Package sc.fiji.snt.analysis.curation

Class PlausibilityCheck.SignalQuality

java.lang.Object
sc.fiji.snt.analysis.curation.PlausibilityCheck.DeepCheck
sc.fiji.snt.analysis.curation.PlausibilityCheck.SignalQuality
Enclosing class:
PlausibilityCheck
public static class PlausibilityCheck.SignalQuality extends PlausibilityCheck.DeepCheck
Assesses local image signal quality around traced paths and flags those in regions with poor contrast. For each path, voxel intensities are sampled in a local neighborhood; signal and background are separated by percentile thresholds, and the contrast ratio (signal median / background median) is computed.

This check requires image data to be provided via setImage(RandomAccessibleInterval) before scanning. If no image is set, the check returns an empty list.

Reference: Zhang et al., Nature Methods (2024), doi:10.1038/s41592-024-02401-8.

  • Field Details

    • AUTO_THRESHOLD

      public static final double AUTO_THRESHOLD
      Sentinel value indicating the threshold should be inferred from image stats.
      See Also:

  • Constructor Details

    • SignalQuality

      public SignalQuality()

  • Method Details

    • getName

      public String getName()
      Specified by:
      getName in class PlausibilityCheck.DeepCheck
      Returns:
      a short human-readable name for this check

    • setMinContrast

      public void setMinContrast(double contrast)
      Sets the minimum signal-to-background contrast ratio below which a path is flagged. Set to AUTO_THRESHOLD to infer from image statistics.
      Parameters:
      contrast - ratio ≥ 1.0, or AUTO_THRESHOLD

    • getMinContrast

      public double getMinContrast()
      Returns:
      the current minimum contrast threshold

    • setImage

      public void setImage(net.imglib2.RandomAccessibleInterval<? extends net.imglib2.type.numeric.RealType<?>> image)
      Provides the image data for signal quality assessment.
      Parameters:
      image - the image (3D RAI); null to clear

    • setImageStats

      public void setImageStats(double min, double max)
      Sets image-level statistics used to auto-compute the contrast threshold when getMinContrast() == AUTO_THRESHOLD.
      Parameters:
      min - image minimum intensity
      max - image maximum intensity

    • hasImage

      public boolean hasImage()
      Returns:
      whether image data has been provided

    • scan

      public List<PlausibilityCheck.Warning> scan(Collection<Path> paths)
      Description copied from class: PlausibilityCheck.DeepCheck
      Scans a collection of paths for plausibility issues.
      Specified by:
      scan in class PlausibilityCheck.DeepCheck
      Parameters:
      paths - the paths to scan
      Returns:
      list of warnings (empty if no issues found)