Package sc.fiji.snt.analysis.curation
package sc.fiji.snt.analysis.curation
Classes for curation of reconstructions, as implemented by the "Curation Assistant".
- Author:
- Tiago Ferreira
-
ClassDescriptionFactory for the small histogram buttons sitting next to threshold spinners in the Curation Assistant.Defines Which side of the threshold(s) constitutes a flagged value.Reserved
cur:*path tags used to record a path's review status after it has been examined in the Curation Assistant.Four-bucket breakdown returned byCurationTags.partitionByReviewStatus(Tree).InfersPlausibilityCheckthresholds from a collection of referenceTrees.Aggregated calibration results from a set of reference trees.Summary for a single calibrated parameter.Framework for evaluating the morphological plausibility of path operations and reconstructions.Flags terminal branches whose endpoint lies suspiciously close to the image's field-of-view boundary.Warns when the bifurcation angle at a fork is outside a plausible range.Detects regions where two unconnected paths run parallel to each other for an extended distance.Warns when a path has radii assigned, but they are all identical (likely unfitted defaults).Detects suspicious crossings between paths viaCrossoverFinder: X-shape near-coincidences where two paths almost touch.A heavier check that scans an entire collection of paths for issues.Warns when the child path's initial direction deviates sharply from the parent's tangent at the branch point (potential U-turn).Classifies how an error propagates through the reconstruction.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.Warns when two consecutive forks on the same parent path are implausibly close together.Flags nodes whose radius is zero, negative, orNaN.A lightweight check that evaluates the plausibility of a single fork operation (parent + child + branch index).Full distribution of a check's raw measurements across a reconstruction, collected without applying the warning threshold.Warns when the child neurite's radius at the fork point exceeds the parent's radius at the branch point.Detects abrupt radius jumps between adjacent nodes within a path.Detects sustained radius increases along a path (neurites should generally taper distally).Severity levels for plausibility warnings.Assesses local image signal quality around traced paths and flags those in regions with poor contrast.Warns when a primary path starts far from any soma node.Warns when a terminal path is suspiciously short.Flags terminal branches whose endpoint sits suspiciously close to a node on a non-ancestor path.Warns when child and parent have very different tortuosity (contraction).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.A plausibility warning produced by a check.Flags paths whose Z-extent is implausibly small relative to their length.Monitors tracing and editing operations for morphological plausibility.Listener interface for warning list changes.