TELEMICROSCOPY & DISTRIBUTED PROCESSING

望远显微镜

• 批准号: 6220658
• 负责人: STEPHEN J YOUNG
• 金额: $ 7.69万
• 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/6220658
• 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.

我们正在开发一个控制 NCMIR Intermediate 的系统 通过互联网远程使用电压电子显微镜 (IVEM) 轻松分配计算密集型任务，例如 电子显微镜断层扫描所需的高性能 电脑。 设计了初步系统来测试可行性 远程控制并在 SIGGRAPH 和 1992 年超级计算会议。由于 这次示威活动引起了人们的兴趣和积极响应 NCRR 我们一直在开发更完善的系统。 我们的最终目标 就是把IVEM和相关的图像处理和分析 软件成为可供全国研究人员使用的网络资源 作为国家信息基础设施的一部分。 我们期望 远程操作将增加资源的访问和使用， 促进更广泛的数据采集和分析 协作项目，并允许更有效地利用资源 职员。 为了开展这个广泛的项目，我们感到鼓舞 NCRR 将寻求额外资金来支持这些项目的发展 遥感显微镜项目的各个方面主要与远程相关 操作并超越增强功能的开发 显微镜的本地使用和相关计算。 因此， 我们提交了一份关于“微观数字合作实验室”的提案 解剖学 (CMDA)”由 NSF 作为国家挑战赛资助 1994 年 9 月获得资助。Mark Ellisman 是 PI，Sid Karin 是董事 圣地亚哥超级计算机中心 (SDSC) 和 Don Greenberg， 康奈尔大学计算机图形学项​​目主任是 共同PI。 NCMIR 和 SDSC 主要负责整体 CMDA系统设计，包括任务管理、网络 通信，增强控制显微镜的功能， 以及开发改进的用户界面。 康奈尔大学是 专注于先进渲染方法的开发 企业错误指标。 这笔 NSF 拨款资助了大部分 望远镜项目的工作。 这笔资金提供 除了开发远程控制器之外，NCMIR 还具有其他优势 控制系统，因为许多 CMDA 活动，特别是那些 与显微镜自动化相关，与目标具有协同作用 的资源。 此外，该项目还支持并增强 与 SDSC（现在是 NPACI）进行互惠互利的互动。 作为 NSF 实地考察团队给予我们积极评价的结果 荣获 NSF 创意延伸奖，再增加两年 对 CMDA 项目的支持将持续到 1999 年 9 月。 CMDA 的早期版本在 Supercomputing 95 上进行了演示 1995 年 12 月在圣地亚哥举行的会议，Young 等人对此进行了描述 等人。 （Int. J. 超级计算机应用和高性能 计算，10：170-181，1996）。 当前的 CMDA (CMDA 1.0) 结合了 NCMIR 开发的例程来实现电子自动化 显微镜聚焦和配准以及顺序操作 采集马赛克和断层扫描倾斜系列所需的。 与加州大学伯克利分校的研究人员进行了初步测试，并且是第一个 1997 年 3 月开始与合作研究人员广泛使用 俄勒冈大学。 这些测试的结果已经 表明远程交互在进行协作方面的价值 研究。 此外，他们还提供了重要的反馈 系统导致的变化正在纳入下一个 版本，CMDA 2.0。 CMDA 项目最近被认定为 最先进的下一代技术。 NCMIR受邀参加 在10月举行的Internet 2.0会议上演示该系统 1997 年在华盛顿特区。 CMDA项目最近被选为 全球信息下一代类别决赛入围者 基础设施的竞争，是全行业的竞争。 获胜者 本次比赛的结果将于1998年4月20日公布。 经过第二个广泛的设计阶段，重点是扩展 当前系统的功能，下一个版本 CMDA II 现已发布 正在进行测试和最终开发。 如 CMDA II 中所述 设计文件中，新的 CMDA II 软件架构将 将许多改进融入到当前的 CMDA I 系统中。 其中包括涉及无限的协作能力 用户数量，并增强系统和数据安全性。 CMDA II 还结合了图像数据压缩以实现更快速的传输 在远程会话期间从 microsocpe 获取的数据。 新的 设计结合了CORBA 接口。 这种语言和平台 独立的分布式处理接口将方便远程 获得用于断层扫描重建的高性能计算， 分析和可视化。 在相关的研究项目中，部分 NCRR 向 Sid Karin 提供的另一项资源拨款支持 “国家生物计算资源”（NBCR），我们已经实施 迭代和简单的 R 加权断层扫描重建 SDSC 的大规模并行 400 节点 Intel Paragon 计算机以及 最近将此程序移植到 Cray T3E。 我们还有 开发了这些重建平台的远程接口。 一个专业 当前时期的重点是增加数量 使用 CMDA 的远程站点。 为了实现这一目标，我们延长了 结合基于网络的技术的初始设计，包括初始 使用基于网络的用户界面，使用来自 显微镜提供增强的显微镜交互控制 增强自动化功能。 独立于平台的网络 接口将使大量用户能够使用 CMDA 研究人员。 作为此设计的一部分，我们已经编写并正在测试 基于 HDF 文件格式的数据组织系统 Gridset。 基于网络的交互式显微镜控制器的测试目前正在进行中 与俄勒冈州、蒙大拿州和纽约的 NCMIR 合作者正在进行中。 最后，今年我们向 NIH/NCRR 提交了一份提案 呼吁为合作试验台提供补充拨款。 这 提案将扩大远程仪器/合作 活动包括其他 NCRR 资源并将受益于 新成立的国家伙伴关系提供的资源 先进的计算基础设施。