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 SPW.xsd to the 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

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 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 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