManager.getPaths - Returns all the paths.

• SNTService.getPaths - Gets the paths currently listed in the Path Manager

• PathAndFillManager.getPathsFiltered - Returns the ‘de facto’ Paths.

• PathAndFillManager.getPathsInROI - No description available

• PathAndFillManager.getPathsStructured - No description available

• NodeProfiler.getPlot - No description available

• PathProfiler.getPlot - Gets the plot profile as an ImageJ plot (all channels included).

• Viewer2D.getPlot - Gets the current plot as a XYPlot object

• PathAndFillManager.getPlugin - Gets the SNT instance.

• GroupedTreeStatistics.getPolarHistogram - Gets the relative frequencies histogram for a univariate measurement as a polar (rose) plot assuming a data range…

• ConvexHull2D.getPolygon - No description available

• DefaultSearchNode.getPredecessor - No description available

• BiSearchNode.getPredecessorFromGoal - No description available

• BiSearchNode.getPredecessorFromStart - No description available

• SNTService.getPriority - No description available

• Tree.getProperties has examples - Returns the Properties instance holding the persistent set of properties. Useful to associate metadata to this tree….

• SkeletonConverter.getPruneMode - Gets the loop pruning strategy.

• FlyCircuitLoader.getReader - Gets the SWC data associated with the specified cell ID as a reader

• NeuroMorphoLoader.getReader - Gets the SWC data (‘CNG version’) associated with the specified cell ID as a reader

• RemoteSWCLoader.getReader - No description available

• SNTService.getRecViewer - Returns a reference to an opened Reconstruction Viewer (standalone instance). *

• FlyCircuitLoader.getReconstructionURL - Gets the URL of the SWC file associated with the specified cell ID.

• NeuroMorphoLoader.getReconstructionURL - Gets the URL of the SWC file (‘CNG version’) associated with the specified cell ID.

• RemoteSWCLoader.getReconstructionURL - No description available

• Viewer3D.getRecorder - Gets the script recorder for this viewer, optionally creating one if needed.

• StrahlerAnalyzer.getRelativeExtensionAngle - Computes the relative extension angle for a StrahlerAnalyzer branch by finding the parent direction from the graph…

• BiSearch.getResult - No description available

• FillerThread.getResult - No description available

• SearchThread.getResult - No description available

• TracerThread.getResult - No description available

• Tree.getRoot - Gets the first node of the main primary path of this tree

• StrahlerAnalyzer.getRootAssociatedBranches - No description available

• StrahlerAnalyzer.getRootNumber - No description available

• SkeletonConverter.getRootRoiStrategy - Gets the current root ROI strategy. Returns the strategy used for handling root ROIs during skeleton conversion. If no…

• ConvexHullAnalyzer.getRoundness - Gets the roundness of the convex hull, which measures how round or circular the convex hull is. Values closer to 1…

• SNTTable.getRowCount - No description available

• SNTTable.getRowHeader - No description available

• SNTTable.getRowIndex - No description available

• MouseLightLoader.getSWC - Gets all the data associated with this reconstruction in the SWC format.

• PathAndFillManager.getSWCFor - Converts a collection of connected Path objects into SWC points for export. SWC is the standardized format used for…

• Tree.getSWCTypeNames - Gets the set of SWC type labels present in this tree with optional soma inclusion in a readable form.

• Tree.getSWCTypes - Gets the set of SWC types present in this tree with optional soma inclusion.

• MouseLightLoader.getSampleInfo - Gets sample information for this neuron.

• SciViewSNT.getSciView - Gets the SciView instance currently in use.

• SNTService.getSciViewSNT - No description available

• ShollAnalyzer.getSecondaryMaxima - No description available

• PathAndFillManager.getSelectedPaths - Gets all paths selected in the GUI

• SNTService.getSelectedPaths - Gets the paths currently selected in the Path Manager list.

• SkeletonConverter.getSingleGraph - Generates a single `DirectedWeightedGraph`s by combining getGraphs()’s list into a single, combined graph. Typically,…

• SkeletonConverter.getSingleTree - Generates a single Tree from getSingleGraph(). If a ROI-based centroid has been set, Root is converted to a single…

• ShollAnalyzer.getSingleValueMetrics - No description available

• ConvexHullAnalyzer.getSize - Gets the size (area or volume) of the convex hull, which is the area for 2D hulls or the volume for 3D hulls.

• Tree.getSkeleton - Retrieves the rasterized skeleton of this tree at 1:1 scaling.

• Tree.getSkeleton2D - Retrieves a 2D projection of the rasterized skeleton of this tree at 1:1 scaling.

• MouseLightLoader.getSomaCompartment - Gets the brain compartment containing the soma.

• MouseLightLoader.getSomaLocation - Gets the soma location for this neuron.

• Tree.getSomaNodes - Gets the list of all nodes tagged as Path.SWC_SOMA.

• Fill.getSourcePaths - Returns the set of source paths for the filled structure.

• Fill.getSourcePathsStringHuman - No description available

• Fill.getSourcePathsStringMachine - No description available

• BiSearchNode.getState - No description available

• BiSearchNode.getStateFromGoal - No description available

• BiSearchNode.getStateFromStart - No description available

• SNTService.getStatistics - Returns a TreeStatistics instance constructed from current Paths.

• PathFitter.getSucceeded - Checks whether the fit succeeded.

• PathResult.getSuccess - No description available

• SNTTable.getSummaryRow - No description available

• NodeProfiler.getTable - No description available

• SNTService.getTable - Returns a reference to SNT’s main table of measurements.

• RootAngleAnalyzer.getTaggedGraph - No description available

• RootAngleAnalyzer.getTaggedTree - Returns a recolored copy of the analyzed tree with the root angles assigned to its node values.

• SWCPoint.getTags - Gets the tags associated with this point.

• Fill.getThreshold - No description available

• FillerThread.getThreshold - No description available

• Tree.getTips - Gets the end points (tips) of the graph. This is simply an alias for DirectedWeightedGraph.getTips().

• Viewer2D.getTitle - Gets the plot display title.

• ConvexHullAnalyzer.getTree - Gets the tree being analyzed.

• FlyCircuitLoader.getTree - Gets the collection of Paths for the specified cell ID

• InsectBrainLoader.getTree - Gets the collection of Paths for the specified cell ID

• MouseLightLoader.getTree - Script-friendly method to extract the entire neuron as a collection of Paths.

• NeuroMorphoLoader.getTree - Gets the collection of Paths for the specified cell ID

• RemoteSWCLoader.getTree - No description available

• SNTService.getTree - Gets the collection of paths listed in the Path Manager as a Tree object.

• Viewer3D.getTree - Gets the tree associated with the specified label.

• SciViewSNT.getTreeAsSceneryNode - Gets the specified Tree as a Scenery Node.

• AllenCompartment.getTreePath - Gets the tree path of this compartment. The TreePath is the list of parent compartments that uniquely identify this…

• SNTService.getTrees - Gets the collection of paths listed in the Path Manager as a Tree object.

• SkeletonConverter.getTrees - Generates a list of Trees from the skeleton image. Each Tree corresponds to one connected component of the graph…

• Viewer3D.getTrees - Returns all trees added to this viewer.

• Annotation3D.getType - Gets the type of this annotation.

• SNTService.getUI - Returns a reference to SNT’s UI.

• AllenCompartment.getUUID - No description available

• BoundingBox.getUnit - Gets the length unit of voxel spacing

• ConvexHullAnalyzer.getUnit - Returns the physical unit associated with the specified metric.

• PointInImage.getUnscaledPoint - Converts the coordinates of this point into pixel units if this point is associated with a Path.

• SWCPoint.getUnscaledPoint - No description available

• NodeProfiler.getValues - Gets the profile for the specified path as a map of lists of pixel intensities (profile indices as keys)

• PathProfiler.getValues - Gets the profile for the specified path as a map of lists, with distances (or indices) stored under X_VALUES…

• SNTService.getVersion - No description available

• Annotation3D.getVolume - No description available

• Fill.getVolume - Returns the Fill volume. It assumes that the volume is just the number of sub-threshold nodes multiplied by x_spacing *…

• BiSearchNode.getX - No description available

• DefaultSearchNode.getX - No description available

• PointInImage.getX - No description available

• SNTPoint.getX - No description available

• SWCPoint.getX - No description available

• SearchNode.getX - No description available

• PathProfiler.getXYPlot - Gets the plot profile as an PlotService plot. It is recommended to call…

• BiSearchNode.getY - No description available

• DefaultSearchNode.getY - No description available

• PointInImage.getY - No description available

• SNTPoint.getY - No description available

• SWCPoint.getY - No description available

• SearchNode.getY - No description available

• BiSearchNode.getZ - No description available

• DefaultSearchNode.getZ - No description available

• PointInImage.getZ - No description available

• SNTPoint.getZ - No description available

• SWCPoint.getZ - No description available

• SearchNode.getZ - No description available

H

• BoundingBox.hasDimensions - No description available

• BiSearchNode.heapDecreaseKey - No description available

• BiSearchNode.heapInsert - No description available

• BoundingBox.height - No description available

I

• AllenCompartment.id - No description available

• InsectBrainCompartment.id - No description available

• InsectBrainLoader.idExists - Checks whether the neuron to be loaded was found in the database.

• MouseLightLoader.idExists - Checks if the neuron ID exists in the database.

• Frangi.in - No description available

• Tubeness.in - No description available

• AllenCompartment.includes - No description available

• Tree.indexOf - Returns the index of the specified Path in this Tree.

• BoundingBox.inferSpacing - Infers the voxel spacing of this box from the inter-node distances of a Collection of SWCPoints.

• Frangi.initialize - No description available

• NodeProfiler.initialize - No description available

• PathProfiler.initialize - No description available

• SNTService.initialize - Initializes SNT.

• Tubeness.initialize - No description available

• WekaModelLoader.initialize - No description available

• BoundingBox.intersection - Retrieves the intersection cuboid between this bounding with another bounding box. It is assumed both boxes share the…

• ConvexHull2D.intersection - No description available

• ConvexHull3D.intersection - No description available

• ConvexHull2D.intersectionBox - No description available

• ConvexHull3D.intersectionBox - No description available

• Tree.is3D - Assesses whether this Tree has depth.

• SNTService.isActive - Gets whether SNT is running.

• Viewer3D.isActive - Checks whether this instance is currently active

• Tree.isAnnotated - Checks if the nodes of this Tree have been assigned BrainAnnotations (neuropil labels).

• ConvexHullAnalyzer.isCanceled - No description available

• NodeProfiler.isCanceled - No description available

• PathProfiler.isCanceled - No description available

• WekaModelLoader.isCanceled - No description available

• AllenCompartment.isChildOf - Assesses if this annotation is a child of a specified compartment.

• InsectBrainCompartment.isChildOf - No description available

• Annotation3D.isColorCodeAllowed - No description available

• Viewer3D.isDarkModeOn - Checks if scene is being rendered under dark or light background.

• FlyCircuitLoader.isDatabaseAvailable - Checks whether a connection to the FlyCircuit database can be established.

• NeuroMorphoLoader.isDatabaseAvailable - Checks whether a connection to the NeuroMorpho database can be established.

• RemoteSWCLoader.isDatabaseAvailable - No description available

• Tree.isEmpty - Checks if this Tree is empty.

• NodeProfiler.isInputResolved - No description available

• PathProfiler.isInputResolved - No description available

• WekaModelLoader.isInputResolved - No description available

• MultiTreeColorMapper.isIntegerScale - No description available

• NodeColorMapper.isIntegerScale - No description available

• TreeColorMapper.isIntegerScale - No description available

• Viewer2D.isIntegerScale - No description available

• AllenCompartment.isMeshAvailable - Checks whether a mesh is known to be available for this compartment.

• InsectBrainCompartment.isMeshAvailable - No description available

• MultiTreeColorMapper.isNodeMapping - No description available

• TreeColorMapper.isNodeMapping - No description available

• Viewer2D.isNodeMapping - No description available

• NodeProfiler.isOutputResolved - No description available

• PathProfiler.isOutputResolved - No description available

• WekaModelLoader.isOutputResolved - No description available

• AllenCompartment.isParentOf - Assesses if this annotation is the parent of the specified compartment.

• InsectBrainCompartment.isParentOf - No description available

• PointInImage.isReal - No description available

• SWCPoint.isReal - No description available

• NodeProfiler.isResolved - No description available

• PathProfiler.isResolved - No description available

• WekaModelLoader.isResolved - No description available

• Viewer3D.isSNTInstance - Checks whether this instance is SNT’s Reconstruction Viewer.

• PointInImage.isSameLocation - No description available

• SWCPoint.isSameLocation - No description available

• BoundingBox.isScaled - Checks whether this BoundingBox is spatially calibrated, i.e., if voxel spacing has been specified

• Viewer3D.isSplitDendritesFromAxons - Checks whether axons and dendrites of imported Trees are set to be imported as separated objects.

• SNTColor.isTypeDefined - Checks if an SWC type has been defined.

L

• Tree.list - Gets all the paths from this tree.

• SNTService.loadGraph - No description available

• Viewer3D.loadMesh - Loads a Wavefront .OBJ file. Files should be loaded _before_ displaying the scene, otherwise, if the scene is already…

• Viewer3D.loadRefBrain - Loads the surface mesh of a supported reference brain/neuropil. Internet connection may be required.

• SNTService.loadTracings - Loads the specified tracings file.

• SNTService.loadTree - Loads the specified tree. Note that if SNT has not been properly initialized, spatial calibration mismatches may occur….

• SNTService.log - No description available

• Viewer3D.logSceneControls - Logs API calls controlling the scene (view point, bounds, etc.) to Script Recorder (or Console if Script Recorder is…

M

• MultiTreeColorMapper.map - Description copied from class: ColorMapper

• NodeColorMapper.map - Maps nodes after the specified measurement. Mapping bounds are automatically determined.

• TreeColorMapper.map - Colorizes a tree after the specified measurement. Mapping bounds are automatically determined.

• Viewer2D.map - No description available

• MultiTreeColorMapper.mapRootDistanceToCentroid - No description available

• MultiTreeColorMapper.mapTrees - No description available

• TreeColorMapper.mapTrees - Colorizes a list of trees, with each tree being assigned a LUT index.

• Viewer2D.mapTrees - No description available

• RootAngleAnalyzer.max - No description available

• RootAngleAnalyzer.mean - No description available

• RootAngleAnalyzer.meanDirection - Returns the mean direction of the fitted von Mises distribution.

• Viewer3D.mergeAnnotations - Merges a collection of annotations into a single object.

• RootAngleAnalyzer.min - No description available

N

• AllenCompartment.name - No description available

• InsectBrainCompartment.name - No description available

• SNTService.newRecViewer - Instantiates a new standalone Reconstruction Viewer.

O

• Frangi.ops - No description available

• Tubeness.ops - No description available

• BoundingBox.origin - Retrieves the origin of this box.

• BoundingBox.originOpposite - Retrieves the origin opposite of this box.

• Frangi.out - No description available

• Tubeness.out - No description available

P

• PathChangeListener.pathChanged - No description available

• BiSearch.pointsConsideredInSearch - No description available

• FillerThread.pointsConsideredInSearch - No description available

• SearchThread.pointsConsideredInSearch - No description available

• TracerThread.pointsConsideredInSearch - No description available

• NodeProfiler.preview - No description available

• PathProfiler.preview - No description available

• WekaModelLoader.preview - No description available

• SWCPoint.previous - Returns the preceding node (if any)

• BiSearch.printStatus - No description available

• FillerThread.printStatus - No description available

• SearchThread.printStatus - No description available

• TracerThread.printStatus - No description available

R

• PathFitter.readPreferences - No description available

• Viewer3D.rebuild - Rebuilds (repaints) a scene object (e.g., a Tree after being modified elsewhere)

• Viewer3D.recordRotation - Records an animated rotation of the scene as a sequence of images.

• SNTService.registerEventHandlers - No description available

• NodeProfiler.removeInput - No description available

• PathProfiler.removeInput - No description available

• WekaModelLoader.removeInput - No description available

• NodeProfiler.removeOutput - No description available

• PathProfiler.removeOutput - No description available

• WekaModelLoader.removeOutput - No description available

• SciViewSNT.removeTree - Removes the specified Tree.

• BiSearch.reportFinished - No description available

• FillerThread.reportFinished - No description available

• SearchThread.reportFinished - No description available

• TracerThread.reportFinished - No description available

• NodeProfiler.resolveInput - No description available

• PathProfiler.resolveInput - No description available

• WekaModelLoader.resolveInput - No description available

• NodeProfiler.resolveOutput - No description available

• PathProfiler.resolveOutput - No description available

• WekaModelLoader.resolveOutput - No description available

• BiSearch.run - No description available

• ConvexHullAnalyzer.run - No description available

• FillerThread.run - No description available

• Frangi.run - No description available

• NodeProfiler.run - No description available

• PathProfiler.run - No description available

• SearchThread.run - No description available

• TracerThread.run - No description available

• Tubeness.run - No description available

• WekaModelLoader.run - No description available

S

• MouseLightLoader.save - Convenience method to save JSON data.

• MultiViewer2D.save - No description available

• SNTService.save - Saves all the existing paths to a file.

• MouseLightLoader.saveAsJSON - Convenience method to save JSON data to a local directory.

• MouseLightLoader.saveAsSWC - Convenience method to save SWC data to a local directory.

• BoundingBox.scale - No description available

• PointInImage.scale - Scales this point coordinates.

• SWCPoint.scale - No description available

• SNTColor.setAWTColor - Re-assigns an AWT color.

• MultiViewer3D.setAnimationEnabled - No description available

• PointInImage.setAnnotation - Description copied from interface: SNTPoint

• SNTPoint.setAnnotation - Assigns a neuropil annotation (e.g., atlas compartment) to this point.

• SWCPoint.setAnnotation - Description copied from interface: SNTPoint

• MultiViewer2D.setAxesVisible - No description available

• Viewer2D.setAxesVisible - No description available

• Annotation3D.setBoundingBoxColor - Determines whether the mesh bounding box should be displayed.

• Annotation3D.setColor - Script friendly method to assign a color to the annotation.

• SWCPoint.setColor - Sets the color of this point.

• MultiViewer2D.setColorBarLegend - No description available

• SkeletonConverter.setConnectComponents - Sets whether to connect nearby skeleton components. Controls whether disconnected skeleton components should be…

• ConvexHullAnalyzer.setContext - No description available

• NodeProfiler.setContext - No description available

• PathProfiler.setContext - No description available

• SNTService.setContext - No description available

• WekaModelLoader.setContext - No description available

• PathFitter.setCrossSectionRadius - Sets the max radius (side search) for constraining the fit.

• Viewer2D.setDefaultColor - Sets the default (fallback) color for plotting paths.

• BoundingBox.setDimensions - Sets the dimensions of this bounding box using uncalibrated (pixel) lengths.

• ShollAnalyzer.setEnableCurveFitting - Sets whether curve fitting computations should be performed.

• Frangi.setEnvironment - No description available

• Tubeness.setEnvironment - No description available

• Viewer2D.setEqualizeAxes - /** Sets whether the axes should be equalized (same scale). When enabled, both X and Y axes will use the same scale to…

• PathResult.setErrorMessage - No description available

• BiSearchNode.setFFromGoal - No description available

• BiSearchNode.setFFromStart - No description available

• BiSearchNode.setFrom - No description available

• DefaultSearchNode.setFrom - No description available

• BiSearchNode.setFromGoal - No description available

• BiSearchNode.setFromStart - No description available

• BiSearchNode.setGFromGoal - No description available

• BiSearchNode.setGFromStart - No description available

• MultiViewer3D.setGap - No description available

• MultiViewer2D.setGridlinesVisible - No description available

• Viewer2D.setGridlinesVisible - No description available

• DefaultSearchNode.setHandle - No description available

• BiSearchNode.setHeapHandle - No description available

• BiSearchNode.setHeapHandleFromGoal - No description available

• BiSearchNode.setHeapHandleFromStart - No description available

• PointInImage.setHemisphere - No description available

• SNTPoint.setHemisphere - No description available

• SWCPoint.setHemisphere - No description available

• PathFitter.setImage - Sets the target image

• SNTService.setInfo - No description available

• Frangi.setInput - No description available

• NodeProfiler.setInput - No description available

• PathProfiler.setInput - No description available

• Tubeness.setInput - No description available

• WekaModelLoader.setInput - No description available

• NodeProfiler.setInputs - No description available

• PathProfiler.setInputs - No description available

• WekaModelLoader.setInputs - No description available

• ConvexHullAnalyzer.setLabel - Sets the optional description for the analysis

• NodeStatistics.setLabel - Sets a descriptive label to this statistic analysis to be used in histograms, etc.

• MultiViewer3D.setLabels - No description available

• MultiViewer2D.setLayoutColumns - No description available

• MultiViewer3D.setLayoutColumns - No description available

• SkeletonConverter.setLengthThreshold - Sets the minimum component length necessary to avoid pruning. This value is only used if pruneByLength is true….

• SkeletonConverter.setMaxConnectDist - Sets the maximum distance for connecting skeleton components. Specifies the maximum distance within which disconnected…

• Fill.setMetric - Sets the cost metric for the filled structure.

• PathProfiler.setMetric - No description available

• MultiTreeColorMapper.setMinMax - No description available

• NodeColorMapper.setMinMax - Description copied from class: ColorMapper

• TreeColorMapper.setMinMax - No description available

• Viewer2D.setMinMax - No description available

• GroupedTreeStatistics.setMinNBins - Sets the minimum number of bins when assembling histograms.

• MultiTreeColorMapper.setNaNColor - No description available

• NodeColorMapper.setNaNColor - No description available

• TreeColorMapper.setNaNColor - No description available

• Viewer2D.setNaNColor - No description available

• PathProfiler.setNodeIndicesAsDistances - Sets whether the profile abscissae should be reported in real-word units (the default) or node indices (zero-based)….

• PathFitter.setNodeRadiusFallback - No description available

• NodeProfiler.setNodeStep - No description available

• SkeletonConverter.setOrigIP - Sets the original ImagePlus to be used during voxel-based loop pruning. See AnalyzeSkeleton documentation Specifies the…

• BoundingBox.setOrigin - Sets the origin for this box, i.e., its (xMin, yMin, zMin) vertex.

• BoundingBox.setOriginOpposite - Sets the origin opposite for this box, i.e., its (xMax, yMax, zMax) vertex.

• MultiViewer2D.setOutlineVisible - No description available

• Viewer2D.setOutlineVisible - No description available

• Frangi.setOutput - No description available

• NodeProfiler.setOutput - No description available

• PathProfiler.setOutput - No description available

• Tubeness.setOutput - No description available

• WekaModelLoader.setOutput - No description available

• NodeProfiler.setOutputs - No description available

• PathProfiler.setOutputs - No description available

• WekaModelLoader.setOutputs - No description available

• PathResult.setPath - No description available

• PointInImage.setPath - Associates a Path with this node

• SWCPoint.setPath - No description available

• ShollAnalyzer.setPolynomialFitRange - Sets the polynomial fit range for linear Sholl statistics.

• BiSearchNode.setPosition - No description available

• DefaultSearchNode.setPredecessor - No description available

• BiSearchNode.setPredecessorFromGoal - No description available

• BiSearchNode.setPredecessorFromStart - No description available

• Viewer2D.setPreferredSize - Sets the preferred size of the plot to a constant value.

• SWCPoint.setPrevious - Sets the preceding node in the reconstruction

• SNTService.setPriority - No description available

• PathFitter.setProgressCallback - No description available

• SkeletonConverter.setPruneByLength - Sets whether to prune components below a threshold length from the result.

• SkeletonConverter.setPruneEnds - Sets whether to prune end branches during skeleton analysis. Controls whether terminal branches should be pruned during…

• SkeletonConverter.setPruneMode - Sets the loop pruning strategy. See AnalyzeSkeleton documentation

• NodeProfiler.setRadius - No description available

• PathProfiler.setRadius - No description available

• PathFitter.setReplaceNodes - Sets whether fitting should occur “in place”.

• NodeProfiler.setResolved - No description available

• WekaModelLoader.setResolved - No description available

• SkeletonConverter.setRootRoi - Sets the Roi enclosing the nodes to be set as root(s) in the final graphs. Must be called before retrieval of any…

• SNTColor.setSWCType - Re-assigns a SWC type integer flag

• SciViewSNT.setSciView - Sets the SciView to be used.

• PathFitter.setScope - Sets the fitting scope.

• NodeProfiler.setShape - Sets the shape of the iterating cursor.

• SkeletonConverter.setShortestPath - Sets whether to calculate the longest shortest-path in the skeleton result.

• PathFitter.setShowAnnotatedView - Sets whether an interactive image of the result should be displayed.

• SkeletonConverter.setSilent - Sets whether to run skeleton analysis in silent mode. Setting this to false will display both the tagged skeleton image…

• Annotation3D.setSize - Sets the annotation width.

• Fill.setSourcePaths - Sets the source paths for the filled structure using a set of paths.

• FillerThread.setSourcePaths - No description available

• BoundingBox.setSpacing - Sets the voxel spacing.

• Fill.setSpacing - No description available

• BiSearchNode.setState - No description available

• BiSearchNode.setStateFromGoal - No description available

• BiSearchNode.setStateFromStart - No description available

• FillerThread.setStopAtThreshold - Whether to terminate the fill operation once all nodes less than or equal to the distance threshold have been explored….

• FillerThread.setStoreExtraNodes - Whether to store above-threshold nodes in the Fill object. The default is true.

• PathResult.setSuccess - No description available

• SWCPoint.setTags - Sets the tags associated with this point.

• Fill.setThreshold - Sets the distance threshold for the filled structure.

• FillerThread.setThreshold - No description available

• MultiViewer2D.setTitle - Sets the title of this Viewer’s frame.

• MultiViewer3D.setTitle - Sets the title of the Viewer’s frame.

• Viewer2D.setTitle - Sets the plot display title.

• Annotation3D.setTransparency - Script friendly method to assign a transparency to the annotation.

• BoundingBox.setUnit - Sets the default length unit for voxel spacing (typically um, for SWC reconstructions)

• SkeletonConverter.setVerbose - Sets whether to run skeleton analysis in verbose mode. Controls whether the skeleton analysis should provide detailed…

• MultiViewer3D.setViewMode - No description available

• PathStraightener.setWidth - Sets the width of the straightened path image.

• Annotation3D.setWireframeColor - Assigns a wireframe color to the annotation.

• BiSearchNode.setX - No description available

• MultiViewer2D.setXrange - Sets a manual range for the viewers’ X-axis. Calling setXrange(-1, -1) enables auto-range (the default). Must be called…

• Viewer2D.setXrange - Sets a manual range for the viewers’ X-axis. Calling setXrange(-1, -1) enables auto-range (the default). Must be called…

• BiSearchNode.setY - No description available

• MultiViewer2D.setYrange - Sets a manual range for the viewers’ Y-axis. Calling setYrange(-1, -1) enables auto-range (the default). Must be called…

• Viewer2D.setYrange - Sets a manual range for the viewers’ Y-axis. Calling setYrange(-1, -1) enables auto-range (the default). Must be called…

• BiSearchNode.setZ - No description available

• BoundingBox.shift - No description available

• MultiViewer2D.show - No description available

• MultiViewer3D.show - No description available

• Viewer2D.show - Displays the current plot on a dedicated frame *

• ConvexHull2D.size - No description available

• ConvexHull3D.size - No description available

• MultiTreeColorMapper.sortedMappedTrees - No description available

• SNTUtils.static addViewer - No description available

• SNTColor.static alphaColor - Adds an alpha component to an AWT color.

• Frangi.static apply - No description available

• Tubeness.static apply - No description available

• ImpUtils.static applyColorTable - No description available

• ColorMaps.static applyPlasma - Applies the “plasma” colormap to the specified (non-RGB) image

• ColorMaps.static applyViridis - Applies the “viridis” colormap to the specified (non-RGB) image

• ImpUtils.static ascii - Converts the specified image into ascii art.

• AllenUtils.static assignAnnotationsFromNodeValues - Assigns brain annotations (interpreted as CCF IDs) to node values for all paths in a Tree. This method is the inverse…

• AllenUtils.static assignHemisphereTags - No description available

• AllenUtils.static assignToLeftHemisphere - Assigns a tree to the left hemisphere by mirroring it if necessary.

• AllenUtils.static assignToRightHemisphere - Assigns a tree to the right hemisphere by mirroring it if necessary.

• Tree.static assignUniqueColors - Assigns distinct colors to a collection of Trees.

• SNTColor.static average - Averages a collection of colors

• SNTPoint.static average - Computes the average position of a collection of SNTPoints.

• ImpUtils.static binarize - No description available

• VFBUtils.static brainBarycentre - Returns the spatial centroid of an adult Drosophila template brain.

• ZBAtlasUtils.static brainBarycentre - Returns the spatial centroid of the template brain.

• AllenUtils.static brainCenter - Returns the spatial centroid of the Allen CCF.

• SNTUtils.static buildDate - Retrieves Sholl Analysis implementation date

• ImpUtils.static calibrationToAxes - No description available

• StrahlerAnalyzer.static classify - No description available

• SNTChart.static closeAll - Closes all open charts

• SWCPoint.static collectionAsReader - Converts a collection of SWC points into a Reader.

• SNTColor.static colorToString - Returns the color encoded as hex string with the format #rrggbbaa.

• SNTChart.static combine - Combines a collection of charts into a multipanel montage.

• ImpUtils.static combineSkeletons - No description available

• NodeStatistics.static computeNearestNeighborDistances - Computes nearest neighbor distances. Assigns the computed value to the v value of each point

• SNTColor.static contrastColor - Returns a suitable ‘contrast’ color.

• ImpUtils.static convertRGBtoComposite - No description available

• ImpUtils.static convertTo32bit - No description available

• ImpUtils.static convertTo8bit - No description available

• ImpUtils.static convertToSimple2D - Converts the specified image into an easy displayable form, i.e., a non-composite 2D image If the image is a timelapse,…

• ImpUtils.static create - No description available

• PathAndFillManager.static createFromFile - Creates a PathAndFillManager instance from imported data

• PathAndFillManager.static createFromGraph - Create a new PathAndFillManager instance from the graph.

• PathAndFillManager.static createFromNodes - Creates a PathAndFillManager instance from a collection of reconstruction nodes.

• ImgUtils.static createIntervals - Partition the source dimensions into a list of Intervals with given dimensions. If the block dimensions are not…

• ImgUtils.static crop - No description available

• ImpUtils.static crop - Crops the image around non-background values. Does nothing if the image does not have non-background values.

• SNTUtils.static csvQuoteAndPrint - No description available

• ImpUtils.static demo - Returns one of the demo images bundled with SNT image associated with the demo (fractal) tree.

• MouseLightLoader.static demoTrees - Returns a collection of four demo reconstructions NB: Data is cached locally. No internet connection required.

• ColorMaps.static discreteColors - No description available

• ColorMaps.static discreteColorsAWT - No description available

• RemoteSWCLoader.static download - No description available

• SNTUtils.static downloadToTempFile - Downloads a file from the specified URL to a temporary file

• ImgUtils.static dropSingletonDimensions - No description available

• SNTUtils.static error - No description available

• MouseLightLoader.static extractNodes - Extracts reconstruction(s) from a JSON file.

• SNTUtils.static extractReadableTimeStamp - No description available

• MouseLightLoader.static extractTrees - No description available

• SNTUtils.static fileAvailable - No description available

• CrossoverFinder.static find - Entry point: detect crossover events for a collection of paths using the given config.

• SNTUtils.static findClosestPair - No description available

• ImgUtils.static findSpatialAxisIndices - No description available

• ImgUtils.static findSpatialAxisIndicesWithFallback - No description available

• SWCPoint.static flush - Prints a list of points as space-separated values.

• SNTUtils.static formatDouble - No description available

• MultiTreeStatistics.static fromCollection - No description available

• PathStatistics.static fromCollection - No description available

• TreeStatistics.static fromCollection - Creates a TreeStatistics instance from a group of Trees and a specific metric for convenient retrieval of histograms

• SNTTable.static fromFile - Script-friendly method for loading tabular data from a file/URL.

• Tree.static fromFile - Script-friendly method for loading a Tree from a reconstruction file.

• FillerThread.static fromFill - No description available

• SNTColor.static fromHex - Returns an AWT Color from a (#)RRGGBB(AA) hex string.

• ColorMaps.static get - Returns a ‘core’ color table from its title

• NeuroMorphoLoader.static get - Convenience method for retrieving SWC data,

• MouseLightQuerier.static getAllIDs - Gets all available neuron IDs from the database.

• MouseLightLoader.static getAllLoaders - Gets the loaders for all the cells publicly available in the MouseLight database.

• MultiTreeStatistics.static getAllMetrics - Description copied from class: TreeStatistics

• PathStatistics.static getAllMetrics - Gets the terminal branches from the analyzed paths. Returns paths that have children, representing non-terminal…

• TreeStatistics.static getAllMetrics - Gets the list of supported metrics.

• InsectBrainUtils.static getAllNeuronIDs - No description available

• InsectBrainUtils.static getAllSpecies - No description available

• AllenUtils.static getAnatomicalPlane - Retrieves the anatomical plane matching the specified cartesian plane.

• AllenUtils.static getAxisDefiningSagittalPlane - Gets the axis defining the sagittal plane.

• SNTUtils.static getBackupCopies - Retrieves a list of time-stamped backup files associated with a TRACES file

• InsectBrainUtils.static getBrainCompartments - No description available

• InsectBrainUtils.static getBrainJSON - No description available

• InsectBrainUtils.static getBrainMeshes - No description available

• ImpUtils.static getCT - No description available

• ImgUtils.static getCalibration - No description available

• AllenUtils.static getCartesianPlane - Retrieves the Cartesian plane matching the specified anatomical plane.

• ImpUtils.static getChannel - No description available

• AllenUtils.static getCompartment - Constructs a compartment from its CCF name or acronym

• SNTUtils.static getContext - Convenience method to access the context of the running Fiji instance

• ImgUtils.static getCtSlice - No description available

• ImgUtils.static getCtSlice3d - Get a view of the ImagePlus at the specified channel and frame.

• ImpUtils.static getCurrentImage - No description available

• SNTUtils.static getDecimalFormat - No description available

• RootAngleAnalyzer.static getDensityPlot - No description available

• PersistenceAnalyzer.static getDescriptors - Gets a list of supported descriptor functions for persistence analysis. Returns the string identifiers for all…

• SNTColor.static getDistinctColors - Returns distinct colors based on Kenneth Kelly’s 22 colors of maximum contrast (black and white excluded). More details…

• SNTColor.static getDistinctColorsAWT - No description available

• SNTColor.static getDistinctColorsHex - No description available

• SNTUtils.static getElapsedTime - No description available

• ImpUtils.static getForegroundRect - Returns the cropping rectangle around non-background values.

• ImpUtils.static getFrame - No description available

• AllenUtils.static getHemisphere - Checks the hemisphere a neuron belongs to.

• AllenUtils.static getHighestOntologyDepth - Gets the maximum number of ontology levels in the Allen CCF.

• RootAngleAnalyzer.static getHistogram - No description available

• MouseLightQuerier.static getIDs - Gets neuron IDs matching the specified collection of IDs or DOIs.

• SNTUtils.static getInstance - No description available

• ImpUtils.static getMIP - No description available

• VFBUtils.static getMesh - Retrieves the mesh associated with the specified VFB id.

• MultiTreeColorMapper.static getMetrics - Gets the list of supported mapping metrics.

• MultiTreeStatistics.static getMetrics - Gets the list of metrics supported by MultiTreeStatistics. Returns all the metrics that can be computed for groups of…

• NodeColorMapper.static getMetrics - Gets the list of supported mapping metrics.

• NodeStatistics.static getMetrics - Gets the list of supported metrics.

• PathStatistics.static getMetrics - No description available

• ShollAnalyzer.static getMetrics - No description available

• TreeColorMapper.static getMetrics - Gets the list of supported mapping metrics.

• Viewer2D.static getMetrics - No description available

• ImpUtils.static getMinMax - No description available

• MouseLightLoader.static getNeuronCount - Gets the number of cells publicly available in the MouseLight database.

• MouseLightQuerier.static getNeuronCount - Gets the number of cells publicly available in the MouseLight database.

• AllenUtils.static getOntologies - Gets a flat (non-hierarchical) list of all the compartments of the specified ontology depth.

• ImgUtils.static getOrigin - No description available

• ImgUtils.static getOrigins - No description available

• PCAnalyzer.static getPrincipalAxes - Computes the principal axes for a collection of SNTPoints.

• SNTUtils.static getReadableVersion - No description available

• SNTUtils.static getReconstructionFiles - Retrieves a list of reconstruction files stored in a common directory matching the specified criteria.

• VFBUtils.static getRefBrain - Retrieves the surface mesh of an adult Drosophila template brain. No Internet connection is required, as these meshes…

• ZBAtlasUtils.static getRefBrain - Retrieves the surface mesh (outline) of the zebrafish template brain.

• AllenUtils.static getRootMesh - Retrieves the surface contours for the Allen Mouse Brain Atlas (CCF), bundled with SNT.

• Tree.static getSWCTypeMap - Returns the SWC Type flags used by SNT.

• SNTUtils.static getSanitizedUnit - No description available

• MultiTreeColorMapper.static getSingleValueMetrics - Gets the list of single-value mapping metrics.

• ImpUtils.static getSliceLabels - No description available

• InsectBrainUtils.static getSpeciesNeuronIDs - No description available

• TreeProperties.static getStandardizedCompartment - No description available

• ImpUtils.static getSystemClipboard - Retrieves an ImagePlus from the system clipboard

• SNTUtils.static getTimeStamp - No description available

• AllenUtils.static getTreeModel - Retrieves the Allen CCF hierarchical tree data.

• SNTUtils.static getUniquelySuffixedFile - No description available

• SNTUtils.static getUniquelySuffixedTifFile - No description available

• PCAnalyzer.static getVariancePercentages - Computes the variance percentages for an array of principal axes. This is a convenience method that returns the…

• AllenUtils.static getXYZLabels - No description available

• VFBUtils.static getXYZLabels - No description available

• ZBAtlasUtils.static getXYZLabels - No description available

• ColorMaps.static glasbeyColorsAWT - No description available

• ImpUtils.static imageTypeToString - No description available

• ImgUtils.static imgPlusToCalibration - No description available

• ImgUtils.static impToRealRai5d - Wrap an ImagePlus to a RandomAccessibleInterval such that the number of dimensions in the resulting rai is 5 and the…

• SNTColor.static interpolateNullEntries - Replaces null colors in an array with the average of flanking non-null colors.

• ImpUtils.static invertLut - No description available

• ImpUtils.static isBinary - No description available

• SNTUtils.static isContextSet - No description available

• InsectBrainLoader.static isDatabaseAvailable - Checks whether a connection to the Insect Brain Database can be established.

• MouseLightLoader.static isDatabaseAvailable - Checks whether a connection to the MouseLight database can be established.

• MouseLightQuerier.static isDatabaseAvailable - Checks whether a connection to the MouseLight database can be established.

• VFBUtils.static isDatabaseAvailable - Checks whether a connection to the Virtual Fly Brain database can be established.

• ZBAtlasUtils.static isDatabaseAvailable - Checks whether a connection to the FishAtlas database can be established.

• SNTUtils.static isDebugMode - Assesses if SNT is running in debug mode

• AllenUtils.static isLeftHemisphere - No description available

• ImpUtils.static isPointVisible - Checks if a given point (in image coordinates) is currently visible in an image

• SNTUtils.static isReconstructionFile - No description available

• ImpUtils.static isVirtualStack - No description available

• Tree.static listFromDir - Retrieves a list of Trees from reconstruction files stored in a common directory matching the specified criteria.

• SNTUtils.static log - No description available

• AllenCompartment.static main - No description available

• AllenUtils.static main - No description available

• ConvexHull2D.static main - No description available

• ConvexHull3D.static main - No description available

• ConvexHullAnalyzer.static main - Main method for testing and demonstration purposes. Creates a ConvexHullAnalyzer instance using demo data and runs the…

• FlyCircuitLoader.static main - No description available

• GroupedTreeStatistics.static main - No description available

• InsectBrainLoader.static main - No description available

• MouseLightLoader.static main - No description available

• MouseLightQuerier.static main - No description available

• MultiTreeColorMapper.static main - No description available

• MultiViewer2D.static main - No description available

• MultiViewer3D.static main - No description available

• NeuroMorphoLoader.static main - No description available

• NodeColorMapper.static main - No description available

• NodeProfiler.static main - No description available

• NodeStatistics.static main - No description available

• PathProfiler.static main - No description available

• PathStraightener.static main - Main method for testing and demonstration purposes. Creates a PathStraightener instance using demo data and displays…

• PersistenceAnalyzer.static main - No description available

• RootAngleAnalyzer.static main - No description available

• SciViewSNT.static main - No description available

• ShollAnalyzer.static main - No description available

• SkeletonConverter.static main - No description available

• StrahlerAnalyzer.static main - No description available

• TreeColorMapper.static main - No description available

• VFBUtils.static main - No description available

• Viewer2D.static main - No description available

• ImgUtils.static maxDimension - No description available

• Annotation3D.static meshToDrawable - No description available

• ImpUtils.static nextZoomLevel - No description available

• SNTPoint.static of - No description available

• ImpUtils.static open - No description available

• PCAnalyzer.static orientTowardDirection - Orients principal axes so the primary axis points toward a reference direction, i.e., the primary axis is oriented to…

• PCAnalyzer.static orientTowardTips - Convenience method to orient existing principal axes toward a tree’s tips centroid. For several topologies, this…

• ImgUtils.static outOfBounds - Checks if pos is outside the bounds given by min and max

• ImpUtils.static previousZoomLevel - No description available

• ImgUtils.static raiToImp - Convert a RandomAccessibleInterval to an ImagePlus. If the input has 3 dimensions, the 3rd dimension is treated as…

• SNTUtils.static randomPaths - Generates a list of random paths. Only useful for debugging purposes

• ImpUtils.static removeIsolatedPixels - No description available

• ImpUtils.static removeSlices - No description available

• SNTUtils.static removeViewer - No description available

• ImpUtils.static rotate90 - Rotates an image 90 degrees.

• ImpUtils.static sameCTDimensions - No description available

• ImpUtils.static sameCalibration - No description available

• ImpUtils.static sameXYZDimensions - No description available

• ImpUtils.static save - Saves the specified image.

• MouseLightQuerier.static setCCFVersion - Sets the version of the Common Coordinate Framework to be used by the Querier.

• SNTUtils.static setContext - No description available

• SNTUtils.static setDebugMode - Enables/disables debug mode

• SNTUtils.static setIsLoading - No description available

• ImpUtils.static setLut - No description available

• SkeletonConverter.static skeletonize - Convenience method to skeletonize a thresholded image using Skeletonize3D_.

• SkeletonConverter.static skeletonizeTimeLapse - Convenience method to skeletonize a thresholded time-lapse using Skeletonize3D_.

• AllenUtils.static splitByHemisphere - No description available

• ImgUtils.static splitIntoBlocks - Partition the source rai into a list of IntervalView with given dimensions. If the block dimensions are not multiples…

• SNTUtils.static startApp - Convenience method to start up SNT’s GUI.

• SNTUtils.static stripExtension - No description available

• ImgUtils.static subInterval - Get an N-D sub-interval of an N-D image, given two corner points and specified padding. If necessary, the computed…

• ImgUtils.static subVolume - Get a 3D sub-volume of an image, given two corner points and specified padding. If the input is 2D, a singleton…

• ConvexHullAnalyzer.static supportedMetrics - Gets the list of metrics supported by ConvexHullAnalyzer.

• RootAngleAnalyzer.static supportedMetrics - No description available

• ImpUtils.static toDataset - No description available

• ImgUtils.static toImagePlus - No description available

• ImpUtils.static toImgPlus - No description available

• ImpUtils.static toImgPlus3D - No description available

• ImpUtils.static toStack - No description available

• AllenUtils.static transferAnnotationIdsToNodeValues - Transfers brain annotation IDs to node values for all paths in a Tree. This is useful for preserving annotation…

• MultiTreeColorMapper.static unMap - No description available

• NodeColorMapper.static unMap - No description available

• TreeColorMapper.static unMap - No description available

• SNTColor.static valueOf - No description available

• ImgUtils.static wrapWithAxes - No description available

• ImpUtils.static zoomTo - No description available

• PathStraightener.straighten - No description available

• SciViewSNT.syncPathManagerList - (Re)loads the current list of Paths in the Path Manager list.

T

• GroupedTreeStatistics.tTest - Computes a two-sample, two-tailed t-test P-value for two of groups being analyzed. It is assumed that data fulfills…

• BoundingBox.toBoundingBox3d - No description available

• PointInImage.transform - No description available

• SWCPoint.transform - No description available

• SNTColor.type - Retrieves the SWC type

U

• NodeProfiler.uncancel - No description available

• WekaModelLoader.uncancel - No description available

• NodeProfiler.unresolveInput - No description available

• WekaModelLoader.unresolveInput - No description available

• NodeProfiler.unresolveOutput - No description available

• WekaModelLoader.unresolveOutput - No description available

• BoundingBox.unscaledOrigin - Retrieves the origin of this box in unscaled (“pixel” units)

• BoundingBox.unscaledOriginOpposite - Retrieves the origin opposite of this box in unscaled (“pixel” units)

• SNTService.updateViewers - Script-friendly method for updating (refreshing) all viewers currently in use by SNT. Does nothing if no SNT instance…

V

• MultiViewer3D.viewers - No description available

W

• BoundingBox.width - No description available

• Fill.writeNodesXML - No description available

• Fill.writeXML - No description available

X

• SWCPoint.xSeparationFromPreviousPoint - Returns the X-distance from previous point.

Y

• SWCPoint.ySeparationFromPreviousPoint - Returns the Y-distance from previous point.

Z

• SWCPoint.zSeparationFromPreviousPoint - Returns the Z-distance from previous point.

See Also

• API Documentation

• Class Index

• Constants Index