[ome-devel] OME.tiff with FLIM time gates that are not equally spaced in time

[Laine, Romain]

Excellent, thanks Ian !

From: ome-devel <ome-devel-bounces at lists.openmicroscopy.org.uk> on behalf of "Munro, Ian" <i.munro at imperial.ac.uk>
Reply-To: OME External Developer List <ome-devel at lists.openmicroscopy.org.uk>
Date: Tuesday, 17 July 2018 at 13:20
To: OME External Developer List <ome-devel at lists.openmicroscopy.org.uk>
Subject: Re: [ome-devel] OME.tiff with FLIM time gates that are not equally spaced in time

Hi Romain

Attached is a little Matlab script to create a FLIM OME-TIFF.
The first section just creates some dummy data.
The second part (after the tic at line 28) uses the bio-formats Matlab plugin to write this to a file.
Note that the variable “delays’ can contain any strings not just the regularly spaced ones used here.

This is quite old code now so maybe someone from the core OME team could have a quick look and see if it’s still ok?
In particular this line:

java.lang.System.setProperty('javax.xml.transform.TransformerFactory', 'com.sun.org.apache.xalan.internal.xsltc.trax.TransformerFactoryImpl’);

may no longer be required.
Also we used to have problems when overwriting existing files. If this has since been addressed,
then this section:

if exist(outputPath, 'file') == 2
    delete(outputPath);
end

May no longer be required.
Hope that helps.

Best wishes.

Ian






On 17 Jul 2018, at 12:38, Laine, Romain <r.laine at ucl.ac.uk<mailto:r.laine at ucl.ac.uk>> wrote:

Hi Ian,
Many thanks.
Code example would be great, please !
I am currently using MATLAB, is this a limitation?

Cheers,

Romain


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