Hanchuan Peng, Zongcai Ruan, Fuhui Long, Julie H. Simpson, and Eugene Myers (2010) "V3D enables real-time 3D visualization and quantitative analysis of large-scale biological image data sets," Nature Biotechnology, 28(4): 348-353. PDF(The first Vaa3D paper; introduces the entire system)
Hanchuan Peng, Alessandro Bria, Zhi Zhou, Giulio Iannello, and Fuhui Long (2014) "Extensible visualization and analysis for multidimensional images using Vaa3D," Nature Protocols, 9(1): 193-208. PDF(The second major Vaa3D paper; introduces 10 widely useful procedures for using and extending the system)
Hanchuan Peng, et al. (2014) "Virtual finger boosts three-dimensional imaging and microsurgery as well as terabyte volume image visualization and analysis," Nature Communications, 5: 4342. PDF(The third major Vaa3D paper; introduces Virtual Finger functions and applications of Vaa3D for a wide range of applications)
Alessandro Bria, Giulio Iannello, Leonardo Onofri, Hanchuan Peng, et al. (2016) "TeraFly: real-time 3D visualization and 3D annotation of terabytes of multidimensional volumetric images," Nature Methods (in press) (The TeraFly engine for very large scale image visualization and annotation)
A few additional publications
Hanchuan Peng, Phuong Chung, Fuhui Long, Lei Qu, Arnim Jenett, Andrew Seeds, Eugene Myers, and Julie Simpson (2011) "BrainAligner: 3D registration atlases of Drosophila brains," Nature Methods, 8(6): 493-498. PDF(Introduce the Vaa3D-AtlasViewer for very large set of 3D registered/aligned images)
Lei Qu, Fuhui Long, Xiao Liu, Stuart Kim, Gene Myers, and Hanchuan Peng (2011) ""Simultaneous recognition and segmentation of cells: application in C. elegans," Bioinformatics, 27(20): 2895-2902, 2011. PDF(Vaa3D plugin on the simultaneous segmentation of recognition of cells)
Yang Yu, and Hanchuan Peng (2011) "Automated high speed stitching of large 3D microscopic images," Proc. IEEE ISBI'2011, 238-241. PDF(Vaa3D plugin on 3D stitching of images, i.e. iStitch)
Hanchuan Peng, Zongcai Ruan, Deniz Atasoy, and Scott Sternson (2010) "Automatic reconstruction of 3D neuron structures using a graph-augmented deformable model," Bioinformatics, 26: i38-i46. PDF(Vaa3D-Neuron GD (graph-augmented deformable model) algorithm)
Lei Qu, and Hanchuan Peng (2010) "A principal skeleton algorithm for standardizing confocal images of fruit fly nervous systems," Bioinformatics, 26(8): 1091-1097. PDF(Vaa3D plugin on the principal skeleton deformable model)
Shing Chun Benny Lam, Zongcai Ruan, Ting Zhao, Fuhui Long, Arnim Jenett, Julie Simpson, Eugene Myers, Hanchuan Peng (2010) "Segmentation of center brains and optic lobes in 3D confocal images of adult fruit fly brains," Methods, 50(2): 63-69. PDF(Vaa3D plugin on the 3D optic lobe segmentation)