DEVELOPMENT OF SOFTWARE FOR AUTOMATED DATA ACQUISITION

自动数据采集软件的开发

• 批准号: 8362523
• 负责人: DAVID N MASTRONARDE
• 金额: $ 4.26万
• 依托单位: UNIVERSITY OF COLORADO
• 依托单位国家: 美国
• 财政年份: 2011
• 资助国家: 美国
• 起止时间: 2011-05-01 至 2012-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8362523
• 关键词: Cell physiology; Cellular Structures; Data; Development; Dose; Funding; Grant; Hour; Institutes; Instruction; Intervention; Laboratories; Manuscripts; Microscope; National Center for Research Resources; Principal Investigator; Procedures; Process; Publications; Queensland; Research; Research Infrastructure; Research Institute; Resources; Running; Series; Source; Training; United States National Institutes of Health; Universities; Update; Work; cost; 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. Primary support for the subproject and the subproject's principal investigator may have been provided by other sources, including other NIH sources. The Total Cost listed for the subproject likely represents the estimated amount of Center infrastructure utilized by the subproject, not direct funding provided by the NCRR grant to the subproject or subproject staff. 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.

这个子项目是许多利用资源的研究子项目之一 由NIH/NCRR资助的中心拨款提供。子项目的主要支持 子项目的主要研究者可能是由其他来源提供的， 包括其它NIH来源。 列出的子项目总成本可能 代表子项目使用的中心基础设施的估计数量， 而不是由NCRR赠款提供给子项目或子项目工作人员的直接资金。 我们的自动倾斜系列采集程序SerialEM继续允许快速数据采集和有效使用Tecnai显微镜。 过去一年的努力包括以下发展。 1)在我们为F20获得这样的相机后，来自16位相机和4端口读出相机的数据处理得到了改进。 2)当EMBL的Johanna Hoog广泛使用蒙太奇时，蒙太奇的剩余问题得到了解决。 3)当使用能量滤波器时，实施相对低剂量的程序以重新对准零损耗峰。 该程序在倾斜系列期间以设定的间隔自动运行，无需操作员干预。 4)安装过程和说明得到了改进，因此现在可以更容易地向新用户提供初始软件包，并提供和安装程序更新。 SerialEM目前正在其他实验室的至少三个Tecnais上使用（Burnham Institute的T12，12个月内约250/小时; Scripps Research Institute的TF 20，11个月内约60 GB;以及昆士兰州大学的新TF 30，7个月内约250小时和约90 GB数据）。 其他几个实验室要么安装了该程序，要么获得了它的软件包。SerialEM已由劳伦斯伯克利国家实验室的Tobin Fricke移植到JEOL 3100显微镜上运行，经过一些努力，现在它的运行情况似乎令人满意。 几个实验室与可比的显微镜想运行该计划，和JEOL美国公司。有兴趣推动这一进程。 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联系人。 SerialEM的手稿已提交出版。