Package sc.fiji.snt.analysis

package sc.fiji.snt.analysis

Analysis of Trees.

Author:

Tiago Ferreira

Related Packages

Package	Description
sc.fiji.snt	SNT core classes
sc.fiji.snt.analysis.curation	Classes for curation of reconstructions, as implemented by the "Curation Assistant".
sc.fiji.snt.analysis.detection	Feature detectors for traced paths.
sc.fiji.snt.analysis.graph	Classes for handling neuronal reconstructions as graphs
sc.fiji.snt.analysis.growth	Classes for growth analysis of neurites across time
sc.fiji.snt.analysis.sholl	Sholl analysis of Images, pre-sampled data and Trees.

Class	Description
AbstractConvexHull	Parent class for convex hull analysis
AnalysisUtils	Static utilities for sc.fiji.analysis.
AnnotationMapper	A specialized ColorMapper for applying color-coded mappings to 3D annotations.
CircularModels	Shared utilities for circular modeling, including von Mises fits.
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.
GroupedTreeStatistics	Computes statistics from Tree groups.
MultiSpectralRefiner	Post-hoc refinement of traced paths in multispectral (e.g., Brainbow) images.
MultiSpectralRefiner.Parameters	Immutable parameter set for multispectral refinement.
MultiTreeColorMapper	Class for color coding groups of Trees.
MultiTreeStatistics	Computes summary and descriptive statistics from univariate properties of Tree groups.
NodeColorMapper	Class for color coding of NodeStatistics results.
NodeProfiler	Command to retrieve node profiles (plots of voxel intensities sampled across Path nodes).
NodeStatistics<T extends PointInImage>	Computes summary and descriptive statistics from a Collection of nodes, including convenience methods to plot distributions of such data.
PathProfiler	Command to retrieve Path profiles (plots of voxel intensities values along a Path)
PathStatistics	A specialized version of TreeStatistics for analyzing individual paths without considering their connectivity relationships.
PathStraightener	Command to "straighten" an image using Path coordinates.
PCAnalyzer	Utility class for performing Principal Component Analysis (PCA) on various SNT data structures including Trees, Paths, and collections of SNTPoints.
PCAnalyzer.PrincipalAxis	Represents a principal axis containing the direction vector and associated variance (eigenvalue) from Principal Component Analysis.
PeripathDetector	Deprecated. Use PeripathDetector instead.
PeripathDetector.Config	Deprecated. Use PeripathDetector.Config instead.
PeripathDetector.Detection	Deprecated. Use Detection instead.
PersistenceAnalyzer	Performs persistent homology analysis on neuronal Trees.
ProfileProcessor<T extends net.imglib2.type.numeric.RealType<T>>	Profile intensities within local neighborhoods around Path PointInImages
ProfileProcessor.Metric
ProfileProcessor.Shape
RoiConverter	Converts SNT Paths into (IJ1) ROIs.
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.
TreeAnalyzer	Deprecated. Use TreeStatistics instead
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.