- accessToValidImageData() - Method in class sc.fiji.snt.SNT
-
- acronym() - Method in class sc.fiji.snt.annotation.AllenCompartment
-
- acronym() - Method in interface sc.fiji.snt.annotation.BrainAnnotation
-
- actionPerformed(ActionEvent) - Method in class sc.fiji.snt.FillManagerUI
-
- actionPerformed(ActionEvent) - Method in class sc.fiji.snt.gui.ShollAnalysisDialog
-
Deprecated.
- actionPerformed(ActionEvent) - Method in class sc.fiji.snt.gui.SWCImportOptionsDialog
-
- add(int, int, int, double, int, boolean) - Method in class sc.fiji.snt.Fill
-
- add(Path) - Method in class sc.fiji.snt.Tree
-
Adds a new Path to this Tree.
- add(Object) - Method in class sc.fiji.snt.viewer.Viewer3D
-
Script friendly method to add a supported object (
Tree,
OBJMesh,
AbstractDrawable, etc.) to this viewer.
- addAsLinesTo3DViewer(Image3DUniverse, Color, ImagePlus) - Method in class sc.fiji.snt.Path
-
Deprecated.
- addColorBarLegend(ColorTable, double, double) - Method in class sc.fiji.snt.viewer.Viewer2D
-
Adds a color bar legend (LUT ramp).
- addColorBarLegend() - Method in class sc.fiji.snt.viewer.Viewer2D
-
Adds a color bar legend (LUT ramp) to the viewer.
- addColorBarLegend(ColorTable, double, double) - Method in class sc.fiji.snt.viewer.Viewer3D
-
Adds a color bar legend (LUT ramp) using default settings.
- addColorBarLegend(ColorTable, double, double, Font, int, int) - Method in class sc.fiji.snt.viewer.Viewer3D
-
Adds a color bar legend (LUT ramp).
- addColorChangedListener(ColorChangedListener) - Method in class sc.fiji.snt.gui.ColorChooserButton
-
- addDiscsTo3DViewer(Image3DUniverse, Color, ImagePlus) - Method in class sc.fiji.snt.Path
-
Deprecated.
- addDiscsTo3DViewer(Image3DUniverse, Color3f, ImagePlus) - Method in class sc.fiji.snt.Path
-
Deprecated.
- addLabel(String) - Method in class sc.fiji.snt.viewer.Viewer3D
-
Adds an annotation label to the scene.
- addListener(SNTListener) - Method in class sc.fiji.snt.SNT
-
- addMesh(OBJMesh) - Method in class sc.fiji.snt.viewer.Viewer3D
-
Loads a Wavefront .OBJ file.
- addNode(PointInImage) - Method in class sc.fiji.snt.Path
-
Appends a node to this Path.
- addNode(SearchNode, boolean) - Method in class sc.fiji.snt.SearchThread
-
- addPath(Path) - Method in class sc.fiji.snt.PathAndFillManager
-
Adds a new path.
- addPathAndFillListener(PathAndFillListener) - Method in class sc.fiji.snt.PathAndFillManager
-
Adds a PathAndFillListener.
- addPathPointsToShollList(Path, double, double, double, List<ShollAnalysisDialog.ShollPoint>) - Static method in class sc.fiji.snt.gui.ShollAnalysisDialog
-
Deprecated.
- addProgressListener(SearchProgressCallback) - Method in class sc.fiji.snt.ManualTracerThread
-
- addProgressListener(SearchProgressCallback) - Method in class sc.fiji.snt.SearchThread
-
- addProgressListener(SearchProgressCallback) - Method in class sc.fiji.snt.TubularGeodesicsTracer
-
- addSeparator(JComponent, String, boolean, GridBagConstraints) - Static method in class sc.fiji.snt.gui.GuiUtils
-
- addSeparator(JComponent, JLabel, boolean, GridBagConstraints) - Static method in class sc.fiji.snt.gui.GuiUtils
-
- addTo3DViewer(Image3DUniverse, Color, ImagePlus) - Method in class sc.fiji.snt.Path
-
Deprecated.
- addTo3DViewer(Image3DUniverse, Color3f, ImagePlus) - Method in class sc.fiji.snt.Path
-
Deprecated.
- addTooltip(JComponent, String) - Method in class sc.fiji.snt.gui.GuiUtils
-
- addToResultsTable() - Method in class sc.fiji.snt.gui.ShollAnalysisDialog.ShollResults
-
Deprecated.
- addTree(Tree) - Method in class sc.fiji.snt.PathAndFillManager
-
- addTree(Tree) - Method in class sc.fiji.snt.SciViewSNT
-
Adds a tree to the associated SciView instance.
- addTree(Tree) - Method in class sc.fiji.snt.viewer.Viewer2D
-
Appends a tree to the viewer using default options.
- addTree(Tree, ColorRGB) - Method in class sc.fiji.snt.viewer.Viewer2D
-
Appends a tree to the viewer.
- addTree(Tree, String, ColorTable, double, double) - Method in class sc.fiji.snt.viewer.Viewer2D
-
Appends a tree to the viewer rendered after the specified measurement.
- addTree(Tree, String, String) - Method in class sc.fiji.snt.viewer.Viewer2D
-
Appends a tree to the viewer rendered after the specified measurement.
- addTree(Tree, String, String, double, double) - Method in class sc.fiji.snt.viewer.Viewer2D
-
Appends a tree to the viewer rendered after the specified measurement.
- addTree(Tree) - Method in class sc.fiji.snt.viewer.Viewer3D
-
Adds a tree to this viewer.
- addTrees(List<Tree>, String) - Method in class sc.fiji.snt.viewer.Viewer2D
-
Adds a list of trees while assigning each tree to a LUT index.
- addViewer(Viewer3D) - Static method in class sc.fiji.snt.SNTUtils
-
- aliases() - Method in class sc.fiji.snt.annotation.AllenCompartment
-
- aliases() - Method in interface sc.fiji.snt.annotation.BrainAnnotation
-
- AllenCompartment - Class in sc.fiji.snt.annotation
-
Defines an Allen Reference Atlas (ARA) [Allen Mouse Common Coordinate
Framework] annotation.
- AllenCompartment(UUID) - Constructor for class sc.fiji.snt.annotation.AllenCompartment
-
Instantiates a new ARA annotation from an UUID (as used by MouseLight's
database).
- AllenCompartment(int) - Constructor for class sc.fiji.snt.annotation.AllenCompartment
-
Instantiates a new ARA annotation from its identifier.
- AllenUtils - Class in sc.fiji.snt.annotation
-
- allPointsIterator() - Method in class sc.fiji.snt.PathAndFillManager
-
- AllPointsIterator() - Constructor for class sc.fiji.snt.PathAndFillManager.AllPointsIterator
-
- alphaColor(Color, double) - Static method in class sc.fiji.snt.util.SNTColor
-
Adds an alpha component to a AWT color.
- analyzeWithShollAnalysisPlugin(String, double) - Method in class sc.fiji.snt.gui.ShollAnalysisDialog.ShollResults
-
Deprecated.
- annotateLine(Collection<? extends SNTPoint>, String) - Method in class sc.fiji.snt.viewer.Viewer3D
-
Adds a line annotation to this viewer.
- annotatePoint(SNTPoint, String) - Method in class sc.fiji.snt.viewer.Viewer3D
-
Adds an highlighting point annotation to this viewer.
- annotatePoints(Collection<? extends SNTPoint>, String) - Method in class sc.fiji.snt.viewer.Viewer3D
-
Adds a scatter (point cloud) annotation to this viewer.
- annotateSurface(Collection<? extends SNTPoint>, String) - Method in class sc.fiji.snt.viewer.Viewer3D
-
Computes a Delaunay surface from a collection of points and adds it to the
scene as an annotation.
- Annotation3D - Class in sc.fiji.snt.viewer
-
An Annotation3D is a triangulated surface or a cloud of points (scatter)
rendered in
Viewer3D that can be used to highlight nodes in a
Tree or locations in a
mesh.
- anySelected() - Method in class sc.fiji.snt.PathAndFillManager
-
Checks whether at least one Path is currently selected in the UI.
- applyCanvasOffset(double, double, double) - Method in class sc.fiji.snt.Tree
-
Specifies the offset to be used when rendering this Tree in a
TracerCanvas.
- applyIcon(AbstractButton, float, IconFactory.GLYPH) - Static method in class sc.fiji.snt.gui.IconFactory
-
- asPath(double, double, double, String) - Method in class sc.fiji.snt.SearchNode
-
- asPathReversed(double, double, double, String) - Method in class sc.fiji.snt.SearchNode
-
- assignToLeftHemisphere(Tree) - Static method in class sc.fiji.snt.annotation.AllenUtils
-
- assignToRightHemisphere(Tree) - Static method in class sc.fiji.snt.annotation.AllenUtils
-
- assignValues() - Method in class sc.fiji.snt.analysis.PathProfiler
-
- assignValues(Path) - Method in class sc.fiji.snt.analysis.PathProfiler
-
Retrieves pixel intensities at each node of the Path storing them as Path
values
- assignValues(boolean) - Method in class sc.fiji.snt.SNTService
-
Assigns pixel intensities at each Path node, storing them as Path values.
- autoTrace(PointInImage, PointInImage, PointInImage) - Method in class sc.fiji.snt.SNT
-
Automatically traces a path from a point A to a point B.
- autoTrace(List<PointInImage>, PointInImage) - Method in class sc.fiji.snt.SNT
-
Automatically traces a path from a list of points and adds it to the active
PathAndFillManager instance.
- average(Collection<Color>) - Static method in class sc.fiji.snt.util.SNTColor
-
Averages a collection of colors
- average(Collection<T>) - Static method in interface sc.fiji.snt.util.SNTPoint
-
- AXES_NORMAL - Static variable in class sc.fiji.snt.gui.ShollAnalysisDialog
-
Deprecated.
- AXON - Static variable in class sc.fiji.snt.io.MouseLightLoader
-
The Constant AXON.
- AXON - Static variable in class sc.fiji.snt.io.MouseLightQuerier
-
The Constant AXON.