Package sc.fiji.snt.analysis.detection

Class AlongPathDetector

java.lang.Object

sc.fiji.snt.analysis.detection.AlongPathDetector

public class AlongPathDetector
extends Object

Detects features (boutons, varicosities) along traced paths by analyzing longitudinal radius and intensity profiles. This complements PeripathDetector, which detects features in perpendicular cross-sections around paths.

The detection algorithm is inspired by the bouton detection in the CAR platform (Zhang et al., Nature Methods, 2024). At each node, the radius is compared to the average radius of its neighbors within a sliding window. A node is flagged as a candidate if its radius exceeds the neighbor average by a configurable factor (default 1.5×). Optionally, an intensity threshold can be applied using on-skeleton intensity sampled from the image. Adjacent candidates are merged via greedy non-maximum suppression.

Usage:

   AlongPathDetector.Config cfg = new AlongPathDetector.Config()
       .swellingFactor(1.5)     // flag nodes ≥ 1.5× neighbor average
       .windowSize(5)           // compare against 5 neighbors each side
       .minIntensity(120)       // minimum on-skeleton intensity (8-bit)
       .mergingDistance(3.0);   // NMS radius in calibrated units
   List<Detection> boutons = AlongPathDetector.detect(paths, image, cfg);
 

Author:

Tiago Ferreira

See Also:

• PeripathDetector
• Detection
• DetectorUtils

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static final class	AlongPathDetector.Config	Configuration for along-path detection with builder-like setters.

Method Summary

Modifier and Type	Method	Description
static <T extends net.imglib2.type.numeric.RealType<T>> List<Detection>	detect(Collection<Path> paths, net.imglib2.RandomAccessibleInterval<? extends net.imglib2.type.numeric.RealType<?>> img, AlongPathDetector.Config cfg)	Detects swellings (boutons/varicosities) along the given paths by analyzing the longitudinal radius profile and, optionally, on-skeleton image intensity.
static List<Detection>	detect(Collection<Path> paths, AlongPathDetector.Config cfg)	Convenience overload that performs radius-only detection (no image).

Methods inherited from class java.lang.Object

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

Method Details

detect

public static <T extends net.imglib2.type.numeric.RealType<T>>
List<Detection> detect(Collection<Path> paths,
 net.imglib2.RandomAccessibleInterval<? extends net.imglib2.type.numeric.RealType<?>> img,
 AlongPathDetector.Config cfg)

Detects swellings (boutons/varicosities) along the given paths by analyzing the longitudinal radius profile and, optionally, on-skeleton image intensity.

Parameters:

paths - the paths to analyze (must have radii for radius-based detection)

img - the image for intensity filtering; may be null if intensity filtering is not needed (minIntensity ≤ 0)

cfg - detection parameters

Returns:

list of detections, deduplicated and optionally assigned to nearest path

Throws:

IllegalArgumentException - if paths is null/empty, or if intensity filtering is requested but no image is provided

detect

public static List<Detection> detect(Collection<Path> paths,
 AlongPathDetector.Config cfg)

Convenience overload that performs radius-only detection (no image).

Parameters:

paths - the paths to analyze

cfg - detection parameters (minIntensity should be ≤ 0)

Returns:

list of detections