Colloquy Cycle SS 2007

Current Schedule
Previous Schedules

In the summer term of 2007 the following talks will be organized by our Institute. The talks are partially financed by the "Arbeitskreis Graphische Datenverarbeitung" of the OCG (Austrian Computer Society)

• Colloquy Cycle WS06/07
• Colloquy Cycle SS06
• Colloquy Cycle WS05/06
• Colloquy Cycle SS05
• Colloquy Cycle WS04/05
• Colloquy Cycle SS04
• Colloquy Cycle WS03/04
• Colloquy Cycle SS03
• Colloquy Cycle WS02/03
• Colloquy Cycle SS02
• Colloquy Cycle WS01/02
• Colloquy Cycle SS01
• Colloquy Cycle WS00/01
• Colloquy Cycle SS00
• Colloquy Cycle WS99/00
• Colloquy Cycle SS99
• Colloquy Cycle WS98/99
• Colloquy Cycle SS98
• Colloquy Cycle WS97/98
• Colloquy Cycle SS97
• Colloquy Cycle WS96/97

Yun Jang, Swiss National Supercomputing Centre

Functional approximation of scattered data is a popular technique for compactly representing various types of datasets in computer graphics, including surface, volume, and vector datasets. Typically, sums of Gaussians or similar radial basis functions are used in the functional approximation and PC graphics hardware is used to quickly evaluate and render these datasets. While truncated radially symmetric basis functions are quick to evaluate and simple for encoding optimization, they are not the most appropriate choice for data that is not radially symmetric and are especially problematic for representing linear, planar, and many non-spherical structures. Therefore, the functional approximation system is extended to using more general basis functions, such as ellipsoidal basis functions(EBFs) that provide greater compression and visually more accurate encodings of volumetric scattered datasets. In addition to static data approximation, temporal data is encoded using results from encoding previous timestep to speed the encoding time. Moreover, as a part of visual analytics, we developed tools for zoonotic syndromic surveillance, linked animal and human visual analytics for healthcare surveillance, network visualization, etc. In this talk, We will introduce these visual analytics tools and discuss their applications.
 

Francois Faure, University Joseph Fourier

SOFA is a new open source framework primarily targeted at medical simulation research. Based on an advanced software architecture, it allows to (1)~create complex and evolving simulations by combining new algorithms with algorithms already included in SOFA; (2) modify most parameters of the simulation~--~deformable behavior, surface representation, solver, constraints, collision algorithm, etc.~--~by simply editing an XML file; (3) build complex models from simpler ones using a scene-graph description; (4) efficiently simulate the dynamics of interacting objects using abstract equation solvers; and (5) reuse and easily compare a variety of available methods. In this paper we highlight the key concepts of the SOFA architecture and illustrate its potential through a series of examples.
 

Josef Neumüller, Zentrum für Anatomie und Zellbiologie

ET is a powerful tool for visualization of the highly dynamic structures of organelles in living cells. Although investigation using transmission electron microscopy requires fixed and embedded material which is stable in high vacuum and under a high voltage electron beam, the modern preparation method of high pressure fixation (HPF) allows obtaining snapshots from the arrangement of organelles in living cells in relation to a particular experimental condition.
In order to obtain appropriate 3D data, tilt series from semithin sections (200-300 nm), cut in parallel to the plane of the monolayer of cell cultures, are performed using a Tecnai-20 200KV transmission electron microscope (FEI, Eindhoven, The Netherlands) equipped with an eucentric goniometer. In addition a rotation holder (Gatan, Inc., Pleasanton, USA) is used for orientation of rod-like structures parallel to the tilt axis and also for dual axis acquisition. Series of tilted images (range: -70° to +70°) are acquired with a tilt increment of 1°. After holder calibration, dislocations in x, y and z axis are corrected by the Explore 3D acquisition software (FEI). The volume of the semithin sections is reconstructed by the back projection method into serial slices using the software package Inspect 3D (FEI). This software implicates also an alignment tool using cross correlation which is prerequisite for an appropriate reconstruction. Dual axis reconstruction requires acquisition of perpendicular orientated tilt series. It is performed using the Matlab software platform and an advanced version of the "Tomo Toolbox", kindly provided by Dr. Jürgen Plitzko, Dept. of Molecular Structural Biology (Head: Prof. Dr. Wolfgang Baumeister), Max Planck Institute of Biochemistry in Martinsried near Munich.
3D models are performed by tracing the structures of interest in every slice with colored contours that are merged in the Z axis by the help of the Amira 3.0 software (Mercury Computer Systems, Merignac Cedex, France). Models, generated in this way can be rotated in the space and presented as movie.
The aim of this presentation is to introduce interesting applications from cell biology and to discuss problems and limitations in 3D visualization using the commercial software as described above.
 

David Williams, City University London

Curved Planar Reformation (CPR) has proved to be a practical and widely used tool for the visualization of curved tubular structures within the human body. It has been useful in medical procedures involving the examination of blood vessels and the spine. However, it is more difficult to use it for large, tubular, structures such as the trachea and the colon because abnormalities may be smaller relative to the size of the structure and may not have such distinct density and shape characteristics.
Our new approach (which we call 'Volumetric CPR') improves on this situation by using volume rendering for hollow regions and standard CPR for the surrounding tissue. This effectively combines gray scale contextual information with detailed color information from the area of interest. The approach is successfully used with each of the standard CPR types and the resulting images are promising as an alternative to virtual flythroughs.
We show that lighting is non-trivial because of the deformation which occurs when the three dimensional curved tubular structure is mapped to a two dimensional image plane. We show how lighting and shading is computed in this scenario and how it can be used to maximize the users understanding of the surface.
Lastly, we demonstrate that our new approach is a useful tool for displaying additional information not typically available during a flythrough, such as real-time surface coverage data or translucency rendering. We also show that, because the Volumetric CPR provides and alternative view on the colon, it increases surface coverage from 86.8% (for a flythrough in each direction) to 99.2%; significantly improving the chances of detecting abnormalities.
 

Marco Tarini, Universita' degli Studi di Pisa

QuteMol is an open source (GPL), interactive, /high quality molecular visualization system/. It exploits the current GPU capabilites through OpenGL shaders to offer an array of innovative visual effects. QuteMol visualization techniques are aimed at improving clarity and an easier understanding of the 3D shape and structure of large molecules or complex proteins.
In this talk, the individual techniques implemented in QuteMol are presented. These include:

• Real Time Ambient Occlusion
• Depth Aware Silhouette Enhancement
• Ball and Sticks, Space-Fill and Liquorice visualization modes
• High resolution antialiased snapshots for creating publication quality renderings
• Automatic generation of animated gifs of rotating molecules for web pages animations
• Interactive rendering of large molecules and protein (>100k atoms)
• Standard PDB input

Ernesto Coto, Universidad Central de Venezuela, Venezuela

The watershed transform from markers is a popular image segmentation operator in mathematical morphology. The Image Foresting Transform (IFT) watershed is a common method to compute the watershed transform from markers, which has been successfully applied in practice, but which unfortunately consumes too much memory when applied to three-dimensional medical datasets. This is a considerable limitation on the applicability of the IFT watershed, as the size of medical datasets keeps increasing with a faster pace than physical memory technology develops. We describe the O-IFT watershed, a new type of IFT watershed based on the O-Buffer theoretical framework, and introduces an efficient data representation which reduces the memory consumption of the algorithm while maintaining its low computational complexity. Furthermore, a new implementation of the priority queue is introduced, which reduces its memory consumption. The O-IFT watershed makes it possible to apply a watershed transformation from markers to large medical datasets.
 

Robert S. Laramee, University of Wales Swansea, UK

Swirl and tumble motion are two important, common fluid flow patterns from computational fluid dynamics (CFD) simulations typical of automotive engine simulation. We study and visualize swirl and tumble flow using several advanced flow visualization techniques: direct, geometric, texture-based, and feature-based. When illustrating these methods, we describe the relative strengths and weaknesses of each approach across multiple spatlo-temporal domains typical of an engineer's analysis. The result is the most comprehensive, systematic search for swirl and tumble motion ever performed. Based on this investigation we offer perspectives on where and when these techniques are best applied in order to visualize the behavior of swirl and tumble motion.