Bilkent University
Department of Computer Engineering


Cell Cycle Phase Identification Using Time-Lapse Fluorescence Microscopy


Prof. Kannappan Palaniappan
University of Missouri

Fluorescently tagged proteins such as GFP-PCNA produce rich dynamically varying textural patterns of foci distributed in the nucleus. This enables the behavioral study of sub-cellular structures during different phases of the cell cycle. The varying punctuate patterns of fluorescence, drastic changes in SNR, shape and position during mitosis and abundance of touching cells, however, require more sophisticated algorithms for reliable automatic cell segmentation and lineage analysis. Since the cell nuclei are non-uniform in appearance, a distribution-based modeling of foreground classes is essential. The recently proposed graph partitioning active contours (GPAC) algorithm supports region descriptors and flexible distance metrics. We extend GPAC for fluorescence-based cell segmentation using regional density functions and dramatically improve its efficiency for segmentation from O(N4) to O(N2), for an image with N2 pixels, making it practical and scalable for high throughput microscopy imaging studies.

Short bio: Kannappan Palaniappan is an associate professor in the Dept. of Computer Science at the University of Missouri-Columbia, where he co-founded the Multimedia Communications and Visualization Laboratory. K. Palaniappan received the B.A.Sc. and M.A.Sc. degrees in Systems Design Engineering from the University of Waterloo, Canada and the Ph. D. degree in Electrical and Computer Engineering from the University of Illinois, Urbana-Champaign in 1991. He was at NASA Goddard Space Flight Center from 1991 to 1996 working in the Laboratory for Atmospheres, where he co-established the high performance visualization and analysis laboratory (VAL). He developed the world's first massively parallel algorithm hurricane motion tracking and deformable motion modeling using the 64 thousand processor Maspar, one of the world's largest supercomputers at the time. While at NASA he also invented the Interactive Image SpreadSheet (IISS) system for visualization of extremely large Earth Observing System geophysical datasets using grid computing over high performance networks. Many visualizations created with colleagues at NASA have been widely used in television, print, museums, and web sites. One of the most prominent being the BlueMarble image of Earth which is a global mosaic produced using EOS MODIS satellite imagery that is used in GoogleMaps, GoogleEarth, Microsoft VirtualEarth and other web geospatial applications.

Palaniappan has worked at the University of Maryland Institute for Advanced Computer Studies. He has been an Air Force Summer Faculty Fellow (2007 - 2010) at the Air Force Research Lab in Rome, NY and Army Research Lab in Adelphi, MD where his focus has been the development of high performance embedded computing algorithms for the analysis of very large scale persistent imagery and high bandwidth streaming video using multicore clusters.

At the University of Missouri he co-founded the NSF vBNS high speed research network, the NASA Center of Excellence in Remote Sensing and the Visualization Lab. His research interests include biomedical imaging, satellite imaging, level set-based segmentation, video tracking, non-rigid motion analysis, content-based image retrieval and scientific visualization. In the biomedical image analysis area Palaniappan's lab works on cell cycle analysis, cell spreading measurement, cell motility in wound healing, cancer cell migration, tissue dynamics and morphogenesis, and histopathology tissue classification.

Palaniappan received the William T. Kemper Fellowship for Teaching Excellence (2002), the highest award for teaching from the University of Missouri. He received the prestigious Boeing Welliver Faculty Fellowship (2004), the University Space Research Association Creativity and Innovation science award (1993), the NASA Outstanding Achievement Award (1993), and the Natural Sciences and Engineering Research Council of Canada scholarship (1982-1988). NASA awarded him the Public Service Medal (2001) one of NASA’s highest honors, for pioneering contributions to scientific visualization and analysis tools for understanding petabyte-sized archives of NASA datasets.


DATE: 27 August, 2010, Friday @ 13:30