Changes for January 2015

The list of the key changes for the January 2015 major release of the OME-XML data model. This schema release will tie in with the Bio-Formats 5.1 release.

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, except ome.xsd which version number is 2.

This schema uses the new namespace:

http://www.openmicroscopy.org/Schemas/[NameSpaceTitle]/2015-01/

For the OME schema

http://www.openmicroscopy.org/Schemas/OME/2015-01/

and the schema file is located at

http://www.openmicroscopy.org/Schemas/OME/2015-01/ome.xsd

Overview of changes

  • This version introduces a major new system of specifying units for the values stored as lengths, times, pressures, angles, temperatures, electric potentials (voltages), powers and frequencies. For more information see the OME system of units.

  • Many annotation points have been added and some removed. Objects in the model are now directly annotatable or have a 1 to 1 relationship with an object that is.

BinaryFile

  • There are no significant changes to this component.

OME

  • Expanded documentation for AcquisitionDate describing supported precision.

  • Updated documentation for NDFilter to reflect usage

  • Added Annotation points (AnnotationRef) to:
    Instrument
    Objective
    Detector
    Filter
    Dichroic
    LightPath
    LightSource
  • Added attributes to store:
    Pixels: PhysicalSizeXUnit
    Pixels: PhysicalSizeYUnit
    Pixels: PhysicalSizeZUnit
    Pixels: TimeIncrementUnit
    Plane: DeltaTUnit
    Plane: ExposureTimeUnit
    Plane: PositionXUnit
    Plane: PositionYUnit
    Plane: PositionZUnit
    Channel: PinholeSizeUnit
    Channel: ExcitationWavelengthUnit
    Channel: EmissionWavelengthUnit
    StageLabel: XUnit
    StageLabel: YUnit
    StageLabel: YUnit
    ImagingEnvironment: TemperatureUnit
    ImagingEnvironment: AirPressureUnit
    Objective: WorkingDistanceUnit
    Detector: VoltageUnit
    Filter: CutInUnit
    Filter: CutOutUnit
    Filter: CutInToleranceUnit
    Filter: CutOutToleranceUnit
    LightSource: PowerUnit
    Laser: WavelengthUnit
    Laser: RepetitionRateUnit
    LightSourceSettings: WavelengthUnit
    DetectorSettings: VoltageUnit
    DetectorSettings: ReadOutRateUnit
  • Removed Annotation points from:
    Pixels: AnnotationRef
  • Changed from int to float:
    Channel: ExcitationWavelength
    Channel: EmissionWavelength
    Filter: CutIn
    Filter: CutOut
    Filter: CutInTolerance
    Filter: CutOutTolerance
    Laser: Wavelength
    LightSourceSettings: Wavelength

  • Added a general Map to ImagingEnvironment to store key-value pairs

  • Added a new core type NonNegativeFloat

  • Added a new core element Map and associated complex type MapPairs. This in turn contains a collection of M elements that store a mapped value, each with its associated K key attribute.

  • Defined new enumerations with the permitted values for:
    UnitsLength
    UnitsTime
    UnitsPressure
    UnitsAngle
    UnitsTemperature
    UnitsElectricPotential
    UnitsPower
    UnitsFrequency

  • Added a new GenericExcitationSource to light source types. This uses a Map of key-value pairs to store metadata for a light source that cannot be expressed as one of the other types.

OMERO

OMERO.xsd is not included in this release.

ROI

  • Added Annotation points to:

    Shape: AnnotationRef

  • Added attributes to store:

    ROI: StrokeWidthUnit ROI: FontSizeUnit

SA

  • Added a new MapAnnotation type. This makes use of the new Map element from ome.xsd to store a collection of key-value pairs.

SPW

  • Added attributes to store:

    WellOriginXUnit WellOriginYUnit PositionXUnit PositionYUnit

  • Removed Annotation points from:

    WellSample: AnnotationRef

Upgrading and Downgrading

The XSLT transforms between June 2013 and January 2015 versions are available here:

http://www.openmicroscopy.org/Schemas/Transforms/2013-06-to-2015-01.xsl

http://www.openmicroscopy.org/Schemas/Transforms/2015-01-to-2013-06.xsl