Uses of Record Class
sc.fiji.snt.tracing.auto.SomaUtils.SomaResult

Packages that use SomaUtils.SomaResult

Package	Description
sc.fiji.snt.tracing.auto	Automatic neuron tracing algorithms that reconstruct complete neuronal morphologies from images without user interaction.

Uses of SomaUtils.SomaResult in sc.fiji.snt.tracing.auto

Methods in sc.fiji.snt.tracing.auto that return SomaUtils.SomaResult

Modifier and Type	Method	Description
static SomaUtils.SomaResult	SomaUtils.detectSoma(net.imagej.ImgPlus<?> source)	Full soma detection using ImgPlus with automatic thresholding.
static SomaUtils.SomaResult	SomaUtils.detectSoma(net.imagej.ImgPlus<?> source, double threshold, int zSlice)	Full soma detection using ImgPlus with spacing extracted automatically.
static SomaUtils.SomaResult	SomaUtils.detectSoma(net.imglib2.RandomAccessibleInterval<? extends net.imglib2.type.numeric.RealType<?>> source, double threshold, double[] spacing)	Full soma detection: finds center, floods region, extracts contour.
static SomaUtils.SomaResult	SomaUtils.detectSomaAt(net.imagej.ImgPlus<?> source, long seedX, long seedY, double threshold, int zSlice)	Detects soma at a specific seed point using ImgPlus.
static SomaUtils.SomaResult	SomaUtils.detectSomaAt(net.imglib2.RandomAccessibleInterval<? extends net.imglib2.type.numeric.RealType<?>> source, long seedX, long seedY, double threshold)	Detects soma at a specific seed point.

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

Modifier and Type	Method	Description
static List<SomaUtils.SomaResult>	SomaUtils.detectAllSomas(net.imagej.ImgPlus<?> source)	Detects all somas using ImgPlus with default settings.
static List<SomaUtils.SomaResult>	SomaUtils.detectAllSomas(net.imagej.ImgPlus<?> source, double threshold, int zSlice, double minRadius)	Detects all somas using ImgPlus with automatic spacing.
static List<SomaUtils.SomaResult>	SomaUtils.detectAllSomas(net.imagej.ImgPlus<?> source, double threshold, int zSlice, double minRadius, double minSomaDistance)	Detects all somas using ImgPlus with automatic spacing and NMS.
static List<SomaUtils.SomaResult>	SomaUtils.detectAllSomas(net.imglib2.RandomAccessibleInterval<? extends net.imglib2.type.numeric.RealType<?>> source, double threshold)	Detects all somas using default minimum radius.
static List<SomaUtils.SomaResult>	SomaUtils.detectAllSomas(net.imglib2.RandomAccessibleInterval<? extends net.imglib2.type.numeric.RealType<?>> source, double threshold, double minRadius)	Detects all somas using EDT local maxima approach.
static List<SomaUtils.SomaResult>	SomaUtils.detectAllSomas(net.imglib2.RandomAccessibleInterval<? extends net.imglib2.type.numeric.RealType<?>> source, double threshold, double minRadius, double minSomaDistance)	Detects all somas in a 2D image using EDT + local maxima + NMS.
static List<SomaUtils.SomaResult>	SomaUtils.detectSomasAt(ij.ImagePlus imp, Collection<ij.gui.Roi> rois)	Detects somas at the centroids of the given ROIs.
static List<SomaUtils.SomaResult>	SomaUtils.detectSomasAt(net.imagej.ImgPlus<?> source, List<long[]> seeds)	Detects somas at the given seed coordinates using an ImgPlus.
static List<SomaUtils.SomaResult>	SomaUtils.detectSomasAt(net.imglib2.RandomAccessibleInterval<? extends net.imglib2.type.numeric.RealType<?>> source, List<long[]> seeds)	Detects somas at the given seed coordinates.
static <T extends net.imglib2.type.numeric.RealType<T>> List<SomaUtils.SomaResult>	SomaUtils.filterSomasByIntensity(List<SomaUtils.SomaResult> somas, net.imglib2.RandomAccessibleInterval<T> source)	Filters a list of detected somas by sampling the source image intensity at each soma center and applying Otsu's threshold to separate real (bright) somas from false detections (dim).
static <T extends net.imglib2.type.numeric.RealType<T>> List<SomaUtils.SomaResult>	SomaUtils.filterSomasByThickness(List<SomaUtils.SomaResult> somas, net.imglib2.RandomAccessibleInterval<T> source)	Filters a list of detected somas by their local EDT thickness, using Otsu's method on the EDT value distribution to separate thick (real soma) from thin (artifact) detections.
static <T extends net.imglib2.type.numeric.RealType<T>> List<SomaUtils.SomaResult>	SomaUtils.selectTopSomasByThickness(List<SomaUtils.SomaResult> somas, net.imglib2.RandomAccessibleInterval<T> source, int n)	Selects the top-N somas by EDT thickness (distance to nearest background pixel at each soma's center), ranking by descending EDT value.

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

Modifier and Type	Method	Description
static double	SomaUtils.estimateMinSomaDistance(List<SomaUtils.SomaResult> somas)	Estimates the minimum inter-soma distance from a list of detected somas using single-linkage hierarchical clustering with gap analysis.
static <T extends net.imglib2.type.numeric.RealType<T>> double	SomaUtils.estimateMinSomaDistance(List<SomaUtils.SomaResult> somas, net.imglib2.RandomAccessibleInterval<T> source)	Estimates the minimum inter-soma distance using a hybrid approach: EDT-thickness filtering followed by spatial gap analysis.
static <T extends net.imglib2.type.numeric.RealType<T>> List<SomaUtils.SomaResult>	SomaUtils.filterSomasByIntensity(List<SomaUtils.SomaResult> somas, net.imglib2.RandomAccessibleInterval<T> source)	Filters a list of detected somas by sampling the source image intensity at each soma center and applying Otsu's threshold to separate real (bright) somas from false detections (dim).
static <T extends net.imglib2.type.numeric.RealType<T>> List<SomaUtils.SomaResult>	SomaUtils.filterSomasByThickness(List<SomaUtils.SomaResult> somas, net.imglib2.RandomAccessibleInterval<T> source)	Filters a list of detected somas by their local EDT thickness, using Otsu's method on the EDT value distribution to separate thick (real soma) from thin (artifact) detections.
static <T extends net.imglib2.type.numeric.RealType<T>> List<SomaUtils.SomaResult>	SomaUtils.selectTopSomasByThickness(List<SomaUtils.SomaResult> somas, net.imglib2.RandomAccessibleInterval<T> source, int n)	Selects the top-N somas by EDT thickness (distance to nearest background pixel at each soma's center), ranking by descending EDT value.
List<Tree>	AbstractGWDTTracer.traceMultiSoma(List<SomaUtils.SomaResult> somas)	Traces multiple somas in a single image using a NeuTube-style recovery pass strategy.