Uses of Package
sc.fiji.snt.analysis

Packages that use sc.fiji.snt.analysis

Package	Description
sc.fiji.snt	SNT core classes
sc.fiji.snt.analysis	Analysis of Trees.
sc.fiji.snt.analysis.graph	Classes for handling neuronal reconstructions as graphs
sc.fiji.snt.analysis.sholl.gui	GUI customizations (image overlays, plots, etc.) required for Sholl Analysis.
sc.fiji.snt.analysis.sholl.math	Statistical analysis of Sholl data
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.plugin	SNT add-ons as IJ2 commands
sc.fiji.snt.viewer	Visualization of reconstructions

Classes in sc.fiji.snt.analysis used by sc.fiji.snt

Class	Description
AbstractConvexHull	Parent class for convex hull analysis
SNTTable	Extension of DefaultGenericTable with (minor) scripting conveniences.
TreeStatistics	Computes summary and descriptive statistics from properties of Paths and Nodes in a Tree, including convenience methods to plot distributions of such data.

Classes in sc.fiji.snt.analysis used by sc.fiji.snt.analysis

Class	Description
AbstractConvexHull	Parent class for convex hull analysis
CircularModels.Domain	Domain of the angle data.
CircularModels.VonMisesFit	Immutable summary of a von Mises fit on circular (directional) or axial (orientation) data.
ColorMapper	Parent class for ColorMappers.
ConvexHull2D	Computes the convex hull of a set of 2D points.
ConvexHull3D	Convex hull analysis in 3D.
ConvexHullAnalyzer	Class for Convex Hull measurements of a Tree.
MultiSpectralRefiner	Post-hoc refinement of traced paths in multispectral (e.g., Brainbow) images.
MultiSpectralRefiner.Parameters	Immutable parameter set for multispectral refinement.
MultiTreeStatistics	Computes summary and descriptive statistics from univariate properties of Tree groups.
NodeStatistics	Computes summary and descriptive statistics from a Collection of nodes, including convenience methods to plot distributions of such data.
PCAnalyzer.PrincipalAxis	Represents a principal axis containing the direction vector and associated variance (eigenvalue) from Principal Component Analysis.
ProfileProcessor.Metric
ProfileProcessor.Shape
RootAngleAnalyzer	Class to perform Root angle analysis on a Tree according to Bird and Cuntz 2019, PMID 31167149.
ShollAnalyzer	Class to retrieve Sholl metrics from a Tree.
SNTChart	Extension of ChartPanel modified for scientific publications and convenience methods for plot annotations.
SNTTable	Extension of DefaultGenericTable with (minor) scripting conveniences.
StrahlerAnalyzer	Class to perform Horton-Strahler analysis on a Tree.
TreeColorMapper	Class for color coding Trees.
TreeStatistics	Computes summary and descriptive statistics from properties of Paths and Nodes in a Tree, including convenience methods to plot distributions of such data.
UnknownMetricException	Exception thrown when a requested metric is not available or recognized.

Classes in sc.fiji.snt.analysis used by sc.fiji.snt.analysis.graph

Class	Description
ColorMapper	Parent class for ColorMappers.
NodeStatistics	Computes summary and descriptive statistics from a Collection of nodes, including convenience methods to plot distributions of such data.

Classes in sc.fiji.snt.analysis used by sc.fiji.snt.analysis.sholl.gui

Class	Description
SNTTable	Extension of DefaultGenericTable with (minor) scripting conveniences.

Classes in sc.fiji.snt.analysis used by sc.fiji.snt.analysis.sholl.math

Class	Description
CircularModels.VonMisesFit	Immutable summary of a von Mises fit on circular (directional) or axial (orientation) data.
SNTChart	Extension of ChartPanel modified for scientific publications and convenience methods for plot annotations.
SNTTable	Extension of DefaultGenericTable with (minor) scripting conveniences.

Classes in sc.fiji.snt.analysis used by sc.fiji.snt.gui

Class	Description
SNTTable	Extension of DefaultGenericTable with (minor) scripting conveniences.

Classes in sc.fiji.snt.analysis used by sc.fiji.snt.gui.cmds

Class	Description
MultiSpectralRefiner.Parameters	Immutable parameter set for multispectral refinement.

Classes in sc.fiji.snt.analysis used by sc.fiji.snt.plugin

Class	Description
SNTChart	Extension of ChartPanel modified for scientific publications and convenience methods for plot annotations.
SNTTable	Extension of DefaultGenericTable with (minor) scripting conveniences.
TreeStatistics	Computes summary and descriptive statistics from properties of Paths and Nodes in a Tree, including convenience methods to plot distributions of such data.

Classes in sc.fiji.snt.analysis used by sc.fiji.snt.viewer

Class	Description
AbstractConvexHull	Parent class for convex hull analysis
ColorMapper	Parent class for ColorMappers.
PCAnalyzer.PrincipalAxis	Represents a principal axis containing the direction vector and associated variance (eigenvalue) from Principal Component Analysis.
SNTChart	Extension of ChartPanel modified for scientific publications and convenience methods for plot annotations.
TreeColorMapper	Class for color coding Trees.