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

By Hanchuan Peng, Zongcai Ruan, Fuhui Long, Julie H. Simpson, Eugene W. Myers. Nature Biotechnology, 2010

721 citations recorded by the source corpus.

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.

Subfields: Biophysics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/be7f7288313cde6123c462b6db02ef0863c63a82

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Citations in the corpus

MorphoGraphX: A platform for quantifying morphogenesis in 4D (2015, methodology): “We have also included a range of standard 3D image processing tools, similar to those available in many other softwares ( Fernandez et al., 2010 ; Peng et al., 2010 ; Sommer et al., 2011 ; Federici et al., 2012 ; Mosaliganti et al., 2012 ; Schmidt et al., 2014 ).”
Microscopy Image Browser: A Platform for Segmentation and Analysis of Multidimensional Datasets (2016, methodology): “In other cases, the models may be saved in the TIF format for free packages such as BioImageXD [5], Drishti [36], or Vaa3D (Fig 4) [37].”
Neuron tracing in perspective (2010, methodology): “A more versatile visualization tool is V3D (106), which supports up to 5D rendering (spatially 3D over time and in multiple colors) of image data as well as surface data, relational data that can be described as a graph (such as neuronal data), point clouds, and landmarks.”
Extensible visualization and analysis for multidimensional images using Vaa3D (2014, background): “Combined with advanced rendering modes, such as asynchronous rendering 20 and especially with local 3D viewers, the system is able to visualize multigigabyte images simultaneously at both high speed and high resolution.”
iDISCO: a simple, rapid method to immunolabel large tissue samples for volume imaging. (2014, positive): “Simple 3D projections were performed with VAA3D (Peng et al., 2010) on desktopclass computers.”
Biological Imaging Software Tools (2012, methodology): “The speed usually results from the exploitation of hardware graphics processing engines and careful software optimization such as that used in the Vaa3D software 21 .”