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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.

Version

The version number of all schema files is now 1.

Namespace

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 that the schema file will be located at 

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

Overview of Changes

  • Schema Cleanup
  • Units
  • ROI changes
  • SPW changes
  • Filter Changes

There are a collection of diagrams for the schema that may be useful in understand the changes available, see wiki:ModelOverview v2010-04 .

Schema Cleanup

  • Remove legacy objects
  • Dropping of files
    • AnalysisChain.xsd
    • AnalysisModule.xsd
    • CA.xsd
    • CLI.xsd
    • DataHistory.xsd
    • MLI.xsd
    • STD.xsd
  • Removal of includes in ome.xsd to STD, CA and AML (also CLI & MLI)
  • Removal from OME, Image and Dataset nodes of CustomAttributes
  • Removal from OME Node of SemanticTypeDefinitions

Units

  • Units 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

For more details see ROI v2010-04

  • 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
    • removed ChannelRef [0..*]
    • add TheC to link to Channel [0..1]
    • all the attributes previously on the dropped ShapeDisplayOptions
      • e.g. Fill, Stroke, FontFamily, etc.

  • Text element renamed to Label.

SPW changes

For more details see Screen Plate Well v2010-04

  • Plate now has:

    • added PlateAcquisition [0..*]
    • an attribute Rows
    • an attribute Columns
    • added a unique key WellSampleIndex for the attribute Index in SPW:Well/SPW:WellSample
    • removed DefaultSample

  • ScreenAcquisition has become PlateAcquisition.

  • PlateAcquisition now has:

    • added an optional Description element
    • added an optional Name attribute
    • added an optional MaximumFieldCount attribute

  • Screen now has:

    • removed ScreenAcquisition

  • WellSample now has:

    • added Index

Filter Changes

For more details see Filter And FilterSet v2010-04

  • Filter now has type "Dichroic"
  • New LightPath object (this provides much more flexibility than SecondaryEmissionFilter and SecondaryExcitationFilter)

Other

  • Detector - Changes/Additions
  • LED attributes
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