This is is 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 is 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.
Copyright changes
The copyright of the files has been extended to recognise the contribution of the University of Wisconsin at Madison.
Minimum Specification
A minium specification for a valid OME-XML file has been defined. Further information, including samples, is available at MinimumSpecification.
Versioning
The way version information is recorded in the XSD files has been changed to adhere to best practise. For further information see VersionInformation.
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. Also updated is the Type, 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 combine to form larger pixels.
Laser extended
Lasers can now be set as being 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 The FrequencyDoubled flag has been replaced by the FrequencyMultiplication setting which as an integer can support more systems.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 AuxLightSource and AuxLightSourceRef have been removed as they have been superseded.
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 Magnification has been removed as it have been superseded.
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 now also can contain Plane elements. Attributes have been added to hold PhysicalSizeX, PhysicalSizeY, PhysicalSizeZ, TimeIncrement, WaveStart, and WaveIncrement. These use to be attached to Image.
Filter and Filter Sets rewritten
The previous filter model has been replaced. For further information see FilterAndFilterSet.
Images contracted and expanded
Make "DefaultPixels" field required in Image - done 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 consistant with the region of interest 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. For further information see ScreenPlateWell.
OME-Tiff extensions
The changes necessary to support the OME-Tiff format have been applied - This was the addition of the TiffData element to Pixels as a 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 inforced 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 was written down and existing names corrected as necessary.
for enumerations
Enumerations names will normally use UpperCamelCase, and contain letters & 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.
for attributes
Attributes names will use UpperCamelCase, letters only, no punctuation. Where practical whole words will be used rather then abbreviations.
for elements
Elements 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 is will be for a specific reason that is outline in an annotation present in each place the element is defined.
Miscellaneous corrections
Some spelling mistakes have been corrected. There have been minor changed to the file layouts.
Plane
This has been modified and now contains some of the structures that were in Image.
Notes: in the XSD files the element and attribute names use camelCase and PascalCase. As these are also interepted by WikiFormatting this may result in links to seeming missing pages. These will be display as follows: DummyElememtName?
