[ome-devel] Questions about initial development.

[Curtis Rueden]

Hi Glenn,

> > Finally we deal with a image type called ICS. When importing these
> > images I wish to pass the metadata out of the images and store it. Can
> > someone point me to the place in the code that performed the
> > passing of
> > metadata from an image.
>
> I think that BioFormats supports ICS.  We are working together with
> LOCI (the developers of BioFormats) for tighter integration with OME
> and OMERO, though I do think that its possible right now to convert
> ICS to OME-TIFF in BioFormats, and then import the OME-TIFF into OME
> (and presumably OMERO).  LOCI also developed OME-TIFF, BTW.  This is
> OME-XML turned inside out so that on the outside it is an innocent
> looking regular TIFF file, but on the inside (in the Description
> tag), is the full OME XML metadata goodness.  The pixels are of
> course stored in the regular TIFF way rather than being encoded in
> Base64 and stored in the XML.  The OME back-end has full support for
> reading OME-TIFF.

Yes, Bio-Formats supports ICS, though support has not been thoroughly
exercised. If you find problems with it, we are committed to fixing
bugs. As for converting to OME-TIFF, the library supports doing so,
but there is no user application to do it yet (though it would be
largely trivial to write one). The main reason we haven't provided
such an application is that metadata population from third party
formats to OME-XML should be considered "alpha" status. For any given
format such as ICS, it should not be considered complete or even
necessarily correct -- though the ultimate goal of Bio-Formats is to
be a reference implementation for metadata conversion of all formats,
it currently provides merely an initial attempt at such conversion. We
are actively looking to improve the metadata population for each
format, so if you have ICS data with particular metadata that you feel
should be assigned to particular locations within OME-XML, we would be
greatly interested. You are welcome to contribute to Bio-Formats,
which can be checked out from our Subversion repository by following
the instructions at http://www.loci.wisc.edu/software/.

-Curtis

P.S. to Ilya: Thanks for the excellent and thorough summary of the
state of the two systems. Your writeup is so informative and useful
that I think it would beneficial to post it somewhere on the main web
site, in an "OME and OMERO" section or some such. I would be willing
to create such a page using your words plus a bit more background
information (i.e., OME is mature, while OMERO is experimental). What
do you think?