OME Server

The OME server is a set of software that interacts with a database to manage images, image metadata, image analysis and analysis results. The OME system is capable of leveraging Bio-Formats to import files.

Please note - the OME server is no longer maintained and has now been superseded by the OMERO server. Support for the OME server has been entirely removed in the 5.0.0 version of Bio-Formats; the following instructions can still be used with the 4.4.x versions.

Installation

For OME Perl v2.6.1 and later, the command line installer automatically downloads the latest loci_tools.jar and places it in the proper location. This location is configurable, but is /OME/java/loci_tools.jar by default.

For a list of what was recognized for a particular import into the OME server, go to the Image details page in the web interface, and click the “Image import” link in the upper right hand box.

Bio-Formats is capable of parsing original metadata for supported formats, and standardizes what it can into the OME data model. For the rest, it expresses the metadata in OME terms as key/value pairs using an OriginalMetadata custom semantic type. However, this latter method of metadata representation is of limited utility, as it is not a full conversion into the OME data model.

Bio-Formats is enabled in OME v2.6.1 for all formats except:

  • OME-TIFF
  • Metamorph HTD
  • Deltavision DV
  • Metamorph STK
  • Bio-Rad PIC
  • Zeiss LSM
  • TIFF
  • BMP
  • DICOM
  • OME-XML

The above formats have their own Perl importers that override Bio-Formats, meaning that Bio-Formats is not used to process them by default. However, you can override this behavior (except for Metamorph HTD, which Bio-Formats does not support) by editing an OME database configuration value:

% psql ome

To see the current file format reader list:

ome=# select value from configuration where name='import_formats';
 value
------------------------------------------------------------------------------
['OME::ImportEngine::OMETIFFreader','OME::ImportEngine::MetamorphHTDFormat',
'OME::ImportEngine::DVreader','OME::ImportEngine::STKreader',
'OME::ImportEngine::BioradReader','OME::ImportEngine::LSMreader',
'OME::ImportEngine::TIFFreader','OME::ImportEngine::BMPreader',
'OME::ImportEngine::DICOMreader','OME::ImportEngine::XMLreader',
'OME::ImportEngine::BioFormats']
 (1 row)

To remove extraneous readers from the list:

ome=# update configuration set value='[\'OME::ImportEngine::MetamorphHTDFormat\',
\'OME::ImportEngine::XMLreader\',\'OME::ImportEngine::BioFormats\']' where
name='import_formats';
UPDATE 1
ome=# select value from configuration where name='import_formats';
 value
------------------------------------------------------------------------------
['OME::ImportEngine::MetamorphHTDFormat','OME::ImportEngine::XMLreader',
'OME::ImportEngine::BioFormats']
 (1 row)

To reset things back to how they were:

ome=# update configuration set value='[\'OME::ImportEngine::OMETIFFreader\',
\'OME::ImportEngine::MetamorphHTDFormat\',\'OME::ImportEngine::DVreader\',
\'OME::ImportEngine::STKreader\',\'OME::ImportEngine::BioradReader\',
\'OME::ImportEngine::LSMreader\',\'OME::ImportEngine::TIFFreader\',
\'OME::ImportEngine::BMPreader\',\'OME::ImportEngine::DICOMreader\',
\'OME::ImportEngine::XMLreader\',\'OME::ImportEngine::BioFormats\']' where
name='import_formats';

Lastly, please note that Li-Cor L2D files cannot be imported into an OME server. Since the OME perl server has been discontinued, we have no plans to fix this limitation.

Upgrading

OME server is not supported by Bio-Formats versions 5.0.0 and above. To take advantage of more recent improvements to Bio-Formats, you must switch to OMERO server.

Source Code

The source code for the Bio-Formats integration with OME server spans three languages, using piped system calls in both directions to communicate, with imported pixels written to OMEIS pixels files. The relevant source files are:

  • OmeisImporter.java – omebf Java command line tool
  • BioFormats.pm – Perl module for OME Bio-Formats importer
  • omeis.c – OMEIS C functions for Bio-Formats (search for “bioformats” case insensitively to find relevant sections)