[ImageJ-devel] [ome-devel] strategy and 6D data

Curtis Rueden ctrueden at wisc.edu
Wed Nov 28 14:10:51 CST 2012

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

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.


On Wed, Nov 28, 2012 at 5:11 AM, Munro, Ian <i.munro at imperial.ac.uk> 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
> _______________________________________________
> ome-devel mailing list
> ome-devel at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel
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