Visualization of Volumetric

Data
into the final result. Ultimately, the software should be able to
produce publication quality figures for scientific articles.
Introduction The open-source tomviz software package aims to meet
This article is a short tutorial on the principles of visual- each of these criteria, whilst also being free to download and
izing complex 3D volumetric datasets, demonstrated using use. Tomviz, can be run on Windows, Mac OS, or Linux
tomviz. Across a diverse range of scientific disciplines, operating systems and is available for download at www.tomviz.
understanding the 3D internal structure of material and org. Tomviz can be run on a laptop and can leverage powerful
biological specimens is essential for scientific progress. There GPUs for visualizing large, intricate datasets. We use tomviz
are numerous methods for characterizing the 3D internal to illustrate this tutorial, but the principles outlined apply to
structure of objects at different length scales, including X-ray other software packages, including the free non-commercial
computed tomography [1], transmission electron microscopy Chimera (University of California at San Francisco) and
(TEM) tomography [2,3], scanning transmission electron various commercial software packages. In the following
microscopy (STEM) tomography [4], focused ion beam– sections, we describe the format of 3D datasets and several
scanning electron microscopy (FIB-SEM) tomography [5], techniques that can be used to visualize the data.
and atom-probe tomography [6,7]. Whatever the
Definitions and the User Interface
application, or the technique used, the volumetric datasets
3D datasets. A data cube refers to any 3D (or higher)
generated by these methods require visualization. Data
array of values—such as a stack of 2D black-and-white
visualization adds more than just aesthetic value to
images representing a spatial volume. Unlike crystallographic
scientific research. High-quality and interpretable
visualization is essential for extracting meaningful and surface data, data cubes grow rapidly—a 1024 × 1024 ×
information from complex 3D structures. 1024 data cube of 32-bit values occupies 4.29 gigabytes of
Visualizing 3D volumetric datasets requires specialized memory. Each 3D element in the data cube is termed a voxel,
software, distinguishable from the more familiar 3D visual- analogous to a pixel in a 2D image. In tomography, each voxel
ization of wireframes (used in animated cinema) or molecular in a data cube contains a value that represents intensity at a
coordinates (crystallography). This specialized software point (x,y,z) in the volume, which may relate to the
requires interactive volume rendering tools, surface rendering composition or some other characteristic of the object at that
tools, and the ability to display cross sections through the point. For example, in medical X-ray computed tomography
volume—at a minimum. Visualizations should be reproducible (CT), higher intensity represents denser material; a human
and shareable, enabling other scientists to inspect and validate head has brighter values at points where the hard skull is
data as well as understand the steps taken to turn the raw data located than where soft brain matter is located [1,8]. In
nanoscale STEM tomography, high-Z gold nanoparticles
appear brighter than low-Z silica nanopar- ticles [4]. Because
intensity values are provided at all voxels, not just at material
surfaces, tomography reveals the entire 3D internal structure
of an object [1].
3D data cubes are not limited to spatial volumes. In
a hyperspectral map the third dimension is spectroscopic (x-y-
wavelength, or x-y-energy) [9]. In a black-and-white movie,
the third dimension is time (x-y-time). In a tomographic tilt
series, the data cube contains images at different projection
 https://doi.org/10.1017/S1551929517001213 Published online by Cambridge University
3D Visulization of Volumetric Data

angles (x-y-angle). Although tomographic volume data is the volume, and a slice in the case of Figure 1—are listed in the
most directly interpretable, tomviz is capable of visualizing upper left-hand Pipelines (Figure 1a). As the user adds new
any type of 3D data cube. visualization modules to a dataset, these will be displayed in
Loading volumetric data into tomviz. In tomviz, users the pipeline for that dataset. Each dataset that is opened in
can load a variety of datatypes stored as a TIFF, PNG, raw tomviz is assigned its own pipeline. This allows the user to
binary data, MRC, or HDF5 under “File > Open” in the top easily keep track of all changes made to every dataset. Further
menubar. For convenience, tomviz comes packaged with an properties for each selected visualization module or dataset are
example dataset, a “Star Nanoparticle (Reconstruction),” so shown in the lower left-hand Properties Panel (Figure 1b).
users can immediately explore different visualization In addition to a suite of visualization tools—the subject of
techniques. The dataset contains the 3D structure of a Co2P this tutorial—3D data processing is also integrated into the
hyperbranched nanoparticle; it can be opened from the tomviz user interface. A Python console (Figure 1c) can be
menubar under “Sample Data.” For further exploration of opened from “Tools > Python” Console under the top
visualization techniques, five high-quality electron tomography menubar. Users can execute pre-written python scripts or create
datasets from the peer-reviewed literature have been made their own code using numpy, scipy, or ITK. The Data
publicly available for researchers to use (Levin et. al., 2016). Transform and Tomography menus contain pre-written
The datasets can be accessed under “Sample Datasets > algorithms for image processing, alignment, and tomographic
Download More Datasets,” or they can be downloaded at reconstruction of raw electron microscopy data. After these
https:// dx.doi.org/10.6084/m9.figshare.c.2185342. scripts are executed in Python, they are sent back to tomviz for
The tomviz user interface. New visualizations can be immediate visualization. Data transforms appear in the
added from the Visualization menu or by clicking an icon pipeline in the order in which they are executed. Double-
from the Toolbar: clicking on a transform listed in the pipeline opens a new
window displaying the Python code used to implement the
transformation, which the user may edit if desired. The tomviz
pipeline uniquely preserves all steps for reproducible workflow.
All tomviz visualizations are interactive 3D objects that
After a dataset is loaded, a histogram panel appears
can be rotated by clicking and dragging in the render
(Figure 1d). Colors in the histogram represent a colormap that
window(s). The dataset and its associated visualizations—
quantitatively correlates colors in a visualization to
an outline, a
corresponding

Figure 1: The tomviz graphical user interface for 3D visualization of tomographic data. Once a dataset has been loaded, the data pipeline is populated (a). A variety of visualization
types are available to be used in combination for analysis—with parameters specified in the module properties panel (b). A Python interface offers advanced scientific processing of data
(c). A histogram of voxel intensities is displayed top center (d). The line across the histogram represents the opacity map and can be altered interactively. Here a reconstruction of porous
PtCu nanoparticles is visualized using a volume render (e), a non-orthogonal slice through one particle (f), and a contour surface (g). Tabs, and divisions within a tab, allow multiple
2018 January • www.microscopy-today.com 13
simultaneous renderings and camera angles.

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 https://doi.org/10.1017/S1551929517001213 Published online by Cambridge University
3D Visulization of Volumetric Data

3D Visualization Techniques for

Volumetric Data
Three principal visualization
methods are available in tomviz:
slicing, surface rendering, and
volume rendering. The visualization
method used to produce the final 3D
visualization can be highly variable
depending on the dataset, the
scientific questions to be answered,
and aesthetic preference.
I. Slicing data with planes.
The simplest method for detailed
examination of specific features of the
Figure 2: A volumetric reconstruction of platinum nanoparticles on a carbon nanofiber [10], showing the position of an internal 3D structure of an object is
extracted orthogonal slice. In the extracted slice, platinum nanoparticles (white/orange) can be identified on both the interior to inspect individual 2D sections—or
and exterior surfaces of the nanofiber (magenta). slices—through the 3D dataset. The
tomviz package features two different
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
figure, an orthogonal slice is
extracted from the center of a
reconstruction of platinum
nanoparticles on a carbon nanofiber
support. Platinum nanoparticles can
be seen on both the interior and
exterior surfaces of the nanofiber in
this slice.
Non-orthogonal slicing offers
greater flexibility, allowing users to
Figure 3: Surface renderings of a porous PtCu nanoparticle [10] at different values of intensity and surface opacity. view slices through the
At full opacity, only the exterior of a surface contour is visible. At low intensity, this exterior surface contour corresponds to the reconstruction at any orientation.
exterior surface of the nanoparticle. As the intensity of a surface contour is increased, features of the interior of the particle The orientation and position of a
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. non-orthogonal slice can be adjusted
interactively by clicking and
dragging the axis and slice in the
Render View panel (Figure
dataset values. This color map corresponds only to the dataset 1f) or manually by entering values in
currently selected under Pipelines. Different color maps can the Properties panel (Figure 1b).
be chosen from a list of presets, or the map may be adjusted , allowing multiple visualizations to be shown
interactively by clicking and dragging points on the color bar simultaneously in separate panels, at different viewing angles
underneath the histogram. (Figure 1f, Figure 1g).
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:

2018 January • www.microscopy-today.com 15

 II. Surface rendering. Surface rendering was
originally
applied to volumetric data to offer 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-specified intensity value
using a fast-flying 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).
The 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

16 www.microscopy-today.com • 2018 January

 https://doi.org/10.1017/S1551929517001213 Published online by Cambridge University
3D Visulization of Volumetric Data

Figure 4: Volume renderings of a Co2P 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,

that reflects the features of the sample that they have imaged.
the user can choose to use a fixed color for all surfaces. Figure
In addition, it is important to include the color-opacity map
3 shows different isosurfaces of a porous PtCu nanoparticle
with any published scientific volumetric renderings to aid
with a fixed color, and different combinations of intensity
and opacity. At full opacity, only the exterior of a surface interpretation.
can be visualized. Reducing the opacity of a surface contour Bounding boxes and scale. A bounding box frame
allows the surface of interior structures, such as pores, to be outlines the edges of a dataset, giving the viewer an
visualized. impression of 3D depth perception with a non-orthogonal
III. Volume rendering. Volume rendering was originally perspective on a 2D screen. In the same way that a parallel set
developed to visualize more complex 3D structures with many of train tracks converges into the distance in the real world, so
gray values, which are difficult to visualize by surface rendering do most 3D visualizations—features in the foreground appear
[13]. In volume rendering, each voxel is assigned both a color larger. A bounding box adds more than aesthetic appeal
and an opacity based on its intensity. The gray line overlaying because it helps restore the interpretability of a 3D structure
the histogram of the data in the tomviz interface (Figure 1d) rendered on a 2D screen. Most of all, a bounding box allows
is the opacity map of the visualization, and together with the scientists to put meaningful scale bars along an edge. In
color map, this defines the color-opacity map. Figure 4 shows tomviz, voxel distances can be displayed by selecting “View >
example volume renderings of a Co2P star-shaped nanoparticle Show Axis Grid.” An example visualization with dimensional
at different viewing angles, with their associated color-opacity scales is shown in Figure 5.
maps. In tomviz, the color-opacity map can be adjusted Animation. In addition to 2D figures, an animation of a
interac- tively with dynamically updated 3D visualizations. 3D visualization is an effective method of illustrating the 3D
The user may simply click and drag a point on the gray line structure of an object. In tomviz, an animation tool allows
overlaying the histogram to vary the opacity of different
users to produce simple animations, such as a 360o orbit
voxels in the volume render. In the examples shown in Figure
around a 3D object, or more complex animations by moving
4, the color- opacity map has been set so that the opacity
increases with increasing voxel intensity, and the color the viewing angle between a series of user-specified positions. A
becomes increasingly light with increasing voxel intensity. still from an animation is shown in Figure 6. The full
The range of the color map has been adjusted to enhance the animation is available online in the digital edition of this issue
brightness and contrast of the visualization. Minor adjustments at this web address:
to the color-opacity map can have a noticeable influence on https://doi.org/10.1017/S1551929517001213. This animation
the final appearance of the visualization of an object. It is shows a mixed volume and surface rendering of platinum
essential for users to adjust the color-opacity map to produce nanoparticles decorating a carbon nanofiber of ~170 nm
a volumetric visualization in diameter. The carbon fiber is visualized in black using a
2018 January • www.microscopy-today.com 17
volume render, with the color-opacity map set such that
only voxels

18 www.microscopy-today.com • 2018 January

 surface contour, with the intensity of the contour set such that
only platinum is visible.
Save and share. Whilst a high-quality manuscript figure 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
software can all be shared with other scientists. Simply click
“File > Save State” to share the tomviz state file (*.tvsm) and
volumetric data with colleagues. For scientific 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
software under the 3-clause BSD License that enables any party
to copy, distribute, and make modifications to the software.
This includes government organizations, for-profit and not-for-
profit educational institutions, and commercial organizations,
as well as individuals. Tomviz is hosted on Github
and is open to further contributions from new users.

Figure 5: Volume rendering of the Co2P 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.

Figure 6: Still image from an animation of platinum particles (turquoise color) on a

carbon fiber. 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 fiber are visible.

2018 January • www.microscopy-today.com 19