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

Nature Biotechnology 28, 348–353 (2010) | Download Citation

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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.

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Acknowledgements

This work is supported by Howard Hughes Medical Institute. We thank B. Lam, Y. Yu, L. Qu, and Y. Zhuang (Janelia, HHMI) in helping reconstruction of neurites, Y. Yu and L. Qu (Janelia, HHMI) for developing some V3D plug-ins, S. Kim and X. Liu (Stanford) for C. elegans confocal images, R. Kerr and B. Rollins (Janelia, HHMI) for the 5D C. elegans SPIM images, T. Lee and H. Yu (Janelia, HHMI) for single neuron images, C. Doe (Univ. of Oregon, HHMI) for fruitfly embryo images, A. Jenett (Janelia, HHMI) for fly brain compartments, P. Chung (Janelia, HHMI) for the raw images of fruitfly GAL4 lines, S. Sternson and Y. Aponte (Janelia, HHMI) for the mouse brain image, and K. Eliceiri and C. Rueden (Univ. of Wisconsin, Madison) for assistance in implementing a V3D plug-in. We also thank G. Rubin, and R. Kerr (Janelia, HHMI) for helpful comments on the manuscript.

Author information

Affiliations

  1. Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, USA.

    • Hanchuan Peng
    • , Zongcai Ruan
    • , Fuhui Long
    • , Julie H Simpson
    •  & Eugene W Myers

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Contributions

H.P. designed this research and developed the algorithms and systems, did the experiments and wrote the manuscript. Z.R. and F.L. helped develop the systems. J.H.S. provided raw images for building the neurite atlas. E.W.M. supported the initial proposal of a fast 3D volumetric image renderer. E.W.M., F.L. and J.H.S. helped write the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Hanchuan Peng.

Supplementary information

PDF files

  1. 1.

    Supplementary Text and Figures

    Supplementary Figs. 1–3 and Supplementary Note

Videos

  1. 1.

    Supplementary Video 1

    3D visualization of a 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: two 3D reconstructed neurons.

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    Supplementary Video 2a

    Hierarchical visualization of a fruit fly brain: The global 3D viewer.

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    Supplementary Video 2b

    Hierarchical visualization of a fruit fly brain: Local 3D viewer for region A of Fig. 1c.

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    Supplementary Video 2c

    Hierarchical visualization of a fruit fly brain: The local 3D viewer for region B in Fig. 1c is used for tracing neurite and proofreading the reconstruction in 3D.

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    Supplementary Video 3a

    3D pinpointing methods in V3D: Pinpointing using 2-clicks.

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    Supplementary Video 3b

    3D pinpointing methods in V3D: Pinpointing using 1-click.

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    Supplementary Video 4

    3D counting of neurons in the arcuate nucleus of the hypothalamus of a mouse brain. For better visibility, only a small trunk of data is displayed. Red: AgrP neurons infected with FLEX-AAV-ChR2-td-tomato virus; blue: DAPI staining indicating the cell bodies of neurons; green spheres: markers indicating the locations of neurons.

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    Supplementary Video 5

    5D volumetric image visualization and quantitative measuring for C. elegans neurons. A series of SPIM images (Supplementary Figure 3) were used. The neuron centers 1~8 were directly pinpointed. 3D line segments were defined between them for profiling both voxel intensity and distance between the moving neurons.

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    Supplementary Video 6

    The use of V3D-Neuron in visualization, reconstruction, and proofreading of the 3D morphology of a fruit fly neuron.

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    Supplementary Video 7

    A 3D atlas of 111 stereotyped neurite tracts in a fruit fly brain. The width of a tract indicates the spatial variation of its location.

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    Supplementary Video 8

    V3D-Neuron can display a neuron in multiple ways (see Methods).

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    Supplementary Video 9

    Editing a neuron using V3D-Neuron (see Methods).

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    Supplementary Video 10

    Display of multiple neurons in V3D-Neuron. The first half shows how to display the atlas of fruit fly neurite tracts in Figure 6. The second half shows how to display multiple mouse brain neurons.

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  1. 1.

    Supplementary Software

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    Supplementary Data

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DOI

https://doi.org/10.1038/nbt.1612