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 The FrequencyDoubled flag has been replaced by the FrequencyMultiplication setting which, as an integer, can support more systems.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 AuxLightSource and AuxLightSourceRef have been superseded and therefore removed.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 Magnification has been superseded and therefore removed.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.

Miscellaneous corrections

Some spelling mistakes have been corrected. There have been minor changes to the file layouts.

Plane

This has been modified and now contains some of the structures that were in Image.