Semi-automatic transfer function generation for non-domain specific direct volume rendering

The field of volume rendering is focused on the visualization of three-dimensional data sets. Although it is predominantly used in biomedical applications, volume rendering has proven useful in fields such as meteorology, physics, and fluid dynamics as a means of analyzing features of interest in three-dimensional scalar fields. The features visualized by volume rendering differ by application, though most applications focus on providing the user with a model for understanding the physical structure represented in the data such as materials or the boundaries between materials. One form of volume rendering, direct volume rendering (DVR), has proven to be a particularly powerful tool for visualizing material and boundary structures represented in volume data through the use of transfer functions which map each unit of the data to optical properties such as color and opacity. Specifying these transfer functions in a manner that yields an informative rendering is often done manually by trial and error and has become the topic of much research. While automated techniques for transfer function creation do exist, many rely on domain-specific knowledge and produce less informative renderings than those generated by manually constructed transfer functions. This thesis presents a novel extension to a successful semi-automated transfer function technique in an effort to minimize the time and effort required in creation of informative transfer functions. In particular, the method proposed provides a means for the semi-automatic generation of transfer functions which highlight and classify material boundaries in a non-domain specific manner

Adaptive transfer functions: improved multiresolution visualization of medical models

The final publication is available at Springer via http://dx.doi.org/10.1007/s00371-016-1253-9Medical datasets are continuously increasing in size. Although larger models may be available for certain research purposes, in the common clinical practice the models are usually of up to 512x512x2000 voxels. These resolutions exceed the capabilities of conventional GPUs, the ones usually found in the medical doctors’ desktop PCs. Commercial solutions typically reduce the data by downsampling the dataset iteratively until it fits the available target specifications. The data loss reduces the visualization quality and this is not commonly compensated with other actions that might alleviate its effects. In this paper, we propose adaptive transfer functions, an algorithm that improves the transfer function in downsampled multiresolution models so that the quality of renderings is highly improved. The technique is simple and lightweight, and it is suitable, not only to visualize huge models that would not fit in a GPU, but also to render not-so-large models in mobile GPUs, which are less capable than their desktop counterparts. Moreover, it can also be used to accelerate rendering frame rates using lower levels of the multiresolution hierarchy while still maintaining high-quality results in a focus and context approach. We also show an evaluation of these results based on perceptual metrics.Peer ReviewedPostprint (author's final draft

Interactive Extraction of High-Frequency Aesthetically-Coherent Colormaps

Color transfer functions (i.e. colormaps) exhibiting a high frequency luminosity component have proven to be useful in the visualization of data where feature detection or iso-contours recognition is essential. Having these colormaps also display a wide range of color and an aesthetically pleasing composition holds the potential to further aid image understanding and analysis. However producing such colormaps in an efficient manner with current colormap creation tools is difficult. We hereby demonstrate an interactive technique for extracting colormaps from artwork and pictures. We show how the rich and careful color design and dynamic luminance range of an existing image can be gracefully captured in a colormap and be utilized effectively in the exploration of complex datasets

Finding Nano-\"Otzi: Semi-Supervised Volume Visualization for Cryo-Electron Tomography

Cryo-Electron Tomography (cryo-ET) is a new 3D imaging technique with unprecedented potential for resolving submicron structural detail. Existing volume visualization methods, however, cannot cope with its very low signal-to-noise ratio. In order to design more powerful transfer functions, we propose to leverage soft segmentation as an explicit component of visualization for noisy volumes. Our technical realization is based on semi-supervised learning where we combine the advantages of two segmentation algorithms. A first weak segmentation algorithm provides good results for propagating sparse user provided labels to other voxels in the same volume. This weak segmentation algorithm is used to generate dense pseudo labels. A second powerful deep-learning based segmentation algorithm can learn from these pseudo labels to generalize the segmentation to other unseen volumes, a task that the weak segmentation algorithm fails at completely. The proposed volume visualization uses the deep-learning based segmentation as a component for segmentation-aware transfer function design. Appropriate ramp parameters can be suggested automatically through histogram analysis. Finally, our visualization uses gradient-free ambient occlusion shading to further suppress visual presence of noise, and to give structural detail desired prominence. The cryo-ET data studied throughout our technical experiments is based on the highest-quality tilted series of intact SARS-CoV-2 virions. Our technique shows the high impact in target sciences for visual data analysis of very noisy volumes that cannot be visualized with existing techniques