VCBM 14: Eurographics Workshop on Visual Computing for Biology and Medicine

Permanent URI for this collection

https://diglib.eg.org/handle/10.2312/7762

Browse

Browsing VCBM 14: Eurographics Workshop on Visual Computing for Biology and Medicine by Subject "I.3.7 [Computer Graphics]"

Now showing 1 - 2 of 2
  • Thumbnail Image
    Item
    Visual and Quantitative Analysis of Higher Order Arborization Overlaps for Neural Circuit Research
    (The Eurographics Association, 2014) Swoboda, Nicolas; Moosburner, Judith; Bruckner, Stefan; Yu, Jai Y.; Dickson, Barry J.; Bühler, Katja; Ivan Viola and Katja Buehler and Timo Ropinski
    Neuroscientists investigate neural circuits in the brain of the common fruit fly Drosophila melanogaster to discover how complex behavior is generated. Hypothesis building on potential connections between individual neurons is an essential step in the discovery of circuits that govern a specific behavior. Overlaps of arborizations of two or more neurons indicate a potential anatomical connection, i.e. the presence of joint synapses responsible for signal transmission between neurons. Obviously, the number of higher order overlaps (i.e. overlaps of three and more arborizations) increases exponentially with the number of neurons under investigation making it almost impossible to precompute quantitative information for all possible combinations. Thus, existing solutions are restricted to pairwise comparison of overlaps as they are relying on precomputed overlap quantification. Analyzing overlaps by visual inspection of more than two arborizations in 2D sections or in 3D is impeded by visual clutter or occlusion. This work contributes a novel tool that complements existing methods for potential connectivity exploration by providing for the first time the possibility to compute and visualize higher order arborization overlaps on the fly and to interactively explore this information in its spatial anatomical context and on a quantitative level. Qualitative evaluation with neuroscientists and non-expert users demonstrated the utility and usability of the tool.
  • Thumbnail Image
    Item
    Visualizing Movements of Protein Tunnels in Molecular Dynamics Simulations
    (The Eurographics Association, 2014) Kozlíková, Barbora; Jurcík, Adam; By ka, Jan; Strnad, Ondrej; Sochor, Jirí; Ivan Viola and Katja Buehler and Timo Ropinski
    Analysis and visualization of molecules and their structural features help biochemists and biologists to better understand protein behavior. Studying these structures in molecular dynamics simulations enhances this understanding. In this paper we introduce three approaches for animating specific inner pathways composed of an empty space between atoms, called tunnels. These tunnels facilitate the transport of small molecules, water solvent and ions in many proteins. They help researchers understand the structure-function relationships of proteins and the knowledge of tunnel properties improves the design of new inhibitors. Our methods are derived from selected tunnel representations when each stresses some of the important tunnel properties-width, shape, mapping of physico-chemical properties, etc. Our methods provide smooth animation of the movement of tunnels as they change their length and shape throughout the simulation.