Development/Applications Of Open Microscopy Environment

开放显微镜环境是麻省理工学院的伊利亚·戈德伯格博士三年前在彼得·索格博士的团队中发起的一个项目。其目的是开发一个用于计算细胞生物学的信息框架--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绑定到数据库的应用程序接口(API)组成。该数据库为通过分析图像获得的生物信息提供了语义框架和数据模型。它还跟踪图像本身，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传输。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。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)他最终确定了一个XML模式，并提交给学术和工业团体进行审查，作为光学显微镜图像信息交换的新标准。他们与约西亚·约翰斯顿一起，在OME软件中全面实施了这一标准，用于图像及相关信息的输入和输出。2)Josiah Johnston还在开发基于Web的5维图像查看器方面发挥了重要作用，使这些多维图像可以在没有额外软件的情况下被调用和查看。3)Goldberg和Johnston已经将数据库布局的整个规范迁移到了XML。这允许从存储在传入的OME XML文件中的新类型的信息动态创建数据库字段。4)Goldberg博士和Orlov博士已经开始研究OME的一种新应用--自动图像分类。使用贝叶斯网络，初步迹象表明，我们可以自动对图像进行分类，其精度远远高于幼稚或专业的人类受试者。我们正在进一步改进这项技术，并研究光学显微镜领域以外的应用，包括医学诊断。6)Harry Hochheiser博士正在寻求新的方式来可视化OME提供的复杂的相互关联的信息并与其进行交互。7)与CIT的王博士合作，我们正在尝试在研究所范围内分阶段部署OME，并正在研究这项技术在处理通过BLSA收集的组织阵列方面的应用。

The Open Microscopy Environment is a project started by Dr. Ilya Goldberg at MIT three 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. Since Dr. Goldberg has established his new unit at the NIA, we have seen major developments in OME. 1) He has finalized an XML schema and submited it for review by academic and industrial groups as a new standard for the exchange of image information for light microscopy. Together with Josiah Johnston, they have fully implemented this standard in OME software for both input and output of images and associated information. 2) Josiah Johnston has also been instrumental in developing a web-based 5-dimensional image viewer so that these multi-dimensional images can be recalled and viewed without additional software. 3) Goldberg and Johnston have migrated the entire specification of the database layout to XML. This allows the dynamic creation of database fields from new kinds of information stored in incomming OME XML files. 4) Drs. Goldberg and Orlov have embarked on a new application of OME - automated image classification. Using Bayesian networks, preliminary indications are that we can automatically classify images to a much higher precision than is possible with naive or expert human subjects. we are pursuing further refinements of this technique and investigating applications outside of the light-microscopy area including medical diagnostics. 6) Dr. Harry Hochheiser is pursuing novel ways of visualizing and interacting with the complex inter-related information made available by OME. 7) In collaboration with Dr. Wang at CIT, we are attempting a staged deployment of OME institute-wide, and are investigating the application of this technology for processing the tissue arrays collected through the BLSA.