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).
For further details, please see the:
- documentation http://fiji.sc/AnalyzeSkeleton
- publication: http://www3.interscience.wiley.com/journal/123322233/abstract