[ome-devel] Latest bioformats.jar and metadata

[Curtis Rueden]

Hi Nigel,

> Hi, we are looking at using bioformats.jar.  Jason told me there is a
> new release committed that can export the most up to date OME-XML.  How
> do we get access to this?

There is not yet an official release of the library supporting the 2007-06
OME-XML schema. But Jason is right that the latest development code in our
Subversion repository now has this support. If you like, you can check out
the code from our repository:

https://skyking.microscopy.wisc.edu/svn/java/trunk

Any of command line svn, TortoiseSVN for Windows, or the Subclipse plugin
for Eclipse will work to access the code.

You can build the library from the command line using Ant (try "ant -p" for
a list of targets, just "ant" to create bio-formats.jar, or "ant tools" to
make loci_tools.jar). You will need JDK 1.4 or later (or jikes) in order to
compile it. Alternately, with Eclipse, point your source path at the root
folder, and set the inclusion rule to include only the "loci" subfolder, and
things should compile. You may also want to set the compiler to
1.4-compatible to avoid an avalanche of 1.5-specific compiler warnings.

Please note that this code has not been officially released or announced,
nor thoroughly tested. We are still in the process of finishing the 2007-06
OME-XML support, and though the basic functionality is working, many things
are still missing. Nonetheless, feel free to email me if you encounter bugs.

Alternately, you can wait for an official release. There will probably be a
preliminary release within a week or so including this functionality, though
it will not be finished, and will still default to the 2003/FC version of
OME-XML for now. My best guess is that we will officially make the switch
over to 2007-06 some time next month.

> Also, in the previous version there seemed to be very little metadata in
> the core, almost everything was in the format-specific fields.  Has this
> changed with the new release?  It's much more useful for cross-vendor
> facilities if search can be done over metadata independent of format.

Your statement that "it's much more useful for cross-vendor facilities if
search can be done over metadata independent of format" is the central
principle of Bio-Formats, and one of OME's guiding principles in general.

As such, there are actually three types of metadata in Bio-Formats, which we
call core metadata, original metadata, and OME metadata.

1) "Core metadata" only includes those things necessary to understand the
basic structure of the pixels: image resolution; number of focal planes,
time points, channels, and other dimensional axes; byte order; dimension
order; color arrangement (RGB, indexed color or separate channels); and
thumbnail resolution.

2) "Original metadata" corresponds to the format-specific fields you
mentioned. They are key/value pairs in the original format, with no
guarantee of cross-format naming consistency or compatibility.

3) "OME metadata" is information from #1 and #2 converted by Bio-Formats
into the OME data model. *Performing this conversion is the primary purpose
of Bio-Formats.* Bio-Formats uses its ability to convert proprietary
metadata into OME-XML as part of its integration with the OME and OMERO
servers -- essentially, they are able to populate their databases in a
structured way because Bio-Formats sorts the metadata into the proper
places. This conversion is nowhere near complete or bug free, but we are
constantly working to improve it. We would greatly appreciate any and all
input from users concerning missing or improperly converted metadata fields.

I am working on a "Bio-Formats Metadata Guide" document detailing these
three kinds of metadata and how the Bio-Formats metadata API works. However,
it is far from complete, with many unwritten sections. You can find a draft
in the SVN repository here:

https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/doc/metadata-guide.txt

I have tried to provide a lot of developer documentation online regarding
how to use the Bio-Formats library, and link it all in a cohesive way from
the Bio-Formats web site. If you feel anything is missing, or have trouble
finding what you are looking for, please do not hesitate to ask.

HTH,
Curtis

On Jan 17, 2008 4:57 PM, Nigel Goddard <ngoddard at axiope.com> wrote:
> Hi, we are looking at using bioformats.jar.  Jason told me there is a
> new release committed that can export the most up to date OME-XML.  How
> do we get access to this?
>
> Also, in the previous version there seemed to be very little metadata in
> the core, almost everything was in the format-specific fields.  Has this
> changed with the new release?  It's much more useful for cross-vendor
> facilities if search can be done over metadata independent of format.
>
> thanks for your help,
>
> Nigel Goddard
> Axiope Limited
>
> _______________________________________________
> ome-devel mailing list
> ome-devel at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel
>
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