[ome-users] File format support : Volocity ?

[Steve Baxter]

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
> >
> >
> > This communication is from Cancer Research UK. Our website is at www.cancerresearchuk.org. We are a registered charity in England and Wales (1089464) and in Scotland (SC041666) and a company limited by guarantee registered in England and Wales under number 4325234. Our registered address is Angel Building, 407 St John Street, London, EC1V 4AD. Our central telephone number is 020 7242 0200.
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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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