[ome-users] Flex File Format

[Curtis Rueden]

Hi Ghislain,

Thanks for the detailed answer. I thought that with OMERO.fs, there
> would be a way to import data into OMERO without duplicating of the
> pixel data
> (http://www.openmicroscopy.org/site/documents/data-management/omero4/ser
> ver/fs<http://www.openmicroscopy.org/site/documents/data-management/omero4/ser%0Aver/fs>).
> Perhaps it has not been implemented yet (if not implemented how
> far along is it). Or perhaps I am missing something.
>

My understanding is that what you describe is an eventual goal of OMERO, but
right now OMERO.fs just facilitates import. The trick is that if the pixel
data is not imported (i.e., duplicated) in a standard way, then the server
has to rely on Bio-Formats to parse image planes from the original format on
the fly, every time they are needed (barring a caching scheme of some kind).
So Bio-Formats needs to be really high-performance, which is more feasible
for some formats than others. But LOCI is also very interested in using this
approach to save disk space, so we'll see how things develop going forward.

Cheers,
Curtis

On Wed, May 6, 2009 at 5:53 PM, Ghislain Bonamy <GBonamy at gnf.org> wrote:

> Chris,
>
> Thanks for the detailed answer. I thought that with OMERO.fs, there
> would be a way to import data into OMERO without duplicating of the
> pixel data
> (http://www.openmicroscopy.org/site/documents/data-management/omero4/ser
> ver/fs<http://www.openmicroscopy.org/site/documents/data-management/omero4/ser%0Aver/fs>).
> Perhaps it has not been implemented yet (if not implemented how
> far along is it). Or perhaps I am missing something.
>
> Currently our institutes generates ~6Tb of image data per month. You can
> see how duplicating the data would be an issue. I am sure this problem
> will arise for anyone running HTS projects. Therefore, the ability to
> link the database to the pixel data would be extremely useful.
>
> Best,
>
> Ghislain Bonamy, PhD
> __________________________________________
> Research Investigator
>
> Genomic Institute of the
> Novartis Research
> Foundation
> Department of Molecular & Cell Biology, room G214
> 10675 John Jay Hopkins Drive
> San Diego CA 92121
> USA
>
> +1 (858) 812-1534 (W & F)
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>
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> www.hudsonalpha.org
>
>
> -----Original Message-----
> From: ome-users-bounces at lists.openmicroscopy.org.uk
> [mailto:ome-users-bounces at lists.openmicroscopy.org.uk] On Behalf Of
> Chris Allan
> Sent: Tuesday, May 05, 2009 10:50 AM
> To: Ghislain Bonamy
> Cc: ome-users at lists.openmicroscopy.org.uk;
> Matthew.Smicker at sanofi-aventis.com
> Subject: Re: [ome-users] Flex File Format
>
> On Tue, 2009-05-05 at 10:27 -0700, Ghislain Bonamy wrote:
> > Jason, (or whomever knows the answer to this)
>
> Hi Ghislain, Matthew and others who are interested in Flex and
> interactions with OMERO.
>
> >
> >
> >
> > In the case of the flex file (and other tiff derivative), how does the
> > usage of ome.tiff (or ome.xml) with a pointer to the flex file works?
> > Will OMERO allow this kind of import, even if the flex file format
> > itself is not supported by OMERO (but bioformat, supports the pixel
> > type)?
>
> I think there's some overall confusion about what OMERO does during
> import and its interactions with OME-TIFF and OME-XML.
>
> Firstly, an OMERO import is a duplication of sorts. It reads, using
> Bio-Formats, as much metadata as it can and all of the pixel data from
> the proprietary Flex file and *copies* it to an OMERO server of your
> choosing. OME-XML and/or OME-XML are not involved in this transaction at
> all. The data in OMERO is split; the metadata in the database and the
> pixel data in the flat file OMERO binary repository. You are now free to
> do whatever you like with the Flex files and the copy of the data in
> OMERO.
>
> Along these lines, to answer Matthew's earlier question directly:
>
> ""Does OMERO convert to OME-TIFF upon import of a non-OME-TIFF file?  My
> impression was that it preserved the original format and just used
> Bio-formats to read it?""
>
> No, it does not and no, it creates a copy.
>
> If a Flex file were to contain a valid OME-XML block with the correct
> TiffData tags it would essentially be an OME-TIFF. This effectively buys
> you nothing apart from allowing OME format (OME-XML or OME-TIFF) aware
> software to read the OME-XML block within the TIFF. It *does not* skirt
> the data duplication of import or allow you to check data in and out of
> OMERO freely.
>
> > Best,
> >
> >
> >
> > Ghislain Bonamy, PhD
>
> I'm happy to be more specific if things are still unclear.
>
> Thanks for your interest and the in depth discussion!
>
> -Chris
>
>
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