Implementation of LSIDs in the Open Microscopy Environment

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Biological microscopy has always required an 'imaging' capability: traditionally, an image of a sample was drawn on paper, or with the advent of light-sensitive film, recorded on media that conveniently allowed reproduction. However, the application of digital detectors to microscopy has converted the biological microscope into a quantitative assay device. The clinical and research applications for digital imaging microscopy are enormous, but these applications generate large amounts of data/a single time-lapse image can easily be 500 Mbytes. Four years ago, we began developing a data management tool for digital biological microscopy. Our project, the Open Microscopy Environment (OME; http://openmicroscopy.org) is now the leading provider of open source image management software for biological microscopy. A critical capability in image data management is understanding the source and history of all data. Knowledge of how data was recorded and the specification of the image acquisition system is especially important in biological imaging, as there are a large range of different imaging modalities. We have defined a common data model for biological microscopy that provides the framework for storing and sharing this image data. This structure is referred to as the OME Data Model, and is being used by a number of commercial and independent entities as a biological image data standard. However, the OME Data Model can capture a large amount of information, and it is critical that as much of this information be filled out as possible. Unfortunately filling out complex data forms is time consuming and thus unlikely to be adopted by most users unless it is automated and simplified. A separate project has specified a system of Life Science Identifiers (LSIDs) as unique identifiers for biological data and systems. This proposal seeks funds to support the integration of LSIDs into the OME specification for microscopes. Most importantly, we will build a user tool that stores microscopes configurations and then obtains an LSID for a microscope system that identifiees that system and can be used to describe most of the parameters for a given image acquisition system. A complex instrument specification and configuration can then be indicated by a single mmouse-click. Most importantly, this specification is uniquely identified, stored with all recorded images, and accessible ('resolvable'') by any OME server or other LSID-compliant system.