The Open Microscopy Environment (OME) Data Model and XML file: open tools for informatics and quantitative analysis in biological imaging

By Ilya G. Goldberg, Chris Allan, Jean-Marie Burel, Douglas A. Creager, Andrea Falconi, H. Hochheiser, J. Johnston, Jeff Mellen, Peter K. Sorger, Jason R. Swedlow. Genome Biology, 2005

335 citations recorded by the source corpus.

The Open Microscopy Environment (OME) defines a data model and a software implementation to serve as an informatics framework for imaging in biological microscopy experiments, including representation of acquisition parameters, annotations and image analysis results. OME is designed to support high-content cell-based screening as well as traditional image analysis applications. The OME Data Model, expressed in Extensible Markup Language (XML) and realized in a traditional database, is both extensible and self-describing, allowing it to meet emerging imaging and analysis needs.

Subfields: Biophysics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/cc05bb3132e7d525776e7e9630a608b22ddb0df7

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Biophysics

In Molecular Biology

Citations in the corpus

OME Remote Objects (OMERO): a flexible, model-driven data management system for experimental biology (2012, background): “This is an open specification for microscope image data that defines the elements and relationships for microscope image metadata 3 .”
Metadata matters: access to image data in the real world (2010, methodology): “For many years, the imaging community has expressed a desire to move away from the current ad hoc approach toward more defined standards for metadata representation (Goldberg et al., 2005).”
Visualization of image data from cells to organisms (2010, neutral): “An attempt to overcome these issues is the OMERO platform from the Open Microscopy Environment (OME), which provides a client-server system for managing images and their associated metadata through a common interface 1–3 .”
ImageJ2: ImageJ for the next generation of scientific image data (2017, positive): “For example, the Open Microscopy Environment (OME) defines a data model called OME-XML [42], for which the SCIFIO-OME-XML component provides a suite of translators to and from ImageJ Common data structures.”