Changes for September 2009

The list of the key changes for the September 2009 major release of the ome-xml data model.

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]/2009-09/

For the OME schema

http://www.openmicroscopy.org/Schemas/OME/2009-09/

and that the schema file will be located at

http://www.openmicroscopy.org/Schemas/OME/2009-09/ome.xsd

Overview of changes

Additional Schema file ROI.xsd

This provides support for the new version of the ROI objects. These were moved from the OME namespace to there own namespace and the objects updated to be simpler and more consistent. Existing ROI’s can be updated to the new structure.

• Some support for ROIs in OMERO.xsd has moved to be part of the full schema in ROI.xsd.

MicrobeamManipulation

• MicrobeamManipulation has been moved from Image to Experiment.

At present MicrobeamManipulation is stored directly under an Image with a link to an Experiment. The structure this produces is too flexible and allow loops of references to be created. It is proposed that we move all the MicrobeamManipulation objects to be located under Experiment and replace them in each Image with zero or more MicrobeamManipulationRef objects. This also allows one MicrobeamManipulation operation to be used in more than one Image.

ROI in MicrobeamManipulation and Image

• ROI in MicrobeamManipulation and in Image has been reworked inline with its movement to the top level OME element.

The ROIs used by the MicrobeamManipulation as a ‘Ref’ and stored in Image have been moved to the top level. This allows reuse of the ROI in more than one Image.

Other changes

• LogicalChannel and ChannelComponent have been merged into the new Channel.
• Additional keys and indexes to enforce valid IDs and References, are listed in the OME:OME element.
• Support for the AnalysisModuleLibrary used by the original OME server has been removed.
• Support for the DisplayOptions used by the original OME server has been removed.
• Support for the Region used by the original OME server has been removed.
• All description elements and attributes have become simple description elements based on ‘xsd::string’ that preserve white space.
• The direction of all annotation links has been reversed. Now objects in the model link to annotations, not the other way around.
• Where possible values that are singular are now an attribute of an element, and values that can be multiple are child elements of an element.
• Units are now specified in the schema annotations.
• Pixels now link to Channel.
• It is now possible to define valid Metadata-Only files.
• There are a large number of general changes and updates as part of a major clean up of the types and names used in the schema, to facilitate code generation direct from the schema.