Skip to content

Skeleton Annotation Tools

Skeleton annotation in WEBKNOSSOS allows you to create graph-like structures by placing connected nodes in 3D space. This is particularly useful for tracing neurons and other branching structures.

New Tree Modifier The Skeleton tool enables you to create and edit skeleton annotations:

  • Place nodes with precise positioning
  • Connect nodes to form tree structures
  • Add branches and create complex neural tracings

Basic Concepts

A skeleton annotation consists of:

  • Nodes: Individual points placed in 3D space (created with left-click)
  • Edges: Connections between nodes that form trees
  • Trees: Collections of connected nodes and edges
  • Branch Points: Special nodes marking where a structure splits into multiple paths

The active node is always highlighted with a circle and can be moved by dragging.

Creating Annotations

New Trees

  • Select the Skeleton tool from the toolbar
  • Create a new tree using the toolbar button or press C
  • Each tree can represent a different structure or part of your annotation
  • Trees are listed and can be managed in the right sidebar

Branch Points

  • Mark any node as a branch point using B or the right-click menu
  • Branch points are highlighted with a distinct color
  • All branch points are stored in a first-in, first-out (FIFO) stack
  • Jump to the latest branch point using J to continue working from there

Tool Modes

The following additional modes are available for the skeleton tool beyond the basic functionality:

New Tree Mode Create new Tree

  • Starts a fresh tree structure
  • Useful when annotating multiple separate structures

Single Node Tree Mode Mode Single Node Tree Mode

  • When enabled, creates a new tree for each placed node
  • Perfect for marking individual objects (e.g., cell nuclei)
  • Also known as "Soma-clicking mode"

Merger Mode Merger Mode

  • Enables using skeletons to merge volume segments
  • Useful for correcting over-segmentation
  • Learn more about Merger Mode

Skeleton Keyboard Shortcuts

The following common keyboard shortcuts are handy for speeding up your annotation workflow:

Key Binding Operation
Left Click Create New Node
Left Click Select Node (Mark as Active Node) under the cursor
Left Drag Move around
Left Drag Move the node under the cursor
S Center Camera on Active Node
Del Delete Active Node
B Create Branch Point
J Jump to Last Branch Point
C Create New Tree

Keyboard Shortcuts

For faster workflow, refer to the keyboard shortcuts guide.