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

A

addEdge(Edge) - Method in class sc.fiji.analyzeSkeleton.Graph

Add edge to the graph.

addPoint(Point) - Method in class sc.fiji.analyzeSkeleton.Vertex

Add point to the vertex.

addVertex(Vertex) - Method in class sc.fiji.analyzeSkeleton.Graph

Add vertex to the graph.

AnalyzeSkeleton_ - Class in sc.fiji.analyzeSkeleton

Main class of the ImageJ/Fiji plugin for skeleton analysis.

AnalyzeSkeleton_() - Constructor for class sc.fiji.analyzeSkeleton.AnalyzeSkeleton_

assembleResults() - Method in class sc.fiji.analyzeSkeleton.AnalyzeSkeleton_

Returns the analysis results in a SkeletonResult object.

B

BACK - Static variable in class sc.fiji.analyzeSkeleton.Edge

"back" edge classification constant for Depth-first search (DFS)

C

calculateDistance(Point, Point) - Method in class sc.fiji.analyzeSkeleton.AnalyzeSkeleton_

Calculate Euclidean distance between two points in 3D.

calculateNumberOfVoxels() - Method in class sc.fiji.analyzeSkeleton.SkeletonResult

Calculates and saves the sum of voxels for every tree as the sum of end points, junction voxels and "normal" voxels.

calculateShortestPath - Static variable in class sc.fiji.analyzeSkeleton.AnalyzeSkeleton_

calculate largest shortest path option

centroid(Collection<Point>) - Static method in class sc.fiji.analyzeSkeleton.ita.PointUtils

Returns the center of the given points.

clone(Vertex, Vertex) - Method in class sc.fiji.analyzeSkeleton.Edge

Clones the Edge with all its properties

clone() - Method in class sc.fiji.analyzeSkeleton.Graph

clone() - Method in class sc.fiji.analyzeSkeleton.Point

cloneUnconnected() - Method in class sc.fiji.analyzeSkeleton.Vertex

Clones the Vertex disconnected from its Graph

D

dialogItemChanged(GenericDialog, AWTEvent) - Method in class sc.fiji.analyzeSkeleton.AnalyzeSkeleton_

Disables dialog components that are irrelevant to GUI-based analysis.

displaySkeletons - Static variable in class sc.fiji.analyzeSkeleton.AnalyzeSkeleton_

flag to output the labeled skeletons in a new image

E

Edge - Class in sc.fiji.analyzeSkeleton

This class represents the edge between two vertices in an undirected graph.

Edge(Vertex, Vertex, ArrayList<Point>, double) - Constructor for class sc.fiji.analyzeSkeleton.Edge

Create an edge of specific vertices and list of slab voxels.

Edge(Vertex, Vertex, ArrayList<Point>, double, double, double, double) - Constructor for class sc.fiji.analyzeSkeleton.Edge

Create an edge of specific vertices and list of slab voxels.

END_POINT - Static variable in class sc.fiji.analyzeSkeleton.AnalyzeSkeleton_

end point flag

equals(Object) - Method in class sc.fiji.analyzeSkeleton.Point

Override equals method to compare points.

F

findPointVertex(Vertex[], Point) - Method in class sc.fiji.analyzeSkeleton.AnalyzeSkeleton_

Find vertex in an array given a specific vertex point.

G

getAverageBranchLength() - Method in class sc.fiji.analyzeSkeleton.SkeletonResult

getAverageNeighborhoodValue(ImageStack, Point, int, int, int) - Static method in class sc.fiji.analyzeSkeleton.AnalyzeSkeleton_

Get average neighborhood pixel value of a given point.

getBranches() - Method in class sc.fiji.analyzeSkeleton.SkeletonResult

getBranches() - Method in class sc.fiji.analyzeSkeleton.Vertex

Get branch list.

getColor() - Method in class sc.fiji.analyzeSkeleton.Edge

getColor3rd() - Method in class sc.fiji.analyzeSkeleton.Edge

getEdges() - Method in class sc.fiji.analyzeSkeleton.Graph

Get list of edges in the graph.

getEndPoints() - Method in class sc.fiji.analyzeSkeleton.AnalyzeSkeleton_

Get the list of endpoints in the skeleton image.

getEndPoints() - Method in class sc.fiji.analyzeSkeleton.SkeletonResult

getEndPointsTree() - Method in class sc.fiji.analyzeSkeleton.AnalyzeSkeleton_

Get the list of endpoints in the skeleton image per tree.

getGraph() - Method in class sc.fiji.analyzeSkeleton.SkeletonResult

getGraphs() - Method in class sc.fiji.analyzeSkeleton.AnalyzeSkeleton_

Get the graphs of the current skeletons

getJunctions() - Method in class sc.fiji.analyzeSkeleton.SkeletonResult

getJunctionVoxels() - Method in class sc.fiji.analyzeSkeleton.SkeletonResult

getLabeledSkeletons() - Method in class sc.fiji.analyzeSkeleton.AnalyzeSkeleton_

Get the stack containing all the trees labeld with their corresponding skeleton id.

getLength() - Method in class sc.fiji.analyzeSkeleton.Edge

Get edge length

getLength_ra() - Method in class sc.fiji.analyzeSkeleton.Edge

Get edge length_ra (running average)

getListOfEndPoints() - Method in class sc.fiji.analyzeSkeleton.SkeletonResult

getListOfJunctionVoxels() - Method in class sc.fiji.analyzeSkeleton.SkeletonResult

getListOfSlabVoxels() - Method in class sc.fiji.analyzeSkeleton.SkeletonResult

getListOfStartingSlabVoxels() - Method in class sc.fiji.analyzeSkeleton.SkeletonResult

getMaximumBranchLength() - Method in class sc.fiji.analyzeSkeleton.SkeletonResult

getNeighborhood(ImageStack, Point, int, int, int) - Static method in class sc.fiji.analyzeSkeleton.AnalyzeSkeleton_

Get neighborhood of a pixel in a 3D image (0 border conditions).

getNJunctionAngles(Collection<Vertex>) - Static method in class sc.fiji.analyzeSkeleton.ita.VertexUtils

Calculates the angles between the branches of each vertex.

getNumberOfVoxels() - Method in class sc.fiji.analyzeSkeleton.SkeletonResult

getNumOfTrees() - Method in class sc.fiji.analyzeSkeleton.SkeletonResult

getOppositeVertex(Vertex) - Method in class sc.fiji.analyzeSkeleton.Edge

Get opposite vertex from a given one.

getPixel(ImageStack, int, int, int) - Static method in class sc.fiji.analyzeSkeleton.AnalyzeSkeleton_

Get pixel in 3D image (0 border conditions)

getPoints() - Method in class sc.fiji.analyzeSkeleton.Vertex

Get list of points.

getPredecessor() - Method in class sc.fiji.analyzeSkeleton.Vertex

Get predecessor edge.

getQuadruples() - Method in class sc.fiji.analyzeSkeleton.SkeletonResult

getResultImage(boolean) - Method in class sc.fiji.analyzeSkeleton.AnalyzeSkeleton_

Returns one of the two result images in an ImageStack object.

getRoot() - Method in class sc.fiji.analyzeSkeleton.Graph

Get root vertex.

getShortestPathList() - Method in class sc.fiji.analyzeSkeleton.SkeletonResult

getShortestPathPoints() - Method in class sc.fiji.analyzeSkeleton.AnalyzeSkeleton_

Get the list of points (including junctions and end points) of the largest shortest paths in the skeleton image (one per tree).

getSlabs() - Method in class sc.fiji.analyzeSkeleton.Edge

Get list of slab voxels belonging to the edge.

getSlabs() - Method in class sc.fiji.analyzeSkeleton.SkeletonResult

getSpStartPosition() - Method in class sc.fiji.analyzeSkeleton.SkeletonResult

getTriples() - Method in class sc.fiji.analyzeSkeleton.SkeletonResult

getType() - Method in class sc.fiji.analyzeSkeleton.Edge

Get DFS edge type

getV1() - Method in class sc.fiji.analyzeSkeleton.Edge

Get first vertex.

getV2() - Method in class sc.fiji.analyzeSkeleton.Edge

Get second vertex.

getVertices() - Method in class sc.fiji.analyzeSkeleton.Graph

Get list of vertices in the graph.

getVisitOrder() - Method in class sc.fiji.analyzeSkeleton.Vertex

Get DFS visit order.

Graph - Class in sc.fiji.analyzeSkeleton

This class represents an undirected graph to allow visiting the skeleton in an efficient way

Graph() - Constructor for class sc.fiji.analyzeSkeleton.Graph

Empty constructor.

GraphPruning - Class in sc.fiji.analyzeSkeleton.ita

Utility functions for pruning certain kinds of edges (and nodes) from a Graph.

groupByValence(Collection<Vertex>, int, int) - Static method in class sc.fiji.analyzeSkeleton.ita.VertexUtils

Groups vertices by their valence, i.e.

I

isVertexPoint(Point) - Method in class sc.fiji.analyzeSkeleton.Vertex

Check if a point belongs to the vertex list of points.

isVisited() - Method in class sc.fiji.analyzeSkeleton.Vertex

Check visit status.

J

JUNCTION - Static variable in class sc.fiji.analyzeSkeleton.AnalyzeSkeleton_

junction flag

L

LOWEST_INTENSITY_BRANCH - Static variable in class sc.fiji.analyzeSkeleton.AnalyzeSkeleton_

lowest intensity branch pruning mode index

LOWEST_INTENSITY_VOXEL - Static variable in class sc.fiji.analyzeSkeleton.AnalyzeSkeleton_

lowest pixel intensity pruning mode index

N

NONE - Static variable in class sc.fiji.analyzeSkeleton.AnalyzeSkeleton_

no pruning mode index

P

Point - Class in sc.fiji.analyzeSkeleton

This class represents a 3D point or position on a 3D image.

Point(int, int, int) - Constructor for class sc.fiji.analyzeSkeleton.Point

Create point from integer coordinates.

pointsToString() - Method in class sc.fiji.analyzeSkeleton.Vertex

Convert list of points to String.

PointUtils - Class in sc.fiji.analyzeSkeleton.ita

Utility methods for the classes of the ita package.

processSkeleton(ImageStack) - Method in class sc.fiji.analyzeSkeleton.AnalyzeSkeleton_

Process skeleton: tag image, mark trees and visit.

protectRoi - Static variable in class sc.fiji.analyzeSkeleton.AnalyzeSkeleton_

protective-ROI option (branches inside ROI are spared from pruning)

pruneCyclesModes - Static variable in class sc.fiji.analyzeSkeleton.AnalyzeSkeleton_

prune cycle options

pruneEnds - Static variable in class sc.fiji.analyzeSkeleton.AnalyzeSkeleton_

dead-end pruning option

pruneIndex - Static variable in class sc.fiji.analyzeSkeleton.AnalyzeSkeleton_

prune cycle options index

pruneShortEdges(Graph, double, boolean, boolean) - Static method in class sc.fiji.analyzeSkeleton.ita.GraphPruning

Creates a copy of the graph, where short edges have been removed.

pruneShortEdges(Graph, double, boolean, boolean, double[]) - Static method in class sc.fiji.analyzeSkeleton.ita.GraphPruning

Creates a copy of the graph, where short edges have been removed.

R

removeLoops(Graph) - Static method in class sc.fiji.analyzeSkeleton.ita.GraphPruning

Removes all loop edges from the graph.

removeParallelEdges(Graph) - Static method in class sc.fiji.analyzeSkeleton.ita.GraphPruning

Removes parallel edges from the graph, leaving at most one connection between each vertex pair.

run(ImageProcessor) - Method in class sc.fiji.analyzeSkeleton.AnalyzeSkeleton_

Process the image: tag skeleton and show results.

run(int, boolean, boolean, ImagePlus, boolean, boolean) - Method in class sc.fiji.analyzeSkeleton.AnalyzeSkeleton_

This method is intended for non-interactively using this plugin.

run(int, boolean, boolean, ImagePlus, boolean, boolean, Roi) - Method in class sc.fiji.analyzeSkeleton.AnalyzeSkeleton_

This method is intended for non-interactively using this plugin.

run(int, double, boolean, ImagePlus, boolean, boolean) - Method in class sc.fiji.analyzeSkeleton.AnalyzeSkeleton_

This method is intended for non-interactively using this plugin.

run() - Method in class sc.fiji.analyzeSkeleton.AnalyzeSkeleton_

A simpler standalone running method, for analysis without pruning or showing images.

S

sc.fiji.analyzeSkeleton - package sc.fiji.analyzeSkeleton

sc.fiji.analyzeSkeleton.ita - package sc.fiji.analyzeSkeleton.ita

setAverageBranchLength(double[]) - Method in class sc.fiji.analyzeSkeleton.SkeletonResult

setBranch(Edge) - Method in class sc.fiji.analyzeSkeleton.Vertex

Add a new branch to the vertex.

setBranches(int[]) - Method in class sc.fiji.analyzeSkeleton.SkeletonResult

setColor(double) - Method in class sc.fiji.analyzeSkeleton.Edge

setColor3rd(double) - Method in class sc.fiji.analyzeSkeleton.Edge

setEndPoints(int[]) - Method in class sc.fiji.analyzeSkeleton.SkeletonResult

setGraph(Graph[]) - Method in class sc.fiji.analyzeSkeleton.SkeletonResult

setJunctions(int[]) - Method in class sc.fiji.analyzeSkeleton.SkeletonResult

setJunctionVoxels(int[]) - Method in class sc.fiji.analyzeSkeleton.SkeletonResult

setLength(double) - Method in class sc.fiji.analyzeSkeleton.Edge

Set edge length

setListOfEndPoints(ArrayList<Point>) - Method in class sc.fiji.analyzeSkeleton.SkeletonResult

setListOfJunctionVoxels(ArrayList<Point>) - Method in class sc.fiji.analyzeSkeleton.SkeletonResult

setListOfSlabVoxels(ArrayList<Point>) - Method in class sc.fiji.analyzeSkeleton.SkeletonResult

setListOfStartingSlabVoxels(ArrayList<Point>) - Method in class sc.fiji.analyzeSkeleton.SkeletonResult

setMaximumBranchLength(double[]) - Method in class sc.fiji.analyzeSkeleton.SkeletonResult

setNumberOfVoxels(int[]) - Method in class sc.fiji.analyzeSkeleton.SkeletonResult

setNumOfTrees(int) - Method in class sc.fiji.analyzeSkeleton.SkeletonResult

setPredecessor(Edge) - Method in class sc.fiji.analyzeSkeleton.Vertex

Set predecessor (for DFS).

setQuadruples(int[]) - Method in class sc.fiji.analyzeSkeleton.SkeletonResult

setShortestPathList(ArrayList<Double>) - Method in class sc.fiji.analyzeSkeleton.SkeletonResult

setSlabs(int[]) - Method in class sc.fiji.analyzeSkeleton.SkeletonResult

setSpStartPosition(double[][]) - Method in class sc.fiji.analyzeSkeleton.SkeletonResult

setTriples(int[]) - Method in class sc.fiji.analyzeSkeleton.SkeletonResult

setType(int) - Method in class sc.fiji.analyzeSkeleton.Edge

Set DFS type (BACK or TREE)

setup(String, ImagePlus) - Method in class sc.fiji.analyzeSkeleton.AnalyzeSkeleton_

This method is called once when the filter is loaded.

setVisited(boolean) - Method in class sc.fiji.analyzeSkeleton.Vertex

Set vertex as visited or not.

setVisited(boolean, int) - Method in class sc.fiji.analyzeSkeleton.Vertex

Set vertex as visited or not.

SHORTEST_BRANCH - Static variable in class sc.fiji.analyzeSkeleton.AnalyzeSkeleton_

shortest branch pruning mode index

SHORTEST_PATH - Static variable in class sc.fiji.analyzeSkeleton.AnalyzeSkeleton_

shortest path flag

silent - Variable in class sc.fiji.analyzeSkeleton.AnalyzeSkeleton_

silent run flag, to distinguish between GUI and plugin calls

SkeletonResult - Class in sc.fiji.analyzeSkeleton

Utility class to transfer the analysis results between different plugins.

SkeletonResult(int) - Constructor for class sc.fiji.analyzeSkeleton.SkeletonResult

SLAB - Static variable in class sc.fiji.analyzeSkeleton.AnalyzeSkeleton_

slab flag

T

toString() - Method in class sc.fiji.analyzeSkeleton.Point

Convert point to string.

TREE - Static variable in class sc.fiji.analyzeSkeleton.Edge

"tree" edge classification constant for Depth-first search (DFS)

U

UNDEFINED - Static variable in class sc.fiji.analyzeSkeleton.Edge

not yet defined edge classification constant for Depth-first search (DFS)

V

verbose - Static variable in class sc.fiji.analyzeSkeleton.AnalyzeSkeleton_

boolean flag to display extra information in result tables

Vertex - Class in sc.fiji.analyzeSkeleton

This class represents a vertex or node in a graph.

Vertex() - Constructor for class sc.fiji.analyzeSkeleton.Vertex

Create empty vertex.

VertexUtils - Class in sc.fiji.analyzeSkeleton.ita

Utility methods for analysing the junctions of a Graph.

X

x - Variable in class sc.fiji.analyzeSkeleton.Point

x- coordinate

Y

y - Variable in class sc.fiji.analyzeSkeleton.Point

y- coordinate

Z

z - Variable in class sc.fiji.analyzeSkeleton.Point

z- coordinate

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