Abstract
The Open Microscopy Environment (OME) defines a data model and software implementation to serve as an informatics framework for imaging in biological microscopy experiments.
Highlights
Biological microscopy has always required an 'imaging' capability: traditionally, the image of a sample was drawn on paper, or with the advent of light-sensitive film, recorded on media that conveniently allowed reproduction
Http://genomebiology.com/2005/6/5/R47 glance, it might appear that these requirements can be met by applying some of the tools that underpin modern biology, such as the informatics approaches developed for genomics
In this report we describe the implementation of this system, including details of the Open Microscopy Environment (OME) XML file format, a description of how images are represented both in the file format and in the data model, the application of semantic types for metadata extensibility as well as their use in modular image analysis, and describe recently developed software that makes use of this system and is targeted at end-users
Summary
We have designed and built OME as a data storage, management and analysis system for biological microscopy. (a) The Chain Builder, a tool that enables a user to build analysis chains by ensuring that the input requirements of a given module are satisfied by outputs from previous modules This is achieved by accessing the STs for the inputs and outputs within an OME database. Schema allows this format to satisfy local requirements and enables a strategy for updating schemas to satisfy new, incoming data types This approach provides the infrastructure to support systematic quantitative image analysis, and satisfies an indispensable need as high-throughput imaging gains wider acceptance as an assay system for functional genomic assays. Using the self-describing OME XML file, we can mediate between different data models, and when necessary, update a local model so that it can send or receive data from a different model In this way, OME considers data reports deposited research dialects as a compromise between a universal data language and a universe of separate languages. The current OME system is focused on biological microscopy, its concepts, and much of its architecture, can be adapted to any data-intensive activity
Sign-in/Register to view highlights & summary 
Published Version (
Free)
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call