Development/Applications Of Open Microscopy Environment

开放显微镜环境是三年前由麻省理工学院的Ilya Goldberg博士在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。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)他已经完成了一个XML模式，并将其提交给学术界和工业界，作为光学显微镜图像信息交换的新标准。与Josiah约翰斯顿一起，他们在OME软件中完全实现了图像和相关信息的输入和输出标准。2)Josiah约翰斯顿还帮助开发了一个基于Web的5维图像查看器，以便这些多维图像可以被调用和查看，而无需额外的软件。3)Goldberg和约翰斯顿已经将数据库布局的整个规范迁移到XML。这允许从存储在传入OME XML文件中的新类型信息动态创建数据库字段。4)Goldberg博士和奥尔洛夫博士已经开始了OME的新应用--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，其精度远远高于天真或专家人类受试者。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博士正在寻求新的可视化方式，并与OME提供的复杂的相互关联的信息进行交互。7)在与CIT的王博士的合作中，我们正在尝试在OME研究所范围内进行分阶段部署，并正在研究该技术在处理通过BLSA收集的组织阵列中的应用。

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.