Package sc.fiji.snt.analysis.curation

Class PlausibilityCheck

java.lang.Object

sc.fiji.snt.analysis.curation.PlausibilityCheck

public final class PlausibilityCheck
extends Object

Framework for evaluating the morphological plausibility of path operations and reconstructions. Checks come in two tiers:

• PlausibilityCheck.LiveCheck: lightweight checks that run inline during interactive tracing (at fork, segment, and edit hook points).
• PlausibilityCheck.DeepCheck: heavier checks that scan an entire reconstruction on demand (e.g., overlap detection, global radius analysis).

Both tiers share the same PlausibilityCheck.Warning type and severity model.

Author:

Tiago Ferreira

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	PlausibilityCheck.BranchAngle	Warns when the bifurcation angle at a fork is outside a plausible range.
static class	PlausibilityCheck.ConstantRadii	Warns when a path has radii assigned but they are all identical (likely unfitted defaults).
static class	PlausibilityCheck.DeepCheck	A heavier check that scans an entire collection of paths for issues.
static class	PlausibilityCheck.DirectionContinuity	Warns when the child path's initial direction deviates sharply from the parent's tangent at the branch point (potential U-turn).
static class	PlausibilityCheck.LiveCheck	A lightweight check that evaluates the plausibility of a single fork operation (parent + child + branch index).
static class	PlausibilityCheck.PathOverlap	Detects paths that run very close to each other without being topologically connected.
static class	PlausibilityCheck.RadiusContinuity	Warns when the child neurite's radius at the fork point exceeds the parent's radius at the branch point.
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 enum	PlausibilityCheck.Severity	Severity levels for plausibility warnings.
static class	PlausibilityCheck.SignalQuality	Assesses local image signal quality around traced paths and flags those in regions with poor contrast.
static class	PlausibilityCheck.SomaDistance	Warns when a primary path starts far from any soma node.
static class	PlausibilityCheck.TerminalBranchLength	Warns when a terminal branch is suspiciously short.
static class	PlausibilityCheck.TortuosityConsistency	Warns when child and parent have very different tortuosity (contraction).
static final record	PlausibilityCheck.Warning	A plausibility warning produced by a check.

Method Summary

Methods inherited from class java.lang.Object

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