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:
For the OME schema
and that the schema file will be located at
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.
Experiment(held until next release)
MicrobeamManipulation is stored directly under an
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
MicrobeamManipulation objects to be located under the
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
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
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
several shapes derived from
All elements now have an explicit minOccurs and maxOccurs. All attributes now have a use value ‘optional’ or ‘required’.
PinholeSize type changed
PinholeSize type has changed from ‘xsd:positiveInteger’ to
‘xsd:float’ with units µm.
This element is a stub to act as a placeholder until more values are needed for this type.
Pixels can now contain EITHER
TiffData - previously
the model allowed there to be a mixture of the two, which was not the intended