Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2010 Apr;28(4):348-53.
doi: 10.1038/nbt.1612. Epub 2010 Mar 14.

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

Hanchuan Peng  1 , Zongcai Ruan, Fuhui Long, Julie H Simpson, Eugene W Myers
Affiliations

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

Hanchuan Peng et al. Nat Biotechnol. 2010 Apr.

Abstract

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.

PubMed Disclaimer

Figures

Figure 1
Figure 1
V3D visualization. (a) The use of V3D in visualizing a 3D digital model of a fruit fly brain. Magenta voxels: the 3D volumetric image of a fruit fly brain; green voxels: a 3D GAL4 neurite pattern; colored surface objects of irregular shapes: digital models of various brain compartments; colored tree-like surface objects: 3D reconstructed neurons. (b) The volumetric image rendering speed of V3D visualization engine under synchronous and asynchronous modes. For each image size, both the peak speed (green and yellow bars) and the respective standard deviation (black line-ranges) of at least 10 speed-test trials are shown. The tests were done on a 64bit Redhat Linux machine with a GTX280 graphics card. (c) V3D hierarchical visualization and analysis. Local 3D viewers of different brain regions can be conveniently initialized from the global viewer. Local viewers can have their own color maps and surface objects independent of the global viewer. They can also be used to analyze sub-volumes of an image separately.
Figure 1
Figure 1
V3D visualization. (a) The use of V3D in visualizing a 3D digital model of a fruit fly brain. Magenta voxels: the 3D volumetric image of a fruit fly brain; green voxels: a 3D GAL4 neurite pattern; colored surface objects of irregular shapes: digital models of various brain compartments; colored tree-like surface objects: 3D reconstructed neurons. (b) The volumetric image rendering speed of V3D visualization engine under synchronous and asynchronous modes. For each image size, both the peak speed (green and yellow bars) and the respective standard deviation (black line-ranges) of at least 10 speed-test trials are shown. The tests were done on a 64bit Redhat Linux machine with a GTX280 graphics card. (c) V3D hierarchical visualization and analysis. Local 3D viewers of different brain regions can be conveniently initialized from the global viewer. Local viewers can have their own color maps and surface objects independent of the global viewer. They can also be used to analyze sub-volumes of an image separately.
Figure 1
Figure 1
V3D visualization. (a) The use of V3D in visualizing a 3D digital model of a fruit fly brain. Magenta voxels: the 3D volumetric image of a fruit fly brain; green voxels: a 3D GAL4 neurite pattern; colored surface objects of irregular shapes: digital models of various brain compartments; colored tree-like surface objects: 3D reconstructed neurons. (b) The volumetric image rendering speed of V3D visualization engine under synchronous and asynchronous modes. For each image size, both the peak speed (green and yellow bars) and the respective standard deviation (black line-ranges) of at least 10 speed-test trials are shown. The tests were done on a 64bit Redhat Linux machine with a GTX280 graphics card. (c) V3D hierarchical visualization and analysis. Local 3D viewers of different brain regions can be conveniently initialized from the global viewer. Local viewers can have their own color maps and surface objects independent of the global viewer. They can also be used to analyze sub-volumes of an image separately.
Figure 2
Figure 2
3D pinpointing methods of V3D. (a) 3D pinpointing using 2 mouse-clicks. The color image is a 3D confocal image of neurons, fluorescently tagged for three different transcriptional factors (repo, eve, and hb9) at the same time, in a fruit fly embryo. A and B: non-parallel rays generated at two viewing angles, corresponding to two mouse-clicks; p: the estimated 3D location that is closest to both A and B. (b) 3D pinpointing using 1 mouse-click. p1 to pN: the progressively estimated centers of mass; R1 to RN: the progressively smaller intervals to estimate p1 to pN.
Figure 2
Figure 2
3D pinpointing methods of V3D. (a) 3D pinpointing using 2 mouse-clicks. The color image is a 3D confocal image of neurons, fluorescently tagged for three different transcriptional factors (repo, eve, and hb9) at the same time, in a fruit fly embryo. A and B: non-parallel rays generated at two viewing angles, corresponding to two mouse-clicks; p: the estimated 3D location that is closest to both A and B. (b) 3D pinpointing using 1 mouse-click. p1 to pN: the progressively estimated centers of mass; R1 to RN: the progressively smaller intervals to estimate p1 to pN.
Figure 3
Figure 3
Quantitative measuring of 3D gene expression gradient in a C. elegans confocal image. Green voxels: myo3:GFP-tagged body wall muscle cells; blue voxels: DAPI (4,6-diamidino-2-phenylindole)-tagged nuclei for the entire animal; colored spheres: pinpointed markers; colored line-segments: the line-indicator for measuring along different directions and with different starting and ending locations; line profile graph: the channel-by-channel display of the voxel intensity along a line segment.
Figure 4
Figure 4
V3D-Neuron tracing. (a) Pinpointing terminals of a fruit fly neuron. 3D image: a GFP-tagged neuron produced via twin-spot MARCM; colored spheres: markers defined for the tips of this neuron. (b) 3D reconstructed neuron produced by V3D-Neuron. Colored segments: the automatically reconstructed neurite structures. (c) The skeleton view of the 3D reconstructed neuron.
Figure 4
Figure 4
V3D-Neuron tracing. (a) Pinpointing terminals of a fruit fly neuron. 3D image: a GFP-tagged neuron produced via twin-spot MARCM; colored spheres: markers defined for the tips of this neuron. (b) 3D reconstructed neuron produced by V3D-Neuron. Colored segments: the automatically reconstructed neurite structures. (c) The skeleton view of the 3D reconstructed neuron.
Figure 4
Figure 4
V3D-Neuron tracing. (a) Pinpointing terminals of a fruit fly neuron. 3D image: a GFP-tagged neuron produced via twin-spot MARCM; colored spheres: markers defined for the tips of this neuron. (b) 3D reconstructed neuron produced by V3D-Neuron. Colored segments: the automatically reconstructed neurite structures. (c) The skeleton view of the 3D reconstructed neuron.
Figure 5
Figure 5
The accuracy of V3D-Neuron reconstructions compared with manual reconstructions. (a) Inconsistency of independent trials of reconstructions. e1, e2, e3, e4: examples of the obvious inconsistent parts in manual reconstructions; e5: an example of the inconsistent region in V3D-Neuron reconstructions. (b) The spatial divergence of reconstructed neurons using different methods, each with two independent runs. Also shown in the legend are the average and the standard deviation of the spatial divergence (see Methods) of all neurons. (c) The percent of the neuron structure that noticeably varies in independent reconstructions. Also shown in the legend are the average and the standard deviation of this score over all neurons. SSD: substantial spatial distance.
Figure 5
Figure 5
The accuracy of V3D-Neuron reconstructions compared with manual reconstructions. (a) Inconsistency of independent trials of reconstructions. e1, e2, e3, e4: examples of the obvious inconsistent parts in manual reconstructions; e5: an example of the inconsistent region in V3D-Neuron reconstructions. (b) The spatial divergence of reconstructed neurons using different methods, each with two independent runs. Also shown in the legend are the average and the standard deviation of the spatial divergence (see Methods) of all neurons. (c) The percent of the neuron structure that noticeably varies in independent reconstructions. Also shown in the legend are the average and the standard deviation of this score over all neurons. SSD: substantial spatial distance.
Figure 5
Figure 5
The accuracy of V3D-Neuron reconstructions compared with manual reconstructions. (a) Inconsistency of independent trials of reconstructions. e1, e2, e3, e4: examples of the obvious inconsistent parts in manual reconstructions; e5: an example of the inconsistent region in V3D-Neuron reconstructions. (b) The spatial divergence of reconstructed neurons using different methods, each with two independent runs. Also shown in the legend are the average and the standard deviation of the spatial divergence (see Methods) of all neurons. (c) The percent of the neuron structure that noticeably varies in independent reconstructions. Also shown in the legend are the average and the standard deviation of this score over all neurons. SSD: substantial spatial distance.
Figure 6
Figure 6
An atlas of stereotyped neurite tracts in a fruit fly brain. (a) Statistical models of the 3D reconstructed neurite tracts. Grayscale image: a fruit fly brain; each colored tubular structure: the average of multiple neurite tracts reconstructed from images of the same GAL4 line. The width of the each tract equals twice of the spatial variation of the respective group of reconstructions. (b) Distribution of the spatial variation of all neurite tracts.
Figure 6
Figure 6
An atlas of stereotyped neurite tracts in a fruit fly brain. (a) Statistical models of the 3D reconstructed neurite tracts. Grayscale image: a fruit fly brain; each colored tubular structure: the average of multiple neurite tracts reconstructed from images of the same GAL4 line. The width of the each tract equals twice of the spatial variation of the respective group of reconstructions. (b) Distribution of the spatial variation of all neurite tracts.
See this image and copyright information in PMC

Comment in

  • Connecting the dots in 3D.
    Evanko D. Evanko D. Nat Methods. 2010 May;7(5):344-5. doi: 10.1038/nmeth0510-344a. Nat Methods. 2010. PMID: 20440880 No abstract available.

References

    1. Peng H. Bioimage informatics: a new area of engineering biology. Bioinformatics. 2008;24(17):1827–1836. - PMC - PubMed
    1. Wilt BA, Burns LD, Wei Ho ET, Ghosh KK, Mukamel EA, Schnitzer MJ. Advances in light microscopy for neuroscience. Annual Rev Neurosci. 2009;32:435–506. - PMC - PubMed
    1. Abramoff MD, Magelhaes PJ, Ram SJ. Image Processing with ImageJ. Biophotonics International. 2004;11(7):36–42.
    1. Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE. UCSF Chimera-a visualization system for exploratory research and analysis. J Comput Chem. 2004;25(13):1605–1612. - PubMed
    1. Schroeder W, Martin K, Lorensen B. Visualization Toolkit: An Object-Oriented Approach to 3D Graphics. 4. (Hardcover), Kitware, Inc; Clifton Park, NY: 2006.

Publication types

MeSH terms