Changes for June 2007¶
List of the key changes made for the June 2007 release of the ome-xml data model.
While this may not be a complete list of changes in detail, it should cover all the categories of changes applied to the files. Some changes affect the structure of the data model, some only the names used for concepts, and others only the xsd files themselves.
Overview of changes¶
Copyright changes¶
The copyright of the files has been extended to recognize the contribution of the University of Wisconsin at Madison.
Minimum specification¶
A minimum specification for a valid OME-XML file has been defined. Further information, including samples, is available in the Minimum Specification section.
Version¶
The way version information is recorded in the XSD files has been changed to adhere to best practice. For further information see Version Information.
ChannelInfo renamed and extended¶
This has been renamed to LogicalChannel. It also now has references to
secondary filters for emission and excitation. IlluminationType can now
be ‘NonLinear’, and Mode now has the catch-all type ‘Other’. Settings have
been added for PockelCell lasers.
Detector extended¶
An attribute Zoom has been added for use with confocals. Detector Type
has also been updated; it can now handle ‘EM-CCD’, ‘APD’, and ‘CMOS’
detectors. The EM-CCD detector type meant that an additional attribute was
needed called AmplificationGain.
DetectorRef extended¶
A reference to a detector now has the following addition attributes: a
Voltage; a ReadOutRate, which is speed at which the detector can count
the pixels; and a Binning setting where detector pixels are combined to
form a larger pixels set.
Laser extended¶
Lasers can now be set as the type ‘PockelCell’. A RepetitionRate has
been added. The FrequencyDoubled flag has been replaced by the
FrequencyMultiplication setting which, as an integer, can support more
systems. Laser now allows any other LightSource to be used as the
Pump. AuxLightSource and AuxLightSourceRef have been superseded
and therefore removed.
Objective extended¶
This now has attributes that record the LensNA, WorkingDistance,
ImmersionType, NomimalMagnification (e.g. x60),
CalibratedMagnification (e.g. x60.034), and Correction. The Correction
attribute records the coating applied to the lens. Possible Correction
types are ‘UV’, ‘PlanApo’, ‘PlanFluor’, ‘SuperFluor’, and ‘VioletCorrected’.
Magnification has been superseded and therefore removed.
ObjectiveRef renamed and extended¶
ObjectiveRef is now called ObjectiveSettingsRef. CorrectionCollar,
Medium, and RefractiveIndex have been added as attributes.
Pixels extended¶
Pixels can now contain either BinData or TiffData elements to
store the pixel data. It can now also contain Plane elements. Attributes
have been added to hold PhysicalSizeX, PhysicalSizeY,
PhysicalSizeZ, TimeIncrement, WaveStart, and WaveIncrement.
These were formerly attached to Image.
Filter and Filter Sets rewritten¶
The previous filter model has been replaced.
Images contracted and expanded¶
Image can now contain the following new elements: PlateRef,
AcquiredPixelsRef, ROI, and MicrobeamManipulation. The attribute
DefaultPixels is now required. The attributes PhysicalSizeX,
PhysicalSizeY, PhysicalSizeZ, TimeIncrement, WaveStart, and
WaveIncrement have been moved to Pixels.
Features renamed¶
Throughout the files, Feature and Features have become Region and
Regions. This allows the naming to be consistent with the region of
interest (ROI) model.
Screening Data Model¶
The new file SPW.xsd has been added to hold the Screen/Plate/Well
model. With its creation, Plate and Screen that were in
ome.xsd have been moved and re-written.
OME-Tiff extensions¶
The changes necessary to support the OME-Tiff format have been applied, namely
the addition of the TiffData element to Pixels as an alternative
option to the BinData element.
Internal IDs and LSID changes¶
The ID types used throughout the OME-XML model are designed to support identifiers in two forms, full LSID format and internal-only format. The formats of these are now enforced in an improved way, using new regular expressions. For further information see LSID.
The Image/Experiment Relationship¶
This has been modified.
Naming conventions¶
The naming convention used for attribute, element and enumeration names, already partly implemented, is documented below, and existing names have been corrected as necessary.
Enumerations¶
Enumeration names will normally use UpperCamelCase, and contain letters and numbers and the dash; no spaces and no other punctuation. The ‘-‘ is the only permitted punctuation character (so ‘e-‘ is allowed). Only abbreviations in common use in the field should be used.
Attributes¶
Attribute names will use UpperCamelCase, letters only, no punctuation. Where practical, whole words will be used rather then abbreviations.
Elements¶
Element names will use UpperCamelCase, letters only, no punctuation. Where practical, whole words will be used rather then abbreviations. Element names will normally be unique across all the OME files and where an element name is reused, this will be for a specific reason, which is outlined in an annotation present everywhere the element is defined.
