Changes for June 2012 ===================== The list of the key changes for the June 2012 major release of the ome-xml data model. This schema release will tie in with the Bio-Formats 4.4 release. The new major release of the schema has a new namespace and all version numbers are reset to 1. As a major release, any file that validated correctly using the last major release will probably not validate correctly using this new release. Some files that failed to validate before will now be valid. It is important to update any file readers and writers to understand the changes. The version number of all schema files is now 1. This schema uses the new namespace: :: http://www.openmicroscopy.org/Schemas/[NameSpaceTitle]/2012-06/ For the OME schema :: http://www.openmicroscopy.org/Schemas/OME/2012-06/ and the schema file is located at :: http://www.openmicroscopy.org/Schemas/OME/2012-06/ome.xsd Overview of changes ------------------- - This release is in step with release of Bio-Formats 4.4. - It is preparation for the Major release of OMERO **after** 4.4. - It includes work to allow full code generation of OME Model API direct from the XSD files. - It also includes almost full synchronization of the OME Model with the OMERO Database structure. - The direction of references between Screen, Plate and Well, and between Project, Dataset and Image, have been reversed. - The ROI model has been majorly reworked. - ``Pixels`` has been **DEPRECATED**, but is still required at present. - ``OTF`` and all associated objects have been **REMOVED**. General changes ^^^^^^^^^^^^^^^ - **All** colors are now stored as new type ``Color``. - The default value for all colors is now solid white (due to legacy color default it was totally transparent red). - ``appinfo`` blocks for ``xsd-fu`` have been added to specify plurals. - ``appinfo`` blocks for ``xsd-fu`` have been added to specify abstract objects. BinaryFile ^^^^^^^^^^ - The only change here is the general change adding ``appinfo`` blocks for ``xsd-fu`` to specify plurals. OME ^^^ - ``AcquiredDate`` has been renamed to ``AcquisitionDate`` in ``Image``. - ``ExperimentGroup`` has been renamed to ``Group``. - ``Group`` is now annotatable. - Multiple ``Leader``s are now possible for each ``Group``. - ``Contact`` has been removed from ``Group`` - the transform will convert any existing ``Contact`` to a ``Leader``. - The direction of the references between ``Project``, ``Dataset`` and ``Image`` have been reversed for consistency with other linked objects. - ``DisplayName`` has been removed from ``Experimenter``. - The ``ImageRef`` element has been moved from the :file:`SPW.xsd` to the :file:`ome.xsd` schema file. - ``Pixels`` has been **DEPRECATED**, but is still required. The contents of ``Pixels`` will be moved up to ``Image`` in the next release - it is a legacy of when ``Image`` could have multiple ``Pixels`` sets and has been redundant since the 2009-09 schema fixed the number of ``Pixels`` sets in an ``Image`` at 1. - ``OTF`` and all associated objects have been **REMOVED**. OMERO ^^^^^ :file:`OMERO.xsd` is not included in this release. It has been extensively reworked and expanded as part of the OME Model and OMERO Database synchronization but work on this will continue until the release of the associated OMERO version. The OME Model does not make use of :file:`OMERO.xsd` so will be unaffected by the future release of this single file. .. note:: Some differences must remain between OME Model and OMERO Database for database optimization reasons - these are handled by special cases in our code generation application ``xsd-fu``. ROI ^^^ - All objects defining colors now use the type 'OME:Color' from file:`ome.xsd`. - ``MarkerStart`` and ``MarkerEnd`` have been moved down from ``Shape`` into ``Line``, ``Polyline``. - A ``Polygon`` element (a new type of ``Shape``) has been added. - 'Closed' has been deleted from Polyline (a Closed Polyline is now transformed into a Polygon). - The attribute ``Name`` has been deleted from ``Shape``. - ``Description`` has been deleted from ``Shape``. - ``Visible`` has been added to ``Shape``. - ``Locked`` has been added to ``Shape``. - The ``Fill`` attribute in ``Shape`` has been renamed to ``FillColor``. - The ``Stroke`` attribute in ``Shape`` has been renamed to ``StrokeColor``. - ``Value`` has been deleted from ``Text``. - The ``Text`` element has been renamed to ``Label``. - The ``Label`` attribute in ``Shape`` has been renamed to ``Text``. - ``Transform`` has been converted to the new type ``AffineTransform``. SA ^^ Additional intermediate abstract annotations (``BasicAnnotation``, ``NumericAnnotation``, ``TextAnnotation``, ``TypeAnnotation``) have been added to match OMERO annotation structure. The current annotations have been modified to now extend these. This allows the code generation to group annotations together by intermediate annotation type. The behavior of the current annotations has not changed, and the new intermediate abstract annotations are not used directly. SPW ^^^ - ``FieldIndex`` has been added to ``Plate`` - this means the index of the WellSample displays as the default Field. - The human readable identifier for the screening status has been renamed from 'Status' to 'Type'. - The direction of the references between ``Screen`` and ``Plate`` has been reversed for consistency with other linked objects. - The ``ImageRef`` element has been moved to the :file:`ome.xsd` schema file. Upgrading and Downgrading ------------------------- The XSLT transforms between June 2011 and June 2012 versions are available here: `http://www.openmicroscopy.org/Schemas/Transforms/2011-06-to-2012-06.xsl `_ `http://www.openmicroscopy.org/Schemas/Transforms/2012-06-to-2011-06.xsl `_