3D Visulization of Volumetric Data
Figure 4 : Volume renderings of a Co 2 P nanoparticle [ 10 ] viewed from different perspectives using Grayscale, Plasma, and Viridis color-opacity maps. In these renderings, the dense internal core of the nanoparticle is displayed in lighter, more opaque colors, whilst the branches that protrude from the core are displayed as darker and more transparent colors. The color-opacity maps used in the visualizations are shown below each view of the particle.
the surface is changed, following the color map. Alternatively, the user can choose to use a fi xed color for all surfaces. Figure 3 shows diff erent isosurfaces of a porous PtCu nanoparticle with a fi xed color, and diff erent combinations of intensity and opacity. At full opacity, only the exterior of a surface can be visualized. Reducing the opacity of a surface contour allows the surface of interior structures, such as pores, to be visualized.
III. Volume rendering . Volume rendering was originally developed to visualize more complex 3D structures with many gray values, which are diffi cult to visualize by surface rendering [ 13 ]. In volume rendering, each voxel is assigned both a color and an opacity based on its intensity. T e gray line overlaying the histogram of the data in the tomviz interface ( Figure 1d ) is the opacity map of the visualization, and together with the color map, this defi nes the color-opacity map. Figure 4 shows example volume renderings of a Co 2 P star-shaped nanoparticle at diff erent viewing angles, with their associated color-opacity maps. In tomviz , the color-opacity map can be adjusted interac- tively with dynamically updated 3D visualizations. T e user may simply click and drag a point on the gray line overlaying the histogram to vary the opacity of diff erent voxels in the volume render. In the examples shown in Figure 4 , the color- opacity map has been set so that the opacity increases with increasing voxel intensity, and the color becomes increasingly light with increasing voxel intensity. T e range of the color map has been adjusted to enhance the brightness and contrast of the visualization. Minor adjustments to the color-opacity map can have a noticeable infl uence on the fi nal appearance of the visualization of an object. It is essential for users to adjust the color-opacity map to produce a volumetric visualization
2018 January •
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that refl ects the features of the sample that they have imaged. In addition, it is important to include the color-opacity map with any published scientifi c volumetric renderings to aid interpretation.
Bounding boxes and scale . A bounding box frame outlines the edges of a dataset, giving the viewer an impression of 3D depth perception with a non-orthogonal perspective on a 2D screen. In the same way that a parallel set of train tracks converges into the distance in the real world, so do most 3D visualizations—features in the foreground appear larger. A bounding box adds more than aesthetic appeal because it helps restore the interpretability of a 3D structure rendered on a 2D screen. Most of all, a bounding box allows scientists to put meaningful scale bars along an edge. In tomviz , voxel distances can be displayed by selecting “View > Show Axis Grid.” An example visualization with dimensional scales is shown in Figure 5 .
Animation . In addition to 2D fi gures, an animation of a 3D visualization is an eff ective method of illustrating the 3D structure of an object. In tomviz , an animation tool allows users to produce simple animations, such as a 360 o orbit around a 3D object, or more complex animations by moving the viewing angle between a series of user-specifi ed positions. A still from an animation is shown in Figure 6. T e full animation is available online in the digital edition of this issue at this web address:
https://doi.org/10.1017/S1551929517001213 . T is animation shows a mixed volume and surface rendering of platinum nanoparticles decorating a carbon nanofi ber of ~170 nm in diameter. T e carbon fi ber is visualized in black using a volume render, with the color-opacity map set such that only voxels
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