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。其目的是为计算细胞生物学开发一个信息框架-生物信息学的一个子专业，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将模块与数据库联系起来的应用程序接口（API）组成。该数据库为通过分析图像获得的生物信息提供语义框架和数据模型。它还跟踪图像本身以及对它们执行的所有分析。数据库也是分析模块之间的通信链路，允许多路复用分析算法。最后，整个系统提供了一个基于网络的用户界面，允许远程交互。在过去的3个月里，自从戈德堡博士在NIA建立了他的新单位以来，我们看到了OME的重大发展。1)他开发并发布了一个XML模式，为生物光学显微镜指定了一个图像文件标准。2)在与邓迪大学的Jason Swedlow博士的合作中，我们已经展示了该系统在活培养细胞中进行3-D颗粒识别和跟踪的功能和灵活性。3)在与哈佛化学与细胞生物学研究所的Brian DeDecker和Yan Fang博士的合作中，我们已经进行了几次自动化的基于细胞的成像屏幕，用于影响神经元生长和转录因子核输入的小化合物。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.