Changes for September 2008 ========================== List of the key changes for the September 2008 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]/2008-09/ For the OME schema :: http://www.openmicroscopy.org/Schemas/OME/2008-09/ and that the schema file will be located at :: http://www.openmicroscopy.org/Schemas/OME/2008-09/ome.xsd Overview of Changes ------------------- Additional Schema file SA.xsd ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ This provides support for the new ``StructuredAnnotation`` objects. The list of annotations is: :: XmlAnnotation FileAnnotation ListAnnotation LongAnnotation DoubleAnnotation StringAnnotation BooleanAnnotation TimestampAnnotation Additional Schema file OMERO.xsd ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ This provides support for the specific use of OMERO in the ``StructuredAnnotation`` objects. Each OMERO-specific block is stored in an ``XmlAnnotation``. It is not strictly part of the model as it provides support only to the OMERO system. The schema will be published to show how we are using structured annotations within OMERO. Optional and non-optional Objects ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - The following objects have been made **optional** to allow the import of the metadata from Bio-Formats and maintain consistency: :: OME:Image:CreationDate OME:Image:Pixels:Plane:PlaneTiming:DeltaT OME:Image:Pixels:Plane:PlaneTiming:ExposureTime OME:Experiment:ExperimenterRef OME:Instrument:Microscope OME:Instrument:Objective:CalibratedMagnification OME:Instrument:Objective:LensNA OME:Instrument:Objective:NominalMagnification OME:Instrument:Objective:WorkingDistance OME:Instrument:Filter:TransmittanceRange OME:Instrument:Filter:TransmittanceRange:CutIn OME:Instrument:Filter:TransmittanceRange:CutOut OME:Instrument:Filter:TransmittanceRange:Transmittance OME:StagePosition:PositionX OME:StagePosition:PositionY OME:StagePosition:PositionZ OME:Project:ExperimenterRef ManufactSpec:Manufacturer ManufactSpec:Model ``ManufactSpec`` is the base type for several other objects. - The following objects have been made **optional in the model** but **NOT in the OMERO database** - a value will be generated on import: :: OME:Image:Name OME:Plate:Name OME:Dataset:Name OME:Project:Name OME:Screen:Name - The following objects **are not optional** - but they now support the value 'Unknown': :: OME:Instrument:LightSource:Laser:LaserMedium - Added new UnknownLaserMedia type to union. OME:Instrument:LightSource:Laser:Type - added Unknown. OME:Instrument:LightSource:Arc:Type - added Unknown. OME:Instrument:LightSource:Filament:Type - added Unknown. OME:Instrument:Microscope:Type - added Unknown. OME:Instrument:Objective:Correction - added Unknown. OME:Instrument:Objective:Immersion - added Unknown. OME:Instrument:Detector:Type - added Unknown. MicrobeamManipulation ^^^^^^^^^^^^^^^^^^^^^ - Moving ``MicrobeamManipulation`` from ``Image`` to ``Experiment`` **(held until next release)** 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 the ``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``. - Reworking ``ROI`` in ``MicrobeamManipulation`` **(held until next release)** As a separate issue to above, the ``ROI`` used by the ``MicrobeamManipulation`` should stop being a 'Ref' to one stored in ``Image``. In the current situation, the manipulated ROI is listed along with all the other ROIs. It is not the same though, as the other ROIs could legitimately be adjusted by the user whereas the ``MicrobeamManipulation`` ROI is fixed and should not be changed after the manipulation. This change is being made at this time as the ROI is already being changed. New ROI model ^^^^^^^^^^^^^ The new model has a more powerful ROI model and the display options are now stored as Structured Annotations. Elements added include ``LogicalChannelRef``, ``ShapeID``, ``ROI``, ``Shape``, ``BasicSvgShape`` and several shapes derived from ``BasicSvgShape``. Min/Max/Optional/Required ^^^^^^^^^^^^^^^^^^^^^^^^^ All elements now have an explicit minOccurs and maxOccurs. All attributes now have a use value 'optional' or 'required'. PinholeSize type changed ^^^^^^^^^^^^^^^^^^^^^^^^ The ``PinholeSize`` type has changed from 'xsd:positiveInteger' to 'xsd:float' with units µm. Added LightEmittingDiode ^^^^^^^^^^^^^^^^^^^^^^^^ This element is a stub to act as a placeholder until more values are needed for this type. Pixels ^^^^^^ ``Pixels`` can now contain **EITHER** ``BinData`` or ``TiffData`` - previously the model allowed there to be a mixture of the two, which was not the intended use.