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.