[ome-devel] Storage format for 'fitted' parameter (FLIM) images?

[Melissa Linkert]

Hi Ian,

> I'd somehow got hold of the wrong idea.

No problem.  OpenEXR is certainly on our radar, we're just not there yet.

> How about floating-point .tif if I can work out how to write them?

That should certainly be supported by Bio-Formats/OMERO.

Regards,
-Melissa

On Tue, Mar 13, 2012 at 03:21:51PM +0000, Munro, Ian wrote:
> Thanks Melissa 
> 
> I'd somehow got hold of the wrong idea.
> How about floating-point .tif if I can work out how to write them?
> 
> Ian
> 
> 
> On 13 Mar 2012, at 15:05, Melissa Linkert wrote:
> 
> > Hi Ian,
> > 
> >> I've finally managed to get back to looking at this  problem & in the absence of any feedback on here,
> >> I've started looking at openEXR as an open floating-point  image format for holding processed parameter images.
> >> 
> >> As far as I can tell this is already compatible with bio-formats.
> > 
> > I can't speak to the suitability of OpenEXR for storing FLIM data, but
> > do note that OpenEXR files are not currently supported in
> > OMERO/Bio-Formats.  There are plans to support these files, as noted here:
> > 
> > http://trac.openmicroscopy.org.uk/ome/ticket/4125
> > 
> > ...but the work has not been done yet, and realistically will not be
> > done until after the 4.4 release of OMERO/Bio-Formats.
> > 
> > Regards,
> > -Melissa
> > 
> > On Tue, Mar 13, 2012 at 02:20:18PM +0000, Munro, Ian wrote:
> >> Hi Again.
> >> 
> >> I've finally managed to get back to looking at this  problem & in the absence of any feedback on here,
> >> I've started looking at openEXR as an open floating-point  image format for holding processed parameter images.
> >> 
> >> As far as I can tell this is already compatible with bio-formats.
> >> 
> >> Does anyone have any thoughts or objections?
> >> 
> >> Regards
> >> 
> >> 
> >> Ian
> >> 
> >> 
> >> On 22 Feb 2012, at 12:16,  wrote:
> >> 
> >>> HI all
> >>> 
> >>> At the recent Dundee meeting I described 3 categories of data required to make OMERO compatible with 
> >>> fluorescence lifetime imaging  (FLIM).
> >>> 
> >>> 1) 'raw'  time-resolved intensity data		 (as acquired by the microscope)
> >>> 2) fitted (floating point) parameter 'images'	(generated by fitting software)
> >>> 3) merged RGB maps.					(for inclusion in papers etc)
> >>> 
> >>> Currently the 2nd type is stored as a .csv image by the fitting code that Donald has already included in OMERO.
> >>> There is concern here over this for two reasons:
> >>> 
> >>> 1) iIt is inefficient  in terms of storage.
> >>> 2) There will inevitably be a loss of precision.
> >>> 
> >>> Could we change to another format for this (assuming it isn't too late) ?
> >>> If so what format?
> >>> 
> >>> Any thoughts welcome.
> >>> 
> >>> Regards
> >>> 
> >>> Ian
> >> 
> >> _______________________________________________
> >> ome-devel mailing list
> >> ome-devel at lists.openmicroscopy.org.uk
> >> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel
>