Vaa3D is a 3D rendering program developed out of Jenalia Farm. It can be used for 3D rendering of image stacks but also includes powerful algorithms for tracing neurons and segmentation.


For information, tutorial videos and to download the software visit the Vaa3D website.

Papers regarding the development of this software include:


  • Peng, H., Ruan, Z., Long, F., Simpson, J.H., and Myers, E.W. (2010) “V3D enables real-time 3D visualization and quantitative analysis of large-scale biological image data sets,” Nature Biotechnology, Vol. 28, No. 4, pp. 348-353, DOI: 10.1038/nbt.1612. [ PDF | Supplements ]
  • Peng, H, Ruan, Z., Atasoy, D., and Sternson, S. (2010) “Automatic reconstruction of 3D neuron structures using a graph-augmented deformable model,” Bioinformatics, Vol. 26, pp. i38-i46, 2010. [ PDF ]

Neuron tracing and brain alignment