OME Data Model and File Formats 5.6.3 Documentation

This documentation covers the OME Data Model, OME-XML and OME-TIFF.

The OME Model is a specification for storing data on biological imaging. The model includes image parameters, such as XYZ dimensions and pixels type, as well as extensive metadata on, for example, image acquisition, annotation, and regions of interest (ROIs). This common specification is essential for the exchange of image data between different software packages. OME-XML is a file format used to store data according to the OME Model, serving as a convenient file format for data migration from one site or user to another. OME-TIFF is a multi-plane tiff file that contains OME metadata in the header, in the form of OME-XML. This allows the pixels to be read with any TIFF-compatible program, and the metadata to be extracted with any OME-aware application. Our paper describing the design and implementation of the OME-XML file appeared in Genome Biology.

The OME consortium currently provides three major tools capable of working with OME-XML and OME-TIFF:

• The Bio-Formats library is a full-featured library with many features related to OME-XML, including conversion of third party file format metadata into OME-XML structures. It can write image data to the OME-TIFF format.
• OME Files C++ is a reference implementation of the OME data model and OME-TIFF for C++ developers wishing to support these in their own software. It can read and write OME-TIFF data.
• The OMERO server works directly with OME-XML. It can import data from OME-XML and OME-TIFF, as well as export to OME-TIFF.

If you have used OME-XML, OME-TIFF, Bio-Formats or OMERO in your work please use the correct citations to acknowledge us.

We have received support from several companies who use our file formats, for details see our list of Partners.

Note

The versioning for this documentation reflects updates to any of the components it covers and is therefore incremented more frequently than the Schema version, which only covers the Data Model and for which a version history is provided below.

OME-TIFF

• The OME-TIFF format
• OME-TIFF file structure
• OME-TIFF specification
• OME-TIFF example source code for common operations
• OME-TIFF sample data

OME-XML

• The OME-XML format
• Extracting, processing and validating OME-XML
• OME-XML Java library

OMERO Pyramid

• The OMERO pyramid format

File specifications

• Compliant file specification
• Compliant HCS specification
• Minimum specification

Developer tools and guidelines

• Developer introduction
• Using OME-XML schema elements
• File compression
• Sample image files
• IDs and LSIDs in OME-XML
• The OME system of units
• Enum Tool

The Data Model in detail

Generated documentation for the current version of the entire Schema is also available.

• Current Data Model overview
• Filter and FilterSet
• Screen Plate Well
• Structured Annotations
• ROI model
• 6D, 7D and 8D storage
• Legacy use-case support

Data Model history

• Schema version information
• Changes for June 2016 release 2
• Changes for June 2016
• Changes for January 2015
• Changes for June 2013
• Changes for June 2012
• Changes for June 2011
• Changes for June 2010
• Changes for April 2010
• Changes for September 2009
• Changes for September 2008
• Changes for February 2008
• Changes for June 2007 release 2
• Changes for June 2007