Uses of Class
sc.fiji.snt.SNT

Packages that use SNT

Package	Description
sc.fiji.snt	SNT core classes
sc.fiji.snt.analysis	Analysis of Trees.
sc.fiji.snt.gui	Customizations and commands for SNT's GUI.
sc.fiji.snt.gui.cmds	Scijava-based GUIs for SNT built-in commands.
sc.fiji.snt.seed	Classes for Seed Tracing.
sc.fiji.snt.tracing	Path-finding algorithms for interactive neuron tracing.
sc.fiji.snt.util	Miscellaneous SNT utilities, including classes defining reconstruction nodes.
sc.fiji.snt.viewer	Visualization of reconstructions

Uses of SNT in sc.fiji.snt

Fields in sc.fiji.snt declared as SNT

Modifier and Type	Field	Description
protected SNT	PathAndFillManager.plugin
protected SNT	SNTUI.plugin

Methods in sc.fiji.snt that return SNT

Modifier and Type	Method	Description
SNT	SNTService.getInstance()	Returns a reference to the active SNT instance.
static SNT	SNTUtils.getInstance()
SNT	PathAndFillManager.getPlugin()	Gets the SNT instance.
SNT	SNTService.getPlugin()	Deprecated. use SNTService.getInstance() instead
static SNT	SNTUtils.getPluginInstance()	Deprecated. use SNTUtils.getInstance() instead
SNT	PathManagerUI.getSNT()	Gets the SNT instance associated with this Path Manager.
SNT	SNTService.initialize(boolean startUI)	Initializes SNT.
SNT	SNTService.initialize(ij.ImagePlus imp, boolean startUI)	Initializes SNT.
SNT	SNTService.initialize(String imagePath, boolean startUI)	Initializes SNT.
<T extends net.imglib2.type.numeric.RealType<T>> SNT	SNTService.initialize(net.imagej.ImgPlus<T> img, boolean startUI)	Initializes SNT from an ImgPlus image.
static SNT	SNTUtils.startApp()	Convenience method to start up SNT's GUI.

Methods in sc.fiji.snt with parameters of type SNT

Modifier and Type	Method	Description
protected void	Path.drawPathAsPoints(Graphics2D g2, TracerCanvas canvas, SNT snt)
protected static void	SNTUtils.setPlugin(SNT plugin)

Constructors in sc.fiji.snt with parameters of type SNT

Modifier	Constructor	Description
	AStarRefiner(SNT snt, Path path)	Creates a refiner for a single path, reading search settings (cost function, data structure, secondary/hessian image) live from snt at the time AStarRefiner.call() actually runs.
	AStarRefiner(SNT snt, Path path, SNT.SearchSettingsSnapshot settings)	Creates a refiner for a single path, using a frozen SNT.SearchSettingsSnapshot instead of the live search settings.
	FillManagerUI(SNT plugin)	Instantiates a new Fill Manager Dialog, with no owning SNTUI (e.g. scripts/tests driving a headless-ish SNT instance that never called startUI()).
	FillManagerUI(SNT plugin, SNTUI ui)	Instantiates a new Fill Manager Dialog owned by ui.
	MultiPathTracerCanvas(ij.ImagePlus imp, SNT snt, PathAndFillManager pafm)	Builds the canvas.
protected	PathAndFillManager(SNT plugin)
	PathFitter(SNT plugin, Path path)	Instantiates a new PathFitter.
	PathManagerUI(SNT plugin)	Instantiates a new Path Manager Dialog.
	SciViewSNT(SNT snt)
	SNTPrefs(SNT snt)	Constructs a new SNTPrefs instance for the specified SNT instance.
	SNTUI(SNT plugin)	Instantiates SNT's main UI and associated PathManagerUI and FillManagerUI instances.
	SNTUI(SNT plugin, boolean bigDataMode)	Instantiates SNT's main UI and associated PathManagerUI and FillManagerUI instances.

Uses of SNT in sc.fiji.snt.analysis

Constructors in sc.fiji.snt.analysis with parameters of type SNT

Modifier	Constructor	Description
	PathStraightener(Path path, SNT snt)	Instantiates a new PathStraightener

Uses of SNT in sc.fiji.snt.gui

Constructors in sc.fiji.snt.gui with parameters of type SNT

Modifier	Constructor	Description
	CostPalette(SNT snt, PointInImage startWorld, PointInImage endWorld)
	DemoRunner(SNTUI ui, SNT snt)
	MeasureUI(SNT plugin, Collection<Tree> trees)
	SigmaPalette(SNT snt)

Uses of SNT in sc.fiji.snt.gui.cmds

Fields in sc.fiji.snt.gui.cmds declared as SNT

Modifier and Type	Field	Description
protected SNT	CommonDynamicCmd.snt

Uses of SNT in sc.fiji.snt.seed

Methods in sc.fiji.snt.seed with parameters of type SNT

Modifier and Type	Method	Description
static void	SeedOverlayCanvasHandler.install(TracerCanvas canvas, SNT snt)	Installs the Alt+Click → edit-nearest-seed listener on the given canvas.

Constructors in sc.fiji.snt.seed with parameters of type SNT

Modifier	Constructor	Description
	SeedTableModel(SeedOverlay overlay, SNT snt)	Builds a model with an optional Status column.

Uses of SNT in sc.fiji.snt.tracing

Constructors in sc.fiji.snt.tracing with parameters of type SNT

Modifier	Constructor	Description
protected	AbstractSearch(SNT snt, ij.ImagePlus imagePlus)
protected	AbstractSearch(SNT snt, net.imglib2.RandomAccessibleInterval<? extends net.imglib2.type.numeric.RealType<?>> image)
	BiSearch(SNT snt, int start_x, int start_y, int start_z, int goal_x, int goal_y, int goal_z)
	BiSearch(SNT snt, int start_x, int start_y, int start_z, int goal_x, int goal_y, int goal_z, Cost costFunction, Heuristic heuristic)
	BiSearch(SNT snt, net.imglib2.RandomAccessibleInterval<? extends net.imglib2.type.numeric.RealType<?>> image, int start_x, int start_y, int start_z, int goal_x, int goal_y, int goal_z, Cost costFunction, Heuristic heuristic)
	ManualTracerThread(SNT plugin, double start_x, double start_y, double start_z, double goal_x, double goal_y, double goal_z)
protected	SearchThread(SNT snt, net.imglib2.RandomAccessibleInterval<? extends net.imglib2.type.numeric.RealType<?>> image, Cost costFunction)
	TracerThread(SNT snt, int start_x, int start_y, int start_z, int goal_x, int goal_y, int goal_z)
	TracerThread(SNT snt, int start_x, int start_y, int start_z, int goal_x, int goal_y, int goal_z, Cost costFunction, Heuristic heuristic)
	TracerThread(SNT snt, net.imglib2.RandomAccessibleInterval<? extends net.imglib2.type.numeric.RealType<?>> image, int start_x, int start_y, int start_z, int goal_x, int goal_y, int goal_z, Cost costFunction, Heuristic heuristic)

Uses of SNT in sc.fiji.snt.util

Methods in sc.fiji.snt.util with parameters of type SNT

Modifier and Type	Method	Description
static double[]	SigmaUtils.getDefaultSigma(SNT snt)

Uses of SNT in sc.fiji.snt.viewer

Fields in sc.fiji.snt.viewer declared as SNT

Modifier and Type	Field	Description
protected final SNT	AbstractBigViewer.snt	The SNT instance this viewer is tethered to, or null if no SNT instance is available.

Methods in sc.fiji.snt.viewer that return SNT

Modifier and Type	Method	Description
SNT	AbstractBigViewer.getSNT()

Methods in sc.fiji.snt.viewer with parameters of type SNT

Modifier and Type	Method	Description
static Bvv	Bvv.open(SNT snt)	Convenience factory: creates a BVV instance tethered to the given SNT instance and immediately displays its currently loaded image data.

Constructors in sc.fiji.snt.viewer with parameters of type SNT

Modifier	Constructor	Description
protected	AbstractBigViewer(SNT snt)
protected	AbstractTracer(SNT snt)
	Bdv(SNT snt)	Creates a BDV viewer tethered to an SNT instance.
	Bvv(SNT snt)	Constructor for assembling a BVV instance tethered to SNT.
protected	Viewer3D(SNT snt)