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Welcome to ome-xml.org!
This site provides information on OME-XML, the Open Microscopy Environment's data model and associated file formats.
This site's main focus is on technical details; if you want to dig in right away, head over to the DeveloperInfo page.
The core site for the Open Microscopy Environment is located at http://www.openmicroscopy.org/
What is OME?
OME is an umbrella term that stands for "Open Microscopy Environment" and covers:
- The OME file formats, including OME-XML and OME-TIFF, and the Bio-Formats Java library.
- The OME database systems for microscopy data management and analysis comprising the original OME Server and the OMERO platform.
- The OME consortium, the group behind these efforts.
What is OME-XML? Why should I care?
OME-XML is a project to provide support for the exchange of microscope imaging data within the field of life sciences. Its key aspects include support for collaborative sharing of data between labs who may be using different apparatus, and the safeguarding of crucial metadata associated with image files that can be lost when they are moved across systems (or in many cases never recorded at all).
The term "OME-XML" means two interrelated but distinct things:
- A data model for representing microscopy metadata, for use with microscopy file formats, expressed as an XML schema.
- A file format for storing microscopy information (both pixels and metadata) using the OME-XML 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 (resolution, number of focal planes, number of time points, number of channels, etc.).
- The hardware configuration used to acquire the image planes (microscope, detectors, lenses, filters, etc.).
- The settings used with said hardware (physical size of the image planes in microns, laser gain and offset, channel configuration, etc.).
- The person performing the experiment.
- Some details on the experiment itself, such as a description, what type of experiment (FRET, time lapse, fluorescence lifetime, etc.) and events occurring during the acquisition (laser ablation, stage motion, etc.).
- Additional, custom information you may wish to provide about your experiment in a structured form (known as semantic types).
What is OME-TIFF?
OME-TIFF is a practical, high performance interchange format that encodes the metadata using the OME-XML data model. It is essentially OME-XML turned "inside out," with the OME-XML inside a regular TIFF file, allowing the pixels to be read with any TIFF-compatible program, and the metadata to be extracted with any OME-aware application.
How can I learn more?
Since the level of detail you want regarding OME-XML undoubtably depends on how you want to use it, we have provided links to varying sorts of information.
If you are wondering how OME-XML can help you, take a look at the OME-XML FAQ, and also see the questions above.
If you are a microscopist, check out the non-technical overview of the OME-XML and OME-TIFF formats. If you are looking for software to read files in OME-XML or OME-TIFF format, check out the Bio-Formats plugins for ImageJ.
If you are a software developer interested in working with OME-XML, try reading the technical overview of OME-XML for the OME Server, and perhaps also the OME-TIFF overview, then check out the DeveloperInfo page, which is the main focus of this site.
If you are looking for a publication to read or cite, check out the Genome Biology paper on OME-XML.
