The OME-XML File

The OME-XML File serves as a convenient file format for data migration from one site or user to another. The OME-XML File captures all image acquisition and experimental metadata along with the binary image data and packages it into an easily readable package. More detailed information on OME-XML is available. Also, see our paper describing the design and implementation of the OME-XML File in Genome Biology.

OME-XML files can be read by potentially any software package – you do not need OME image management software to use OME-XML.

Some specific features of the OME-XML File Format:

• OME-XML files may contain one or more sets of 5-D Pixels, for example raw data from a microscope, the deconvolved data, and a volume rendered view.
• OME-XML files contain all the metadata associated with an image, including the experimental (cells, genes, etc.) and acquisition (microscope light sources, fluors, filters, detectors, etc.) metadata.
• OME-XML Image pixels may be stored compressed (or not) directly in XML with base64 encoding. Compression of the pixels and the metadata is supported through widely-available patent-free compression schemes (gzip and bzip2). OME-XML Images are addressable by plane.
• OME-XML files have a built-in mechanism for supporting arbitrary user-defined data that can be used globally or attached to Images, Features (objects inside Images), and Datasets. Mechanisms for OME-compliant systems to populate databases with these user-defined fields is part of the specification. See the Semantic Type Definitions XML Schema, documentation and an example document that defines the core OME Semantic Types.

Again, the OME-XML Schema and use are documented here.

Ongoing Development

The ongoing development of the OME-XML data model can be tracked on http://www.ome-xml.org/. Users can also add work tickets to the system detailing any changes they feel should be made. The site contains details of the changes made for the June 2007 release.

Commercial Support for OME-XML

Bitplane AG and EAMNET have proposed the use of the OME-XML File as an image data migration standard. A C++ class that reads OME-XML has been posted by Peter Majer and Marius Messerli of Bitplane AG on the EAMNET site. Thanks to Peter and Marius for this.

Applied Precision, LLC has released an image visualization tool that reads and writes OME-XML.

Scientific Volume Imaging have included support for the OME-XML file format in there Huygens Software, a collection of Fluorescence Microscope image processing packages. The packages are available for many software platforms.

Improvision joins the ever-increasing list of commercial solution providers that supports OME-TIFF. Support is available in the newest release of Version 4.2.