Real-time multi-scale brain data acquisition, assembly, and analysis using an end-to-end OptIPuter

  • Authors:

  • Rajvikram Singh;Nicholas Schwarz;Nut Taesombut;David Lee;Byungil Jeong;Luc Renambot;Abel W. Lin;Ruth West;Hiromu Otsuka;Sei Naito;Steven T. Peltier;Maryann E. Martone;Kazunori Nozaki;Jason Leigh;Mark H. Ellisman

  • Affiliations:

  • Electronic Visualization Laboratory, University of Illinois at Chicago;Electronic Visualization Laboratory, University of Illinois at Chicago;Department of Computer Science and Engineering, University of California, San Diego;National Center for Microscopy and Imaging Research, University of California, San Diego;Electronic Visualization Laboratory, University of Illinois at Chicago;Electronic Visualization Laboratory, University of Illinois at Chicago;National Center for Microscopy and Imaging Research, University of California, San Diego;National Center for Microscopy and Imaging Research, University of California, San Diego;KDDI Corporation, Chiyoda-ku, Tokyo, Japan;KDDI Labs, Fujimino, Saitama, Japan;National Center for Microscopy and Imaging Research, University of California, San Diego;National Center for Microscopy and Imaging Research, University of California, San Diego;Cybermedia Center, Osaka University, Japan;Electronic Visualization Laboratory, University of Illinois at Chicago;National Center for Microscopy and Imaging Research, University of California, San Diego

  • Venue:
  • Future Generation Computer Systems - IGrid 2005: The global lambda integrated facility
  • Year:
  • 2006

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Abstract

At iGrid 2005 we demonstrated the transparent operation of a biology experiment on a test-bed of globally distributed visualization, storage, computational, and network resources. These resources were bundled into a unified platform by utilizing dynamic lambda allocation, high bandwidth protocols for optical networks, a Distributed Virtual Computer (DVC) [N. Taesombut, A. Chien, Distributed Virtual Computer (DVC): Simplifying the development of high performance grid applications, in: Proceedings of the Workshop on Grids and Advanced Networks, GAN 04, Chicago, IL, April 2004 (held in conjunction with the IEEE Cluster Computing and the Grid (CCGrid2004) Conference)], and applications running over the Scalable Adaptive Graphics Environment (SAGE) [L. Renambot, A. Rao, R. Singh, B. Jeong, N. Krishnaprasad, V. Vishwanath, V. Chandrasekhar, N. Schwarz, A. Spale, C. Zhang, G. Goldman, J. Leigh, A. Johnson, SAGE: The Scalable Adaptive Graphics Environment, in: Proceedings of WACE 2004, 23-24 September 2004, Nice, France, 2004]. Using these layered technologies we ran a multi-scale correlated microscopy experiment [M.E. Maryann, T.J. Deerinck, N. Yamada, E. Bushong, H. Ellisman Mark, Correlated 3D light and electron microscopy: Use of high voltage electron microscopy and electron tomography for imaging large biological structures, Journal of Histotechnology 23 (3) (2000) 261-270], where biologists imaged samples with scales ranging from 20X to 5000X in progressively increasing magnification. This allows the scientists to zoom in from entire complex systems such as a rat cerebellum to individual spiny dendrites. The images used spanned multiple modalities of imaging and specimen preparation, thus providing context at every level and allowing the scientists to better understand the biological structures. This demonstration attempts to define an infrastructure based on OptIPuter components which would aid the development and design of collaborative scientific experiments, applications and test-beds and allow the biologists to effectively use the high resolution real estate of tiled displays.