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

描述(申请人提供)：在过去的二十年里，生物显微镜有了很大的进步，极大地提高了深度渗透、生存能力和辨别能力，这是可以用基于光的方法获得的。近年来在计算方面的显著进步使得先进的多维显微镜方法得到了更多的发展，因为它允许改进的采集能力，包括自动采集、更大的数据集采集、更快的采集和采集时基于硬件的图像处理。然而，尽管取得了这些重大进展，但令人惊讶的是，显微镜领域缺乏一个通用的计算基础设施或框架来帮助显微镜工作者共享数据。也许最令人惊讶的是，甚至没有一种共识的存储文件格式。光学显微镜的大部分采集和分析都是由商业程序完成的，这些程序使用专有的文件格式来存储像素和相关的元数据。开放显微镜环境(OME)基于XML的数据模型具有作为标准交换文件格式的巨大潜力，因为它足够灵活，可以容纳广泛的商业数据，并且可以封装为几种实用的形式。我们提出了以下具体目标，以满足生物光学显微镜中对标准文件格式的需求。具体目的：开发OME-XML作为生物光学显微镜采集的完整数据标准。这一目标需要改进OME-XML元数据字段以支持所有开放源代码和商业显微镜数据要求，创建可利用OME-XML的实用文件格式，扩展我们的生物格式文件格式库以将专有元数据映射到OME-XML，并开发用于读写OME-XML和所有派生格式的本地和跨平台库。该系统将支持来自所有类型光学显微镜的元数据，并将向最终用户和应用程序开发人员提供记录、注释和阅读这些元数据的工具。拟议的系统将有助于克服生物显微镜社区面临的重大数据共享挑战，并将极大地促进生物显微镜数据分析和数据挖掘。公共卫生相关性：活体成像技术揭示了有关疾病发生和发展的重要知识。生物光学显微镜标准交换文件格式的开发将有助于研究人员分析和共享生物医学数据集，从而促进他们对细胞、动物和人类模型中疾病状态的成像研究。

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.