[ome-users] Flex File Format

[Ghislain Bonamy]

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). 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)
+1 (757) 941-4194 (H)
+1 (858) 354-7388 (M)
www.gnf.org

Hudson-Alpha Institute for Biotechnology
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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