OME-XML: Development of a Data Standard for Biological Light Microscopy

OME-XML：生物光学显微镜数据标准的开发

• 批准号: 7452018
• 负责人: Kevin William Eliceiri
• 金额: $ 7.43万
• 依托单位: UNIVERSITY OF WISCONSIN-MADISON
• 依托单位国家: 美国
• 财政年份: 2008
• 资助国家: 美国
• 起止时间: 2008-04-01 至 2010-03-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7452018
• 关键词: Address; Advanced Development; Animals; Biological; Collection; Communities; Consensus; Data; Data Analyses; Data Set; Depth; Development; Discrimination; Disease; Encapsulated; Environment; Extensible Markup Language; Goals; Human; Image; Imaging Techniques; Knowledge; Libraries; Light; Light Microscope; Maps; Metadata; Microscopy; Modeling; Onset of illness; Penetration; Public Health; Reading; Research; Research Infrastructure; Research Personnel; Standards of Weights and Measures; System; Writing; base; data mining; data modeling; file format; image processing; improved; in vivo; light microscopy; open source; programs; tool

DESCRIPTION (provided by applicant): The last twenty years have seen great advances in biological microscopy that have greatly improved the depth penetration, viability and discrimination capabilities that can be obtained with light based approaches. Phenomenal advances in computing in recent years have allowed for the increased development of advanced multidimensional microscopy approaches by allowing for improved acquisition capabilities including automated collection, larger dataset collection, faster collection and hardware based image processing at acquisition. However, despite these significant advances, surprisingly there lacks a common computational infrastructure or framework in microscopy to help microscopists share data. Perhaps most surprising of all, there is not even a consensus storage file format. Much of the acquisition and analysis in light microscopy is being done by commercial programs that use proprietary file formats for their storage of the pixel and associated metadata. The Open Microscopy Environment (OME) XML-based data model has great potential as a standard interchange file format as it is flexible enough to accommodate the wide array of commercial data and can be encapsulated in several practical forms. We propose the following specific aim to address the need for a standard file format in biological light microscopy. Specific aim: To develop OME-XML as a complete data standard for biological light microscopy acquisition. This goal entails the refinement of the OME-XML metadata fields to support all open source and commercial microscopy data requirements, the creation of a practical file format that can utilize OME-XML, expansion of our Bio-Formats file format library for mapping proprietary metadata to OME-XML and the development of native and cross-platform libraries for reading and writing OME-XML and all derived formats. The system will support metadata from all types of light microscopes and will provide tools to both end users and application developers for recording, annotating and reading this metadata. The proposed system will help overcome the significant data sharing challenges facing the biological microscopy community and will greatly facilitate biological microscopy data analysis and data mining. Public Health Relevance: In vivo imaging techniques have revealed significant knowledge about disease onset and progression. The development of a standard interchange file format for biological light microscopy will aid investigators in their analysis and sharing of biomedical datasets and thereby facilitate their imaging research of disease states in cellular, animal and human models.

描述（由申请人提供）：过去二十年来，生物学显微镜的进展很大，这些进步大大提高了深度渗透，生存能力和歧视能力，可以通过基于轻的方法获得。近年来，计算机的惊人进步允许通过提高采集功能，包括自动化收集，较大的数据集收集，更快的收集速度和基于硬件的图像处理，从而增加了高级多维显微镜方法的开发。但是，尽管有这些重大进展，但令人惊讶的是，在显微镜中缺乏常见的计算基础架构或框架来帮助显微镜共享数据。也许最令人惊讶的是，甚至没有共识存储文件格式。光学显微镜中的大部分采集和分析都是通过使用专有文件格式存储像素和相关元数据的商业程序来完成的。开放显微镜环境（OME）基于XML的数据模型具有巨大的潜力作为标准的互换文件格式，因为它具有足够的灵活性，可以容纳各种各样的商业数据，并且可以以几种实际形式封装。我们提出以下特定目的，以满足生物光学显微镜中标准文件格式的需求。具体目的：开发OME-XML作为生物光显微镜采集的完整数据标准。 This goal entails the refinement of the OME-XML metadata fields to support all open source and commercial microscopy data requirements, the creation of a practical file format that can utilize OME-XML, expansion of our Bio-Formats file format library for mapping proprietary metadata to OME-XML and the development of native and cross-platform libraries for reading and writing OME-XML and all derived格式。该系统将支持所有类型的光显微镜的元数据，并将为最终用户和应用程序开发人员提供录制，注释和阅读此元数据的工具。所提出的系统将有助于克服生物学显微镜社区所面临的重大数据共享挑战，并极大地促进生物学显微镜数据分析和数据挖掘。公共卫生相关性：体内成像技术揭示了有关疾病发作和进展的重要知识。用于生物光学显微镜的标准互换文件格式的开发将有助于研究人员的分析和共享生物医学数据集，从而促进其对细胞，动物和人类模型中疾病状态的成像研究。