Changes for June 2016

The list of the key changes for the June 2016 major release of the OME-XML data model. This schema release will tie in with the Bio-Formats 5.2 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.

This schema uses the new namespace:

http://www.openmicroscopy.org/Schemas/OME/2016-06/

All the schema files have been unified into a single ome.xsd file located at this namespace. The version number of this schema file is 1.

Overview of changes

  • This release will be implemented in Bio-Formats 5.2 and OMERO 5.3.
  • This release introduces the concept of Folders, a new model object which may contain Images, ROIs and other Folders, and which has a strict tree hierarchy.

Details

  • The model element Folder was added. A Folder specifies a possibly heterogeneous collection of data and may contain other Folders, Images and ROIs. Data may be in multiple Folders but a Folder may not be in more than one other Folder, giving a strict tree hierarchy. The primary driver for this addition is to allow the organization of ROI elements into hierarchical structures (see this Folders blog post for further discussion).
  • The ROI properties ROI.Namespace, Shape.Linecap and Shape.Visible have been dropped. This simplifies graphical aspects in the data model in favor of more generic enumerated values independent of the rendering framework, making it easier to implement across clients (see this Design issue for an example discussion).
  • The Marker enumeration has been reduced to Arrow only, dropping Circle and Square. This affects the Line.MarkerStart, Line.MarkerEnd, Polyline.MarkerStart and Polyline.MarkerEnd attributes. As with the ROI property changes, these are also intended to simplify the graphical aspects of the data model.

The following are simplifications for code generation purposes and have no functional effects:

  • The model elements LightSource and Shape have become abstract classes, meaning they are now complexTypes in the .xsd. This provides a more intuitive object-oriented design (e.g. Rectangle is a type of Shape rather than Shape containing a Rectangle) and simplifies the data representation (schema) as well as the code generation because two different ways to model inheritance and polymorphism have been changed to one.
  • The MapPairs model element has been removed as an unnecessary container which is superseded by using the maps directly in the generated code.
  • The Map model element has been made a complexType. This element was never used directly, only as a base, so the change allows for the removal of a redundant model object.
  • xsd:appinfo has been extended to provide more detail for enumeration code generation, in particular for units.

Upgrading and Downgrading

The XSLT transforms between January 2015 and June 2016 versions are available here:

http://www.openmicroscopy.org/Schemas/Transforms/2015-01-to-2016-06.xsl

http://www.openmicroscopy.org/Schemas/Transforms/2016-06-to-2015-01.xsl