[ome-devel] Importing OME-TIFFs

[Curtis Rueden]

Hi Matthias,

Apologies for the delay in my reply.

does the import library take care of the metadata stored beside the binary
> image data in a OME-TIFF file? I. e. will all apropiate models be stored in
> the DB like laser, objective, and so on, if values are found in the TIFF?


If you are talking about the OME Perl server, then yes, everything in the
OME-TIFF's XML metadata block is imported, just as though it were an OME-XML
file. The OMERO server does not yet support OME-TIFF, but we are working on
it for the Beta3 release later this spring.

If so, where can I find documents explaining what is recognized during
> import?
>

If you want a list of what was recognized for a particular import into the
OME server, that information is linked from the Image details page in the
web interface. Follow the "Image import" link in the upper right hand box. I
am not sure how to access such a list for an OMERO import; perhaps one of
the OMERO developers can elaborate.

If you are asking for a master list of every metadata field we recognize, be
prepared to dive into some very deep technical water. The OME-XML schema and
server apps are constantly evolving, making it difficult to maintain
extensive technical documentation detailing every metadata field, beyond the
OME-XML schema, program source code itself, and automatically generated
resources like those linked above. But we do make an effort, as you can see
from the web sites: <http://openmicroscopy.org>
<http://ome-xml.org>
<http://loci.wisc.edu/ome/>
<http://trac.openmicroscopy.org.uk/omero>.

Anyway, such a list is essentially what the OME-XML schema itself is, though
support varies across implementations.

First, the (relatively) easy to read stuff:

1) You can browse a nice graphical representation of the 2003 version of the
OME-XML schema at <
http://www.openmicroscopy.org/XMLschemas/OME/latest/ome_xsd/index.html>.

2) The 2007 version of OME-XML has automatically generated documentation at
<
http://cvs.openmicroscopy.org.uk/svn/specification/Documentation/Generated/OME-2007-07/ome.xsd.html
>.

3) You can see all of the metadata fields Bio-Formats can currently convert
from third party formats into the OME data model (and hence render
importable by OMERO) by checking out the Javadoc for the MetadataStore and
MetadataRetrieve interfaces:
<http://www.loci.wisc.edu/software/docs/loci/formats/meta/MetadataStore.html
>
<
http://www.loci.wisc.edu/software/docs/loci/formats/meta/MetadataRetrieve.html
>

4) You can browse a wealth of information about the OME data model,
including changes we have made to OME-XML as it evolves, at <
http://ome-xml.org/>, with most technical details at <
http://ome-xml.org/wiki/DeveloperInfo>. The site is Trac-driven, which means
you get lots of functionality, such as graphical diffs between versions of
the XSD by clicking the Browse button. You can even file tickets to request
features or changes to the schema so that it better meets your needs.

And some less easy to read, but more technically explicit, information:

1) The full OME-XML schemas can be browsed at: <
http://www.openmicroscopy.org/Schemas/>

2) The OME Perl server transforms OME-XML into a flattened "CA" form that
maps directly to the OME semantic type definitions (which map directly to
tables in Postgres). These types are defined in the OME/src/xml/OME/Core
folder of the OME server distribution, and be browsed online at <
http://cvs.openmicroscopy.org.uk/horde/chora/browse.php?f=OME%2Fsrc%2Fxml%2FOME%2FCore%2F
>

3) The OMERO server uses a DB structure that is very similar to the OME-XML
and OME server schemas (since it has to store the same information, after
all), but throws Hibernate into the mix to gain some database agnosticism.
It uses Bio-Formats to map from proprietary formats' metadata values into
the OME data model via the MetadataStore interface, populating the OMERO DB
with an implementation called OMEROMetadataStore:
<
http://trac.openmicroscopy.org.uk/omero/browser/trunk/components/bioformats-omero/src/ome/formats/OMEROMetadataStore.java
>

There is so much information, it can be difficult to organize. If you are
having trouble finding something, please ask!

HTH,
Curtis

On Fri, Feb 8, 2008 at 8:09 AM, Matthias Dunda <Matthias.Dunda at carus-it.com>
wrote:

> Hi all,
>
> does the import library take care of the metadata stored beside the binary
> image data in a OME-TIFF file? I. e. will all apropiate models be stored in
> the DB like laser, objective, and so on, if values are found in the TIFF?
>
> If so, where can I find documents explaining what is recognized during
> import?
>
> Have a nice weekend!
> Matthias
>
> --
> Matthias Dunda, Dipl.-Inform.
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