Vessel Graph Extraction

A vessel graph simplifies the complex 3D structure of vascular systems into a network of nodes (representing branch points or endpoints) and edges (representing vessels or segments connecting the nodes). An algorithm for vessel graph extraction was developed and presented by Dominik Drees (https://doi.org/10.1186/s12859-021-04262-w)

The feature-vortexcorelineextraction.vws provides a Voreen workspace for extracting vesssel graphs from vessel volumes. To access it, follow these steps:
File → Open Workspaces → Workspaces → feature-vesselgraphextraction.vws → Open

Once the workspace is loaded, switch to application mode, where you should see the following interface:

Operations in the Properties Space

• Vessel Volume Input:
  Load the data. The processor is named "Vessel Volume Input" but is actually the standard VolumeSource processor, familiar from other parts of Voreen.
• Sample Mask Volume Input (optional):
  Load an optional mask for the data
• Preprocessing:
  Configure various preprocessing steps for the data. For example Threshold values and surface smoothing can be adjusted here.
• Vessel Graph Extraction:
  Calculate the vessel graph extraction for specific bulge size and a number of refinement iterations.
• Rendering:
  Adjust standard rendering properties as for instance the colormap or the radius of the nodes.
• Data Export:
  Save the vessel graph, edge data or note data in various formats.

Operations in the Canvas Space

• Adjust the camera angle by clicking and hovering.

Extracting the sample vessel graph

If you extract the vessel graph in the sample workspace by first starting the preprocessing and the vessel graph extraction your result should look like