3D Visulization of Volumetric Data
surface contour, with the intensity of the contour set such that only platinum is visible. Save and share . Whilst a high-quality manuscript fi gure can convey a sense of 3D structure, it is no substitute for interactive visualization and exploration of a volumetric dataset. With tomviz , the data, visualization pipeline, and soſt ware can all be shared with other scientists. Simply click “File > Save State” to share the tomviz state fi le (*.tvsm) and volumetric data with colleagues. For scientifi c publication, a screenshot of the visual- ization can be exported using the existing background or a transparent background by executing “File > Save Screenshot.” Open-source license . Tomviz is made freely and publicly available as open-source soſt ware under the 3-clause BSD License that enables any party to copy, distribute, and make modifi cations to the soſt ware. T is includes government organizations, for-profi t and not-for-profi t educational institutions, and commercial organizations, as well as individuals. Tomviz is hosted on Github and is open to further contributions from new users.
Conclusion
Figure 5 : Volume rendering of the Co 2 P nanoparticle from Figure 4 , enclosed in a bounding box with scale markers in nanometers shown on each axis of the box. Using perspective, the bounding box and scale together convey a sense of the 3D size of the particle. The color-opacity map of the volume render is shown underneath the visualization.
High-quality, visualizations of 3D volumetric datasets are essential for interpreting and sharing tomographic data. In this tutorial, we have used the open-source tomviz soſt ware package to review the range in which volumetric data can be represented and explored—including 2D slices, surface contours, volume rendering, and combinations thereof. Ultimately, the fi nal visualization will depend on the questions, goals, and aesthetic of the researcher. Readers are encouraged to explore these techniques further using their own datasets, or using publicly available STEM tomography datasets [ 10 ].
Acknowledgements T is work was supported by DOE Offi ce of Science contract DE-SC0011385. T e authors thank the many open-source developers and electron microscopists who have given valuable feedback and other contributions to the tomviz project. Elliot Padgett acknowledges support from NSF graduate research fellowship, DGE-1650441.
References [1] GN Hounsfi eld , Computed Medical Imaging, Nobel Lectures, Physiology or Medicine 1971-1980, ed. J Lindsten, World Scientifi c Publishing Co. , Singapore , 1992 .
[2] DJ DeRosier and A Klug , Nature 217 ( 1968 ) 130 – 34 . [3] RA Crowther et al ., Proc R Soc London, Ser A 317 ( 1970 ) 319 – 40 .
[4] M Weyland et al ., J Phys Chem B 105 ( 2001 ) 7882 – 86 . [5] BJ Inkson et al ., Scr Mater 45 ( 2001 ) 753 –5 8 . [6] A Cerezo et al ., Rev Sci Instrum 59 ( 1988 ) 862 . [7] A Cerezo et al ., Mater Today 10 ( 12 ) (2007 ) 36 – 42 . [8] DH Phillips and JJ Lannutti , NDT&E International 30 ( 6 ) (1997 ) 339 – 50 .
Figure 6 : Still image from an animation of platinum particles (turquoise color) on a carbon fi ber. The animation is available online in the digital edition of this issue at this web address:
https://doi.org/10.1017/S1551929517001213 .
with an intensity corresponding to the carbon fi ber are visible. T e platinum nanoparticles are visualized using a turquoise
16
[9] P Cueva et al ., Microsc Microanal 18 ( 2012 ) 667 – 75 . [10] BDA Levin et al ., Sci Data 3 ( 2016 ) 160041 . [11] WE Lorenson and HE Cline , ACM SIGGRAPH Computer Graphics 21 ( 4 ) (1987 ) 163 – 9 .
[12] W Schroeder et al ., IEEE 5th Symposium on Large Data Analysis and Visualization (LDAV), Chicago , 2015 , p. 33 – 40 . [13] A Kaufman et al ., Computer 26 ( 7 ) (1993 ) 51 – 64 .
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