Development /Applications Of Open Microscopy Environment

开放显微镜环境是由麻省理工学院的Ilya Goldberg博士两年前在Peter Sorger博士的小组中发起的一个项目。目的是开发计算细胞生物学的信息框架——生物信息学的一个分支，称为“图像信息学”。这个开源框架由一个数据库、几个分析模块和一个应用程序编程接口（API）组成，API将这些模块连接到数据库。该数据库为通过图像分析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，以及对它们进行的所有分析。数据库也是分析模块之间的通信链路，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，允许远程交互。在过去的3个月里，自从Goldberg博士在NIA建立了他的新部门以来，我们看到了OME的重大发展。1)他开发并发布了一个XML Schema，该Schema指定了生物光学显微镜的图像文件标准。2)我们与邓迪大学的Jason Swedlow博士合作，展示了该系统在活培养细胞中进行三维粒子识别和跟踪的功能和灵活性。3)与博士合作。哈佛大学化学和细胞生物学研究所的Brian DeDecker和Yan Fang，我们对影响神经元生长和转录因子核输入的小化合物进行了几次基于细胞的自动成像筛选。有关OME的更多信息请访问http://openmicroscopy.org。

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.