Uses of Class
sc.fiji.snt.analysis.curation.PlausibilityCheck.DeepCheck

Packages that use PlausibilityCheck.DeepCheck

Package	Description
sc.fiji.snt.analysis.curation	Classes for curation of reconstructions, as implemented by the "Curation Assistant".

Uses of PlausibilityCheck.DeepCheck in sc.fiji.snt.analysis.curation

Subclasses of PlausibilityCheck.DeepCheck in sc.fiji.snt.analysis.curation

Modifier and Type	Class	Description
static class	PlausibilityCheck.BoundaryProximity	Flags terminal branches whose endpoint lies suspiciously close to the image's field-of-view boundary.
static class	PlausibilityCheck.BundledPaths	Detects regions where two unconnected paths run parallel to each other for an extended distance.
static class	PlausibilityCheck.Crossovers	Detects suspicious crossings between paths via CrossoverFinder: X-shape near-coincidences where two paths almost touch.
static class	PlausibilityCheck.IntensityValley	Flags localized intensity valleys along a path's intensity profile: discrete dips of one or a few nodes whose intensity is markedly below the surrounding peaks.
static class	PlausibilityCheck.InvalidRadius	Flags nodes whose radius is zero, negative, or NaN.
static class	PlausibilityCheck.RadiusJumps	Detects abrupt radius jumps between adjacent nodes within a path.
static class	PlausibilityCheck.RadiusMonotonicity	Detects sustained radius increases along a path (neurites should generally taper distally).
static class	PlausibilityCheck.SignalQuality	Assesses local image signal quality around traced paths and flags those in regions with poor contrast.
static class	PlausibilityCheck.TerminalNearAncestor	Flags terminal branches whose endpoint sits suspiciously close to a node on a non-ancestor path.
static class	PlausibilityCheck.UncertainTerminal	Flags terminal branches whose final few nodes have low signal/background contrast: the tip's spatial location is poorly determined because the neurite faded into the background before the trace stopped.
static class	PlausibilityCheck.ZExtentRatio	Flags paths whose Z-extent is implausibly small relative to their length.

Methods in sc.fiji.snt.analysis.curation with type parameters of type PlausibilityCheck.DeepCheck

Modifier and Type	Method	Description
<T extends PlausibilityCheck.DeepCheck> T	PlausibilityMonitor.getDeepCheck(Class<T> type)	Convenience method to get a specific deep check by type.

Methods in sc.fiji.snt.analysis.curation that return types with arguments of type PlausibilityCheck.DeepCheck

Modifier and Type	Method	Description
List<PlausibilityCheck.DeepCheck>	PlausibilityMonitor.getDeepChecks()

Methods in sc.fiji.snt.analysis.curation with parameters of type PlausibilityCheck.DeepCheck

Modifier and Type	Method	Description
PlausibilityCheck.Measurements	PlausibilityMonitor.measure(PlausibilityCheck.DeepCheck deepCheck, Collection<Path> paths)	Collects the raw distribution of deepCheck's metric across paths without applying its warning threshold.