[ome-users] nd2 converted TIFF / OME.TIF error in FIJI

[David Gault (Staff)]

Hi Darren,

If you convert the file to TIFF using bfconvert from the Bio-Formats command line tools do you still have the same issue?
https://www.openmicroscopy.org/bio-formats/downloads/
https://docs.openmicroscopy.org/bio-formats/5.9.2/users/comlinetools/conversion.html

If you have one of the converted files showing the issue which is less than 2GB you can upload it to https://www.openmicroscopy.org/qa2/qa/upload/ for us to test.

With Thanks,
David Gault


On 21 Jan 2019, at 16:18, Darren Thomson <darren.thomson at MANCHESTER.AC.UK<mailto:darren.thomson at MANCHESTER.AC.UK>> wrote:

Hello All,

I am unable to import TIFF / OME.TIF into FIJI. I get the following errors upon going through Bioformats Importer.

I converted my .nd2 file in NIS into TIFF (since the nd2 was so large) for readability.

Can anyone help?

Many thanks,


CONSOLE:
Warning:  org.apache.xerces.parsers.SAXParser: Feature 'http://javax.xml.XMLConstants/feature/secure-processing'<http://javax.xml.xmlconstants/feature/secure-processing'> is not recognized.
Warning:  org.apache.xerces.parsers.SAXParser: Property 'http://javax.xml.XMLConstants/property/accessExternalDTD'<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.
EXCEPTION:
(Fiji Is Just) ImageJ 2.0.0-rc-69/1.52i; Java 1.8.0_66 [64-bit]; Windows 7 6.1; 110MB of 26000MB (<1%)
java.lang.ArithmeticException: / by zero
                at loci.formats.MetadataTools.populatePixelsOnly(MetadataTools.java:293)
                at loci.formats.MetadataTools.populateMetadata(MetadataTools.java:251)
                at loci.formats.MetadataTools.populatePixels(MetadataTools.java:151)
                at loci.formats.in.OMETiffReader.initFile(OMETiffReader.java:1181)
                at loci.formats.FormatReader.setId(FormatReader.java:1397)
                at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:499)
                at loci.plugins.in.ImportProcess.execute(ImportProcess.java:142)
                at loci.plugins.in.Importer.showDialogs(Importer.java:140)
                at loci.plugins.in.Importer.run(Importer.java:76)
                at loci.plugins.LociImporter.run(LociImporter.java:78)
                at ij.IJ.runUserPlugIn(IJ.java:228)
                at ij.IJ.runPlugIn(IJ.java:192)
                at ij.Executer.runCommand(Executer.java:137)
                at ij.Executer.run(Executer.java:66)
                at java.lang.Thread.run(Thread.java:745)


Dr Darren Thomson | Experimental Officer
Manchester Fungal Infection Group (MFIG)<http://research.bmh.manchester.ac.uk/mfig>
Tel: (+44) (0)161 306 2457
Email: darren.thomson at manchester.ac.uk<mailto:darren.thomson at manchester.ac.uk>
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Manchester Fungal Infection Group
NUS Gold Award Winners 2016 for Lab Sustainability
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