|release| DocumentationOME Data Model and File Formats
This documentation covers the OME Data Model, OME-XML and OME-TIFF.
The OME Model is a specification for storing data on biological imaging. The model includes image parameters, such as XYZ dimensions and pixels type, as well as extensive metadata on, for example, image acquisition, annotation, and regions of interest (ROIs). This common specification is essential for the exchange of image data between different software packages. OME-XML is a file format used to store data according to the OME Model, serving as a convenient file format for data migration from one site or user to another. OME-TIFF is a multi-plane tiff file that contains OME metadata in the header, in the form of OME-XML. This allows the pixels to be read with any TIFF-compatible program, and the metadata to be extracted with any OME-aware application. Our paper describing the design and implementation of the OME-XML file appeared in Genome Biology.
The OME consortium currently provides three major tools capable of working with OME-XML and OME-TIFF:
- The :bf:`Bio-Formats <>` library is a full-featured library with many features related to OME-XML, including conversion of third party file format metadata into OME-XML structures. It can write image data to the OME-TIFF format.
- :ome-files:`OME Files C++ <>` is a reference implementation of the OME data model and OME-TIFF for C++ developers wishing to support these in their own software. It can read and write OME-TIFF data.
- The :omero:`OMERO server <>` works directly with OME-XML. It can import data from OME-XML and OME-TIFF, as well as export to OME-TIFF.
If you have used OME-XML, OME-TIFF, Bio-Formats or OMERO in your work please use the :citing:`correct citations <>` to acknowledge us.
We have received support from several companies who use our file formats, for details see our list of :partners:`Partners <>`.
The versioning for this documentation reflects updates to any of the components it covers and is therefore incremented more frequently than the Schema version, which only covers the Data Model and for which a version history is provided below.
.. toctree:: :maxdepth: 1 :titlesonly: ome-tiff/index ome-tiff/file-structure ome-tiff/specification ome-tiff/code ome-tiff/data
.. toctree:: :maxdepth: 1 :titlesonly: ome-xml/index ome-tiff/tools ome-xml/java-library
.. toctree:: :maxdepth: 1 :titlesonly: omero-pyramid/index
.. toctree:: :maxdepth: 1 :titlesonly: specifications/index specifications/compliant-hcs specifications/minimum
Developer tools and guidelines
.. toctree:: :maxdepth: 1 :titlesonly: developers/index developers/using-ome-xml developers/compression developers/sample-files developers/id-and-lsid developers/ome-units developers/EnumTool
The Data Model in detail
Generated documentation for the :schema_doc:`current version of the entire Schema <ome.html>` is also available.
.. toctree:: :maxdepth: 1 :titlesonly: developers/model-overview developers/filter-and-filterset developers/screen-plate-well developers/structured-annotations developers/roi developers/6d-7d-and-8d-storage developers/legacy/index
Data Model history
.. toctree:: :maxdepth: 1 :titlesonly: schemas/index schemas/june-2016-2 schemas/june-2016 schemas/january-2015 schemas/june-2013 schemas/june-2012 schemas/june-2011 schemas/june-2010 schemas/april-2010 schemas/september-2009 schemas/september-2008 schemas/february-2008 schemas/june-2007-2 schemas/june-2007
.. toctree:: :hidden: schemas/september-2007