Compliant file specification
============================


This was developed in conjunction with the April 2010 release of the
OME-XML Model and the samples have been updated to the June 2016 release.

A "compliant" specification OME file has been defined. This is not the
minimum required for the display of an image (for this, see :doc:`Minimum
Specification <minimum>`). This is the information a file should contain to 
authoritatively describe an imaging experiment, so that another person could, 
with the same sample and microscope, reproduce the data recorded in the file. 
Therefore, an 'OME Compliant' file should be as complete
as possible, but only contain metadata relevant to a specific imaging
experiment i.e. all of the fields listed below
that are relevant to the experiment should be completed. As an example,
PockelCellSetting would not be used in most wide-field microscopy
experiments, but would be mandatory for many multi-photon imaging
experiments.

Sample structure
----------------

Two samples of this structure are shown below. They were generated by
opening a propriety file (Olympus .oib and DeltaVision .dv,
respectively) in ImageJ, using the Bio-Formats plugin with the *Display
OME-XML Metadata* option checked. A few additional
attributes were then manually added to the files to make them compliant.

Sample structure one:

.. literalinclude:: olympus.ome.xml

Sample structure two:

.. literalinclude:: deltavision.ome.xml

.. note::
    The data (BinData element content) in these sample was removed for
    reasons of length.

Alternative valid forms:

-  would have a ``TiffData`` block instead of the ``BinData`` block
   (this would be used in the header of an OME-TIFF file)
-  would have a ``MetadataOnly`` block instead of the ``BinData``
   block (this would be used as a companion to one or more ``BinaryOnly``
   OME-TIFF files)

.. note:: A units system was added in January 2015. This sample assumes the
   default unit for each value is used.

Definitions of values stored
----------------------------

The figure :ref:`figure-spec-stored` is ©2010 Linkert et al. Figure originally
published as Figure 2, 
Linkert et al (2010), J. Cell Biol. 189(5):777-782
(http://jcb.rupress.org/content/189/5/777)

.. note:: AcquiredDate was renamed to AcquisitionDate in June 2012

.. _figure-spec-stored:

.. figure:: /images/OME-schema-table-formatted_final.png
   :align: center
   :alt: Definitions of values stored

   Definitions of values stored
   
   ©2010 Linkert et al. Figure originally published as Figure 2, Linkert et
   al (2010), J. Cell Biol. 189(5):777-782