The OME-XML format

OME-XML is a file format for storing microscopy information (both pixels and metadata) using the OME Data Model.

Note

OME-XML as a file format is superseded by OME-TIFF, which is the preferred container format for image data making use of the OME Data Model.

The purpose of OME-XML is to provide a rich, extensible way to save information concerning microscopy experiments and the images acquired therein, including:

  • dimensional parameters defining the scope of the image pixels (e.g. resolution, number of focal planes, number of time points, number of channels)
  • the hardware configuration used to acquire the image planes (e.g. microscope, detectors, lenses, filters)
  • the settings used with said hardware (e.g. physical size of the image planes in microns, laser gain and offset, channel configuration)
  • the person performing the experiment
  • some details regarding the experiment itself, such as a description, the type of experiment (e.g. FRET, time lapse, fluorescence lifetime) and events occurring during acquisition (e.g. laser ablation, stage motion)
  • additional custom information you may wish to provide about your experiment in a structured form (known as Structured Annotations)

Features and applications

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. The paper describing the design and implementation of the OME-XML file appeared in Genome Biology.

Note

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 (e.g. cells, genes) and acquisition (e.g. microscope light sources, filters, detectors) metadata.
  • OME-XML Image pixels may be stored compressed 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 Structured Annotations XML Schema section.

The OME-XML Schema .xsd files and technical documentation are available on the Schema pages.