To the Editor —
New popular microscopy techniques such as structured illumination microscopy (SIM), selective plane illumination microscopy (SPIM) and optical projection tomography (OPT) as well as many other biomedical imaging modalities (magnetic resonance imaging (MRI), X-ray computed tomography) generate an explosive amount of volumetric data. Techniques such as SPIM capture >50 million voxels per minute, generating tens of terabytes of data per sample1. It is now possible to image whole organs and even animals at single-cell resolution to produce so-called digital embryos2. While highly specialized software packages are available for the analysis and visualization of such data, their use requires expert skills and they are often expensive. Furthermore, their capacity to share data is limited and there are no means for interactive exploration of the data by third parties.
We wish to inform the readers of Nature Photonics that we have developed an easy-to-use and powerful open-source visualization tool that enables researchers to share their volumetric image data online. The tool, called First Person Bioimage (FPBioimage), allows third parties to view and interact with datasets in their entirety. It can be downloaded for free at our website http://fpb.ceb.cam.ac.uk. FPBioimage provides the viewer with an immersive experience for the exploration of complex 3D data. It makes use of the latest graphics capabilities embedded in all modern web browsers, and therefore no separate software is required for viewing. The tool is fast and user responsive, requires no training for use, and includes advanced rendering and data manipulation capabilities. Data can be intuitively explored from a 'first-person perspective', akin to navigating virtual space in modern computer games, allowing users to conceptualize and contextualize details in the data to aid biological and physical interpretation (see Supplementary Movie 1).
Figure 1 shows screenshots of datasets obtained with OPT3, MRI4 and light-sheet microscopy2, demonstrating different rendering and data manipulation capabilities. Although the tool was originally conceived for use in conjunction with bioimaging data, it is suited for the visualization of any volumetric data. Other examples shown in Supplementary Figs 1–8 include the volumetric visualization of atomic wavefunctions and 3D electric fields in photonic devices. We have also ported FPBioimage to the Android and iOS mobile platforms for viewing on hand-held devices. For a truly immersive experience of the data the mobile app supports a virtual reality mode for viewing with a virtual reality headset (see Supplementary Movie 2).
From a researcher's perspective the tool now makes it possible to easily share volumetric data globally, providing anyone full and interactive access to the data via a web browser. In future, we hope this changes the way research data are shared and suggest that publishers will use the software as a tool for online publication. Data can thus be shared in their entirety, moving on from the current practice of providing selective views or movies shown from a single perspective, which are not capable of providing a full understanding of the data.
References
Reynaud, E., Peychi, J., Huisken, J. & Tomancak, P. Nat. Methods 12, 30–34 (2015).
Chhetri, R. et al. Nat. Methods 12, 1171–1178 (2015).
Sharpe, J. et al. Science 296, 541–545 (2002).
Levoy, M. IEEE Comput. Graph. Appl. 8, 29–37 (1988).
Acknowledgements
We thank M. Mantle, P. Keller, R. Chhetri, J. Swoger and J. McGinty for the provision of volumetric image data. This work was sponsored by the Engineering and Physical Sciences Research Council (EPSRC) UK, the Medical Research Council (MRC) UK and the Wellcome Trust.
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Supplementary Figures
An example of FPBioimage rendering a magnetic resonance imaging (MRI) scan of a human head, obtained from the Stanford Volume Archive1. (PDF 15520 kb)
Supplementary Movie 1
Supplementary Movie 1 (MP4 30598 kb)
Supplementary Movie 2
Supplementary Movie 2 (MP4 29796 kb)
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Fantham, M., Kaminski, C. A new online tool for visualization of volumetric data. Nature Photon 11, 69 (2017). https://doi.org/10.1038/nphoton.2016.273
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DOI: https://doi.org/10.1038/nphoton.2016.273
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