Open microscopy environment
Open microscopy environment
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开放式显微镜环境
DOI：
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发表时间：
2005
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通讯作者：
I. Goldberg
中科院分区：
文献类型：
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作者：
I. Goldberg
仅提供摘要形式。开放显微镜环境（OME）是一个用于管理和分析生物显微镜中图像数据和元数据的框架。生物显微镜图像可以以许多不同的方式收集，并且可以代表许多不同种类的信息，这些信息随着不断发展的技术和实验目标而不断变化。一个完全涵盖生物显微镜范围的框架不能依赖于固定的数据模型-它必须被设计为适应不断变化的信息学需求。流体数据模型所面临的挑战与语义Web所解决的挑战相似，主要是支持任意或用户定义的语义和本体。然而，分析框架面临着额外的挑战，除了管理语义：定义分析单元之间的转换语义结构，定义聚合的分析单元，以表示工作流，接口算法的实现，和维护数据的起源或历史。协作科学环境还要求这些本地定义的语义和转换完全可传输，以供后续审查或分析。OME将这些组件整合到针对最终用户生物学家的数据库支持系统中。本演示将简要描述OME的各个组件：语义层（语义类型-ST），用于ST之间转换的分析单元（分析模块），工作流单元（分析链），工作流处理器（分析引擎）和可移植性层（OME XML）。一个复杂的工作流程的例子，也将说明如何使用该系统进行自动图像分类。
Summary form only given. The Open Microscopy Environment (OME) is a framework for the management and analysis of image data and metadata in biological microscopy. Biological microscopy images can be collected in many different ways, and may represent many different kinds of information which changes continually with evolving technology and experimental goals. A framework that fully encompasses biological microscopy in scope cannot rely on a fixed data model - it must be designed to accommodate ever-changing informatics needs. The challenge posed by a fluid data model is similar to one addressed by the semantic web, principally support for arbitrary or user-defined semantics and ontologies. However, an analysis framework faces additional challenges besides the management of semantics: definition of analytic units as transforms between semantic constructs, definition of aggregates of analytic units to represent work flows, interfaces to algorithm implementations, and maintenance of data provenance or history. A collaborative scientific environment also demands that these locally defined semantics and transforms be fully transportable for subsequent review or analysis. OME incorporates these components in a database-backed system targeted at end-user biologists. This presentation will briefly describe the various components of OME: the semantic layer (Semantic Types - STs), the analytical un its used to transform between STs (Analysis Modules), the units of work flow (Analysis Chains), the work-flow processor (Analysis Engine), and the transportability layer (OME XML). An example of a complex work flow will also be presented illustrating how this system is used for automated image classification.