Analyze Skeleton

marielaureb's picture
Workflow Author: 

Ignacio Arganda-Carreras

Workflow Language: 
Output data type: 
table result, image of the skeleton
Comment / Instructions: 

This plugin tags all pixel/voxels in a skeleton image and then counts all its junctions, triple and quadruple points and branches, and measures their average and maximum length. The tags are shown in a new window displaying every tag in a different color. You can find it under Plugins>Skeleton>Analyze Skeleton (2D/3D). See Skeletonize3D for an example of how to produce skeleton images.

The voxels are classified into three different categories depending on their 26 neighbors:

End-point voxels: if they have less than 2 neighbors.
Junction voxels: if they have more than 2 neighbors.
Slab voxels: if they have exactly 2 neighbors.

End-point voxels are displayed in blue, slab voxels in orange and junction voxels in purple.

Notice here that, following this notation, the number of junction voxels can be different from the number of actual junctions since some junction voxels can be neighbors of each other.

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