Package sc.fiji.snt.tracing.auto

Interface AutoTracer

All Known Implementing Classes:
AbstractAutoTracer, AbstractGWDTTracer, BinaryTracer, DiskBackedGWDTTracer, GWDTTracer, SparseGWDTTracer
public interface AutoTracer
Interface for automatic neuron tracers that reconstruct complete neuronal morphologies from images.

Implementations include both grayscale-based tracers (e.g., GWDTTracer) and skeleton-based tracers (e.g., BinaryTracer).

Author:
Tiago Ferreira

  • Nested Class Summary

    Nested Classes
    Modifier and Type
    Interface
    Description
    static enum 
    AutoTracer.SeedRole
    Role a SeedPoint plays in a tracing run.

  • Field Summary

    Fields
    Modifier and Type
    Field
    Description
    static final int
    ROI_CENTROID
    Rooting strategy: A single tree is created with all branches connected to the geometric centroid of the soma ROI.
    static final int
    ROI_CENTROID_WEIGHTED
    Rooting strategy: A single tree is created with all branches connected to a weighted centroid computed from nodes inside the soma ROI.
    static final int
    ROI_CONTAINED
    Rooting strategy: Trees are rooted on nodes contained within the soma ROI.
    static final int
    ROI_EDGE
    Rooting strategy: Separate trees are created for each neurite exiting the soma ROI.
    static final int
    ROI_UNSET
    Rooting strategy: Tree is rooted at an algorithm-specific point (e.g., seed point for grayscale tracers, arbitrary endpoint for binary tracers).

  • Method Summary

    Modifier and Type
    Method
    Description
    default EnumSet<AutoTracer.SeedRole>
    honoredSeedRoles()
     
    default void
    setRoots(Collection<SeedPoint> seeds)
    Hands the tracer a collection of seeds to use as roots in this run.
    default void
    setTips(Collection<SeedPoint> seeds)
    Hands the tracer a collection of seeds to use as tips / targets in this run.
    default void
    setWaypoints(Collection<SeedPoint> seeds)
    Hands the tracer a collection of seeds to use as waypoints (path constraints) in this run.
    default Tree
    trace()
    Traces the neuronal structure and returns a single merged Tree.
    List<Tree>
    traceTrees()
    Traces the neuronal structure and returns a list of Trees.

  • Field Details

    • ROI_UNSET

      static final int ROI_UNSET
      Rooting strategy: Tree is rooted at an algorithm-specific point (e.g., seed point for grayscale tracers, arbitrary endpoint for binary tracers). Any soma-marking ROI is ignored.
      See Also:

    • ROI_EDGE

      static final int ROI_EDGE
      Rooting strategy: Separate trees are created for each neurite exiting the soma ROI. Nodes inside the ROI are excluded from the output trees.
      See Also:

    • ROI_CENTROID

      static final int ROI_CENTROID
      Rooting strategy: A single tree is created with all branches connected to the geometric centroid of the soma ROI.
      See Also:

    • ROI_CENTROID_WEIGHTED

      static final int ROI_CENTROID_WEIGHTED
      Rooting strategy: A single tree is created with all branches connected to a weighted centroid computed from nodes inside the soma ROI.
      See Also:

    • ROI_CONTAINED

      static final int ROI_CONTAINED
      Rooting strategy: Trees are rooted on nodes contained within the soma ROI. Unlike ROI_EDGE, nodes inside the ROI are included in the analysis.
      See Also:

  • Method Details

    • setRoots

      default void setRoots(Collection<SeedPoint> seeds)
      Hands the tracer a collection of seeds to use as roots in this run. Default: no-op. Concrete tracers that consume root seeds override.
      Parameters:
      seeds - candidate roots; may be null or empty

    • setTips

      default void setTips(Collection<SeedPoint> seeds)
      Hands the tracer a collection of seeds to use as tips / targets in this run. Default: no-op. Concrete tracers that consume tip seeds override.
      Parameters:
      seeds - candidate tips; may be null or empty

    • setWaypoints

      default void setWaypoints(Collection<SeedPoint> seeds)
      Hands the tracer a collection of seeds to use as waypoints (path constraints) in this run. Default: no-op. Concrete tracers that consume waypoint seeds override.
      Parameters:
      seeds - candidate waypoints; may be null or empty

    • honoredSeedRoles

      default EnumSet<AutoTracer.SeedRole> honoredSeedRoles()
      Returns:
      the AutoTracer.SeedRoles this tracer actually honors. Callers (e.g. an "Autotrace from Seeds" wrapper command) can use this to gate UI choices and to error early when the user picks a role the tracer ignores. Default: empty set.

    • traceTrees

      List<Tree> traceTrees()
      Traces the neuronal structure and returns a list of Trees.
      Returns:
      list of traced trees, or empty list if tracing fails

    • trace

      default Tree trace()
      Traces the neuronal structure and returns a single merged Tree.

      Default implementation merges all trees from traceTrees().

      Returns:
      the traced tree, or null if tracing fails