Computer Vision for Computational Optics
Thursday, 14 April, 10:00am-10:50am
Abstract
Our group has been actively pursuing the idea that with great microscopes and great informatics we will be able to truly digitize models of cells, tissues, and organisms through time with information about the genetic and proteomic states of each cell. The belief is that these atlases, combined with optical observations of labeled entities, will accelerate the life sciences by allowing us to visualize these systems from any vantage point and as a system, thus leading to many discoveries such as the nature of the genetic control of fly wing development.
We have made significant progress on hard segmentation and tracking problems with the use of AI techniques developed in the computer vision community. We will present several examples of current projects that exemplify various such techniques and present the quality of results we obtain with them.
Despite these improvements we still find ourselves at the limit of what can be determined because of the limited resolution and contrast of the imagery. Fortunately, advances in microscope componentry such as adaptive optics, spatial light modulators, and ultra high-speed cameras present opportunities for improving the underlying imagery. We will report on microscope development projects in our lab, where the aim is to improve resolution by making multiple observations of a volume and from them computing a better reconstruction of the object under observation. We think better microscopy through computation and dynamic onboard control of acquisitions is an emerging trend that we generally call computational optics.
Biography
In 2012 Gene Myers joined a growing group of computational biologists in Dresden as the founding director of a new Systems Biology Center that is being built as part of an extension of the Max-Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG). His group focuses on engineering specialized light microscopes for cell biology and analyzing the imagery produces by such microscopes. Previously Gene had been a group leader at the HHMI Janelia Farm Research Campus (JFRC) since its inception in 2005. Gene came to the JFRC from UC Berkeley where he was on the faculty of Computer Science from 2003 to 2005. From 1998 to 2002 he was the Vice President of Informatics Research at Celera Genomics where he and his team determined the sequences of the Drosophila, Human, and Mouse genomes using the whole genome shotgun technique that he advocated in 1996. Prior to that Gene was on the faculty of the University of Arizona for 17 years and he received his Ph.D in Computer Science from the University
of Colorado in 1981.
His research interests include the design and analysis of algorithms for problems in computational molecular biology, image analysis of bioimages, and light microscopy with a focus on building models of the cell and cellular systems from imaging data. He is best known for the development of BLAST – the most widely used tool in bioinformatics, and for the paired-end whole genome shotgun sequencing protocol and the assembler he developed at Celera that delivered the fly, human, and mouse genomes in a three year period. He has also written many seminal papers on the theory of sequence comparison.
He was awarded the IEEE 3rd Millenium Achievement Award in 2000, the Newcomb Cleveland Best Paper in Science award in 2001, and the ACM Kanellakis Prize in 2002. He was voted the most influential scientist in bioinformatics in 2001 by Genome Technology Magazine and was elected to the National Academy of Engineering in 2003. In 2004 he won the International Max-Planck Research Prize and in 2005 was selected as one of two distinguished alumni (with David Haussler) at his alma-mater, the University of Colorado.
In 2006 Gene was inducted into Leopoldina, the German Academy of Science and awarded an honorary doctorate at ETH, Zurich.
Other plenary speakers
| Milan ŠONKA | Michael HAWRYLYCZ | K. Kirk SHUNG | ||
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