[ome-users] Flex File Format

[Chris Allan]

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