Uses of Package
sc.fiji.snt.util

Packages that use sc.fiji.snt.util

Package	Description
sc.fiji.snt	SNT core classes
sc.fiji.snt.analysis	Analysis of Trees.
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.sholl	Sholl analysis of Images, pre-sampled data and Trees.
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.analysis.sholl.parsers	Parsers to retrieve Sholl profiles from multiple sources (2D/3D images, reconstructions, and tables)
sc.fiji.snt.annotation	Classes handling neuropil annotations and atlases metadata.
sc.fiji.snt.filter	Filters for detection of tube-like structures
sc.fiji.snt.gui	Customizations and commands for SNT's GUI.
sc.fiji.snt.hyperpanes	Classes implementing SNT's XY, ZY, and XZ canvases.
sc.fiji.snt.io	Classes for importing reconstructions into SNT.
sc.fiji.snt.seed
sc.fiji.snt.tracing.auto	Automatic neuron tracing algorithms that reconstruct complete neuronal morphologies from images without user interaction.
sc.fiji.snt.util	Miscellaneous SNT utilities, including classes defining reconstruction nodes.
sc.fiji.snt.viewer	Visualization of reconstructions
sc.fiji.snt.viewer.geditor	Classes implementing SNT's Graph Viewer

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

Class	Description
BoundingBox	A BoundingBox contains information (including spatial calibration) of a tracing canvas bounding box, i.e., the minimum bounding cuboid containing all nodes (SNTPoints) of a reconstructed structure.
PointInCanvas	Defines a Point in a tracing canvas in pixel coordinates.
PointInImage	Defines a Point in an image, a node of a traced Path.
SNTPoint	Classes extend this interface implement a point in a 3D space, always using real world coordinates.
SWCPoint	Defines a node in an SWC reconstruction.

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

Class	Description
BoundingBox	A BoundingBox contains information (including spatial calibration) of a tracing canvas bounding box, i.e., the minimum bounding cuboid containing all nodes (SNTPoints) of a reconstructed structure.
PointInImage	Defines a Point in an image, a node of a traced Path.
SNTPoint	Classes extend this interface implement a point in a 3D space, always using real world coordinates.
SWCPoint	Defines a node in an SWC reconstruction.

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

Class	Description
PointInImage	Defines a Point in an image, a node of a traced Path.

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

Class	Description
PointInImage	Defines a Point in an image, a node of a traced Path.

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

Class	Description
SWCPoint	Defines a node in an SWC reconstruction.

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

Class	Description
ShollPoint	Convenience flavor of PointInImage defining 2D/3D points for Sholl Analysis.

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

Class	Description
ShollPoint	Convenience flavor of PointInImage defining 2D/3D points for Sholl Analysis.

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

Class	Description
Logger	The Logger class provides functionality for logging messages with different levels such as info, debug, and warn.
ShollPoint	Convenience flavor of PointInImage defining 2D/3D points for Sholl Analysis.

Classes in sc.fiji.snt.util used by sc.fiji.snt.analysis.sholl.parsers

Class	Description
PointInImage	Defines a Point in an image, a node of a traced Path.
ShollPoint	Convenience flavor of PointInImage defining 2D/3D points for Sholl Analysis.

Classes in sc.fiji.snt.util used by sc.fiji.snt.annotation

Class	Description
SNTPoint	Classes extend this interface implement a point in a 3D space, always using real world coordinates.

Classes in sc.fiji.snt.util used by sc.fiji.snt.filter

Class	Description
PointInImage	Defines a Point in an image, a node of a traced Path.

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

Class	Description
PointInImage	Defines a Point in an image, a node of a traced Path.
SNTColor	A simple class for handling Colors including the ability to map an AWT Color to a SWC type integer tag.
SNTPoint	Classes extend this interface implement a point in a 3D space, always using real world coordinates.

Classes in sc.fiji.snt.util used by sc.fiji.snt.hyperpanes

Class	Description
BoundingBox	A BoundingBox contains information (including spatial calibration) of a tracing canvas bounding box, i.e., the minimum bounding cuboid containing all nodes (SNTPoints) of a reconstructed structure.
PointInCanvas	Defines a Point in a tracing canvas in pixel coordinates.

Classes in sc.fiji.snt.util used by sc.fiji.snt.io

Class	Description
SWCPoint	Defines a node in an SWC reconstruction.

Classes in sc.fiji.snt.util used by sc.fiji.snt.seed

Class	Description
PointInImage	Defines a Point in an image, a node of a traced Path.
SNTPoint	Classes extend this interface implement a point in a 3D space, always using real world coordinates.

Classes in sc.fiji.snt.util used by sc.fiji.snt.tracing.auto

Class	Description
Logger	The Logger class provides functionality for logging messages with different levels such as info, debug, and warn.
SWCPoint	Defines a node in an SWC reconstruction.

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

Class	Description
BoundingBox	A BoundingBox contains information (including spatial calibration) of a tracing canvas bounding box, i.e., the minimum bounding cuboid containing all nodes (SNTPoints) of a reconstructed structure.
CircleCursor3D	Iterate the pixels of an oriented circle in 3-space using Bresenham's algorithm, where the circle is constructed from the unit normal to the circle plane, the center point, and radius.
CrossoverFinder.Config	Immutable configuration with builder-like setters.
CrossoverFinder.CrossoverEvent	One detected crossover event.
ImgUtils.SliceResult	Result of a channel/time slice extraction from an ImgPlus.
PointInCanvas	Defines a Point in a tracing canvas in pixel coordinates.
PointInImage	Defines a Point in an image, a node of a traced Path.
ShollPoint	Convenience flavor of PointInImage defining 2D/3D points for Sholl Analysis.
SNTPoint	Classes extend this interface implement a point in a 3D space, always using real world coordinates.
SWCPoint	Defines a node in an SWC reconstruction.
TreeToRaster	Rasterizes a Tree into a 3D image using frustum (truncated-cone) geometry with partial-volume supersampling.
TreeUtils.EndpointClusterAnalysis	Result of analyzing which endpoint cluster (starts vs ends) is tighter.
TreeUtils.EndpointMatch	Result of finding the closest endpoints between two paths.

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

Class	Description
BoundingBox	A BoundingBox contains information (including spatial calibration) of a tracing canvas bounding box, i.e., the minimum bounding cuboid containing all nodes (SNTPoints) of a reconstructed structure.
SNTPoint	Classes extend this interface implement a point in a 3D space, always using real world coordinates.

Classes in sc.fiji.snt.util used by sc.fiji.snt.viewer.geditor

Class	Description
SWCPoint	Defines a node in an SWC reconstruction.