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