Invited SpeakersProfile Details

GABRIEL WITTUM
GABRIEL WITTUM Professor, Applied Mathematics and Computational Science At
Computer, Electrical and Mathematical Science and Engineering Division, KAUST

Biography

Professor Wittum’s research focuses on a general approach to modelling and simulation of problems from empirical sciences, in particular using high performance computing (HPC). Particular areas of focus include: the development of advanced numerical methods for modelling and simulation, such as fast solvers like parallel adaptive multi-grid methods, allowing for application to complex realistic models; the development of corresponding simulation frameworks and tools; and the efficient use of top-level supercomputers for that purpose. These methods and tools are applied towards problem-solving in fields including computational fluid dynamics, environmental research, energy research, finance, neuroscience, pharmaceutical technology and beyond.

All sessions by GABRIEL WITTUM

  • Day 3Wednesday, April 12th
10:30 am

The Neuron Reconstruction Algorithm

Modern microscopic techniques enable imaging of three-dimensional neuron morphologies in intact brain tissue. In principle it is now possible to automatically reconstruct the dendritic branching patterns of neurons from 3D fluorescence image stacks. In practice however, the signal-to-noise ratio can be low, in particular in the case of thin dendrites or axons imaged relatively deep in the tissue. Here we present a nonlinear anisotropic diffusion filter that enhances the signal-to-noise ratio while preserving the original dimensions of the structural elements. The key idea is to use structural information in the raw data — the local moments of inertia — to locally control the strength and direction of diffusion filtering. A cylindrical dendrite, for example, is effectively smoothed only parallel to its longitudinal axis, not perpendicular to it. The filter is a valuable general tool for smoothing cellular processes and is well suited for preparing data for subsequent image segmentation and cell reconstruction.

References:
P. J. Broser, R. Schulte, A. Roth, F. Helmchen, J. Waters, S. Lang, B. Sakmann, G. Wittum: Nonlinear anisotropic diffusion filtering of three-dimensional image data from 2-photon microscopy. Journal of Biomedical Optics 9(6), 1253–1264 (2004)
Queisser, G., H. Bading, M. Wittmann, G. Wittum: Filtering, reconstruction and measurement of the geometry of neuron cell nuclei based on confocal microscopy data, Journal of Biomedical Optics, Jan 2008.
Daniel Jungblut, Andreas Vlachos, Gerlind Schuldt, Nadine Zahn, Thomas Deller, Gabriel Wittum: SpineLab – a Tool for Three Dimensional Cell Morphology Reconstruction. J Biomed Opt., 17(7), (2012)

KAUST 10:30 - 11:00 Details