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3D Skeletonization Extension


3D Skeletonization Extension is an Aphelion™ Dev extension1 that derives a skeletonized of a 3D binary image. The resulting skeleton is a 3D connected graph whose lines have the thickness of one voxel. This Skeletonization process is based on advanced work performed at the Ecole des Mines de Paris (France) and Monash University (Australia).

Load the image 3D_Skeleton_fig1 Load the image 3D_Skeleton_fig2

Branched structure example and skeletonization result

3D Skeletonization Extension employs a robust and highly accurate process that is especially well-suited to the analysis of intricate objects like branched structures (see Figure 1). The module's output is a set of one-voxel thickness branches represented in a tree-like structure (see Figure 2). The resulting Skeletonization data is stored as an Aphelion ObjectSet that contains the attributes that define the skeleton. These include:

  • Branch index;
  • Level of branch in the hierarchy;
  • Branch length (raw and calibrated);
  • Length from each branch to the root;
  • Associated skeleton label;
  • Mother branch index;
  • Number and index of each child branch; and
  • Node coordinates in the 3D space.

While the 3D Skeletonization Extension process specifies the root of the skeleton (i.e., the last node of an extremity), the user can manually specify a different root node. When a new root node is chosen, the tree structure and associated attributes are then automatically recomputed. This method enables the user to exhaustively analyze each connected component of the skeleton.

Typical Skeletonization applications include analysis of blood vessels, neural systems, and any other tree-like structure in 3D space. 3D skeletons greatly enhance a user's ability to quickly extract quantitative data from complex 3D structures.

Main benefits of the Aphelion 3D Skeletonization Extension:

  • Rapid generation and display of a one-voxel thickness skeleton
  • Representation of the skeleton as a tree-like structure
  • Computation of a comprehensive set of skeleton attributes
  • User selection of a different root node causes recomputation of the skeleton
  • Skeleton structure available in spreadsheet form for further statistical analysis

1 3D Skeletonization Extension is a plug-in for Aphelion Dev. It also requires the 3D Image Processing Extension to be installed and executable. The 3D Image Display Extension is highly recommended.