OME at LOCI –
Software – Bio-Formats — OME server
OME
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.
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.
If you wish to read certain kinds of compressed DICOM files, you will
need to
set up the optional native libraries.
If you wish to read compressed SVS files, you will need to
set up the optional native library.
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. We are working to resolve this issue; see
this
Trac ticket for details.
You can upgrade your OME server installation to take advantage of a
new Bio-Formats release
by overwriting the old loci_tools.jar with the new one.
Last update: Friday, August 29, 2008
