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Fail to open OME file after updating the fiji

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Fail to open OME file after updating the fiji

Postby Suwinn » Wed Feb 15, 2017 9:57 am

Hi there,

Before updating the Fiji,when i drag and drop the ome.tiff file to the fiji window, all the meta data looked fine. After I updated it i got the following error and most of the meta data was not shown. I noticed that the previous biodata version is bio-formats_plugins-5.1.10.jar and the new updated biodata version is bio-formats_plugins-5.3.3.jar.


->I also tried to update the Java version to 8 but it does'nt work.

->I also got the warning [WARN] Could not transform version 2013-06 OME-XML. What does that mean?


Warning: org.apache.xerces.jaxp.SAXParserImpl$JAXPSAXParser: Property 'http://www.oracle.com/xml/jaxp/properties/entityExpansionLimit' is not recognized.
Warning: org.apache.xerces.parsers.SAXParser: Feature 'http://javax.xml.XMLConstants/feature/secure-processing' is not recognized.
Warning: org.apache.xerces.parsers.SAXParser: Property 'http://javax.xml.XMLConstants/property/accessExternalDTD' is not recognized.
Warning: org.apache.xerces.parsers.SAXParser: Property 'http://www.oracle.com/xml/jaxp/properties/entityExpansionLimit' is not recognized.
Warning: org.apache.xerces.jaxp.SAXParserImpl$JAXPSAXParser: Property 'http://www.oracle.com/xml/jaxp/properties/entityExpansionLimit' is not recognized.
Warning: org.apache.xerces.parsers.SAXParser: Property 'http://javax.xml.XMLConstants/property/accessExternalDTD' is not recognized.
Warning: org.apache.xerces.parsers.SAXParser: Property 'http://www.oracle.com/xml/jaxp/properties/entityExpansionLimit' is not recognized.
[WARN] Could not transform version 2013-06 OME-XML.
Reading IFDs
Populating metadata
Checking comment style
Populating OME metadata


Thanks
Su
Suwinn
 
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Re: Fail to open OME file after updating the fiji

Postby dgault » Wed Feb 15, 2017 10:46 am

Hi Su,

We received a similar report to this issue last week and currently have some ongoing investigation as to the cause of this problem - https://github.com/openmicroscopy/bioformats/issues/2705. It appears to be caused by a clash of dependencies required for the XML transforms.

This does look slightly different though as it has failed to upgrade from 2013-06 OME-XML, would it be possible to upload a sample file showing this problem to https://www.openmicroscopy.org/qa2/qa/upload/ for further testing?

With Thanks,
David Gault
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Re: Fail to open OME file after updating the fiji

Postby Suwinn » Wed Feb 15, 2017 11:21 am

Hi David,
Thanks for ur reply. I uploaded a file name cy5 555.ome.tiff file for ur investigation.

Thanks
su
Suwinn
 
Posts: 8
Joined: Thu Oct 13, 2016 1:38 pm


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