A B C D E F G H I J L M N O P Q R S T U V W X Y Z

S

save(String) - Method in class sc.fiji.snt.SNTService

Saves all the existing paths to a file.

save(String) - Method in class sc.fiji.snt.Tree

Saves this Tree to a .TRACES (XML, compressed) file.

save(String) - Method in class sc.fiji.snt.viewer.MultiViewer2D

saveAsJSON(String) - Method in class sc.fiji.snt.io.MouseLightLoader

Convenience method to save JSON data to a local directory.

saveAsSWC(String) - Method in class sc.fiji.snt.io.MouseLightLoader

Convenience method to save SWC data to a local directory.

saveAsSWC(String) - Method in class sc.fiji.snt.Tree

Saves this Tree to an SWC file.

saveFile(String, File, List<String>) - Method in class sc.fiji.snt.gui.GuiUtils

saveFill() - Method in class sc.fiji.snt.SNT

saveSnapshot() - Method in class sc.fiji.snt.viewer.Viewer3D

Saves a snapshot of current scene as a PNG image.

saveSnapshot(String) - Method in class sc.fiji.snt.viewer.Viewer3D

Saves a snapshot of current scene as a PNG image to the specified path.

sc.fiji.snt - package sc.fiji.snt

SNT core classes

sc.fiji.snt.analysis - package sc.fiji.snt.analysis

Analysis of Trees.

sc.fiji.snt.analysis.graph - package sc.fiji.snt.analysis.graph

Classes for handling neuronal reconstructions as graphs

sc.fiji.snt.analysis.sholl - package sc.fiji.snt.analysis.sholl

Sholl analysis of Trees.

sc.fiji.snt.annotation - package sc.fiji.snt.annotation

Classes handling neuropil annotations and atlases metadata.

sc.fiji.snt.event - package sc.fiji.snt.event

Utilities for TrakEM2 interaction

sc.fiji.snt.gui - package sc.fiji.snt.gui

Customizations and commands for SNT's GUI.

sc.fiji.snt.gui.cmds - package sc.fiji.snt.gui.cmds

Scijava-based GUIs for SNT built-in commands.

sc.fiji.snt.hyperpanes - package sc.fiji.snt.hyperpanes

Classes implementing SNT's XY, ZY, and XZ canvases.

sc.fiji.snt.io - package sc.fiji.snt.io

Classes for importing reconstructions into SNT.

sc.fiji.snt.plugin - package sc.fiji.snt.plugin

SNT add-ons as IJ2 commands

sc.fiji.snt.util - package sc.fiji.snt.util

Miscellaneous SNT utilities, including classes defining reconstruction nodes.

sc.fiji.snt.viewer - package sc.fiji.snt.viewer

Visualization of reconstructions

scale(double, double, double) - Method in class sc.fiji.snt.Tree

Scales the tree by the specified factors.

scale(double, double, double, double) - Method in class sc.fiji.snt.Tree

Scales the tree by the specified factors.

scale(double, double, double) - Method in class sc.fiji.snt.util.PointInImage

Scales this point coordinates.

scaledMicrometer(double, int) - Static method in class sc.fiji.snt.gui.GuiUtils

Returns a more human readable representation of a length in micrometers.

SciViewSNT - Class in sc.fiji.snt

Bridges SNT to SciView, allowing Trees to be rendered as Scenery objects

SciViewSNT(Context) - Constructor for class sc.fiji.snt.SciViewSNT

Instantiates a new SciViewSNT instance.

SciViewSNT(SciView) - Constructor for class sc.fiji.snt.SciViewSNT

Instantiates SciViewSNT from an existing SciView instance.

SearchInterface - Interface in sc.fiji.snt

Tracer classes implementing searches between two points should implement this interface.

SearchNode - Class in sc.fiji.snt

SearchNode(int, int, int, float, float, SearchNode, byte) - Constructor for class sc.fiji.snt.SearchNode

SearchProgressCallback - Interface in sc.fiji.snt

searchStatus - Variable in class sc.fiji.snt.SearchNode

SearchThread - Class in sc.fiji.snt

Implements a common thread that explores the image using a variety of strategies, e.g., to trace tubular structures or surfaces.

SearchThread(ImagePlus, float, float, boolean, boolean, boolean, int, long) - Constructor for class sc.fiji.snt.SearchThread

selectColor(Color) - Method in class sc.fiji.snt.gui.ColorMenu

selectNone() - Method in class sc.fiji.snt.gui.ColorMenu

selectPath(Path, boolean) - Method in class sc.fiji.snt.SNT

selectSWCColor(SNTColor) - Method in class sc.fiji.snt.gui.ColorMenu

SEND_TO_TRAKEM2 - Static variable in class sc.fiji.snt.event.SNTEvent

setAnimationEnabled(boolean) - Method in class sc.fiji.snt.viewer.Viewer3D

Toggles the Viewer's animation.

setAnnotation(BrainAnnotation) - Method in class sc.fiji.snt.util.PointInImage

setAnnotation(BrainAnnotation) - Method in interface sc.fiji.snt.util.SNTPoint

Assigns a neuropil annotation (e.g., atlas compartment) to this point.

setAnnotation(BrainAnnotation) - Method in class sc.fiji.snt.util.SWCPoint

setAnnotationsColor(Color) - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanesCanvas

setAnnotationsColorAllPanes(Color) - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanes

setAutoDismiss(JDialog) - Static method in class sc.fiji.snt.gui.GuiUtils

setAWTColor(Color) - Method in class sc.fiji.snt.util.SNTColor

Re-assigns a AWT color.

setAxesVisible(boolean) - Method in class sc.fiji.snt.viewer.MultiViewer2D

setAxesVisible(boolean) - Method in class sc.fiji.snt.viewer.Viewer2D

setBoundingBox(BoundingBox) - Method in class sc.fiji.snt.Tree

Associates a bounding box to this tree.

setBoundingBoxColor(ColorRGB) - Method in class sc.fiji.snt.viewer.Annotation3D

Determines whether the mesh bounding box should be displayed.

setBoundingBoxColor(ColorRGB) - Method in class sc.fiji.snt.viewer.OBJMesh

Determines whether the mesh bounding box should be displayed.

setBounds(float, float, float, float, float, float) - Method in class sc.fiji.snt.viewer.Viewer3D

Sets a manual bounding box for the scene.

setCanvasLabel(String) - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanesCanvas

Sets the string to be rendered on canvas' upper left corner.

setCanvasLabelAllPanes(String) - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanes

setCanvasOffset(PointInCanvas) - Method in class sc.fiji.snt.Path

Specifies a translation offset when rendering this Path in a TracerCanvas.

setCenter(int) - Method in class sc.fiji.snt.analysis.sholl.TreeParser

Computes the center of the Profile.

setCenter(PointInImage) - Method in class sc.fiji.snt.analysis.sholl.TreeParser

Sets the center of the profile.

setColor(Color) - Method in class sc.fiji.snt.Path

Sets this path color.

setColor(ColorRGB) - Method in class sc.fiji.snt.Tree

Assigns a color to all the paths in this tree.

setColor(String) - Method in class sc.fiji.snt.Tree

Assigns a color to all the paths in this tree.

setColor(ColorRGB, double) - Method in class sc.fiji.snt.viewer.Annotation3D

Assigns a color to the annotation.

setColor(String, double) - Method in class sc.fiji.snt.viewer.Annotation3D

Script friendly method to assign a color to the annotation.

setColor(String) - Method in class sc.fiji.snt.viewer.Annotation3D

Script friendly method to assign a color to the annotation.

setColor(String, double) - Method in class sc.fiji.snt.viewer.OBJMesh

Script friendly method to assign a color to the mesh.

setColor(ColorRGB, double) - Method in class sc.fiji.snt.viewer.OBJMesh

Assigns a color to the mesh.

setColorBarLegend(String, double, double) - Method in class sc.fiji.snt.viewer.MultiViewer2D

setColorBarLegend(ColorTable, double, double) - Method in class sc.fiji.snt.viewer.MultiViewer2D

setColorRGB(ColorRGB) - Method in class sc.fiji.snt.Path

Sets this path color.

setCrosshairs(double, double, double, boolean) - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanesCanvas

Deprecated.

setCTposition(int, int) - Method in class sc.fiji.snt.Path

Sets the hyperstack position of this Path

setCurrentPath(Path) - Method in class sc.fiji.snt.SNT

setCursorText(String) - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanesCanvas

Sets the string to be appended to the current cursor.

setCursorTextAllPanes(String) - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanes

setDebugMode(boolean) - Static method in class sc.fiji.snt.SNTUtils

Enables/disables debug mode

setDefaultColor(ColorRGB) - Method in class sc.fiji.snt.viewer.Viewer2D

Sets the default (fallback) color for plotting paths.

setDefaultColor(ColorRGB) - Method in class sc.fiji.snt.viewer.Viewer3D

Sets the default color for rendering Trees.

setDefaultThickness(float) - Method in class sc.fiji.snt.viewer.Viewer3D

Sets the line thickness for rendering Trees that have no specified radius.

setDimensions(int, int, int) - Method in class sc.fiji.snt.util.BoundingBox

Sets the dimensions of this bounding box using uncalibrated (pixel) lengths.

setDrawCrosshairs(boolean) - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanesCanvas

setDrawCrosshairsAllPanes(boolean) - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanes

setDrawDiametersXY(boolean) - Method in class sc.fiji.snt.SNT

setEditableNode(int) - Method in class sc.fiji.snt.Path

Tags the specified point position as 'editable'.

setEnableDarkMode(boolean) - Method in class sc.fiji.snt.viewer.Viewer3D

Enables/disables "Dark Mode" mode

setEnableDebugMode(boolean) - Method in class sc.fiji.snt.SNTUI

Enables/disables debug mode

setEnableDebugMode(boolean) - Method in class sc.fiji.snt.viewer.Viewer3D

Enables/disables debug mode

setEndJoin(Path, PointInImage) - Method in class sc.fiji.snt.Path

setFillList(String[]) - Method in class sc.fiji.snt.FillManagerUI

setFillList(String[]) - Method in class sc.fiji.snt.PathManagerUI

setFillList(String[]) - Method in class sc.fiji.snt.SNT

setFillThreshold(double) - Method in class sc.fiji.snt.SNT

setFillThresholdFrom(double, double, double) - Method in class sc.fiji.snt.SNT

setFillTransparent(boolean) - Method in class sc.fiji.snt.FillManagerUI

setFont(Font, float, ColorRGB) - Method in class sc.fiji.snt.viewer.Viewer3D

Sets the font for label annotations

setFrameSize(int, int) - Method in class sc.fiji.snt.viewer.Viewer3D

Resizes the viewer to the specified dimensions.

setFrom(SearchNode) - Method in class sc.fiji.snt.SearchNode

setGridlinesVisible(boolean) - Method in class sc.fiji.snt.viewer.MultiViewer2D

setGridlinesVisible(boolean) - Method in class sc.fiji.snt.viewer.Viewer2D

setHeadless(boolean) - Method in class sc.fiji.snt.PathAndFillManager

Sets whether this PathAndFillManager instance should run headless.

setLabel(String) - Method in class sc.fiji.snt.Tree

Sets an identifying label for this Tree.

setLabel(String) - Method in class sc.fiji.snt.viewer.OBJMesh

setLabelLocation(float, float) - Method in class sc.fiji.snt.viewer.Viewer3D

Sets the location for annotation labels

setLayoutColumns(int) - Method in class sc.fiji.snt.viewer.MultiViewer2D

setMaxRadius(int) - Method in class sc.fiji.snt.PathFitter

Sets the max radius (side search) for constraining the fit.

setMetric(String) - Method in class sc.fiji.snt.Fill

setMinMax(double, double) - Method in class sc.fiji.snt.analysis.ColorMapper

Sets the LUT mapping bounds.

setName(String) - Method in class sc.fiji.snt.Path

Sets this Path's name.

setNodeAnnotation(BrainAnnotation, int) - Method in class sc.fiji.snt.Path

Assigns an annotation to an existing node.

setNodeColor(Color, int) - Method in class sc.fiji.snt.Path

Sets the node color.

setNodeColors(Color[]) - Method in class sc.fiji.snt.Path

Sets the node colors.

setNodeIndicesAsDistances(boolean) - Method in class sc.fiji.snt.analysis.PathProfiler

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

setNodeValue(double, int) - Method in class sc.fiji.snt.Path

Assigns the "value" property to this node.

setNodeValues(double[]) - Method in class sc.fiji.snt.Path

Sets the path "values", the array containing the numeric property assigned to path nodes, typically voxel intensities.

setOrigin(PointInImage) - Method in class sc.fiji.snt.util.BoundingBox

Sets the origin for this box, i.e., the Box's SE vertex (lower left corner)

setOutlineVisible(boolean) - Method in class sc.fiji.snt.viewer.MultiViewer2D

setOutlineVisible(boolean) - Method in class sc.fiji.snt.viewer.Viewer2D

setPaneOwner(PaneOwner) - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanesCanvas

setPath(Path) - Method in class sc.fiji.snt.util.PointInImage

Associates a Path with this node

setPathList(String[], Path, boolean) - Method in class sc.fiji.snt.FillManagerUI

setPathList(String[], Path, boolean) - Method in class sc.fiji.snt.PathManagerUI

setPathList(String[], Path, boolean) - Method in class sc.fiji.snt.SNT

setPredecessor(SearchNode) - Method in class sc.fiji.snt.SearchNode

setPreferredSize(int, int) - Method in class sc.fiji.snt.viewer.Viewer2D

Sets the preferred size of the plot to a constant value.

setPreviousPoint(SWCPoint) - Method in class sc.fiji.snt.util.SWCPoint

Sets the preceding node in the reconstruction

setProgressCallback(int, MultiTaskProgress) - Method in class sc.fiji.snt.PathFitter

setRadii(double[]) - Method in class sc.fiji.snt.Path

Assigns radii to this Path

setRadii(double) - Method in class sc.fiji.snt.Tree

Assigns a fixed radius to all the nodes in this tree.

setRadius(double) - Method in class sc.fiji.snt.Path

Assigns a fixed radius to all the nodes of this Path

setReplaceNodes(boolean) - Method in class sc.fiji.snt.PathFitter

Sets whether fitting should occur "in place".

setSaveCompressedTraces(boolean) - Method in class sc.fiji.snt.SNTPrefs

setSaveWinLocations(boolean) - Method in class sc.fiji.snt.SNTPrefs

setSceneUpdatesEnabled(boolean) - Method in class sc.fiji.snt.viewer.Viewer3D

Sets whether the scene should update (refresh) every time a new reconstruction (or mesh) is added/removed from the scene.

setSciView(SciView) - Method in class sc.fiji.snt.SciViewSNT

Sets the SciView to be used.

setScope(int) - Method in class sc.fiji.snt.PathFitter

Sets the fitting scope.

setSecondaryImage(File) - Method in class sc.fiji.snt.SNT

Specifies the 'secondary image' to be used during a tracing session.

setSecondaryImageMinMax(float, float) - Method in class sc.fiji.snt.SNT

setSelected(boolean) - Method in class sc.fiji.snt.Path

setSelectedColor(Color, boolean) - Method in class sc.fiji.snt.gui.ColorChooserButton

setSelectedPaths(HashSet<Path>, Object) - Method in class sc.fiji.snt.FillManagerUI

setSelectedPaths(HashSet<Path>, Object) - Method in class sc.fiji.snt.PathManagerUI

setSelectedPaths(HashSet<Path>, Object) - Method in class sc.fiji.snt.SNT

setShowAnnotatedView(boolean) - Method in class sc.fiji.snt.PathFitter

Sets whether an interactive image of the result should be displayed.

setShowOnlySelectedPaths(boolean) - Method in class sc.fiji.snt.SNT

setSigmaAndMax(double, double) - Method in class sc.fiji.snt.HessianCaller

setSinglePane(boolean) - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanes

setSize(float) - Method in class sc.fiji.snt.viewer.Annotation3D

Sets the annotation width.

setSnapshotDir(String) - Method in class sc.fiji.snt.viewer.Viewer3D

Sets the directory for storing snapshots.

setSomasDisplayed(Collection<String>, boolean) - Method in class sc.fiji.snt.viewer.Viewer3D

Toggles the visibility of somas for subset of trees.

setSomasDisplayed(boolean) - Method in class sc.fiji.snt.viewer.Viewer3D

Toggles the visibility of somas for all trees in the scene.

setSourcePaths(Path[]) - Method in class sc.fiji.snt.Fill

setSourcePaths(Set<Path>) - Method in class sc.fiji.snt.Fill

setSourcePaths(Collection<Path>) - Method in class sc.fiji.snt.FillerThread

setSpacing(double, double, double, String) - Method in class sc.fiji.snt.Fill

setSpacing(double, double, double, String) - Method in class sc.fiji.snt.util.BoundingBox

Sets the voxel spacing.

setStartJoin(Path, PointInImage) - Method in class sc.fiji.snt.Path

setStatus(String) - Method in class sc.fiji.snt.gui.SNTSearchableBar

setStatusLabelPlaceholder(String) - Method in class sc.fiji.snt.gui.SNTSearchableBar

setStepSize(double) - Method in class sc.fiji.snt.analysis.sholl.TreeParser

Sets the radius step size.

setStrokeWidth(int) - Method in class sc.fiji.snt.analysis.RoiConverter

Sets the line width of converted segment paths.

setSWCType(int) - Method in class sc.fiji.snt.Path

Sets the SWC type.

setSWCType(String) - Method in class sc.fiji.snt.Tree

Assigns an SWC type label to all the Paths in this Tree.

setSWCType(int) - Method in class sc.fiji.snt.util.SNTColor

Re-assigns a SWC type integer flag

setSystemLookAndFeel() - Static method in class sc.fiji.snt.gui.GuiUtils

setTable(DefaultGenericTable) - Method in class sc.fiji.snt.analysis.TreeAnalyzer

Sets the Analyzer table.

setTable(DefaultGenericTable, String) - Method in class sc.fiji.snt.analysis.TreeAnalyzer

Sets the table.

setTemporaryPath(Path) - Method in class sc.fiji.snt.SNT

setThreads(int) - Method in class sc.fiji.snt.SNTPrefs

setThreshold(double) - Method in class sc.fiji.snt.Fill

setThreshold(double) - Method in class sc.fiji.snt.FillerThread

setTitle(String) - Method in class sc.fiji.snt.viewer.Viewer2D

Sets the plot display title.

setTmpMsgTimeOut(int) - Method in class sc.fiji.snt.gui.GuiUtils

setTreesThickness(Collection<String>, float) - Method in class sc.fiji.snt.viewer.Viewer3D

Applies a constant thickness (line width) to a subset of rendered trees.

setTreesThickness(float) - Method in class sc.fiji.snt.viewer.Viewer3D

Applies a constant thickness to all rendered trees.

setType(int) - Method in class sc.fiji.snt.Tree

Assigns an SWC type label to all the Paths in this Tree.

setUnit(String) - Method in class sc.fiji.snt.util.BoundingBox

Sets the default length unit for voxel spacing (typically um, for SWC reconstructions)

setUp() - Method in class sc.fiji.snt.Tracing2DTest

setUp() - Method in class sc.fiji.snt.Tracing3DTest

setUp() - Method in class sc.fiji.snt.TreeAnalyzerTest

setUseFitted(boolean) - Method in class sc.fiji.snt.Path

Sets whether the fitted flavor of this Path should be used.

setView(int) - Method in class sc.fiji.snt.analysis.RoiConverter

Sets the exporting view for segment paths (XY by default).

setViewMode(Viewer3D.ViewMode) - Method in class sc.fiji.snt.viewer.Viewer3D

Renders the scene from a specified camera angle.

setViewPoint(double, double) - Method in class sc.fiji.snt.viewer.Viewer3D

Renders the scene from a specified camera angle using polar coordinates relative to the the center of the scene.

setViewPointCC(double, double) - Method in class sc.fiji.snt.viewer.Viewer3D

Calls Viewer3D.setViewPoint(double, double) using Cartesian coordinates.

setVisible(String, boolean) - Method in class sc.fiji.snt.viewer.Viewer3D

Toggles the visibility of a rendered Tree, a loaded OBJ mesh, or an annotation.

setZPositionAllPanes(int, int, int) - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanes

ShollAnalysisDialog - Class in sc.fiji.snt.gui

Deprecated.

ShollAnalysisDialog(double, double, double, SNT) - Constructor for class sc.fiji.snt.gui.ShollAnalysisDialog

Deprecated.

ShollAnalysisDialog.ShollPoint - Class in sc.fiji.snt.gui

Deprecated.

ShollAnalysisDialog.ShollResults - Class in sc.fiji.snt.gui

Deprecated.

ShollAnalysisPlugin - Class in sc.fiji.snt.plugin

Deprecated.

ShollAnalysisPlugin() - Constructor for class sc.fiji.snt.plugin.ShollAnalysisPlugin

Deprecated.

ShollResults(List<ShollAnalysisDialog.ShollPoint>, ImagePlus, boolean, int, double, double, double, String, int, int, double, boolean) - Constructor for class sc.fiji.snt.gui.ShollAnalysisDialog.ShollResults

Deprecated.

ShollTracingsCmd - Class in sc.fiji.snt.plugin

Implements both the "Analyze:Sholl:Sholl Analysis (From Tracings)..." and SNT's "Start Sholl Analysis..." commands

ShollTracingsCmd() - Constructor for class sc.fiji.snt.plugin.ShollTracingsCmd

show(Graph<V, E>) - Static method in class sc.fiji.snt.analysis.graph.GraphUtils

Displays a graph in a dedicated window featuring UI commands for interactive visualization and export options.

show() - Method in class sc.fiji.snt.viewer.MultiViewer2D

show() - Method in class sc.fiji.snt.viewer.Viewer3D

Displays the Viewer and returns a reference to its frame.

show(int, int) - Method in class sc.fiji.snt.viewer.Viewer3D

Displays the viewer under specified dimensions.

ShowCorrespondencesCmd - Class in sc.fiji.snt.gui.cmds

Command for highlighting the correspondences between two reconstructions in the Legacy 3D Viewer

ShowCorrespondencesCmd() - Constructor for class sc.fiji.snt.gui.cmds.ShowCorrespondencesCmd

showCorrespondencesTo(File, Color, double) - Method in class sc.fiji.snt.SNT

Deprecated.

showHTMLDialog(String, String) - Static method in class sc.fiji.snt.gui.GuiUtils

showMessage(String, String) - Method in class sc.fiji.snt.SNTUI

showMIPOverlays(double) - Method in class sc.fiji.snt.SNT

Overlays a semi-transparent MIP (8-bit scaled) of the data being traced over the tracing canvas(es).

showPlot() - Method in class sc.fiji.snt.viewer.Viewer2D

Displays the current plot on a dedicated frame

showStatus(int, int, String) - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanes

showStatus(int, int, String) - Method in interface sc.fiji.snt.hyperpanes.PaneOwner

showStatus(int, int, String) - Method in class sc.fiji.snt.SNT

showStatus(String, boolean) - Method in class sc.fiji.snt.SNTUI

Updates the status bar.

SigmaPalette - Class in sc.fiji.snt.gui

Implements SNT 'Sigma wizard'.

SigmaPalette(SNT, HessianCaller) - Constructor for class sc.fiji.snt.gui.SigmaPalette

similarCalibrations(Calibration, Calibration) - Static method in class sc.fiji.snt.SNTUtils

size() - Method in class sc.fiji.snt.Path

Returns the number of nodes of this path

size() - Method in class sc.fiji.snt.PathAndFillManager

Returns the number of Paths in the PathAndFillManager list.

size() - Method in class sc.fiji.snt.Tree

Retrieves the number of paths in this tree.

skeletonize(ImagePlus, int) - Method in class sc.fiji.snt.Tree

SkeletonizerCmd - Class in sc.fiji.snt.plugin

Convenience command for converting Paths into skeleton images

SkeletonizerCmd() - Constructor for class sc.fiji.snt.plugin.SkeletonizerCmd

smallButton(String) - Static method in class sc.fiji.snt.gui.GuiUtils

SNT - Class in sc.fiji.snt

Implements the SNT plugin.

SNT(Context, ImagePlus) - Constructor for class sc.fiji.snt.SNT

Instantiates SNT in 'Tracing Mode'.

SNT(Context, PathAndFillManager) - Constructor for class sc.fiji.snt.SNT

Instantiates SNT in 'Analysis Mode'

SNT_PAUSED - Static variable in class sc.fiji.snt.SNTUI

Flag specifying all SNT are temporarily disabled (all user interactions are waived back to ImageJ)

SNTColor - Class in sc.fiji.snt.util

A simple class for handling Colors including the ability to map an AWT Color to a SWC type integer tag.

SNTColor(Color, int) - Constructor for class sc.fiji.snt.util.SNTColor

Instantiates a new SNT color.

SNTColor(Color) - Constructor for class sc.fiji.snt.util.SNTColor

Instantiates a new SNT color without SWC type association

SNTEvent - Class in sc.fiji.snt.event

SNTEvent(int) - Constructor for class sc.fiji.snt.event.SNTEvent

SNTLegacyLoaderCmd - Class in sc.fiji.snt.gui.cmds

Command for Launching SNT when user selects 'Simple Neurite Tracer' from Ij's menu hierarchy.

SNTLegacyLoaderCmd() - Constructor for class sc.fiji.snt.gui.cmds.SNTLegacyLoaderCmd

SNTListener - Interface in sc.fiji.snt.event

SNTLoaderCmd - Class in sc.fiji.snt.gui.cmds

Command for Launching SNT

SNTLoaderCmd() - Constructor for class sc.fiji.snt.gui.cmds.SNTLoaderCmd

SNTPoint - Interface in sc.fiji.snt.util

Classes extend this interface implement a point in a 3D space, always using real world coordinates.

SNTPrefs - Class in sc.fiji.snt

Class handling SNT preferences.

SNTPrefs(SNT) - Constructor for class sc.fiji.snt.SNTPrefs

SNTSearchableBar - Class in sc.fiji.snt.gui

Implements a SearchableBar following SNT's UI.

SNTSearchableBar(Searchable) - Constructor for class sc.fiji.snt.gui.SNTSearchableBar

SNTService - Class in sc.fiji.snt

Service for accessing and scripting the active instance of SNT.

SNTService() - Constructor for class sc.fiji.snt.SNTService

SNTUI - Class in sc.fiji.snt

Implements SNT's main dialog.

SNTUI(SNT) - Constructor for class sc.fiji.snt.SNTUI

Instantiates SNT's main UI and associated PathManagerUI and FillManagerUI instances.

SNTUtils - Class in sc.fiji.snt

Static utilities for SNT

SOMA - Static variable in class sc.fiji.snt.io.MouseLightLoader

The Constant SOMA.

SOMA - Static variable in class sc.fiji.snt.io.MouseLightQuerier

The Constant SOMA.

sortedMappedTrees() - Method in class sc.fiji.snt.analysis.MultiTreeColorMapper

spacing_units - Variable in class sc.fiji.snt.Fill

start() - Method in class sc.fiji.snt.HessianCaller

startElement(String, String, String, Attributes) - Method in class sc.fiji.snt.PathAndFillManager

startFillerThread(FillerThread) - Method in class sc.fiji.snt.SNT

startFillingPaths(Set<Path>) - Method in class sc.fiji.snt.SNT

startHessian(String, double, double, boolean) - Method in class sc.fiji.snt.SNT

startUI() - Method in class sc.fiji.snt.SNT

STOPPING - Static variable in class sc.fiji.snt.SearchThread

StrahlerCmd - Class in sc.fiji.snt.plugin

Command to perform Horton-Strahler analysis on a Tree.

StrahlerCmd(Tree) - Constructor for class sc.fiji.snt.plugin.StrahlerCmd

stringToColor(String) - Static method in class sc.fiji.snt.util.SNTColor

Returns an AWT Color from a (#)RRGGBB(AA) hex string.

stripExtension(String) - Static method in class sc.fiji.snt.SNTUtils

subTree(String...) - Method in class sc.fiji.snt.Tree

Extracts the subset of paths matching the specified criteria (script friendly method)

subTree(int...) - Method in class sc.fiji.snt.Tree

Extracts the subset of paths matching the specified criteria.

succeeded() - Method in class sc.fiji.snt.gui.SWCImportOptionsDialog

SUCCESS - Static variable in class sc.fiji.snt.SearchThread

successful() - Method in class sc.fiji.snt.analysis.sholl.TreeParser

summarize(boolean) - Method in class sc.fiji.snt.analysis.TreeAnalyzer

Outputs a summary of the current analysis to the Analyzer table using the default Tree label.

summarize(String, boolean) - Method in class sc.fiji.snt.analysis.TreeAnalyzer

Outputs a summary of the current analysis to the Analyzer table.

SWC_APICAL_DENDRITE - Static variable in class sc.fiji.snt.Path

Flag specifying the SWC type 'apical dendrite'.

SWC_APICAL_DENDRITE_LABEL - Static variable in class sc.fiji.snt.Path

String representation of Path.SWC_APICAL_DENDRITE

SWC_AXON - Static variable in class sc.fiji.snt.Path

Flag specifying the SWC type 'axon'.

SWC_AXON_LABEL - Static variable in class sc.fiji.snt.Path

String representation of Path.SWC_AXON

SWC_CUSTOM - Static variable in class sc.fiji.snt.Path

Flag specifying the SWC type 'custom'.

SWC_CUSTOM_LABEL - Static variable in class sc.fiji.snt.Path

String representation of Path.SWC_CUSTOM

SWC_DENDRITE - Static variable in class sc.fiji.snt.Path

Flag specifying the SWC type '(basal) dendrite'.

SWC_DENDRITE_LABEL - Static variable in class sc.fiji.snt.Path

String representation of Path.SWC_DENDRITE

SWC_END_POINT - Static variable in class sc.fiji.snt.Path

Deprecated.

SWC_END_POINT_LABEL - Static variable in class sc.fiji.snt.Path

String representation of Path.SWC_END_POINT

SWC_FORK_POINT - Static variable in class sc.fiji.snt.Path

Deprecated.

SWC_FORK_POINT_LABEL - Static variable in class sc.fiji.snt.Path

String representation of Path.SWC_FORK_POINT

SWC_SOMA - Static variable in class sc.fiji.snt.Path

Flag specifying the SWC type 'soma'.

SWC_SOMA_LABEL - Static variable in class sc.fiji.snt.Path

String representation of Path.SWC_SOMA

SWC_UNDEFINED - Static variable in class sc.fiji.snt.Path

Flag specifying the SWC type 'undefined'.

SWC_UNDEFINED_LABEL - Static variable in class sc.fiji.snt.Path

String representation of Path.SWC_UNDEFINED

SWCImportOptionsDialog - Class in sc.fiji.snt.gui

Implements a dialog for importing SWC files into SNT with advanced options.

SWCImportOptionsDialog(String) - Constructor for class sc.fiji.snt.gui.SWCImportOptionsDialog

SWCPoint - Class in sc.fiji.snt.util

Defines a node in an SWC reconstruction.

SWCPoint(int, int, double, double, double, double, int) - Constructor for class sc.fiji.snt.util.SWCPoint

SWCTypeFilterCmd - Class in sc.fiji.snt.gui.cmds

Implements PathManagerUI's SWC-type filtering Command.

SWCTypeFilterCmd() - Constructor for class sc.fiji.snt.gui.cmds.SWCTypeFilterCmd

SWCTypeOptionsCmd - Class in sc.fiji.snt.gui.cmds

Implements PathManagerUI's SWC-SWC-type tagging Options Command.

SWCTypeOptionsCmd() - Constructor for class sc.fiji.snt.gui.cmds.SWCTypeOptionsCmd

SwingSafeResult - Class in sc.fiji.snt.gui

Utility class that ensures EDT execution.

SwingSafeResult() - Constructor for class sc.fiji.snt.gui.SwingSafeResult

syncPathManagerList() - Method in class sc.fiji.snt.viewer.Viewer3D

(Re)loads the current list of Paths in the Path Manager list.

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