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 Summary

Fields

Modifier and Type	Field	Description
static final double	AUTO_THRESHOLD	Sentinel value indicating the threshold should be inferred from image stats.

Constructor Summary

Constructors

Constructor	Description
SignalQuality()

Method Summary

Modifier and Type	Method	Description
double	getMinContrast()
String	getName()
double	getResolvedThreshold()
boolean	hasImage()
boolean	hasValidStats()
PlausibilityCheck.Measurements	measure(Collection<Path> paths)	Computes the full distribution of this check's metric across paths, without applying the warning threshold.
void	prepareImage(net.imglib2.RandomAccessibleInterval<? extends net.imglib2.type.numeric.RealType<?>> rai)	Sets the image and computes its full-volume min/max stats by scanning every voxel.
List<PlausibilityCheck.Warning>	scan(Collection<Path> paths)	Scans a collection of paths for plausibility issues.
void	setImage(net.imglib2.RandomAccessibleInterval<? extends net.imglib2.type.numeric.RealType<?>> image)	Provides the image data for signal quality assessment.
void	setImageStats(double min, double max)	Sets image-level statistics used to auto-compute the contrast threshold when getMinContrast() == AUTO_THRESHOLD.
void	setMinContrast(double contrast)	Sets the minimum signal-to-background contrast ratio below which a path is flagged.

Methods inherited from class sc.fiji.snt.analysis.curation.PlausibilityCheck.DeepCheck

impactKind, isEnabled, setEnabled

Methods inherited from class java.lang.Object

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

Field Details

AUTO_THRESHOLD

public static final double AUTO_THRESHOLD

Sentinel value indicating the threshold should be inferred from image stats.

See Also:

• Constant Field Values

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

prepareImage

public void prepareImage(net.imglib2.RandomAccessibleInterval<? extends net.imglib2.type.numeric.RealType<?>> rai)

Sets the image and computes its full-volume min/max stats by scanning every voxel. Use this instead of setImage(net.imglib2.RandomAccessibleInterval<? extends net.imglib2.type.numeric.RealType<?>>) + setImageStats(double, double) when the caller wants the resolved auto-threshold to reflect the actual image range, independent of any lazily-populated stats elsewhere.

Should always be called from a worker thread.

Parameters:

rai - the image data; null clears the image and stats.

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)

getResolvedThreshold

public double getResolvedThreshold()

Returns:

the resolved threshold (auto-derived from image stats when the spinner is set to AUTO_THRESHOLD). Exposed so the curation UI can draw the marker at the effective cutoff even in auto mode.

hasValidStats

public boolean hasValidStats()

Returns:

true when a full-volume scan has populated the min/max intensity stats (i.e., prepareImage(net.imglib2.RandomAccessibleInterval<? extends net.imglib2.type.numeric.RealType<?>>) has run). Used by sibling checks (e.g., PlausibilityCheck.UncertainTerminal) to decide whether to borrow this check's resolved threshold or scan the volume themselves.

measure

public PlausibilityCheck.Measurements measure(Collection<Path> paths)

Description copied from class: PlausibilityCheck.DeepCheck

Computes the full distribution of this check's metric across paths, without applying the warning threshold. Default implementation returns PlausibilityCheck.Measurements.EMPTY; subclasses override to enable per-check histogram popups in the Curation Assistant.

Overrides:

measure in class PlausibilityCheck.DeepCheck

Parameters:

paths - the paths to evaluate; null or empty yields PlausibilityCheck.Measurements.EMPTY.

Returns:

a PlausibilityCheck.Measurements record; never null.