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

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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.