Tomography produces complex volumetric datasets containing the entire internal structure and density of an object in three dimensions (3D). Interpreting volumetric data requires 3D visualization but needs specialized software distinguishable from more familiar tools used in animation for 3D surface data. This tutorial reviews 3D visualization techniques for volumetric data using the open-source tomviz software package. A suite of tools including two-dimensional (2D) slices, surface contours, and full volume rendering provide quantitative and qualitative analysis of volumetric information. The principles outlined here are applicable to a wide range of 3D tomography techniques and can be applied to volumetric datasets beyond materials characterization.

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BackgroundBecause of the difficulties involved in learning and using 3D modeling and rendering software, many scientists hire programmers or animators to create models and animations. This both slows the discovery process and provides opportunities for miscommunication. Working with multiple collaborators, a tool was developed (based on a set of design goals) to enable them to directly construct models and animations.ResultsSketchBio is presented, a tool that incorporates state-of-the-art bimanual interaction and drop shadows to enable rapid construction of molecular structures and animations. It includes three novel features: crystal-by-example, pose-mode physics, and spring-based layout that accelerate operations common in the formation of molecular models. Design decisions and their consequences are presented, including cases where iterative design was required to produce effective approaches.ConclusionsThe design decisions, novel features, and inclusion of state-of-the-art techniques enabled SketchBio to meet all of its design goals. These features and decisions can be incorporated into existing and new tools to improve their effectiveness.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2105-15-334) contains supplementary material, which is available to authorized users.

Electron tomography (ET) is widely used for 3D characterization of biological and material systems at nano-scales and meso-scales [1,2]. The success of an ET experiment critically depends on many image processing steps including tilt series alignment, tomographic reconstruction, segmentation, and visualization. Because each step demands unique algorithms developed by researchers from different fields of expertise, electron microscopists must piece together multiple software tools-making the workflow inefficient and non-reproducible. Here, we present the first full release of tomviz, v.1.0, an advanced and open platform that achieves high-throughput ET by providing state of the art functionality from basic image filters to 3D segmentation.tomviz offers a broad collection of reconstruction methods, from traditional weighted back projection (favored by biological applications) to more advanced optimization-based techniques such as the totalvariation minimization method [3] that utilizes the concept of compressed sensing. To lower the barrier of complicated algorithms that involve multiple steps and parameters, the software provides live updates and image inspection tools that facilitate parameter selection and convergence test.In addition to reconstruction, users can perform 2D tilt series processing such as background subtraction and noise filtering. With automatic alignment methods for image translation and tilt axis, it's possible to obtain reasonable reconstruction from raw data with a single click. Manual alignments are also supported with intuitive and flexible user interface. All data transforms are tracked step-by-step in a pipeline and can be shared among different computers.For large 3D data sets, tomviz performs fast and interactive visualization and segmentation by combining the popular Insight Toolkit (ITK) and the Visualization Toolkit (VTK) [4]. The platform offers a variety of GPU-accelerated rendering modes beyond traditional 3D volumetric rendering by including adjustable lighting and maximum intensity projections. Many common morphology transformation and segmentation functions are also included. With more than 100 color maps available and tools for editing axis labels, users can easily to generate publication-quality figures and animations.tomviz is open source and available for Windows, Mac OS X, and Linux. It is designed for intuitive graphical use by scientists, and built in C++ and Python (with built-in Numpy, Scipy, FFTW and wrapped ITK/VTK). The package comes with sample ET data sets [5] and flexible plug-in capabilities for users to implement their own algorithms and applications, making the software a valuable resource for learning electron tomography and testing new techniques. The software has an active user base with over 2,500 downloads and a multitude of electron microscopists participating in its development.