TELEMICROSCOPY & DISTRIBUTED PROCESSING

望远显微镜

• 批准号: 6121805
• 负责人: STEPHEN J YOUNG
• 金额: $ 2.78万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN DIEGO
• 依托单位国家: 美国
• 财政年份: 1999
• 资助国家: 美国
• 起止时间: 1999-05-15 至 2000-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/6121805
• 关键词: bioengineering /biomedical engineering; biomedical equipment development; biomedical resource; biotechnology; building /facility design /renovation; technology /technique

We are developing a system to control the NCMIR Intermediate Voltage Electron Microscope (IVEM) remotely over the Internet and to easily distribute computationally intensive tasks such as those required for electron microscope tomography to high performance computers. A preliminary system was designed to test the feasibility of remote control and demonstrated at the SIGGRAPH and the Supercomputing conferences in 1992. As a result of the success of this demonstration and the interest and positive response from the NCRR we have been developing a more refined system. Our ultimate goal is to turn the IVEM and associated image processing and analysis software into a network resource available to researchers nationwide as part of the National Information Infrastructure. We expect that remote operation will increase access and use of the resource, facilitate more extensive data acquisition and analyses for collaborative projects, and allow more efficient use of the resource staff. To carry out this extensive project, we were encouraged by the NCRR to seek additional funding to support development of those aspects of the telemicroscopy project primarily related to remote operation and going beyond the development of enhancements for the local use of the microscope and associated computation. Accordingly, we submitted a proposal for a "Collaboratory for Microscopic Digital Anatomy (CMDA)" that was funded by the NSF as a National Challenge grant in September 1994. Mark Ellisman is PI and Sid Karin, Director of the San Diego Supercomputer Center (SDSC) and Don Greenberg, Director of Cornell University Program of Computer Graphics are Co-PIs. NCMIR and SDSC are primarily responsible for the overall system design of the CMDA including task management, network communication, enhancement of functions controlling the microscope, and the development of an improved user interface. Cornell is focusing on the development of advanced rendering methods that will in corporate error metrics. This NSF grant funds the major portion of the work on the telemicroscopy project. This funding provides additional benefits to the NCMIR beyond the develop of a remote control system since many of the CMDA activities, in particular those associated with microscope automation, are synergistic with the goals of the resource. In addition, the project supports and enhances a mutually beneficial interaction with the SDSC (and now the NPACI). As the result of a positive reviews by NSF site visit teams we were awarded an NSF Creativity Extension Award, adding two more years of support to the CMDA project which will carry it to September of 1999. An early version of the CMDA was demonstrated at the Supercomputing 95 conference in San Diego in December 1995 and is described in Young et al. (Int. J. Supercomputer Applications and High Performance Computing, 10: 170-181, 1996). The present CMDA (CMDA 1.0) incorporates routines developed by NCMIR to automate electron microscope focus and registration as well as the sequential operations required for acquisition of mosaics and tomographic tilt series. Initial testing with researchers at UC Berkeley, and the first intensive use began in March 1997 with collaborative researchers at the University of Oregon. Results of these tests have already indicated the value of remote interaction in conducting collaborative research. In addition, they have provided important feedback on the system leading to changes which are being incorporated into the next version, CMDA 2.0. The CMDA project has been recently recognized as a state-of-the-art next generation technology. NCMIR was i nvited to demonstrate the system at the Internet 2 conference held in October 1997 in Washington DC. The CMDA project has been recently selected as a finalist in the Next Generation category of the Global Information Infrastrucure competition, an industry-wide competition. The winner of this competition will be announced on April 20, 1998. After a second extensive design period focused on extending the functionality of the current system, the next version, CMDA II, is now undergoing testing and final development. As described in the CMDA II design document, the new CMDA II software architecture will incorporate numerous improvements into the current CMDA I system. These include the capability of collaboration involving an unlimited number of users, and enhanced system and data security. The CMDA II also incorporates image data compression for more rapid transmission of data acquired from the microsocpe during remote sessions. The new design incorporates a CORBA interface. This language and platform independent distributed processing interface will facilitate remote access to high performance computing for tomographic reconstruction, analysis, and visualization. In a related research project, partly supported by another NCRR-sponsored Resource grant to Sid Karin, the "National Biological Computing Resource" (NBCR), we have implemented both iterative and simple R-weighted tomographic reconstruction on the massively parallel 400 node Intel Paragon computer at the SDSC and have recently ported this program to the Cray T3E. We have also developed a remote interface these reconstruction platforms. A major emphasis in the current period is to bring on an increasing number of remote sites using the CMDA. To accomplish this, we have extended the initial design to incorporate web-based technology, including initial work with a web-based user interface using video images from the microscope to provide enhanced interactive control of the microscope to augment automated functions. The platform-independent web interface will enable use of the CMDA by a large number of researchers. As part of this design, we have written and are testing a data organization system, Gridset, based on the HDF file format. Tests of the web-based interactive microscope controller are currently underway with NCMIR collaborators in Oregon, Montana, and New York. Finally, during this year we have submitted a proposal to the NIH/NCRR call for supplementary grant to on collaboratory test-beds. This proposal will expand of the teleinstrumentation / collaboratory activities to include other NCRR resources and will benefit from resources provided by the newly established National Partnership for Advanced Computing Infrastructure.

我们正在开发一种控制NCMIR中级的系统