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 :doc:`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 :doc:`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 The ``FrequencyDoubled`` flag has been replaced by the ``FrequencyMultiplication`` setting which, as an integer, can support more systems.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 ``AuxLightSource`` and ``AuxLightSourceRef`` have been superseded and therefore removed.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 :file:`SPW.xsd` has been added to hold the Screen/Plate/Well model. With its creation, ``Plate`` and ``Screen`` that were in :file:`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 :doc:`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``.