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OME Data Model and File Formats |release| Documentation

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 <>`.

Note

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.

OME-TIFF

.. toctree::
    :maxdepth: 1
    :titlesonly:

    ome-tiff/index
    ome-tiff/file-structure
    ome-tiff/specification
    ome-tiff/code
    ome-tiff/data


OME-XML

.. toctree::
    :maxdepth: 1
    :titlesonly:

    ome-xml/index
    ome-tiff/tools
    ome-xml/java-library

OMERO Pyramid

.. toctree::
    :maxdepth: 1
    :titlesonly:

    omero-pyramid/index

File specifications

.. 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
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