EPFL has developed an add-on for Blender that loads centerlines generated by VMTK into Blender, and writes meshes from Blender so that they can be easily read by VMTK. The add-on includes a simple mesh-cleaning routine that helps the VMTK tool function better on Blender meshes. There are also a couple tools that perform useful functions using the centerlines in Blender, including generating cross-sectional surfaces, projecting objects (for example vesicle spheres) onto the centerline, and detecting swellings (for example boutons) in the mesh.
The tool is available free for download from GitHub, full instructions with example images are available here: http://wiki.blender.org/index.php/Extensions:2.6/Py/Scripts/NeuroMorph/Centerline_Tools
The tool has been developed part of the NeuroMorph project at EPFL.
Thanks to Anne Jorstad and her team for the effort and contribution.