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

G

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

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

Returns the Path at the specified position.

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

Gets the IDs of all the cells publicly available in the MouseLight database.

getAnalyzer(boolean) - Method in class sc.fiji.snt.SNTService

Returns a TreeAnalyzer instance constructed from current Paths.

getAncestors(int) - Method in class sc.fiji.snt.annotation.AllenCompartment

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

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

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

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

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

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

Returns an estimated volume of this path.

getAvalailableLuts() - Method in class sc.fiji.snt.analysis.TreeColorMapper

Gets the available LUTs.

getAxonNodes() - Method in class sc.fiji.snt.io.MouseLightQuerier

Extracts the nodes of the axonal arbor of loaded neuron.

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

Returns the center of this annotation bounding box.

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

Returns the BoundingBox enclosing all nodes of all existing Paths.

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

Gets the bounding box associated with this tree.

getBoundingBox(boolean) - Method in class sc.fiji.snt.Tree

Gets the bounding box associated with this tree.

getBranchPointMap() - Method in class sc.fiji.snt.plugin.StrahlerCmd

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

Gets the position of all the branch points in the analyzed tree.

getButton(IconFactory.GLYPH) - Static method in class sc.fiji.snt.gui.IconFactory

getButtonIcon(IconFactory.GLYPH, float) - Static method in class sc.fiji.snt.gui.IconFactory

getButtonIcon(IconFactory.GLYPH) - Static method in class sc.fiji.snt.gui.IconFactory

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

Gets the cable length.

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

Gets the spatial calibration of this Path.

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

Creates a Calibration object using information from this BoundingBox

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

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

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

Returns the center coordinates

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

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

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

Returns the spatial centroid of the specified (hemi)mesh.

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

Gets the hyperstack channel associated with this Path.

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

Gets the current viewer as a JFreeChart object

getChildren() - Method in class sc.fiji.snt.annotation.AllenCompartment

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

getChildren(int) - Method in class sc.fiji.snt.annotation.AllenCompartment

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

getChoice(String, String, String[], String) - Method in class sc.fiji.snt.gui.GuiUtils

getChosenTypes(Context) - Static method in class sc.fiji.snt.gui.cmds.SWCTypeFilterCmd

getColor(String, Color) - Method in class sc.fiji.snt.gui.GuiUtils

getColor(String, Color, String...) - Method in class sc.fiji.snt.gui.GuiUtils

Simplified color chooser.

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

Gets the color of this Path

getColorFilterMenu() - Method in class sc.fiji.snt.gui.PathManagerUISearchableBar

getColorMap() - Method in class sc.fiji.snt.gui.cmds.SWCTypeOptionsCmd

getColorRGB(String, Color, String...) - Method in class sc.fiji.snt.gui.GuiUtils

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

Gets the color of this Path

getColorTable(String) - Method in class sc.fiji.snt.analysis.TreeColorMapper

getCompartment(int) - Static method in class sc.fiji.snt.annotation.AllenUtils

Constructs a compartment from its CCF id

getCompartment(String) - Static method in class sc.fiji.snt.annotation.AllenUtils

Constructs a compartment from its CCF name or acronym

getCompartment(String) - Method in class sc.fiji.snt.io.MouseLightQuerier

Gets a traced compartment of the loaded cell.

getConfirmation(String, String) - Method in class sc.fiji.snt.gui.GuiUtils

getConfirmation(String, String, String, String) - Method in class sc.fiji.snt.gui.GuiUtils

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

getCorrespondences(PathAndFillManager, double) - Method in class sc.fiji.snt.PathAndFillManager

For each point in this PathAndFillManager, find the corresponding point on the other one.

getCountMap() - Method in class sc.fiji.snt.plugin.StrahlerCmd

getCriticalValue() - Method in class sc.fiji.snt.gui.ShollAnalysisDialog.ShollResults

Deprecated.

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

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

getDecimalFormat(double, int) - Static method in class sc.fiji.snt.SNTUtils

getDendriteMaximum() - Method in class sc.fiji.snt.gui.ShollAnalysisDialog.ShollResults

Deprecated.

getDendriteNodes() - Method in class sc.fiji.snt.io.MouseLightQuerier

Extracts the nodes of the dendritic arbor of loaded neuron.

getDescriptiveStats(String) - Method in class sc.fiji.snt.analysis.TreeStatistics

Computes the DescriptiveStatistics for the specified measurement.

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

Gets the box diagonal

getDimensions(boolean) - Method in class sc.fiji.snt.util.BoundingBox

Gets this BoundingBox dimensions.

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

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

getDistinctColors(int) - Static method in class sc.fiji.snt.util.SNTColor

Returns distinct colors based on Kenneth Kelly's 22 colors of maximum contrast (black and white excluded).

getDouble(String, String, Number) - Method in class sc.fiji.snt.gui.GuiUtils

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

Returns the AbstractDrawable associated with this annotation.

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

Returns the DrawableVBO associated with this mesh

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

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

Gets the position of the node tagged as 'editable', if any.

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

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

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

getFillManager() - Method in class sc.fiji.snt.SNTUI

Gets the Fill Manager dialog.

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

Gets the fitted version ('flavor') of this Path.

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

Gets the hyperstack frame position associated with this Path.

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

Assembles a DirectedGraph from this Tree.

getGraphics2D(Graphics) - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanesCanvas

getHessianCaller(String) - Method in class sc.fiji.snt.SNT

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

getHighestOntologyDepth() - Static method in class sc.fiji.snt.annotation.AllenUtils

Gets the maximum number of ontology levels in the Allen CCF.

getHistogram(String) - Method in class sc.fiji.snt.analysis.TreeStatistics

Gets the relative frequencies histogram for a univariate measurement.

getIcon(IconFactory.GLYPH, float, Color) - Static method in class sc.fiji.snt.gui.IconFactory

Creates a new icon from a Font Awesome glyph.

getIconHeight() - Method in class sc.fiji.snt.gui.FADerivedIcon

getIconWidth() - Method in class sc.fiji.snt.gui.FADerivedIcon

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

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

Gets the identifier of this Path

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

Returns this Viewer's id.

getIDs(AllenCompartment) - Static method in class sc.fiji.snt.io.MouseLightQuerier

Gets the IDs of the cells publicly available in the MouseLight database having the soma associated with the specified compartment.

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

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

getImagePlus(int) - Method in class sc.fiji.snt.SNT

Gets the Image associated with a view pane.

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

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

Gets an empty image capable of holding the skeletonized version of this tree.

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

Gets all the data associated with this reconstruction as a JSON object.

getJTree() - Method in class sc.fiji.snt.PathManagerUI

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

Returns the identifying label of this tree.

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

Gets the annotation label

getLabelsImage(ImagePlus, ColorTable) - Method in class sc.fiji.snt.analysis.sholl.TreeParser

Gets the labels image.

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

Gets the length of this Path

getLengthMap() - Method in class sc.fiji.snt.plugin.StrahlerCmd

getListIcon(IconFactory.GLYPH) - Static method in class sc.fiji.snt.gui.IconFactory

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

Retrieves the pixel data of the main image currently loaded in memory as an ImagePlus object.

getMaxDistanceSquared() - Method in class sc.fiji.snt.gui.ShollAnalysisDialog.ShollResults

Deprecated.

getMaxRadius() - Method in class sc.fiji.snt.PathFitter

Gets the current max radius

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

Gets the path mean radius.

getMenuIcon(IconFactory.GLYPH) - Static method in class sc.fiji.snt.gui.IconFactory

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

getMesh() - Method in class sc.fiji.snt.annotation.AllenCompartment

getMesh() - Method in interface sc.fiji.snt.annotation.BrainAnnotation

getMesh(String) - Static method in class sc.fiji.snt.annotation.VFBUtils

Retrieves the mesh associated with the specified VFB id.

getMesh(String, ColorRGB) - Static method in class sc.fiji.snt.annotation.VFBUtils

Retrieves the mesh associated with the specified VFB id.

getMetric() - Method in class sc.fiji.snt.Fill

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

getMinMax() - Method in class sc.fiji.snt.analysis.ColorMapper

Returns the mapping bounds

getMIP(ImagePlus) - Static method in class sc.fiji.snt.SNTUtils

getMorphoFilterMenu() - Method in class sc.fiji.snt.gui.PathManagerUISearchableBar

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

getMultiViewer() - Method in class sc.fiji.snt.analysis.TreeColorMapper

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

Gets this Path's name.

getNeuronCount() - Static method in class sc.fiji.snt.io.MouseLightLoader

Gets the number of cells publicly available in the MouseLight database.

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

Returns the list holding the subsequent nodes in the reconstructed structure after this one.

getNode() - Method in class sc.fiji.snt.NearPoint

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

Gets the node at the specified position.

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

Returns the neuropil annotation associated with this node.

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

Gets the node color.

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

Gets the node colors.

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

Gets the first node index associated with the specified image coordinates.

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

Gets the radius of the specified node.

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

Extracts the nodes (single-point soma, axonal and dendritic arbor) of the loaded neuron.

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

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

getNodes() - Method in class sc.fiji.snt.io.MouseLightQuerier

Extracts the nodes (single-point soma, axonal and dendritic arbor) of the loaded neuron.

getNodes(String) - Method in class sc.fiji.snt.io.MouseLightQuerier

Script-friendly method to extract the nodes of a compartment.

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

Gets all the nodes (path points) forming this tree.

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

getNodeUnscaled() - Method in class sc.fiji.snt.NearPoint

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

Returns the "value" property of this node.

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

Gets the no.

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

Returns the OBJFile associated with this mesh

getOntologies() - Static method in class sc.fiji.snt.annotation.AllenUtils

Gets the Allen CCF as a flat (non-hierarchical) collection of ontologies.

getOntologyDepth() - Method in class sc.fiji.snt.annotation.AllenCompartment

Gets the ontology depth of this compartment.

getOptions(String, String[], boolean[], String) - Method in class sc.fiji.snt.gui.GuiUtils

getOrCreateSciViewSNT() - Method in class sc.fiji.snt.SNTService

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

Gets the branching order of this Path

getOriginalFilename() - Method in class sc.fiji.snt.gui.ShollAnalysisDialog.ShollResults

Deprecated.

getParent() - Method in class sc.fiji.snt.annotation.AllenCompartment

Gets the parent of this compartment

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

Returns the set of parsed Paths.

getPath() - Method in class sc.fiji.snt.NearPoint

getPath(int) - Method in class sc.fiji.snt.PathAndFillManager

Returns the Path at the specified position in the PathAndFillManager list.

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

Returns the Path associated with this node (if any)

getPathAndFillManager() - Method in class sc.fiji.snt.PathManagerUI

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

getPathAndFillManager() - Method in class sc.fiji.snt.SNTService

Returns the PathAndFillManager associated with the current SNT instance.

getPathFromID(int) - Method in class sc.fiji.snt.PathAndFillManager

Returns the Path with the specified id.

getPathFromName(String, boolean) - Method in class sc.fiji.snt.PathAndFillManager

Returns the Path with the specified name.

getPathIndex(Path) - Method in class sc.fiji.snt.PathAndFillManager

Gets the index of a Path

getPathManager() - Method in class sc.fiji.snt.SNTUI

Gets the Path Manager dialog.

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

Returns all the paths.

getPaths() - Method in class sc.fiji.snt.SNTService

Gets the paths currently listed in the Path Manager

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

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

getPathsStructured(Collection<Path>) - Method in class sc.fiji.snt.PathAndFillManager

getPersistentConfirmation(String, String) - Method in class sc.fiji.snt.gui.GuiUtils

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

Gets the plot profile as an IJ1 Plot.

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

Gets the current plot as a XYPlot object

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

Gets the SNT instance.

getPlugin() - Method in class sc.fiji.snt.SNTService

Returns a reference to the active SNT plugin.

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

getPoint3fList() - Method in class sc.fiji.snt.Path

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

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

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

Returns the preceding node (if any)

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

Retrieves the primary branches of the analyzed Tree.

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

Gets the cable length of primary branches.

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

Retrieves all the Paths in the analyzed Tree tagged as primary.

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

getRange(String, String, float[]) - Method in class sc.fiji.snt.gui.GuiUtils

getRatioMap() - Method in class sc.fiji.snt.plugin.StrahlerCmd

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

getReader(String) - Method in class sc.fiji.snt.io.FlyCircuitLoader

Gets the SWC data associated with the specified cell ID as a reader

getReader(String) - Method in class sc.fiji.snt.io.NeuroMorphoLoader

Gets the SWC data ('CNG version') associated with the specified cell ID as a reader

getReader(String) - Method in interface sc.fiji.snt.io.RemoteSWCLoader

getReconstructionURL(String) - Method in class sc.fiji.snt.io.FlyCircuitLoader

Gets the URL of the SWC file associated with the specified cell ID.

getReconstructionURL(String) - Method in class sc.fiji.snt.io.NeuroMorphoLoader

Gets the URL of the SWC file ('CNG version') associated with the specified cell ID.

getReconstructionURL(String) - Method in interface sc.fiji.snt.io.RemoteSWCLoader

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

Gets the Reconstruction Viewer.

getRecViewer() - Method in class sc.fiji.snt.SNTService

Returns a reference to SNT's Reconstruction Viewer.

getRecViewer(int) - Method in class sc.fiji.snt.SNTService

Returns a reference to an opened Reconstruction Viewer (standalone instance).

getRefBrain(String) - Static method in class sc.fiji.snt.annotation.VFBUtils

Retrieves the surface mesh of an adult Drosophila template brain.

getRefBrain() - Static method in class sc.fiji.snt.annotation.ZBAtlasUtils

Retrieves the surface mesh (outline) of the zebrafish template brain.

getRegressionGradient() - Method in class sc.fiji.snt.gui.ShollAnalysisDialog.ShollResults

Deprecated.

getRegressionIntercept() - Method in class sc.fiji.snt.gui.ShollAnalysisDialog.ShollResults

Deprecated.

getRegressionRSquare() - Method in class sc.fiji.snt.gui.ShollAnalysisDialog.ShollResults

Deprecated.

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

getResult() - Method in class sc.fiji.snt.FillerThread

getResult(Callable<T>) - Static method in class sc.fiji.snt.gui.SwingSafeResult

getResult() - Method in class sc.fiji.snt.ManualTracerThread

getResult() - Method in interface sc.fiji.snt.SearchInterface

getResult() - Method in class sc.fiji.snt.TracerThread

getResult() - Method in class sc.fiji.snt.TubularGeodesicsTracer

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

Gets the first node of the main primary path of this tree

getRootMesh(ColorRGB) - Static method in class sc.fiji.snt.annotation.AllenUtils

Retrieves the surface contours for the Allen Mouse Brain Atlas (CCF), bundled with SNT.

getRootNumber() - Method in class sc.fiji.snt.plugin.StrahlerCmd

getSampledCounts() - Method in class sc.fiji.snt.gui.ShollAnalysisDialog.ShollResults

Deprecated.

getSampledDistances() - Method in class sc.fiji.snt.gui.ShollAnalysisDialog.ShollResults

Deprecated.

getScaledPoint() - Method in class sc.fiji.snt.util.PointInCanvas

Converts the pixels coordinates of this point into a physical location if this point is associated with a Path.

getSciView() - Method in class sc.fiji.snt.SciViewSNT

Gets the SciView instance currently in use.

getSciViewSNT() - Method in class sc.fiji.snt.SNTService

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

Gets the SciView Viewer.

getSearchable() - Method in class sc.fiji.snt.PathManagerUI

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

Retrieves the 'secondary image' data currently loaded in memory as an ImagePlus object.

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

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

Gets a section between two nodes of this Path.

getSelectedColor() - Method in class sc.fiji.snt.gui.ColorChooserButton

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

Gets all paths selected in the GUI

getSelectedPaths(boolean) - Method in class sc.fiji.snt.PathManagerUI

Gets the paths currently selected in the Manager's JTree list.

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

getSelectedPaths() - Method in class sc.fiji.snt.SNTService

Gets the paths currently selected in the Path Manager list.

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

getShollRegressionCoefficient() - Method in class sc.fiji.snt.gui.ShollAnalysisDialog.ShollResults

Deprecated.

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

getSNT() - Method in class sc.fiji.snt.PathManagerUI

getSoma() - Method in class sc.fiji.snt.io.MouseLightQuerier

Retrieves the soma (single-point representation) of the loaded neuron.

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

Gets the centroid position of all nodes tagged as Path.SWC_SOMA

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

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

getState() - Method in class sc.fiji.snt.SNTUI

Gets the current UI state.

getStatistics(boolean) - Method in class sc.fiji.snt.SNTService

Returns a TreeStatistics instance constructed from current Paths.

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

Gets the Strahler-Horton root number of the analyzed tree

getString(String, String, String) - Method in class sc.fiji.snt.gui.GuiUtils

getSucceeded() - Method in class sc.fiji.snt.PathFitter

Checks whether the fit succeeded.

getSuggestedSuffix() - Method in class sc.fiji.snt.gui.ShollAnalysisDialog.ShollResults

Deprecated.

getSummaryStats(String) - Method in class sc.fiji.snt.analysis.TreeStatistics

Computes the SummaryStatistics for the specified measurement.

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

Gets all the data associated with this reconstruction in the SWC format.

getSWCcolor(int) - Static method in class sc.fiji.snt.Path

Gets the default SWC colors used by SNT.

getSWCFor(Collection<Path>) - Method in class sc.fiji.snt.PathAndFillManager

Gets the list of SWCPoints associated with a collection of Paths.

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

Gets the SWC type.

getSWCtypeName(int, boolean) - Static method in class sc.fiji.snt.Path

Gets the SWC type label associated with the specified type flag.

getSWCtypeNames() - Static method in class sc.fiji.snt.Path

Gets the list of string representations of non-redundant SWC types (i.e., excluding Path.SWC_FORK_POINT_LABEL, and Path.SWC_FORK_POINT_LABEL

getSWCtypes() - Static method in class sc.fiji.snt.Path

Gets the list of non-redundant SWC types (i.e., excluding the redundant types Path.SWC_FORK_POINT_LABEL, and Path.SWC_FORK_POINT_LABEL

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

Extracts the SWC-type flags present in this Tree.

getTabbedPaneIcon(IconFactory.GLYPH) - Static method in class sc.fiji.snt.gui.IconFactory

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

Gets the table currently being used by the Analyzer

getTable() - Method in class sc.fiji.snt.SNTService

Returns a reference to SNT's main table of measurements.

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

Retrieves the terminal branches of the analyzed Tree.

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

Gets the cable length of terminal branches

getThreads() - Method in class sc.fiji.snt.SNTPrefs

getThreadStatus() - Method in class sc.fiji.snt.ManualTracerThread

getThreadStatus() - Method in class sc.fiji.snt.SearchThread

getThreshold() - Method in class sc.fiji.snt.Fill

getThreshold() - Method in class sc.fiji.snt.FillerThread

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

Gets the position of all the tips in the analyzed tree.

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

Gets the plot display title.

getTree(String) - Method in class sc.fiji.snt.io.FlyCircuitLoader

Gets the collection of Paths for the specified cell ID

getTree(String, ColorRGB) - Method in class sc.fiji.snt.io.MouseLightLoader

Extracts a cell compartment as a collection of Paths.

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

Script-friendly method to extract a compartment as a collection of Paths.

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

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

getTree(String) - Method in class sc.fiji.snt.io.NeuroMorphoLoader

Gets the collection of Paths for the specified cell ID

getTree(String) - Method in interface sc.fiji.snt.io.RemoteSWCLoader

getTree(boolean) - Method in class sc.fiji.snt.SNTService

Gets the collection of paths listed in the Path Manager as a Tree object.

getTreeAsSceneryNode(Tree) - Method in class sc.fiji.snt.SciViewSNT

Gets the specified Tree as a Scenery Node.

getTreeModel(boolean) - Static method in class sc.fiji.snt.annotation.AllenUtils

Retrieves the Allen CCF hierarchical tree data.

getTreePath() - Method in class sc.fiji.snt.annotation.AllenCompartment

Gets the tree path of this compartment.

getTubenessImp() - Method in class sc.fiji.snt.gui.cmds.ComputeTubenessImg

getType() - Method in class sc.fiji.snt.event.SNTEvent

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

Gets the main UI.

getUI() - Method in class sc.fiji.snt.SNTService

Returns a reference to SNT's UI.

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

Gets the length unit of voxel spacing

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

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

getUnscaledPoint(int) - Method in class sc.fiji.snt.util.PointInImage

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

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

Gets whether the fitted 'flavor' of this Path is in use.

getValues(Path) - Method in class sc.fiji.snt.analysis.PathProfiler

Gets the profile for the specified path as a map of lists, with distances stored under PathProfiler.X_VALUES ("x-values") and intensities under PathProfiler.Y_VALUES ("y-values").

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

Returns the mesh vertices.

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

Returns the mesh vertices.

getVolume() - Method in class sc.fiji.snt.Fill

Returns the Fill volume.

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

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

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

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

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

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

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

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

Gets the plot profile as an PlotService plot.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

getZYXZ(ImagePlus, int) - Static method in class sc.fiji.snt.hyperpanes.MultiDThreePanes

GraphUtils - Class in sc.fiji.snt.analysis.graph

GuiUtils - Class in sc.fiji.snt.gui

Misc.

GuiUtils(Component) - Constructor for class sc.fiji.snt.gui.GuiUtils

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

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