V3D enables real-time 3D visualization and quantitative analysis of large-scale biological image data sets

• Published in: Nature biotechnology 2010-04, Vol.28 (4), p.348-353
• Main Authors: Peng, Hanchuan, Ruan, Zongcai, Long, Fuhui, Simpson, Julie H, Myers, Eugene W
• Format: Article
• Language: English
• Subjects: 3-D graphics; 631/1647/245/2221; 692/700/1421/65; Agriculture; Bioinformatics; Biological and medical sciences; Biomedical and Life Sciences; Biomedical Engineering/Biotechnology; Biomedical research; Biomedicine; Biotechnology; Brain; Computational biology; Computer Graphics; Computer programs; Databases, Factual; Diverse techniques; Ergonomics; Fundamental and applied biological sciences. Psychology; General aspects. Models. Methods; Image Interpretation, Computer-Assisted - methods; Image processing; Imaging systems; Imaging, Three-Dimensional - methods; Information Storage and Retrieval - methods; Life Sciences; Medical imaging; Microscopy; Microscopy - methods; Molecular and cellular biology; Probes; Properties; Radiology Information Systems; Technology application; Three-dimensional graphics; User-Computer Interface; Vertebrates: nervous system and sense organs
• ISSN: 1087-0156; 1546-1696
• DOI: 10.1038/nbt.1612

High-throughput imaging generates massive data sets that are difficult to quantitatively analyze by hand. Peng et al . describe customizable software for visualizing and working with multi-gigabyte three-dimensional images in real time. The V3D system provides three-dimensional (3D) visualization of gigabyte-sized microscopy image stacks in real time on current laptops and desktops. V3D streamlines the online analysis, measurement and proofreading of complicated image patterns by combining ergonomic functions for selecting a location in an image directly in 3D space and for displaying biological measurements, such as from fluorescent probes, using the overlaid surface objects. V3D runs on all major computer platforms and can be enhanced by software plug-ins to address specific biological problems. To demonstrate this extensibility, we built a V3D-based application, V3D-Neuron, to reconstruct complex 3D neuronal structures from high-resolution brain images. V3D-Neuron can precisely digitize the morphology of a single neuron in a fruitfly brain in minutes, with about a 17-fold improvement in reliability and tenfold savings in time compared with other neuron reconstruction tools. Using V3D-Neuron, we demonstrate the feasibility of building a 3D digital atlas of neurite tracts in the fruitfly brain.