Open Microscopy Environment

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

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

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

Thanks
su

Just as a follow up to this thread for anyone interested, there was extended discussion and investigation into this issue with more in depth details as part of the GitHub issue https://github.com/openmicroscopy/biofo ... ssues/2705

A suitable fix has not yet been established but a design issue is open on the Bio-Formats 5.x board which can be followed for future updates - https://trello.com/c/3yxt3pyt/115-xalan ... zer-review