Changes for April 2010

List of key changes for April 2010 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]/2010-04/

For the OME schema

http://www.openmicroscopy.org/Schemas/OME/2010-04/

and the schema file is located at

http://www.openmicroscopy.org/Schemas/OME/2010-04/ome.xsd

Overview of components changed

  • schema cleanup

  • units

  • ROI changes

  • SPW changes

  • Filter changes

Schema cleanup

The following legacy objects have been removed:

  • AnalysisChain.xsd

  • AnalysisModule.xsd

  • CA.xsd

  • CLI.xsd

  • DataHistory.xsd

  • MLI.xsd

  • STD.xsd

This required the removal of references to them from ome.xsd; the removal of CustomAttributes from OME, Image and Dataset nodes; and the removal of SemanticTypeDefinitions from the OME Node.

Units

  • Units were defined for everything in

    • ome.xsd

    • ROI.xsd

    • SPW.xsd

Follow some examples:

Physical size of a pixel in microns[um]
The Z-section this plane is for. [units:none]
This is the name of the fluorophore used to produce this channel [plain text string]

ROI changes

  • ROI now has:

    • an optional Description element

    • an optional Name attribute

    • an optional Namespace

  • Shape now has:

    • an abstract marker in an appinfo

    • an optional Name attribute

    • ChannelRef [0..\*] removed

    • TheC added linked to Channel [0..1]

    • all the attributes previously on the dropped ShapeDisplayOptions e.g. Fill, Stroke, FontFamily, etc.

  • The Text element has been renamed to Label.

SPW changes

  • Plate now has:

    • PlateAcquisition [0..\*] added

    • an attribute Rows

    • an attribute Columns

    • a unique key WellSampleIndex added for the attribute Index in SPW:Well/SPW:WellSample

    • DefaultSample removed

  • ScreenAcquisition has become PlateAcquisition.

  • PlateAcquisition now has:

    • an optional Description element added

    • an optional Name attribute added

    • an optional MaximumFieldCount attribute added

  • Screen now has ScreenAcquisition removed.

  • WellSample now has Index added.

Filter changes

  • Filter now has type ‘Dichroic’.

  • There is a new LightPath object (this provides much more flexibility than SecondaryEmissionFilter and SecondaryExcitationFilter).

Other

  • There have been changes and additions made to Detector.

  • The lack of LED attributes was explained in documentation.