[ome-users] question about image format conversion

[Curtis Rueden]

Hi Linda,

You're not doing anything wrong. More likely OME has limitations that
prevent it from behaving in the way that you expect.

When you say that OME is "losing the metadata," which pieces of
information are important to your organization? What were you
expecting to happen? Do you want to preserve all the key/value pairs
in their original format? Doing so is possible, but if the information
is not converted to a standard data model, it will be of limited
utility since it will not be represented in a common structure with
other data.

The issue of metadata is very important, but also deceptively complex.
OME converts proprietary metadata into the OME data model. But many
kinds of metadata currently fall outside the scope of that model.

Bio-Formats is capable of parsing all the original metadata for
MetaMorph TIFF and STK formats, and can even express that metadata in
OME terms as custom semantic types -- though this is the "key/value
pair" approach of limited use I mentioned above, not a full conversion
of everything into the OME data model. This behavior is enabled in OME
v2.6.1, but only for formats that are not handled with a separate OME
perl format importer. Unfortunately, STK and TIFF both have their own
perl importers that override Bio-Formats, meaning BF is not used to
process those formats. However, you can override this behavior 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';
++++++++++

However, after attempting to test this approach today, I discovered
that the latest release of Bio-Formats is broken with respect to OME.
I'll be working on fixing it as soon as I can, and notify the list
when I do.

-Curtis

On Jan 9, 2008 7:48 AM, Linda Sperling <linda.sperling at cgm.cnrs-gif.fr> wrote:
> Hello,
>
> I am testing OME server with the intention of using it to manage image data,
> mostly acquired in MetaMorph TIFF format (which puts the metadata into tags
> that I guess are not standard).
>
> It seems that I cannot import this format into the OME data server (using
> the web interface -- haven't tried command line import) without losing the
> metadata. Idem for metamorph STK format. Am I doing something wrong?
>
> If not, is there a work around? For example, is there a tool for doing
> command-line conversion before import?
>
> Thanks,
>
>
> Linda Sperling
> Centre de Génétique Moléculaire
> CNRS
> Avenue de la Terrasse
> 91198 Gif-sur-Yvette CEDEX
> FRANCE
>
> sperling at cgm.cnrs-gif.fr
> +33 (0)1 69 82 32 09 (telephone)
> +33 (0)1 69 82 31 50 (fax)
> http://paramecium.cgm.cnrs-gif.fr/
>
>
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