- call() - Method in class sc.fiji.snt.PathFitter
-
Takes the signal from the image specified in the constructor to fit
cross-section circles around the nodes of input path.
- CallLegacyShollPlugin - Class in sc.fiji.snt.plugin
-
Command to invoke the legacy "Sholl Analysis (Tracings)..." IJ1 plugin
- CallLegacyShollPlugin() - Constructor for class sc.fiji.snt.plugin.CallLegacyShollPlugin
-
- cancel() - Method in class sc.fiji.snt.gui.cmds.CommonDynamicCmd
-
- cancel(String) - Method in class sc.fiji.snt.gui.cmds.CommonDynamicCmd
-
- cancel() - Method in class sc.fiji.snt.plugin.ShollTracingsCmd
-
- CANCELLED - Static variable in class sc.fiji.snt.SearchThread
-
- cancelPath() - Method in class sc.fiji.snt.SNT
-
Cancels the temporary path.
- cancelSearch(boolean) - Method in class sc.fiji.snt.SNT
-
- cancelTemporary() - Method in class sc.fiji.snt.SNT
-
- canvasResized() - Method in class sc.fiji.snt.PathAndFillManager
-
Deprecated.
- captureView(String, boolean) - Method in class sc.fiji.snt.SNTService
-
Retrieves a WYSIWYG 'snapshot' of a tracing canvas.
- centeredMsg(String, String) - Method in class sc.fiji.snt.gui.GuiUtils
-
- changeState(int) - Method in class sc.fiji.snt.SNTUI
-
Changes this UI to a new state.
- changeUIState(int) - Method in class sc.fiji.snt.SNT
-
- ChooseDatasetCmd - Class in sc.fiji.snt.gui.cmds
-
Implements the 'Choose Tracing Image (From Open Image)...' command.
- ChooseDatasetCmd() - Constructor for class sc.fiji.snt.gui.cmds.ChooseDatasetCmd
-
- clear() - Method in class sc.fiji.snt.PathAndFillManager
-
Deletes all paths and fills.
- clearAll() - Static method in class sc.fiji.snt.SNTPrefs
-
- clone() - Method in class sc.fiji.snt.Path
-
- clone() - Method in class sc.fiji.snt.Tree
-
- clone() - Method in class sc.fiji.snt.util.BoundingBox
-
- closeAndResetAllPanes() - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanes
-
- closeAndResetAllPanes() - Method in class sc.fiji.snt.SNT
-
- CLOSED_FROM_GOAL - Static variable in class sc.fiji.snt.SearchThread
-
- CLOSED_FROM_START - Static variable in class sc.fiji.snt.SearchThread
-
- collapseAllTreeNodes(JTree) - Static method in class sc.fiji.snt.gui.GuiUtils
-
- collectionAsReader(Collection<SWCPoint>) - Static method in class sc.fiji.snt.util.SWCPoint
-
Converts a collection of SWC points into a Reader.
- color() - Method in class sc.fiji.snt.util.SNTColor
-
Retrieves the AWT color
- colorChanged(Color) - Method in interface sc.fiji.snt.gui.ColorChangedListener
-
- ColorChangedListener - Interface in sc.fiji.snt.gui
-
- ColorChooserButton - Class in sc.fiji.snt.gui
-
Creates a JButton holding a color chooser.
- ColorChooserButton(Color) - Constructor for class sc.fiji.snt.gui.ColorChooserButton
-
- ColorChooserButton(Color, String) - Constructor for class sc.fiji.snt.gui.ColorChooserButton
-
- ColorChooserButton(Color, String, double, int) - Constructor for class sc.fiji.snt.gui.ColorChooserButton
-
- colorCode(Collection<String>, String, ColorTable) - Method in class sc.fiji.snt.viewer.Viewer3D
-
- colorCode(String, String, ColorTable) - Method in class sc.fiji.snt.viewer.Viewer3D
-
- ColorMapper - Class in sc.fiji.snt.analysis
-
Parent class for ColorMappers.
- ColorMapper() - Constructor for class sc.fiji.snt.analysis.ColorMapper
-
- ColorMapReconstructionCmd - Class in sc.fiji.snt.gui.cmds
-
Implements Reconstruction Viewer's 'Color coding' commands.
- ColorMapReconstructionCmd() - Constructor for class sc.fiji.snt.gui.cmds.ColorMapReconstructionCmd
-
- ColorMenu - Class in sc.fiji.snt.gui
-
Generates a simplified color widget holding both predetermined colors and
user-defined ones.
- ColorMenu(String) - Constructor for class sc.fiji.snt.gui.ColorMenu
-
- colorToString(Color) - Static method in class sc.fiji.snt.util.SNTColor
-
Returns the color encoded as hex string with the format #rrggbbaa.
- COMMON_MEASUREMENTS - Static variable in class sc.fiji.snt.analysis.TreeAnalyzer
-
- CommonDynamicCmd - Class in sc.fiji.snt.gui.cmds
-
Command class for GUI commands extending DynamicCommand
- CommonDynamicCmd() - Constructor for class sc.fiji.snt.gui.cmds.CommonDynamicCmd
-
- CompareFilesCmd - Class in sc.fiji.snt.gui.cmds
-
Command for opening two SWC/traces files in a dedicated Reconstruction
Viewer.
- CompareFilesCmd() - Constructor for class sc.fiji.snt.gui.cmds.CompareFilesCmd
-
- compareTo(ShollAnalysisDialog.ShollPoint) - Method in class sc.fiji.snt.gui.ShollAnalysisDialog.ShollPoint
-
Deprecated.
- compareTo(NearPoint) - Method in class sc.fiji.snt.NearPoint
-
- compareTo(Path) - Method in class sc.fiji.snt.Path
-
- compareTo(SearchNode) - Method in class sc.fiji.snt.SearchNode
-
- compareTo(SWCPoint) - Method in class sc.fiji.snt.util.SWCPoint
-
- compute() - Method in class sc.fiji.snt.plugin.StrahlerCmd
-
- compute(Iterator<? extends SNTPoint>) - Method in class sc.fiji.snt.util.BoundingBox
-
Computes a new positioning so that this box encloses the specified point
cloud.
- ComputeSecondaryImg - Class in sc.fiji.snt.gui.cmds
-
Implements the "Generate Secondary Image" command.
- ComputeSecondaryImg() - Constructor for class sc.fiji.snt.gui.cmds.ComputeSecondaryImg
-
- ComputeTubenessImg - Class in sc.fiji.snt.gui.cmds
-
Implements the "Cache All Hessian Computations" command.
- ComputeTubenessImg() - Constructor for class sc.fiji.snt.gui.cmds.ComputeTubenessImg
-
- confirmTemporary() - Method in class sc.fiji.snt.SNT
-
- containedBy(AllenCompartment) - Method in class sc.fiji.snt.annotation.AllenCompartment
-
Assesses if this annotation is a child of a specified compartment.
- contains(AllenCompartment) - Method in class sc.fiji.snt.annotation.AllenCompartment
-
Assesses if this annotation is parent of a specified compartment.
- contains(PointInImage) - Method in class sc.fiji.snt.Path
-
Check whether this Path contains the specified point
- contains(BoundingBox) - Method in class sc.fiji.snt.util.BoundingBox
-
Checks whether the specified BoundingBox is enclosed by this one .
- contentAdded(Content) - Method in class sc.fiji.snt.PathAndFillManager
-
Deprecated.
- contentChanged(Content) - Method in class sc.fiji.snt.PathAndFillManager
-
Deprecated.
- contentRemoved(Content) - Method in class sc.fiji.snt.PathAndFillManager
-
Deprecated.
- contentSelected(Content) - Method in class sc.fiji.snt.PathAndFillManager
-
Deprecated.
- contrastColor(Color) - Static method in class sc.fiji.snt.util.SNTColor
-
Returns a suitable 'contrast' color.
- convertBranchPoints(Overlay) - Method in class sc.fiji.snt.analysis.RoiConverter
-
Converts all the branch points associated with the parsed paths into
PointRois
- convertPaths(Overlay) - Method in class sc.fiji.snt.analysis.RoiConverter
-
Converts paths into 2D polyline ROIs (segment paths)
- convertTips(Overlay) - Method in class sc.fiji.snt.analysis.RoiConverter
-
Converts all the tips associated with the parsed paths into
PointRois
- convertTo8bit(ImagePlus) - Static method in class sc.fiji.snt.SNTUtils
-
- createCanvas(ImagePlus, int) - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanes
-
- createCanvas(ImagePlus, int) - Method in class sc.fiji.snt.SNT
-
- createFromFile(String) - Static method in class sc.fiji.snt.PathAndFillManager
-
Creates a PathAndFillManager instance from imported data
- createFromNodes(Collection<SWCPoint>) - Static method in class sc.fiji.snt.PathAndFillManager
-
Creates a PathAndFillManager instance from a collection of reconstruction
nodes.
- createGraph(Collection<SWCPoint>, boolean) - Static method in class sc.fiji.snt.analysis.graph.GraphUtils
-
Creates a DirectedGraph from a collection of reconstruction nodes.
- createGraph(Tree) - Static method in class sc.fiji.snt.analysis.graph.GraphUtils
-
Creates a DirectedGraph from a Tree.
- createIcon(Color, int, int) - Static method in class sc.fiji.snt.gui.GuiUtils
-
- createTree(DefaultDirectedGraph<SWCPoint, ?>) - Static method in class sc.fiji.snt.analysis.graph.GraphUtils
-
Creates a
Tree from a graph.
- crossingsAtDistanceSquared(double) - Method in class sc.fiji.snt.gui.ShollAnalysisDialog.ShollResults
-
Deprecated.
- csvQuoteAndPrint(PrintWriter, Object) - Static method in class sc.fiji.snt.SNTUtils
-
- ctrlKey() - Static method in class sc.fiji.snt.gui.GuiUtils
-
- CustomizeObjCmd - Class in sc.fiji.snt.gui.cmds
-
Command for customizing an OBJ mesh in Reconstruction Viewer
- CustomizeObjCmd() - Constructor for class sc.fiji.snt.gui.cmds.CustomizeObjCmd
-
- CustomizeTreeCmd - Class in sc.fiji.snt.gui.cmds
-
Command for customizing a Tree in Reconstruction Viewer
- CustomizeTreeCmd() - Constructor for class sc.fiji.snt.gui.cmds.CustomizeTreeCmd
-