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TeraFly: real-time three-dimensional visualization and annotation of terabytes of multidimensional volumetric images

Nature Methods volume 13, pages 192–194 (2016)Cite this article

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To the Editor:

New sample preparation and high-throughput light-sheet microscopy techniques1 are increasingly capable of generating multidimensional (3D and higher) images easily exceeding the terabyte size. This has posed a significant challenge for scalable interactive visualization and quantitative annotation of such big image data. A common practice is to design a data-streaming and visualization tool to supply and display small parts of an image volume when needed2,3. However, existing tools allow only 2D slice-based rendering of 3D image stacks. Such 2D approaches not only are time consuming and low throughput but also bring bias to the understanding of intrinsic 3D properties of bioimage data4. A free, open-source and cross-platform software tool for true 3D visualization and 3D annotation of very large multidimensional volumes is highly desired (Supplementary Note 1).

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Figure 1: Overview of TeraFly image and surface-object visualization.

References

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Acknowledgements

We thank F.S. Pavone, L. Sacconi, L. Silvestri, J.P. Ghobril, R. Tsien, H. Zeng, P. Keller and E. Betzig for providing the data sets we used in this work, as well as for the useful discussions that helped us in the requirement analysis of our tool.

Author information

Author notes

  1. hanchuanp@alleninstituite.org.

Authors and Affiliations

  1. Department of Engineering, University Campus Bio-Medico of Rome, Rome, Italy

    Alessandro Bria, Giulio Iannello & Leonardo Onofri

  2. Department of Electrical and Information Engineering, University of Cassino and Southern Lazio, Cassino, Italy

    Alessandro Bria

  3. Allen Institute for Brain Science, Seattle, Washington, USA

    Alessandro Bria & Hanchuan Peng

Authors
  1. Alessandro Bria
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  2. Giulio Iannello
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  3. Leonardo Onofri
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  4. Hanchuan Peng
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Supplementary information

Supplementary Text

Supplementary Notes 1–7 (PDF 3429 kb)

Supplementary Video 1

Instant three-dimensional visualization of a 0.8-terabyte image. Image: entire brain of a L1-GFP mouse acquired using light sheet microscopy (courtesy of F.S. Pavone, L. Sacconi, L. Silvestri). In this video, the user zooms-in and out with the mouse scroll through all image resolution levels. (AVI 18657 kb)

Supplementary Video 2

Instant three-dimensional visualization of a 110-gigabyte image stored in BigDataViewer HDF5 format. Image: entire cerebellum of a L1-GFP mouse acquired using light sheet microscopy (courtesy of F.S. Pavone, L. Sacconi, L. Silvestri). Compared to Supplementary Video 1, in which the image was stored in TeraFly's format, this video shows again a real-time visualization performance, thus demonstrating that TeraFly does not rely on the optimization of the input data organization. (MP4 40395 kb)

Supplementary Video 3

Three-dimensional proofreading of automatic Purkinje cell counts in a 110-gigabyte image. Image: entire cerebellum of a L1-GFP mouse acquired using confocal light sheet microscopy (courtesy of F.S. Pavone, L. Sacconi, L. Silvestri). In this video, the user first sets up the proofreading session by choosing the volume of interest coordinates, blocks overlap and blocks size and then starts the block-by-block scan. Empty blocks are quickly skipped thanks to a scrollable instant preview of blocks content. Using a series of Virtual Finger-based display and annotation tools, fast and accurate proofreading of cell counts is achieved. (AVI 50063 kb)

Supplementary Video 4

Two-dimensional proofreading of automatic Purkinje cell counts with ImageJ (Cell Counter plugin). Image: 300×300×300 voxels image stack from entire cerebellum of a L1-GFP mouse acquired using light sheet microscopy (courtesy of F.S. Pavone, L. Sacconi, L. Silvestri). Compared to Supplementary Video 2, this video shows the difference in terms of proofreading speed and precision between TeraFly (3D-based) and ImageJ Cell Counter (2D-based). Specifically, here it is more difficult to locate false positives, since markers are too small and overlaid only on a single slice. (AVI 11048 kb)

Supplementary Video 5

Two-dimensional proofreading of automatic Purkinje cell counts with MaMuT/BigDataViewer. Image: 1,020×1,020×1,020 voxels image stack from entire cerebellum of a L1-GFP mouse acquired using light sheet microscopy (courtesy of F.S. Pavone, L. Sacconi, L. Silvestri. Compared to Supplementary Video 2, this video shows the difference in terms of proofreading speed and precision between TeraFly (3D-based) and MaMuT/BigDataViewer (2D-based). Specifically, here the removal of false positives is done slice-by-slice with several user operations, whereas in TeraFly it can be done directly in 3D with just one mouse right-stroke. (MP4 128922 kb)

Supplementary Video 6

Vaa3D-TeraFly-assisted three-dimensional tracing of a rat neuron. Image: rat neuron image acquired using 2-photon microscopy (courtesy of R. Tisen). In this video, the user zooms-in through all image resolution scales to trace neurites of various thickness. (MP4 336820 kb)

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Bria, A., Iannello, G., Onofri, L. et al. TeraFly: real-time three-dimensional visualization and annotation of terabytes of multidimensional volumetric images. Nat Methods 13, 192–194 (2016). https://doi.org/10.1038/nmeth.3767

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