DEVELOPMENT OF SOFTWARE FOR AUTOMATED DATA ACQUISITION

自动数据采集软件的开发

• 批准号: 8170817
• 负责人: DAVID N MASTRONARDE
• 金额: $ 4.98万
• 依托单位: UNIVERSITY OF COLORADO
• 依托单位国家: 美国
• 财政年份: 2010
• 资助国家: 美国
• 起止时间: 2010-05-01 至 2011-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8170817
• 关键词: Bite; Computer Retrieval of Information on Scientific Projects Database; Data; Development; Dose; Funding; Grant; Hour; Institutes; Institution; Instruction; Intervention; Laboratories; Manuscripts; Microscope; Procedures; Process; Publications; Queensland; Research; Research Institute; Research Personnel; Resources; Running; Series; Source; Training; United States National Institutes of Health; Universities; Update; Work; data acquisition; improved; interest; programs; software development

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. Our program for automated tilt series acquisition, SerialEM, has continued to allow rapid data acquisition and effective use of our Tecnai microscopes. Efforts in the past year included the following developments. 1) The handling of data from 16-bit cameras and from 4-port readout cameras was improved after we obtained such a camera for our F20. 2) Remaining problems with montaging were worked out when Johanna Hoog from the EMBL used montaging extensively. 3) A relatively low-dose procedure was implemented for realigning the zero-loss peak when using an energy filter. The procedure is run automatically at a set interval during a tilt series and eliminates the need for operator intervention. 4) Installation procedures and instructions were improved, so that it is now easier to provide an initial package to new users and to provide and install program updates. SerialEM is now being used on at least three Tecnais in other laboratories (a T12 at the Burnham Institute, approximately 250/hours in 12 months; a TF20 at Scripps Research Institute, approximately 60 GB in 11 months; and a new TF30 at the University of Queensland, approximately 250 hours and approximately 90 GB of data in 7 months). Several other laboratories have either installed the program or obtained packages for it. SerialEM has been ported to run on a JEOL 3100 microscope by Tobin Fricke at the Lawrence Berkeley National Laboratories, and after some effort it now appears to run satisfactorily. Several laboratories with comparable microscopes would like to run the program, and JEOL USA, Inc. is interested in facilitating this process. An informal arrangement has been worked out whereby Jaap Brink from JEOL will help users to install the program and provide a first contact for training and assistance. A manuscript on SerialEM has been submitted for publication.

这个子项目是许多研究子项目中利用 资源由NIH/NCRR资助的中心拨款提供。子项目和 调查员(PI)可能从NIH的另一个来源获得了主要资金， 并因此可以在其他清晰的条目中表示。列出的机构是 该中心不一定是调查人员的机构。 我们的倾斜系列自动采集程序SerialEM继续支持快速数据采集和有效使用我们的Tecnai显微镜。过去一年的努力包括以下事态发展。1)在为我们的F20获得这样的摄像头后，改进了来自16位摄像头和4端口读出摄像头的数据处理。2)当EMBL的约翰娜·胡格广泛使用蒙太奇时，蒙太奇的遗留问题得到了解决。3)在使用能量滤光片时，实现了相对低剂量的零损耗峰重新对准。该程序在倾斜系列期间以设定的间隔自动运行，不需要操作员干预。4)改进了安装程序和说明，以便现在更容易向新用户提供初始包以及提供和安装程序更新。SerialEM现在至少在其他实验室的三个TecNai上使用(伯纳姆研究所的T12，12个月约250次/小时；斯克里普斯研究所的TF20，11个月约60 GB；昆士兰大学的新TF30，约250小时，7个月约90 GB数据)。其他几个实验室要么安装了该程序，要么获得了该程序的软件包。劳伦斯伯克利国家实验室的托宾·弗里克已经将SerialEM移植到JEOL 3100显微镜上运行，经过一些努力，它现在似乎运行得令人满意。几个拥有类似显微镜的实验室希望运行该计划，JEOL USA，Inc.有兴趣促进这一过程。已经制定了一项非正式安排，JEOL的Jaap Brink将帮助用户安装该程序，并提供培训和援助的第一次联系。一份关于SerialEM的手稿已经提交出版。