[ome-devel] OME-Tiff writing using LOCI calls from MATLAB, and ModuloAlongT annotation

[Andrew Patterson]

Hello Gary,

I am coming to this discussion late and you may only be talking about dummy test data, but I was wonder why your Experiment Description would be that large?

This is normally used for a few lines of text that can be displayed to the user, perhaps in a tool-tip, to help then tell similarly named experiments apart.
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2013-06/ome_xsd.html#Experiment_Description

If you have a quantity of data you wish to store the better location might be an annotation on a Dataset, Project, Experimenter, or Image.
CommentAnnotation can store a long string.
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2013-06/SA_xsd.html#CommentAnnotation
Or XMLAnnotation more structured data.
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2013-06/SA_xsd.html#XMLAnnotation

Hope this helps,

Andrew


On 27 Oct 2014, at 15:20, "Yellen, Gary" <gary_yellen at hms.harvard.edu> wrote:

> Ian – I did give this a try and it did not fix either the file size or the slow speed problem. 
> Also, I reduced the size of the metadata (at least, of the ExperimentDescription string) by 5 KB, and the file size was reduced only by this amount.  So at least this particular metadata item is not being duplicated.
> Best,
> Gary
>  
> From: ome-devel [mailto:ome-devel-bounces at lists.openmicroscopy.org.uk] On Behalf Of Munro, Ian
> Sent: Monday, October 27, 2014 9:02 AM
> Cc: ome-devel at lists.openmicroscopy.org.uk
> Subject: Re: [ome-devel] OME-Tiff writing using LOCI calls from MATLAB, and ModuloAlongT annotation
>  
> Hi Again Gary 
>  
> Good to know that you’ve found a solution. However,  I find it puzzling that the files are different sizes.
> We had a problem where bio-formats was writing multiple copies of the xml when called from Matlab.
> The work-around was to add the following line:
>  
> java.lang.System.setProperty('javax.xml.transform.TransformerFactory', 'com.sun.org.apache.xalan.internal.xsltc.trax.TransformerFactoryImpl’);
>  
> to the Matlab code as in the example that I sent.
> Perhaps this might help.
>  
> Regards
>  
> Ian 
> _______________________________________________
> ome-devel mailing list
> ome-devel at lists.openmicroscopy.org.uk
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