[ome-users] ome-users Digest, Vol 50, Issue 11

[Scott Grieshaber]

Hello,

I have a general question about the future plans and direction of the  
omero insight client.  We have been using the archive original file  
option in the 3.2 addition to allow us to recover the 5D data sets for  
external analysis using both bitplane and ImageJ.  Both of these  
applications support the OME.TIFF file format.  My question is why  
does the omero insight client not write out OME.TIFF files from the  
data in the database?  LOCI supports both reading and writing ome.tiff  
files in ImageJ.  Is this a design decision or just something not  
implemented yet?

Scott

Scott Grieshaber Ph.D.
Assistant Professor
University of Florida
Department of Oral Biology
School of Dentistry
PO BOX 100424 Room D5-33D
1600 SW Archer Road
Gainesville FL 32610
(352) 273-8856
sgriesha at ufl.edu

On May 6, 2009, at 7:00 AM, ome-users-request at lists.openmicroscopy.org.uk 
  wrote:

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> Today's Topics:
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>   1. Re: Flex File Format (Chris Allan)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 05 May 2009 18:49:37 +0100
> From: Chris Allan <callan at blackcat.ca>
> Subject: Re: [ome-users] Flex File Format
> To: Ghislain Bonamy <GBonamy at gnf.org>
> Cc: ome-users at lists.openmicroscopy.org.uk,
> 	Matthew.Smicker at sanofi-aventis.com
> Message-ID:
> 	<1241545777.31590.41.camel at shadowblade.openmicroscopy.org.uk>
> Content-Type: text/plain
>
> 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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> End of ome-users Digest, Vol 50, Issue 11
> *****************************************