[ome-users] OME TIFF from Andor Fusion software produces errors

[James Wainwright]

Hi Bio-formats team!

I'm pretty sure that I was previously able to open OME TIFFs that our
latest microscopy software, Fusion, generates.

I just tried opening both a recent (today in the latest version of Fusion)
and older (late 2016) file and they both fail to fully open in FIJI using
the Bio-formats plugin.

Both generate the following error:

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.
[WARN] SamplesPerPixel mismatch: OME=-1, TIFF=1
Reading IFDs
Populating metadata
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] Error untangling IFDs; the OME-TIFF file may be malformed (IFD #24
missing).

With LOTS of the "[WARN] Error untangling" lines after that.


I have uploaded a test file for you using the OMERO upload tool. The file
is called:

"2018-03-13_15.51.33_Sample Prefix_WAINWRIGHT James_Protocol_F0.tif"

Please let me know if the problem with our generation of the file or the
Bio-formats import?

I will also let our development team know.

Many thanks!

James
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