Uses of Class
sc.fiji.snt.seed.SeedPoint

Packages that use SeedPoint

Package	Description
sc.fiji.snt	SNT core classes
sc.fiji.snt.seed	Classes for Seed Tracing.
sc.fiji.snt.tracing.auto	Automatic neuron tracing algorithms that reconstruct complete neuronal morphologies from images without user interaction.

Uses of SeedPoint in sc.fiji.snt

Methods in sc.fiji.snt with parameters of type SeedPoint

Modifier and Type	Method	Description
static Color	SeedOverlayRenderer.colorForSeed(net.imglib2.display.ColorTable table, Color unknownConfidenceColor, SeedOverlay.ColorMode mode, SeedPoint s, double low, double high, double depthFalloff, Map<SeedPoint,Integer> seedIndexMap, Map<String,Integer> categoryOrdinals)	Dispatches to the per-mode color computation.

Method parameters in sc.fiji.snt with type arguments of type SeedPoint

Modifier and Type	Method	Description
static Color	SeedOverlayRenderer.colorForSeed(net.imglib2.display.ColorTable table, Color unknownConfidenceColor, SeedOverlay.ColorMode mode, SeedPoint s, double low, double high, double depthFalloff, Map<SeedPoint,Integer> seedIndexMap, Map<String,Integer> categoryOrdinals)	Dispatches to the per-mode color computation.

Uses of SeedPoint in sc.fiji.snt.seed

Methods in sc.fiji.snt.seed that return SeedPoint

Modifier and Type	Method	Description
SeedPoint	SeedOverlay.get(int index)
SeedPoint	SeedOverlay.nearest(double x, double y, double z, double maxDistance)	Returns the seed closest to (x, y, z) in physical units, or null if the overlay is empty or no seed lies within maxDistance.
SeedPoint	SeedOverlay.removeAt(int index)	Removes the seed at the given (data-list) index.

Methods in sc.fiji.snt.seed that return types with arguments of type SeedPoint

Modifier and Type	Method	Description
static List<SeedPoint>	LabelsToSeeds.compute(ij.ImagePlus imp, double minConfidence, String type, String source)	Computes one SeedPoint per non-zero label in imp.
List<SeedPoint>	SeedOverlay.filtered()	Returns a new list of seeds whose confidence falls in [lowConfidence, highConfidence].
Set<SeedPoint>	SeedOverlay.getSelectedSeeds()
List<SeedPoint>	SeedOverlay.list()	Returns a defensive snapshot of all held seeds (a fresh ArrayList, safe to iterate while the overlay continues to mutate on another thread).
List<SeedPoint>	SeedOverlay.CsvImportResult.seeds()	Returns the value of the seeds record component.
List<SeedPoint>	SeedOverlay.topKByConfidence(int k)	Returns up to k seeds from the visible range ([lowConfidence, highConfidence]) with the highest confidence.
static List<SeedPoint>	SeedRois.toSeeds(ij.gui.Roi[] rois, ij.ImagePlus imp, double confidence, String type, String source)	Converts the given ROIs to seeds.
static List<SeedPoint>	SeedRois.toSeeds(ij.gui.Roi[] rois, ij.ImagePlus imp, double confidence, String type, String source, double[] offset)	As SeedRois.toSeeds(Roi[], ImagePlus, double, String, String), additionally correcting for SNT#getWorldOriginOffset(): world = pixel * spacing + offset.

Methods in sc.fiji.snt.seed with parameters of type SeedPoint

Modifier and Type	Method	Description
void	SeedOverlay.add(SeedPoint seed)	Adds a single seed.
double	SeedPoint.distanceSquaredTo(SeedPoint other)	Squared 3D Euclidean distance to another seed (physical units).
int	SeedOverlay.indexOf(SeedPoint seed)	Returns the index of seed in the data list, or -1 if absent.
boolean	SeedOverlay.isSelected(SeedPoint seed)
boolean	SeedOverlay.remove(SeedPoint seed)	Removes a single seed by reference equality.
boolean	SeedOverlay.replaceAt(int index, SeedPoint replacement)	Replaces the seed at the given index.

Method parameters in sc.fiji.snt.seed with type arguments of type SeedPoint

Modifier and Type	Method	Description
void	SeedOverlay.addAll(Collection<? extends SeedPoint> batch)	Bulk-adds seeds.
int	SeedOverlay.removeAll(Collection<? extends SeedPoint> batch)	Bulk-removes seeds by reference equality.
void	SeedOverlay.replaceAll(Collection<? extends SeedPoint> replacement)	Replaces the current contents with the given seeds.
int	SeedOverlay.replaceAllAt(Map<Integer,SeedPoint> replacements)	Bulk-replaces seeds at multiple positions, firing listeners and invalidating the spatial index once at the end.
int	SeedOverlay.scaleConfidence(Collection<SeedPoint> seeds, double factor)	Multiplies the confidence of seeds by factor, clamping each result to [0, 1].
int	SeedOverlay.scaleRadius(Collection<SeedPoint> seeds, double factor)	Multiplies the physical radius of seeds by factor, clamping each result to >= 0 (radius has no upper bound, unlike confidence).
void	SeedOverlay.setSelectedSeeds(Collection<? extends SeedPoint> selection)	Replaces the selection set.
static List<ij.gui.Roi>	SeedRois.toRois(Collection<SeedPoint> seeds, ij.ImagePlus imp)	Converts the given seeds to ROIs.
static List<ij.gui.Roi>	SeedRois.toRois(Collection<SeedPoint> seeds, ij.ImagePlus imp, double[] offset)	As SeedRois.toRois(Collection, ImagePlus), additionally correcting for SNT#getWorldOriginOffset(): pixel = (world - offset) / spacing.

Constructor parameters in sc.fiji.snt.seed with type arguments of type SeedPoint

Modifier	Constructor	Description
	CsvImportResult(List<SeedPoint> seeds, int skipped)	Creates an instance of a CsvImportResult record class.

Uses of SeedPoint in sc.fiji.snt.tracing.auto

Methods in sc.fiji.snt.tracing.auto that return types with arguments of type SeedPoint

Modifier and Type	Method	Description
List<SeedPoint>	RootDetector.detect(Collection<Tree> trees)	Detects root-convergence candidates pooled across every Tree in trees - deliberately not per-tree, since the whole point is catching fragments that live in structurally unrelated Trees (or unconnected primary paths within one).
List<SeedPoint>	TuftDetector.detect(Tree tree, List<TuftDetector.Type> types)	Detects tufts across several node populations in tree in a single pooled pass: candidates from every requested TuftDetector.Type are merged into one KDTree/scoring/suppression run, so a tuft that happens to show up in more than one (e.g. a fork sitting right next to a tip) is still reported once, rather than once per type.
List<SeedPoint>	TuftDetector.detect(Tree tree, TuftDetector.Type type)	Detects tufts of the given type in tree.

Method parameters in sc.fiji.snt.tracing.auto with type arguments of type SeedPoint

Modifier and Type	Method	Description
void	AbstractGWDTTracer.setRoots(Collection<SeedPoint> seeds)	Sets the run's root from a collection of seeds.
default void	AutoTracer.setRoots(Collection<SeedPoint> seeds)	Hands the tracer a collection of seeds to use as roots in this run.
void	BinaryTracer.setRoots(Collection<SeedPoint> seeds)	Sets the run's root from a collection of seeds. v1 takes the first seed and bridges to the existing BinaryTracer.setRootRoi(Roi, int) API by synthesizing an oval ROI around the seed (diameter derived from radius, with a minimum of one voxel when radius is unset) and using AutoTracer.ROI_CENTROID placement.
void	AbstractGWDTTracer.setTips(Collection<SeedPoint> seeds)	Configures the run's tips.
default void	AutoTracer.setTips(Collection<SeedPoint> seeds)	Hands the tracer a collection of seeds to use as tips / targets in this run.
void	AbstractGWDTTracer.setWaypoints(Collection<SeedPoint> seeds)	Configures the run's waypoints.
default void	AutoTracer.setWaypoints(Collection<SeedPoint> seeds)	Hands the tracer a collection of seeds to use as waypoints (path constraints) in this run.