Hi Curtis
Thans for the feedback. It's much appreciated.
Actually I oversimplified as our code is a Matlab GUI wrapping cross-platform
c++ fitting code so bringing this together with slim may be relatively easy as
the 2 GUIs seem to have a lot of common features.
In the shorter term I think we need to use the same strategy to store data in
OMERO.
Clearly you have a better feel for the downsides of the ModuloAlong? solution
than we do so can I ask how you intend to store your data in OMERO?
Regards
Ian
On 28 Nov 2012, at 20:10, Curtis Rueden wrote:
Hi Ian,
Thanks for this update; very informative. It looks like you have done a lot to
bring FLIM processing into OMERO, which is great.
I want to draw your attention to some very similar work we are doing within
ImageJ:
http://loci.wisc.edu/software/slim-plugin
The SLIM Plugin is an ImageJ plugin (written in Java, of course), which uses
the SLIM-curve library (written in cross-platform C) to perform the curve
fitting (of TCSPC data).
> The Imperial/Photonics Group’s main FLIM analysis software is
> internally named “GlobalProcessing”. It is written in MATLAB and
> provides state of the art fitting of time domain data for both
> laser-scanning time-correlated single photon (TCSPC) and wide-field
> time-gated FLIM images.
Perhaps GlobalProcessing and SLIM-curve could join forces? It is much easier to
access C code from Java than MATLAB code, but there are clearly features in
GlobalProcessing missing from SLIM-curve (e.g., wide-field), and vice versa.
> 1) We intend to standardise on encoding FLIM data using ModuloAlongT.
Personally, I dislike ModuloAlongT, especially as a long-term solution. There
are certain dimension orders that are simply impossible using it (e.g., XYbCZT,
where "b" is lifetime bins, and T is actual time points). I would much favor us
developing a true N-dimensional OME data model, and using that, moving forward.
> 2) Where should the functionality currently in IC-importer fit into
> the OMERO eco-system?
I agree that this functionality would work well as a Bio-Formats reader.
Regards,
Curtis
On Wed, Nov 28, 2012 at 5:11 AM, Munro, Ian
<[email protected]<mailto:[email protected]>> wrote:
Hello all
Please find attached a document describing where the work of the Imperial
satellite currently stands.
We've reached a point where our group is making decisions, regarding the
handling of data with a 6th dimension,
that may well have future implications for the OMERO clients or for other
groups working with 5+ dimensions.
As a result we're looking for any feedback/improvements that anyone can offer
on our current approach
In particular the 3 areas highlighted on the second page of the document.
Thanks in advance for your time.
Ian
Ian
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