Open Microscopy Environment

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Hi All again!

In our FLIMfit application, we found an Omero image loading bug when trying to access an image from later (5.0.2) server with newer (5.0.5) OMEROMatlab. The bug was reproduced on both PC and Mac.

The reason is that, when looking for xml Modulo annotation, this code produces empty annotations

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metadataService = session.getMetadataService();
map = metadataService.loadAnnotations(specifier, java.util.Arrays.asList(objId), java.util.Arrays.asList( 'ome.model.annotations.XmlAnnotation'), annotators, omero.sys.ParametersI());
annotations = map.get(objId);


The alternative method is to use “getObjectAnnotations.m” function (part of OMEROMatlab) - but it also returns empty annotations.

When instead one tries to access in-sync (5.0.5 "octopus" server with 5.0.5 OMEROMatlab) – both methods work normally.

Presumably, these things should be backward compatible? - so it is likely a metadata issue.

Best,
Y.

Hi Yuriy,

I was unable to reproduce your issue. I imported a sample file with an XML annotation, 6x4y1z1t1c8b-swatch-xmlannotation-svg.ome, into a local OMERO 5.0.2 server and ran the following code using OMERO.matlab 5.0.5:

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>> c=loadOmero('localhost');
--------------------------
OMERO.matlab Toolbox
5.0.5-ice35-b47
--------------------------

>> s=c.createSession('user,password);
>> disp(s.getConfigService().getVersion())
5.0.2

>> xmlAnnotation = getImageXmlAnnotations(s, 2802)

xmlAnnotation =

omero.model.XmlAnnotationI@779822a7


Eveything works as far as I can tell. Can you try to reproduce this test on your local 5.0.2 server and let me know if you get the same output?

Best,
Sebastien

Thanks Sebastien,

yepp You are right - it finds annotation correctly, when given such test.

..maybe I made mistake on usage when in FLIMfit code - will investigate and come back.

Cheers,
Y.

yes - there was mistake on usage, however not in the code, and not incompatibility between Omero versions, but on data.

I tried to load images transferred to Omero some time ago by previous versions of Insight, when FLIM-ModuloAlongT convention wasn't strictly followed.

Data on octopus (5.0.5) were imported recently, so everything was OK with Modulo, whereas among our data on Imperial's server (5.0.2) there are still some rarities without, or using unconventional Modulo.

We can consider maybe on restoring this compatibility, to work with historical data placed in Omero, but unlikely as there are not many of such data.
So the conclusion : issue closed.

Thanks again
Y.