OME file formats

Users meeting

June 1, 2016

Sébastien Besson

OME File Formats

OME-TIFF file format

  • Based on the TIFF specification
  • OME metadata stored as OME-XML within the ImageDescription tag of the first IFD

OME-TIFF file format

  • Supports multi-dimensional, multi-image files

    • See artifical OME-TIFF samples

    OME-TIFF large datasets

    • TIFF specification limited to 4GB (32-bit pointers)
    • Limitations for large data volumes
      • Complex multi-dimensional datasets
      • High-Content-Screening data

    Solution 1: BigTiff

    • OME-TIFF supports BigTIFF format
    • Use of 64-bit based offsets overcomes 4GB limit

    Solution 2: distribution across multiple files

    See the multi-file OME-TIFF sample

    Solution 2: distribution across multiple files

    See the master OME-TIFF sample

    Solution 2: distribution across multiple files

    See the companion OME-XML sample

    Extended metadata

    • Store flexible metadata not defined in the OME Data Model
    • Use structured annotations to store key/value pairs
    <OME xmlns="http://www.openmicroscopy.org/Schemas/OME/2015-01"
...
    <AnnotationRef ID="Annotation:1"/>
  </Image>
    <MapAnnotation ID="Annotation:1">
      <Description>Additional metadata description</Description>
      <Value>
        <M K="Key-1">Value-1</M>
        <M K="Key-2">Value-2</M>
      </Value>
    </MapAnnotation>
  </StructuredAnnotations>
</OME>
    See the OME-XML sample

    Tools and software

    • Bio-Formats tools
      • validation (xmlvalid)
      • reading (showinf)
      • modification (tiffcomment)
    • Reference C++ implementation for working with OME Files

    Future directions

    • More extension points
    • New HDF5-based file format

    Questions?

    Model Changes

    Class Hierarchies

    • LightSource
      Arc, Filament, GenericExcitationSource, Laser, LightEmittingDiode
    • Shape
      Ellipse, Label, Line, Mask, Point, Polygon, Polyline, Rectangle

    Model Changes

    Single namespace

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

    Model Changes

    Drop ROI Properties

    Drop from model,

    • ROI.Namespace
    • Shape.LineCap
    • Shape.Visible

    Model Changes

    Drop (Poly)Line Markers

    • Drop Circle and Square
    • Arrow markers remain
    • Also added to OMERO model

    Model Changes

    New: Folders

    • Folders may contain:
      Folders, ROIs, Images
    • Folder hierarchy is a strict tree:
      a Folder may have only one parent

    Model Changes

    Folders and Images

    • Images are associated with Folders,
      • directly via ImageRef or
      • indirectly via ROIRef
    • OMERO.insight, .web initially support only the latter

    Model Changes

    Folder Example

    <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>