Open Microscopy Environment

Hallo everybody,
we found a problem in OMERO if no light source is used or at least if the metadata does not contain info about the light source.
We made some measurements in FEI (former TILLPhotonics) Live Acquisition (LA), with a monochromator as a light source. Unfortunately this limits the acqusition speed to for us useless values . So we fixed the wavelength of the monochromator and recorded in LA without setting the light source, so now faster speeds are possible . Now we tried to import the data in OMERO and got the following error:

java.lang.RuntimeException: Failure response on import!
Category: ::omero::grid::ImportRequest
Name: import-request-failure
Parameters: {message=omero.ApiUsageException
serverStackTrace = "ome.conditions.ApiUsageException: Missing reference handler for LightSource:eacd2d8f-2579-46c7-9b6a-a39ee13287b9(null) --> omero.model.LightSettings:

And here is the link to the tiff and xml file, as well as the full exception.

https://www.dropbox.com/s/rh7wdxesig36z ... ptions.txt
https://www.dropbox.com/s/7j64g70ocqsunpr/Ctrl00.xml
https://www.dropbox.com/s/zaso18vdlx2i9tq/Ctrl00.tif

We already tried to import without metadata which leas to a successfull import, so problem is definatly in the metadata. This is a workaround but no "solution" to the problem.

Thanks for your help

Benjamin

Dear Benjamin,

The error you are getting is because the OME-XML in the TIFF is invalid:

Code: Select all

% BF_MAX_MEM=4g BF_DEVEL=1 CLASSPATH=./artifacts/loci_tools.jar ./tools/showinf ~/Downloads/Ctrl00.tif -nopix -omexml
...
Parsing schema path
http://www.openmicroscopy.org/Schemas/OME/2013-06/ome.xsd
Validating OME-XML
Key 'ImagePixelsChannelLightSourceSettingsLightSourceIDKeyRef' with value 'LightSource:eacd2d8f-2579-46c7-9b6a-a39ee13287b9' not found for identity constraint of element 'OME'.
Error validating document: 1 errors found

If you look at the LightSource in the file, it's this:

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<OME:LightSource ID="LightSource:1bf2812c-798e-49a3-8afc-9c470ca504fc" Power="150" Manufacturer="FEI Munich" Model="Polychrome V"><OME:Arc Type="Xe" /></OME:LightSource>

But later on, we see this:

Code: Select all

OME:LightSourceSettings ID="LightSource:eacd2d8f-2579-46c7-9b6a-a39ee13287b9" />

This is a reference to a non-existent light source, and this invalid reference is the direct cause of the error.

I'm afraid this is not something we can easily work around: the OME-XML is invalid, and this is most likely due to a problem with the software which wrote it. Is the OME-XML generated by yourselves or by the FEI software? If the former, I would suggest tweaking your code to make sure the LightSourceSettings is valid (or remove entirely). If the latter, I would suggest getting in touch with the software vendor--it's a bug in their code.

Kind regards,
Roger