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.
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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
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.
- 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
- 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
The following additional modes are available for the skeleton tool beyond the basic functionality:
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Create new Tree
- Starts a fresh tree structure
- Useful when annotating multiple separate structures
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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"
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Merger Mode
- Enables using skeletons to merge volume segments
- Useful for correcting over-segmentation
- Learn more about Merger Mode
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 |
!!! tip "Keyboard Shortcuts" For faster workflow, refer to the keyboard shortcuts guide.