[ome-users] File format support : Volocity ?

[Melissa Linkert]

Hi Steve,

> Melissa - I do have some thoughts on how we might be able to add some "niceness" in the .mvd2 file (which is a Metakit database) to make it easier to interpret everything else, or create a reader SDK if there is strong demand from the community. Please feel free to contact me if you would like a chat about this.

I'd certainly be happy to discuss ways to make it easier for Bio-Formats
to support Volocity.  Our two biggest concerns are 1) easing the burden
on users, so that they can directly work with the originally acquired
data and 2) preserving all of the metadata in the original files.  If
Perkin Elmer can help with either of these, we would be quite grateful.

I will be at the ASCB annual meeting this coming week - if you are there as well, that would be a great time to discuss further.  You can stop by the OME/Glencoe Software booths (#615/#617) any time, or contact me off-list to set up a time to chat.  Otherwise, I will be back in touch after ASCB.

Regards,
-Melissa

On Thu, Dec 09, 2010 at 04:31:43PM +0000, Steve Baxter wrote:
> Hi,
> 
> I think the easiest solution at the moment would be to export the data you want as TIFF or OME-TIFF (the plain TIFF from Volocity includes metadata that I believe Bioformats can read). You can export multiple datasets from Volocity in one go by selecting them all and choosing File -> Export...
> 
> The Volocity library format isn't so easy to share unfortunately - much of it is streamed C++ objects and plain binary image data, and sadly we never really designed it with reading by third parties in mind. 
> 
> Melissa - I do have some thoughts on how we might be able to add some "niceness" in the .mvd2 file (which is a Metakit database) to make it easier to interpret everything else, or create a reader SDK if there is strong demand from the community. Please feel free to contact me if you would like a chat about this.
> 
> Cheers,
> 
> Steve
> 
> On 9 Dec 2010, at 15:38, Melissa Linkert wrote:
> 
> > Hi Alex,
> > 
> > We are planning to add support for Volocity database files in Bio-Formats in
> > the not-too-distant future.  For further information, please see this ticket on
> > our issue tracking system:
> > 
> > http://dev.loci.wisc.edu/trac/software/ticket/55
> > 
> > If you would like to be automatically notified whenever we update that
> > ticket, just let me know and I will happily CC you.
> > 
> > Regards,
> > -Melissa
> > 
> > On Thu, Dec 09, 2010 at 03:29:59PM +0000, Alexander Tournier wrote:
> > > Hi,
> > >
> > > we are currently testing OMERO for deployment at Cancer Research UK
> > > in London.
> > > One of the file formats we use regularly is Volocity (currently 5.3)
> > > coming out of Perkin-Elmer spinning disk microscopes.
> > > The current bioformats don't seem to be able to handle Volocity
> > > files/databases.
> > >
> > > Anybody knows how to handle Volocity formats for import into OMERO?
> > > Are there plans for these formats to be supported by bioformats?
> > >
> > > Thanks,
> > > Alex
> > >
> > >
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> 
> Steve Baxter | R&D Leader, PerkinElmer Coventry
> PerkinElmer | For the Better
> steve.baxter at perkinelmer.com
> Phone:  +44 2476 698115
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