Development /Applications Of Open Microscopy Environment

开放式显微镜环境的开发/应用

• 批准号: 6668443
• 负责人: David Schlessinger
• 金额: --
• 依托单位: NATIONAL INSTITUTE ON AGING
• 依托单位国家: 美国
• 资助国家: 美国
• 起止时间: 至
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/6668443
• 关键词: cell biology; image processing; informatics; light microscopy; mathematical model; microscopy; molecular biology information system; molecular shape; structural biology; technology /technique development

The Open Microscopy Environment is a project started by Dr. Ilya Goldberg at MIT two years ago, in the group of Dr. Peter Sorger. The purpose is to develop an information framework for computational cell biology - a sub-specialty of bioinformatics called 'Image Informatics'. This open-source framework consists of a database, several analytic modules, and an application program interface (API) that ties the modules to the database. The database provides a semantic framework and a data model for biological information obtained by analyzing images. It also keeps track of the images themselves, and of all the analyses performed on them. The database is also the communication link between analysis modules permitting the multiplexing of analysis algorithms. Finally, the entire system provides a web-based user interface allowing for remote interaction. During the past 3 months, since Dr. Goldberg has established his new unit at the NIA, we have seen major developments in OME. 1) He has developed and published an XML Schema specifying an image file standard for biological light microscopy. 2) In collaboration with Dr. Jason Swedlow at the University of Dundee, we have demonstrated the functionality and flexibility of this system for performing 3-D particle identification and tracking in living cultured cells. 3) In collaboration with Drs. Brian DeDecker and Yan Fang of the Harvard Institute of Chemistry and Cell Biology, we have performed several automated cell-based imaging screens for small chemical compounds affecting neuronal outgrowth and nuclear import of transcription factors. Further information about OME is available at http://openmicroscopy.org.

开放的显微镜环境是两年前在彼得·索格（Peter Sorger）的小组中，由麻省理工学院（MIT）的伊利亚·戈德堡（Ilya Goldberg）博士发起的项目。目的是为计算细胞生物学开发信息框架 - 一种称为“图像信息学”的生物信息学的亚物种。该开源框架由数据库，几个分析模块和一个将模块与数据库联系起来的应用程序程序接口（API）组成。该数据库为通过分析图像获得的生物信息提供了语义框架和数据模型。它还可以跟踪图像本身以及对它们的所有分析。数据库也是分析模块之间的通信链接，允许分析算法的多路复用。最后，整个系统提供了一个基于Web的用户界面，允许进行远程交互。在过去的三个月中，自戈德伯格博士在NIA建立了他的新部门以来，我们已经看到了OME的重大发展。 1）他已经开发并发布了一个XML模式，该模式指定了用于生物光学显微镜的图像文件标准。 2）与邓迪大学的Jason Swedlow博士合作，我们证明了该系统在活着的培养细胞中执行3-D粒子识别和跟踪的功能和灵活性。 3）与Drs合作。哈佛化学与细胞生物学研究所的Brian Dedecker和Yan Fang，我们为影响神经元的生长和转录因子的核导入的小型化合物进行了几个基于自动的细胞成像筛选。有关OME的更多信息，请访问http://openmicroscopy.org。