File Formats Downloads

File Formats Libraries

Bio-Formats

Developed by the Laboratory for Optical Computational Instrumentation group (LOCI), Bio-Formats is a standalone Java library for reading and writing popular microscopy file formats and is capable of parsing both pixels and metadata for a large number of formats, as well as writing to several formats.

• loci_tools.jar – Complete Bio-Formats bundle with supporting libraries
• bio-formats.jar – Bio-Formats standalone library

See the Bio-Formats Download page for the most up-to-date version of Bio-Formats including daily and trunk builds.

The source code is also available from the Subversion repository

$ svn co https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats formats

File Format Specifications

OME-XML

OME partners at Dundee develop and maintain the OME-XML schemas that represent the data model. The XML namespaces for the current schemas are located on this site. This also where the XSD files are available to download from.

http://www.openmicroscopy.org/Schemas/

OME-XML has its own site at http://www.ome-xml.org/ for documentation and development discussion.

Note: any schemas and documentation below http://www.openmicroscopy.org/XMLschemas/ is preserved for legacy support only. This includes the 2003FC schema used by the original OME server.

OME-TIFF

OME partners at LOCI have developed a variant of the OME-XML File specifically designed for data acquisition and storage. This format, called OME-TIFF, uses OME-XML in the standard TIFF header and stores binary image data in a multi-page TIFF file.

More Details.

File Formats Samples

.ome Samples

• min-sample-2008-02.ome
  • sample created with dummy data to show the shape of a minimal file
• max-sample-2008-02.ome
  • sample created with dummy data showing at least one of everything in a file

.ome.tiff Samples

• single-channel-2003-FC.ome.tif - view embedded XML

• single-channel-2007-06.ome.tif - view embedded XML

• single-channel-2008-02.ome.tif - view embedded XML

  • generated file with placeholder image in three different schemas. The tiff file has OME image frame.

• Iron-Plate-2003-FC.ome.tiff - view embedded XML

• Iron-Plate-2007-06.ome.tiff - view embedded XML

• Iron-Plate-2008-02.ome.tiff - view embedded XML

  • image of the surface of an iron plate in three different schemas with custom attributes. The tiff file has THREE image frames i.e. 1,2,3.

XSLT Transform Samples

There are two transforms available that convert between the hierarchical pre-July 2007 OME schema and a flat CA only representation of that schema.

• From full OME to OME-CA: OME-CA2OME.xslt
• From OME-CA to OME: OME2OME-CA.xslt