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ABSTRACT: The complete characterization of a novel direct detection device (DDD) camera for transmission electron microscopy is reported, for the first time at primary electron energies of 120 and 200 keV. Unlike a standard charge coupled device (CCD) camera, this device does not require a scintillator. The DDD transfers signal up to 65 lines/mm providing the basis for a high-performance platform for a new generation of wide field-of-view high-resolution cameras. An image of a thin section of virus particles is presented to illustrate the substantially improved performance of this sensor over current indirectly coupled CCD cameras.
Ultramicroscopy 03/2010; 110(7):744-7. · 2.47 Impact Factor
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ABSTRACT: A prototype direct detection device (DDD) camera system has shown great promise in improving both the spatial resolution and the signal to noise ratio for electron microscopy at 120-400 keV beam energies (Xuong et al., 2007. Methods in Cell Biology, 79, 721-739). Without the need for a resolution-limiting scintillation screen as in the charge coupled device (CCD), the DDD camera can outperform CCD based systems in terms of spatial resolution, due to its small pixel size (5 microm). In this paper, the modulation transfer function (MTF) of the DDD prototype is measured and compared with the specifications of commercial scientific CCD camera systems. Combining the fast speed of the DDD with image mosaic techniques, fast wide-area imaging is now possible. In this paper, the first large area mosaic image and the first tomography dataset from the DDD camera are presented, along with an image processing algorithm to correct the specimen drift utilizing the fast readout of the DDD system.
Journal of Structural Biology 04/2008; 161(3):352-8. · 3.41 Impact Factor
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Methods in cell biology 02/2007; 79:721-39. · 2.05 Impact Factor
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Methods in cell biology 02/2007; 79:643-60. · 2.05 Impact Factor
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ABSTRACT: The advent of “Grids,” or Grid computing, has led to a fundamental shift in the development of applications for managing and
performing computational or data-intensive analyses. A current challenge faced by the Grid community entails modeling the
work patterns of domain or bench scientists and providing robust solutions utilizing distributed infrastructures. These challenges
spawned efforts to develop “workflows” to manage programs and data on behalf of the end user. The technologies come from multiple
scientific fields, often with disparate definitions, and have unique advantages and disadvantages, depending on the nature
of the scientific process in which they are used. In this chapter, we argue that to maximize the impact of these efforts,
there is value in promoting the use of workflows within a tiered, hierarchical structure where each of these emerging workflow
pieces are interoperable. We present workflow models of the Telescience™ Project1 and BIRN2 architectures as frameworks that manage multiple tiers of workflows to provide tailored solutions for end-to-end scientific
processes.
12/2006: pages 109-125;
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Toyokazu Akiyama,
Yuuichi Teranishi,
Kazunori Nozaki,
Seiichi Kato,
Shinji Shimojo, Steven T Peltier,
Abel Lin,
Tomas Molina,
George Yang,
David Lee,
Mark Ellisman,
Sei Naito,
Atsushi Koike,
Shuichi Matsumoto,
Kiyokazu Yoshida,
Hirotaro Mori
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ABSTRACT: The Cybermedia Center (CMC), Osaka University, is a research institution that offers knowledge and technology resources obtained from advanced researches in the areas of large-scale computation, information and communication, multimedia content and education. Currently, CMC is involved in Japanese national Grid projects such as JGN II (Japan Gigabit Network), NAREGI and BioGrid. Not limited to Japan, CMC also actively takes part in international activities such as PRAGMA. In these projects and international collaborations, CMC has developed a Grid system that allows scientists to perform their analysis by remote-controlling the world's largest ultra-high voltage electron microscope located in Osaka University. In another undertaking, CMC has assumed a leadership role in BioGrid by sharing its experiences and knowledge on the system development for the area of biology. In this paper, we will give an overview of the BioGrid project and introduce the progress of the Telescience unit, which collaborates with the Telescience Project led by the National Center for Microscopy and Imaging Research (NCMIR). Furthermore, CMC collaborates with seven Computing Centers in Japan, NAREGI and National Institute of Informatics to deploy PKI base authentication infrastructure. The current status of this project and future collaboration with Grid Projects will be delineated in this paper.
Journal of Clinical Monitoring and Computing 11/2005; 19(4-5):279-94. · 0.89 Impact Factor
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Jeffrey S Grethe,
Chaitan Baru,
Amarnath Gupta,
Mark James,
Bertram Ludaescher,
Maryann E Martone,
Philip M Papadopoulos, Steven T Peltier,
Arcot Rajasekar,
Simone Santini,
Ilya N Zaslavsky,
Mark H Ellisman
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ABSTRACT: Through support from the National Institutes of Health's National Center for Research Resources, the Biomedical Informatics Research Network (BIRN) is pioneering the use of advanced cyberinfrastructure for medical research. By synchronizing developments in advanced wide area networking, distributed computing, distributed database federation, and other emerging capabilities of e-science, the BIRN has created a collaborative environment that is paving the way for biomedical research and clinical information management. The BIRN Coordinating Center (BIRN-CC) is orchestrating the development and deployment of key infrastructure components for immediate and long-range support of biomedical and clinical research being pursued by domain scientists in three neuroimaging test beds.
Studies in health technology and informatics 02/2005; 112:100-9.
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ABSTRACT: Electron tomography is a powerful tool for deriving three-dimensional (3D) structural information about biological systems within the spatial scale spanning and . With this technique, it is possible to derive detailed models of subcellular components such as organelles and synaptic complexes and to resolve the 3D distribution of their protein constituents in situ. While there continues to be progress towards the integration of high-performance computing technologies with traditional electron tomography processes, there is a significant need for more transparent integration with applications and to minimize the administrative overhead and complexity (resource administration, authentication, scheduling, data delivery) passed on to the non-computer scientist end user. Here we present the “Telescience Portal” (https://gridport.npaci.edu/Telescience) as an example of a fully integrated, web-based solution for performing end-to-end electron tomography. More than just a collection of individual applications, the Portal provides a transparent workflow, where simple intuitive interfaces for grid-enabled parallel computation, resource scheduling, remote instrumentation, advanced image processing and visualization, access to distributed/federated databases, and network-enabled data management and archival are tightly coupled within a secure environment which promotes increased collaboration between researchers. This tightly integrated Telescience system is a test-bed application for using grid resources to accelerate the throughput of data acquisition and processing, increase access to scarce and/or expensive instrumentation, and improve the accuracy of derived data products.
Journal of Parallel and Distributed Computing.
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ABSTRACT: By taking advantage of network-based computing and the recent developments in Web interfaces, centralized research facilities housing specialized and unique imaging instruments along with associated high-performance computing can be made available to researchers for use from their own laboratories. In addition to increasing access and utilization of these facilities, operation over the Internet is expected to enhance research by facilitating collaboration between researchers. We describe the implementation of a platform-independent Web-based system written in Java that supplements automated functions with video-guided interactive, collaborative remote control and data acquisition from an intermediate-high-voltage electron microscope.
Journal of Structural Biology · 3.41 Impact Factor
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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
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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.
Future Generation Computer Systems.
