Package sc.fiji.snt.tracing.auto

Class SomaUtils

java.lang.Object

sc.fiji.snt.tracing.auto.SomaUtils

public class SomaUtils
extends Object

Utilities for automatic soma detection and ROI generation.

Provides methods to detect the soma (cell body) in fluorescent images using a combined EDT-intensity approach, flood fill the region, extract contours, and convert to ImageJ ROIs.

Three detection modes are available:

• detectSoma(net.imagej.ImgPlus<?>, double, int) - Detect single soma (brightest/thickest region)
• detectSomaAt(net.imglib2.RandomAccessibleInterval<? extends net.imglib2.type.numeric.RealType<?>>, long, long, double, double[]) - Detect soma at a specific seed point
• detectAllSomas(net.imglib2.RandomAccessibleInterval<? extends net.imglib2.type.numeric.RealType<?>>, double, double[], double) - Detect all somas in the image

Author:

Tiago Ferreira

See Also:

• AbstractAutoTracer.findRoot(RandomAccessibleInterval, double, double[])

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static final record	SomaUtils.SomaResult	Container for soma detection results.

Field Summary

Fields

Modifier and Type	Field	Description
static final String	OUTPUT_CIRCLE	Output type: Circular ROI with estimated radius
static final String	OUTPUT_CONTOUR	Output type: Area ROI from flood fill contour
static final String	OUTPUT_POINT	Output type: Point ROI at soma center

Method Summary

Modifier and Type	Method	Description
static double	computeMaskArea(net.imglib2.img.Img<net.imglib2.type.logic.BitType> mask, double[] spacing)	Computes the area of a binary mask.
static double[]	computeMaskCentroid(net.imglib2.img.Img<net.imglib2.type.logic.BitType> mask, double[] spacing)	Computes the centroid of a binary mask.
static double	computeOtsuThreshold(net.imglib2.RandomAccessibleInterval<? extends net.imglib2.type.numeric.RealType<?>> source)	Computes Otsu's threshold using ImageJ Ops.
static List<SomaUtils.SomaResult>	detectAllSomas(net.imagej.ImgPlus<?> source)	Detects all somas using ImgPlus with default settings.
static List<SomaUtils.SomaResult>	detectAllSomas(net.imagej.ImgPlus<?> source, double threshold, int zSlice, double minRadius)	Detects all somas using ImgPlus with automatic spacing.
static List<SomaUtils.SomaResult>	detectAllSomas(net.imglib2.RandomAccessibleInterval<? extends net.imglib2.type.numeric.RealType<?>> source, double threshold, double[] spacing)	Detects all somas using default minimum radius.
static List<SomaUtils.SomaResult>	detectAllSomas(net.imglib2.RandomAccessibleInterval<? extends net.imglib2.type.numeric.RealType<?>> source, double threshold, double[] spacing, double minRadius)	Detects all somas using EDT local maxima approach.
static SomaUtils.SomaResult	detectSoma(net.imagej.ImgPlus<?> source)	Full soma detection using ImgPlus with automatic thresholding.
static SomaUtils.SomaResult	detectSoma(net.imagej.ImgPlus<?> source, double threshold, int zSlice)	Full soma detection using ImgPlus with spacing extracted automatically.
static SomaUtils.SomaResult	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	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	detectSomaAt(net.imglib2.RandomAccessibleInterval<? extends net.imglib2.type.numeric.RealType<?>> source, long seedX, long seedY, double threshold, double[] spacing)	Detects soma at a specific seed point.
static Polygon	extractContour(net.imglib2.img.Img<net.imglib2.type.logic.BitType> mask)	Extracts the boundary contour from a binary mask using Moore boundary tracing.
static net.imglib2.img.Img<net.imglib2.type.logic.BitType>	floodFillSoma(net.imglib2.RandomAccessibleInterval<? extends net.imglib2.type.numeric.RealType<?>> source, long seedX, long seedY, double threshold)	Creates a binary mask of the soma region using flood fill from seed point.
static Path	roiToSomaPath(ij.gui.Roi roi, double[] spacing)	Creates a single-node soma Path from an ImageJ ROI.
static Path	roiToSomaPath(ij.gui.Roi roi, Path referencePath)	Creates a single-node soma Path from an ImageJ ROI using calibration from a reference Path.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Details

OUTPUT_POINT

public static final String OUTPUT_POINT

Output type: Point ROI at soma center

See Also:

• Constant Field Values

OUTPUT_CONTOUR

public static final String OUTPUT_CONTOUR

Output type: Area ROI from flood fill contour

See Also:

• Constant Field Values

OUTPUT_CIRCLE

public static final String OUTPUT_CIRCLE

Output type: Circular ROI with estimated radius

See Also:

• Constant Field Values

Method Details

detectSoma

public static SomaUtils.SomaResult detectSoma(net.imagej.ImgPlus<?> source,
 double threshold,
 int zSlice)

Full soma detection using ImgPlus with spacing extracted automatically.

Convenience method that extracts spacing from the ImgPlus calibration.

Parameters:

source - input image (2D or 3D ImgPlus)

threshold - intensity threshold. Use -1 for Otsu, NaN for mean.

zSlice - Z-slice to use (0-indexed), or -1 for middle slice

Returns:

SomaResult containing center, mask, contour, and radius; or null if detection fails

See Also:

• detectSoma(RandomAccessibleInterval, double, double[])

detectSoma

public static SomaUtils.SomaResult detectSoma(net.imagej.ImgPlus<?> source)

Full soma detection using ImgPlus with automatic thresholding.

Convenience method using Otsu's threshold and spacing from ImgPlus calibration.

Parameters:

source - input image (2D or 3D ImgPlus)

Returns:

SomaResult containing center, mask, contour, and radius; or null if detection fails

See Also:

• detectSoma(ImgPlus, double, int)

detectSoma

public static SomaUtils.SomaResult detectSoma(net.imglib2.RandomAccessibleInterval<? extends net.imglib2.type.numeric.RealType<?>> source,
 double threshold,
 double[] spacing)

Full soma detection: finds center, floods region, extracts contour.

Parameters:

source - input image (2D)

threshold - intensity threshold. Use -1 for Otsu, NaN for mean.

spacing - voxel spacing [x, y], or null for unit spacing

Returns:

SomaResult containing center, mask, contour, and radius; or null if detection fails

detectSomaAt

public static SomaUtils.SomaResult detectSomaAt(net.imglib2.RandomAccessibleInterval<? extends net.imglib2.type.numeric.RealType<?>> source,
 long seedX,
 long seedY,
 double threshold,
 double[] spacing)

Detects soma at a specific seed point.

Useful for interactive detection where user clicks near a soma.

Parameters:

source - input image (2D)

seedX - X coordinate of seed point (voxels)

seedY - Y coordinate of seed point (voxels)

threshold - intensity threshold. Use -1 for Otsu, NaN for mean.

spacing - voxel spacing [x, y], or null for unit spacing

Returns:

SomaResult, or null if seed is in background or detection fails

detectSomaAt

public static SomaUtils.SomaResult detectSomaAt(net.imagej.ImgPlus<?> source,
 long seedX,
 long seedY,
 double threshold,
 int zSlice)

Detects soma at a specific seed point using ImgPlus.

Parameters:

source - input image (2D or 3D ImgPlus)

seedX - X coordinate of seed point (voxels)

seedY - Y coordinate of seed point (voxels)

threshold - intensity threshold. Use -1 for Otsu, NaN for mean.

zSlice - Z-slice to use (0-indexed), or -1 for middle slice

Returns:

SomaResult, or null if seed is in background or detection fails

detectAllSomas

public static List<SomaUtils.SomaResult> detectAllSomas(net.imglib2.RandomAccessibleInterval<? extends net.imglib2.type.numeric.RealType<?>> source,
 double threshold,
 double[] spacing,
 double minRadius)

Detects all somas using EDT local maxima approach. Finds local maxima in the distance transform - these correspond to centers of thick structures (somas), not thin structures (neurites).

Parameters:

source - input image (2D)

threshold - intensity threshold. Use -1 for Otsu, NaN for mean.

spacing - voxel spacing [x, y], or null for unit spacing

minRadius - minimum soma radius in voxels to include (filters small debris)

Returns:

list of SomaResult, sorted by radius (largest first); empty list if none found

detectAllSomas

public static List<SomaUtils.SomaResult> detectAllSomas(net.imglib2.RandomAccessibleInterval<? extends net.imglib2.type.numeric.RealType<?>> source,
 double threshold,
 double[] spacing)

Detects all somas using default minimum radius.

Parameters:

source - input image (2D)

threshold - intensity threshold. Use -1 for Otsu, NaN for mean.

spacing - voxel spacing [x, y], or null for unit spacing

Returns:

list of SomaResult, sorted by radius (largest first)

detectAllSomas

public static List<SomaUtils.SomaResult> detectAllSomas(net.imagej.ImgPlus<?> source,
 double threshold,
 int zSlice,
 double minRadius)

Detects all somas using ImgPlus with automatic spacing.

Parameters:

source - input image (2D or 3D ImgPlus)

threshold - intensity threshold. Use -1 for Otsu, NaN for mean.

zSlice - Z-slice to use (0-indexed), or -1 for middle slice

minRadius - minimum soma radius in voxels

Returns:

list of SomaResult, sorted by radius (largest first)

detectAllSomas

public static List<SomaUtils.SomaResult> detectAllSomas(net.imagej.ImgPlus<?> source)

Detects all somas using ImgPlus with default settings.

Parameters:

source - input image (2D or 3D ImgPlus)

Returns:

list of SomaResult, sorted by radius (largest first)

floodFillSoma

public static net.imglib2.img.Img<net.imglib2.type.logic.BitType> floodFillSoma(net.imglib2.RandomAccessibleInterval<? extends net.imglib2.type.numeric.RealType<?>> source,
 long seedX,
 long seedY,
 double threshold)

Creates a binary mask of the soma region using flood fill from seed point.

Parameters:

source - the input image (2D)

seedX - seed X coordinate (voxels)

seedY - seed Y coordinate (voxels)

threshold - pixels above this value are considered foreground

Returns:

binary mask where TRUE = soma region, or null if seed is in background

extractContour

public static Polygon extractContour(net.imglib2.img.Img<net.imglib2.type.logic.BitType> mask)

Extracts the boundary contour from a binary mask using Moore boundary tracing.

Parameters:

mask - binary mask (TRUE = foreground)

Returns:

polygon contour, or null if mask is empty

computeMaskCentroid

public static double[] computeMaskCentroid(net.imglib2.img.Img<net.imglib2.type.logic.BitType> mask,
 double[] spacing)

Computes the centroid of a binary mask.

Parameters:

mask - binary mask

spacing - voxel spacing [x, y] for physical coordinates, or null for voxel coords

Returns:

centroid as [x, y], or null if mask is empty

computeMaskArea

public static double computeMaskArea(net.imglib2.img.Img<net.imglib2.type.logic.BitType> mask,
 double[] spacing)

Computes the area of a binary mask.

Parameters:

mask - binary mask

spacing - voxel spacing [x, y], or null for voxel count

Returns:

area in physical units squared, or voxel count if spacing is null

computeOtsuThreshold

public static double computeOtsuThreshold(net.imglib2.RandomAccessibleInterval<? extends net.imglib2.type.numeric.RealType<?>> source)

Computes Otsu's threshold using ImageJ Ops.

Parameters:

source - the input image

Returns:

Otsu threshold value

roiToSomaPath

public static Path roiToSomaPath(ij.gui.Roi roi,
 Path referencePath)

Creates a single-node soma Path from an ImageJ ROI using calibration from a reference Path.

Parameters:

roi - the ROI to convert (must not be null)

referencePath - a Path from which to extract spacing and units (may be null for pixel units)

Returns:

a single-node soma path, or null if ROI is null

See Also:

• roiToSomaPath(Roi, double[])

roiToSomaPath

public static Path roiToSomaPath(ij.gui.Roi roi,
 double[] spacing)

Creates a single-node soma Path from an ImageJ ROI.

Converts any ROI to a soma path centered at the ROI's centroid. For area ROIs (polygon, oval, freehand, etc.), the radius is estimated from the equivalent circle area. For non-area ROIs (point, line), no radius is assigned.

Parameters:

roi - the ROI to convert (must not be null)

spacing - voxel spacing [x, y, z] for physical coordinates, or null for pixel units

Returns:

a single-node soma path, or null if ROI is null