Skeletonize3D is a Fiji and ImageJ plugin that performs the skeletonization of 2D and 3D binary images (8-bit images). In Fiji, you can find it under Plugins > Skeleton > Skeletonize (2D/3D). If you need to analyze a 2D/3D skeleton image, you may be interested on having a look at AnalyzeSkeleton.
For further details, please visit the documentation site: http://fiji.sc/Skeletonize3D