This is the 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.

Version

• The version number of all schema files is now 1

Namespace

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

• There will be an 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

• There will be an 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 provide support only to the OMERO system. The schema will be published to show how we are using structured annotations within OMERO.

• 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 HAVE NOT been made optional. They do 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
  

• Move 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 MicrobeamManipulations to be located under the Experiment and replace them in each Image with zero or more MicrobeamManipulationRefs. This also allows one MicrobeamManipulation operation to be used in more than one Image.

• Rework 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 as the other ROIs could legitimately be adjusted by the user. The MicrobeamManipulation ROI is however 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 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 maxOccours. 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 um.

• Added LightEmittingDiode

This element is a stub to act as a placeholder until more values are needed for this type.

• Pixels can now contain EITHER BinData or TiffData.

Previously the model allowed there to be a mixture of the two. This was not the intended use.