OME 2016-06 Data Model

June 14, 2016

Mark Carroll, David Gault, Roger Leigh, S├ębastien Besson

Model Changes

  • Namespace unification
  • Class hierarchies
  • ROI Properties
  • Folders

Namespace unification

  • No more Schemas/SA/2015-01,
    Schemas/SPW/2015-01, etc.
  • For 2016 all now in one OME namespace

Namespace unification

OME-XML impact

2015-01 sample
<?xml version="1.0" encoding="UTF-8"?>
<OME xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
     xmlns="http://www.openmicroscopy.org/Schemas/OME/2015-01"
     xmlns:OME="http://www.openmicroscopy.org/Schemas/OME/2015-01"
     xmlns:Bin="http://www.openmicroscopy.org/Schemas/BinaryFile/2015-01"
     xmlns:SPW="http://www.openmicroscopy.org/Schemas/SPW/2015-01"
     xmlns:SA="http://www.openmicroscopy.org/Schemas/SA/2015-01"
     xmlns:ROI="http://www.openmicroscopy.org/Schemas/ROI/2015-01"
     xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2015-01
                         http://www.openmicroscopy.org/Schemas/OME/2015-01/ome.xsd">
2016-06 sample
<?xml version="1.0" encoding="UTF-8"?>
<OME xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
     xmlns="http://www.openmicroscopy.org/Schemas/OME/2016-16"
     xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2016-16
                         http://www.openmicroscopy.org/Schemas/OME/2016-16/ome.xsd">

Class Hierarchies

Data representation and code generation simplification

  • Elements made complexType
    • LightSource
      Arc, Filament, GenericExcitationSource, Laser, LightEmittingDiode
    • Shape
      Ellipse, Label, Line, Mask, Point, Polygon, Polyline, Rectangle
    • Map
      MapAnnotation, GenericExcitationSource, ImagingEnvironment
  • Elements dropped
    • MapPairs
  • Extended usage of xsd:appinfo for enumerations

Class Hierarchies

Shape

2015-01
<ROI ID="3">
    <Union>
      <Shape ID="Shape:3" FillRule="EvenOdd" Text="Hi There!">
        <Rectangle X="1" Y="2" Width="3" Height="4"/>
      </Shape>
      <Shape ID="Shape:4" FillRule="EvenOdd" FontStyle="Normal" FontFamily="serif">
        <Label X="1" Y="1"/>
      </Shape>
    </Union>
  </ROI>
2016-06
  <ROI ID="3">
    <Union>
      <Rectangle ID="Shape:3" FillRule="EvenOdd" Text="Hi There!" X="1" Y="2" Width="3" Height="4"/>
      <Label ID="Shape:4" FillRule="EvenOdd" FontStyle="Normal" FontFamily="serif" X="1" Y="1"/>
    </Union>
  </ROI>

Class Hierarchies

LightSource

2015-01
  <Instrument ID="Instrument:0">
    <LightSource ID="LightSource:0" Power="200" Manufacturer="OME Lights" Model="Ruby60"
                 SerialNumber="A654321">
      <Laser Type="SolidState" LaserMedium="Ruby">
        <Pump ID="LightSource:1"/>
      </Laser>
    </LightSource>
    <LightSource ID="LightSource:1" Power="300" Manufacturer="OME Lights" Model="Arc60"
                 SerialNumber="A123456">
      <Arc Type="Xe"/>
    </LightSource>
2016-06
  <Instrument ID="Instrument:0">
    <Laser ID="LightSource:0" Power="200" PowerUnit="mW" Manufacturer="OME Lights"
               Model="Ruby60" SerialNumber="A654321" Type="SolidState" LaserMedium="Ruby" RepetitionRate="1.2"
               RepetitionRateUnit="MHz" Wavelength="590.5" WavelengthUnit="nm">
      <Pump ID="LightSource:1"/>
    </Laser>
    <Arc ID="LightSource:1" Power="300" PowerUnit="mW" Manufacturer="OME Lights"
               Model="Arc60" SerialNumber="A123456" Type="Xe"/>

Class Hierarchies

MapAnnotation

Bio-Formats 5.1.xm =  new MapAnnotation();
List< MapPair > p = new ArrayList< MapPair>();
p.add(new MapPair("a", "1"));
p.add(new MapPair("b", "1"));
m.setValue(new MapPairs(p));
List< MapPair > p2 = m.getValue().getPairs();
Bio-Formats 5.2.xm =  new MapAnnotation();
List< MapPair > p = new ArrayList< MapPair>();
p.add(new MapPair("a", "1"));
p.add(new MapPair("b", "1"));
m.setValue(pairs);
List< MapPair > p2 = m.getValue();

Class Hierarchies

ImagingEnvironment

Bio-Formats 5.1.xi =  new ImagingEnvironment();
List< MapPair > p = new ArrayList< MapPair>();
p.add(new MapPair("a", "1"));
p.add(new MapPair("b", "1"));
i.setMap(new Map(p));
List< MapPair > p2 = i.getMap().getPairs();
Bio-Formats 5.2.xi =  new ImagingEnvironment();
List< MapPair > p = new ArrayList< MapPair>();
p.add(new MapPair("a", "1"));
p.add(new MapPair("b", "1"));
i.setMap(pairs);
List< MapPair > p2 = i.getMap();

Class Hierarchies

GenericExcitationSource

Bio-Formats 5.1.xg =  new GenericExcitationSource();
List< MapPair > p = new ArrayList< MapPair>();
p.add(new MapPair("a", "1"));
p.add(new MapPair("b", "1"));
g.setMap(new Map(p));
List< MapPair > p2 = g.getMap().getPairs();
Bio-Formats 5.2.xi =  new GenericExcitationSource();
List< MapPair > p = new ArrayList< MapPair>();
p.add(new MapPair("a", "1"));
p.add(new MapPair("b", "1"));
g.setMap(pairs);
List< MapPair > p2 = g.getMap();

ROI Properties

Simplification of graphical aspects of the data model

  • Properties dropped
    • ROI
      ROI.Namespace
    • Shape
      Shape.LineCap, Shape.Visible
  • Marker enumerations dropped
    Circle, Square
  • Arrow markers still available for Line/Polyline

Markers and OMERO

Folders

Allow the organization of ROI elements into hierarchical structures

  • Top-level element that may contain: Folders, ROIs, Images
  • Folder hierarchy is a strict tree: a Folder may have only one parent

Folder: OME-XML

<Folder ID="Folder:1" Name="CMPO">
  <FolderRef ID="Folder:2"/>
  <FolderRef ID="Folder:7"/>
</Folder>
<Folder ID="Folder:7" Name="Cell Component">
  <FolderRef ID="Folder:8"/>
  <ROIRef ID="Roi:14"/>
</Folder>

Folders and OMERO

Folders and Images

  • Images are associated with Folders,
    • directly via ImageRef or
    • indirectly via ROIRef

What's next

  • June: release of 2016-06 schema
  • July: release of OME Files C++ 0.2.0
  • August/September: release of Bio-Formats 5.2.0

Thank you

  • OME team