[ome-users] Problem opening files

[Balaji Ramalingam (Staff)]

Hi,

Thank you for reporting your issue.
It would be great if you could upload your sample files to our QA server,
https://www.openmicroscopy.org/qa2/qa/upload/

This would help us troubleshoot your issue in better detail.

Best,
Balaji



__________________
Mr Balaji Ramalingam
Software Developer

OME Team
College of Life Sciences
University of Dundee






On 29/04/2016 16:49, "Alain Abou Khalil" <alain_aboukhalil at hotmail.com>
wrote:

>Hello,
>
>I am contacting you today to transfer you my problem maybe you can help
>me if you please.
>
>I am trying to open an.iob file. Actually, i have 6 files, i am able to
>open 2 out of these 6 only. The problem that occurs is:
>Exception in thread "BioFormats-ThumbLoader"
>java.lang.IllegalArgumentException: Invalid series: 1
>at loci.formats.FormatReader.seriesToCoreIndex(FormatReader.java:1284)
>at loci.formats.FormatReader.setSeries(FormatReader.java:970)
>at loci.formats.ImageReader.setSeries(ImageReader.java:479)
>at loci.formats.ReaderWrapper.setSeries(ReaderWrapper.java:376)
>at loci.formats.FileStitcher.initReader(FileStitcher.java:1220)
>at loci.formats.FileStitcher.getReader(FileStitcher.java:188)
>at loci.formats.FileStitcher.computeIndices(FileStitcher.java:1196)
>at loci.formats.FileStitcher.getReader(FileStitcher.java:177)
>at loci.formats.FileStitcher.openThumbBytes(FileStitcher.java:518)
>at loci.formats.ReaderWrapper.openThumbBytes(ReaderWrapper.java:361)
>at
>loci.formats.ChannelSeparator.openThumbBytes(ChannelSeparator.java:234)
>at loci.formats.ReaderWrapper.openThumbBytes(ReaderWrapper.java:361)
>at
>loci.formats.DimensionSwapper.openThumbBytes(DimensionSwapper.java:255)
>at loci.formats.ReaderWrapper.openThumbBytes(ReaderWrapper.java:361)
>at loci.formats.ReaderWrapper.openThumbBytes(ReaderWrapper.java:361)
>at loci.formats.ReaderWrapper.openThumbBytes(ReaderWrapper.java:361)
>at
>loci.formats.gui.BufferedImageReader.openThumbImage(BufferedImageReader.ja
>va:100)
>at loci.plugins.in.ThumbLoader.loadThumb(ThumbLoader.java:133)
>at loci.plugins.in.ThumbLoader.run(ThumbLoader.java:115)
>at java.lang.Thread.run(Thread.java:745)²
>
>Another error is the following:
>"java.lang.IndexOutOfBoundsException: Index: 1, Size: 1
>at java.util.ArrayList.rangeCheck(ArrayList.java:653)
>at java.util.ArrayList.get(ArrayList.java:429)
>at ome.xml.model.OME.getImage(OME.java:658)
>at
>ome.xml.meta.OMEXMLMetadataImpl.getImageName(OMEXMLMetadataImpl.java:2316)
>at
>loci.plugins.in.ImportProcess.computeSeriesLabels(ImportProcess.java:729)
>at loci.plugins.in.ImportProcess.initializeStack(ImportProcess.java:559)
>at loci.plugins.in.ImportProcess.execute(ImportProcess.java:147)
>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:216)
>at ij.IJ.runPlugIn(IJ.java:180)
>at ij.Executer.runCommand(Executer.java:137)
>at ij.Executer.run(Executer.java:66)
>at java.lang.Thread.run(Thread.java:745)
>"
>
>I updated my ImageJ as well as the bio formats plug ins but still no
>solution.
>
>Therefore, i am asking kindly for you help.
>
>My OS is the OS X El capitan.
>
>Thank you in advance
>Sincerely yours,
>
>Alain Abou Khalil
>
>
>
>_______________________________________________
>ome-users mailing list
>ome-users at lists.openmicroscopy.org.uk
>http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users


The University of Dundee is a registered Scottish Charity, No: SC015096