Package sc.fiji.snt.analysis
package sc.fiji.snt.analysis
Analysis of
Trees.- Author:
- Tiago Ferreira
-
ClassDescriptionParent class for convex hull analysisStatic utilities for sc.fiji.analysis.A specialized
ColorMapperfor applying color-coded mappings to 3D annotations.Shared utilities for circular modeling, including von Mises fits.Domain of the angle data.Immutable summary of a von Mises fit on circular (directional) or axial (orientation) data.Parent class for ColorMappers.Computes the convex hull of a set of 2D points.Convex hull analysis in 3D.Class for Convex Hull measurements of aTree.Computes statistics fromTreegroups.Post-hoc refinement of traced paths in multispectral (e.g., Brainbow) images.Immutable parameter set for multispectral refinement.Class for color coding groups ofTrees.Computes summary and descriptive statistics from univariate properties ofTreegroups.Class for color coding ofNodeStatisticsresults.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.Command to retrieve Path profiles (plots of voxel intensities values along a Path)A specialized version ofTreeStatisticsfor analyzing individual paths without considering their connectivity relationships.Command to "straighten" an image using Path coordinates.Utility class for performing Principal Component Analysis (PCA) on various SNT data structures including Trees, Paths, and collections of SNTPoints.Represents a principal axis containing the direction vector and associated variance (eigenvalue) from Principal Component Analysis.Deprecated.Deprecated.UsePeripathDetector.Configinstead.Deprecated.UseDetectioninstead.Performs persistent homology analysis on neuronalTrees.ProfileProcessor<T extends net.imglib2.type.numeric.RealType<T>>Profile intensities within local neighborhoods aroundPathPointInImagesConverts SNTPaths into (IJ1) ROIs.Class to perform Root angle analysis on aTreeaccording to Bird and Cuntz 2019, PMID 31167149.Class to retrieve Sholl metrics from aTree.Extension ofChartPanelmodified for scientific publications and convenience methods for plot annotations.Extension ofDefaultGenericTablewith (minor) scripting conveniences.Class to perform Horton-Strahler analysis on aTree.Deprecated.UseTreeStatisticsinsteadClass for color codingTrees.Computes summary and descriptive statistics from properties of Paths and Nodes in aTree, including convenience methods to plot distributions of such data.Exception thrown when a requested metric is not available or recognized.
PeripathDetectorinstead.