3D Visulization of Volumetric Data


3D Visualization Techniques for Volumetric Data T ree principal visualization methods are available in tomviz : slicing, surface rendering, and volume rendering. T e visualization method used to produce the fi nal 3D visualization can be highly variable depending on the dataset, the scientifi c questions to be answered, and aesthetic preference.


I. Slicing data with planes .


Figure 2 : A volumetric reconstruction of platinum nanoparticles on a carbon nanofi ber [ 10 ], showing the position of an extracted orthogonal slice. In the extracted slice, platinum nanoparticles (white/orange) can be identifi ed on both the interior and exterior surfaces of the nanofi ber (magenta).


T e simplest method for detailed examination of specifi c features of the internal 3D structure of an object is to inspect individual 2D sections—or slices—through the 3D dataset. T e tomviz package features two diff erent slice viewing tools. Orthogonal slicing allows users to view slices through the data perpendicular to one of the principal x , y , or z axes. Both the plane ( x , y , or z ), and the position of the slice can be altered interactively in the Properties panel ( Figure 1b ), as can the opacity/transparency of the slice. An example of orthogonal slicing is shown in Figure 2 . In this fi gure, an orthogonal slice is extracted from the center of a reconstruction of platinum nanoparticles on a carbon nanofi ber support. Platinum nanoparticles can be seen on both the interior and exterior surfaces of the nanofi ber in this slice. Non-orthogonal slicing off ers


Figure 3 : Surface renderings of a porous PtCu nanoparticle [ 10 ] at different values of intensity and surface opacity. At full opacity, only the exterior of a surface contour is visible. At low intensity, this exterior surface contour corresponds to the exterior surface of the nanoparticle. As the intensity of a surface contour is increased, features of the interior of the particle become visible. Varying the opacity at lower intensity allows the user to see through the exterior surface and observe the interior surfaces of the nebulous internal pore structure of the particle.


dataset values. T is color map corresponds only to the dataset currently selected under Pipelines . Diff erent color maps can be chosen from a list of presets, or the map may be adjusted interactively by clicking and dragging points on the color bar underneath the histogram. By default, tomviz automatically adds a box outline and an orthogonal slice taken through the volume center in a Render View panel. Users may then add new visualizations of their own to the default Render View panel ( Figure 1e ). Additional Render View panels can be added from the Toolbar: , allowing multiple visualizations to be shown


simultaneously in separate panels, at diff erent viewing angles ( Figure 1f , Figure 1g ).


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greater fl exibility, allowing users to view slices through the reconstruction at any orientation. T e orientation and position of a non-orthogonal slice can be adjusted interactively by clicking and dragging the axis and slice in the Render View panel ( Figure 1f ) or manually by entering values in


the Properties panel ( Figure 1b ). II. Surface rendering . Surface rendering was originally applied to volumetric data to off er a more direct method of visualizing the 3D morphology of structures than 2D slices [ 11 ]. In surface rendering, a surface contour of constant intensity is generated from a user-specifi ed intensity value using a fast-fl ying edges algorithm [ 12 ]. In tomviz , the intensity value of the surface contour can be entered manually or adjusted using a slider in the Properties panel ( Figure 1b ). T e color, opacity/ transparency, and lighting (specularity) of a surface render can also be altered in the Properties panel. Surfaces are rendered in a single color. By default, this color will change as the intensity of


www.microscopy-today.com • 2018 January


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