Visualization and analysis of diffusion tensor fields

technical reportThe power of medical imaging modalities to measure and characterize biological tissue is amplified by visualization and analysis methods that help researchers to see and understand the structures within their data. Diffusion tensor magnetic resonance imaging can measure microstructural properties of biological tissue, such as the coherent linear organization of white matter of the central nervous system, or the fibrous texture of muscle tissue. This dissertation describes new methods for visualizing and analyzing the salient structure of diffusion tensor datasets. Glyphs from superquadric surfaces and textures from reactiondiffusion systems facilitate inspection of data properties and trends. Fiber tractography based on vector-tensor multiplication allows major white matter pathways to be visualized. The generalization of direct volume rendering to tensor data allows large-scale structures to be shaded and rendered. Finally, a mathematical framework for analyzing the derivatives of tensor values, in terms of shape and orientation change, enables analytical shading in volume renderings, and a method of feature detection important for feature-preserving filtering of tensor fields. Together, the combination of methods enhances the ability of diffusion tensor imaging to provide insight into the local and global structure of biological tissue

Curvature-based transfer functions for direct volume rendering: methods and applications

Journal ArticleDirect volume rendering of scalar fields uses a transfer function to map locally measured data properties to opacities and colors. The domain of the transfer function is typically the one-dimensional space of scalar data values. This paper advances the use of curvature information in multi-dimensional transfer functions, with a methodology for computing high-quality curvature measurements. The proposed methodology combines an implicit formulation of curvature with convolution-based reconstruction of the field. We give concrete guidelines for implementing the methodology, and illustrate the importance of choosing accurate filters for computing derivatives with convolution. Curvature-based transfer functions are shown to extend the expressivity and utility of volume rendering through contributions in three different application areas: nonphotorealistic volume rendering, surface smoothing via anisotropic diffusion, and visualization of isosurface uncertainty

Stream bundles - cohesive advection through flow fields

Journal ArticleStreamline advection has proven an effective method for visualizing vector flow field data. Traditional streamlines do not, however, provide for investigating the coarsergrained features of complex datasets, such as the white matter tracts in the brain or the thermal conveyor belts in the ocean. In this paper, we introduce a cohesive advection primitive, called a stream bundle. Whereas traditional streamlines describe the advection patterns of single, infinitesimal micro-particles, stream bundles indicate advection paths for large macro-particles. Implementationally, stream bundles are composed of a collection of individual streamlines (here termed fibers), each of which only advects a short distance before being terminated and re-seeded in a new location. The individual fibers combine to dictate the instantaneous distribution of the bundle, and it is this collective distribution which is used in determining where fibers are reseeded. By carefully controlling the termination and re-seeding policies of the fibers, we can prevent the bundle from becoming frayed in divergent regions. By maintaining a cohesive from, the bundles can indicate the coarse structure of complex vector fields. In this paper, we use stream bundles to investigate the oceanic currents

Transboundary Cooperation: The Best Way to Share Common Responsibility for Future

The Bavarian Forest National Park (BFNP) and Šumava National Park (ŠNP), established in 1969 and 1991, respectively, are located between Prague and Munich. Their long common border accents the transboundary issue regarding nature conservation, ecological corridors and connectivity. Plans to protect this large forest landscape, dating back to the early twentieth century, were never implemented due to the two World Wars and Iron Curtain. Initially, there were many joint activities. Many common projects (e.g., joint information centre, transboundary public transport system, GPS lynx and deer telemetry) were conducted. Both sides have learned a lot during these 25 years of cooperation. The main obstacles in cooperation are economic differences between the regions, language barriers and different policies and laws. There is only one common ecosystem of mountain forests, common populations of lynx, capercaillie or bark beetle, and the partners have to learn how to share their common responsibility for the future. Step by step, the transboundary cooperation is improving, which is very important in good years, but maybe even more important in bad years. The principle stance of the transboundary partner can buffer threatening in the neighbouring national park and support recovery when the crisis is over

Interactive simulation and visualization

Journal ArticleMost of us perform data analysis and visualization only after everything else is finished, which often means that we don't discover errors invalidating the results of our simulation until postprocessing. A better approach would be to improve the integration of simulation and visualization into the entire process so that you can make adjustments along the way. We call this approach computational steering. Computational steering is the capacity to control all aspects of the computational science pipeline-the succession of steps required to solve computational science and engineering problems. When you interactively explore a simulation in time and space, you steer it. In this sense, you can rely on steering to assist in debugging and to modify the computational aspects of your application

Diet and prey selection by snow leopards in the Nepalese Himalayas

Visual attractiveness and rarity often results in large carnivores being adopted as flagship species for stimulating conservation awareness. Their hunting behaviour and prey selection can affect the population dynamics of their prey, which in turn affects the population dynamics of these large carnivores. Therefore, our understanding of their trophic ecology and for-aging strategies is important for predicting their population dynamics and consequently for developing effective conservation programs. Here we concentrate on an endangered species of carnivores, the snow leopard, in the Himalayas. Most previous studies on snow leopard diet lack information on prey availability and/or did not genetically check, whether the identification of snow leopard scats is correct, as their scats are similar to those of other carnivores. We studied the prey of snow leopard in three Himalayan regions in Nepal (Sagarmatha National Park (SNP), Lower Mustang (LM) and Upper Manang (UM) in the Annapurna Conservation Area, during winter and summer in 2014-2016. We collected 268 scats along 139.3 km linear transects, of which 122 were genetically confirmed to belong to snow leopard. Their diet was identified by comparing hairs in scats with our reference collection of the hairs of potential prey. We determined prey availability using 32-48 camera-traps and 4,567 trap nights. In the SNP, the most frequent prey in snow leopard faeces was the Himalayan tahr in both winter and summer. In LM and UM, its main prey was blue sheep in winter, but yak and goat in summer. In terms of relative biomass consumed, yak was the main prey everywhere in both seasons. Snow leopard preferred large prey and avoided small prey in summer but not in winter, with regional differences. It preferred domestic to wild prey only in winter, and in SNP. Unlike most other studies carried out in the same area, our study uses genetic methods for identifying the source of the scat. Studies solely based on visual identification of samples may be strongly biased. Diet studies based on frequency of occurrence of prey tend to overestimate the importance of small prey, which may be consumed more often, but contribute less energy than large prey. However, even assessments based on prey biomass are unlikely to be accurate as we do not know whether the actual size of the prey consumed corresponds to the average size used to calculate the biomass eaten. For example, large adults may be too difficult to catch and therefore mostly young animals are consumed, whose weight is much lower. We show that snow leopard consumes a diverse range of prey, which varies both regionally and seasonally. We conclude that in order to conserve snow leopards it is also necessary to conserve its main wild species of prey, which will reduce the incidence of losses of livestock.The authors thank the Department of National Parks and Wildlife Conservation (Nepal) and National Trust for Nature Conservation (Nepal) for permitting us to conduct this study at ACA and SNP. We thank GA CR (grant No. GB14-36098G), Panthera (US), and Rufford Foundation (UK) for supporting our field and laboratory work