The Open Microscopy Environment: A Collaborative Data Modeling and Software Development Project for Biological Image Informatics

The transition of a microscope’s output from an “image,” recorded on paper or film, to digitally recorded “data” has created new demands for storage, analysis and visualization that are not adequately met in current software packages. The Open Microscopy Environment (OME) Consortium is dedicated to developing open available tools to meet this challenge. We have developed and released the OME data model that provides a thorough description of the image data acquisition, structure and analysis results. An XML representation of the OME data model provides convenient standardized file formats known as OME-XML and OME-TIFF. In addition, OME has built two software tools, the OME and OME Remote Objects (OMERO) servers that enable visualization, management and analysis of multidimensional image data in structures that enable remote access. The OME server provides a flexible data model and an interface into complex analysis workflows. The OMERO server and clients provide image data visualization and management. A major goal for the next year is the provision of well-developed libraries and documentation to support the OME file formats, and enhanced functionality in our OME and OMERO applications to provide complete solutions for imaging in cell biology.

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