[ImageJ-bugs] [Bug 1057] New: Fiji won't open .czi files created by Zeiss Zen2

bugzilla at fiji.sc bugzilla at fiji.sc
Tue Apr 21 04:10:20 CDT 2015


http://fiji.sc/bugzilla/show_bug.cgi?id=1057

            Bug ID: 1057
           Summary: Fiji won't open .czi files created by Zeiss Zen2
           Product: Fiji
           Version: unspecified
          Hardware: Macintosh
                OS: Mac OS
            Status: NEW
          Severity: blocker
          Priority: P5
         Component: Bio-Formats
          Assignee: imagej-bugs at imagej.net
          Reporter: amorbach at mpi-cbg.de

I created some .czi files doing live imaging, smaller files for every timepoint
with 9 stacks per file and one large file having all stacks and all timepoints.
The files were created with the Zeiss LSM 780 NLO Laser Scanning Microscope and
Zen2. Other people working with the same system can open their files. However,
mine won't open on any computer (I tried Windows and Mac, Fiji and ImageJ2). It
gives me this error: 

(Fiji Is Just) ImageJ 2.0.0-rc-29/1.49q; Java 1.6.0_65 [64-bit]; Mac OS X
10.9.5; 59MB of 4155MB (1%)

java.lang.NumberFormatException: null
    at java.lang.Integer.parseInt(Integer.java:417)
    at java.lang.Integer.parseInt(Integer.java:499)
    at
loci.formats.in.ZeissCZIReader.translateExperiment(ZeissCZIReader.java:2173)
    at
loci.formats.in.ZeissCZIReader.translateMetadata(ZeissCZIReader.java:1234)
    at loci.formats.in.ZeissCZIReader.initFile(ZeissCZIReader.java:702)
    at loci.formats.FormatReader.setId(FormatReader.java:1395)
    at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:493)
    at loci.plugins.in.ImportProcess.execute(ImportProcess.java:140)
    at loci.plugins.in.Importer.showDialogs(Importer.java:137)
    at loci.plugins.in.Importer.run(Importer.java:75)
    at loci.plugins.LociImporter.run(LociImporter.java:78)
    at ij.IJ.runUserPlugIn(IJ.java:199)
    at ij.IJ.runPlugIn(IJ.java:163)
    at ij.IJ.runPlugIn(IJ.java:152)
    at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:450)
    at HandleExtraFileTypes.run(HandleExtraFileTypes.java:66)
    at ij.IJ.runUserPlugIn(IJ.java:199)
    at ij.IJ.runPlugIn(IJ.java:163)
    at ij.IJ.runPlugIn(IJ.java:152)
    at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:486)
    at ij.io.Opener.openImage(Opener.java:360)
    at ij.io.Opener.openImage(Opener.java:239)
    at ij.io.Opener.open(Opener.java:106)
    at ij.io.Opener.openAndAddToRecent(Opener.java:288)
    at ij.plugin.DragAndDrop.openFile(DragAndDrop.java:176)
    at ij.plugin.DragAndDrop.run(DragAndDrop.java:152)
    at java.lang.Thread.run(Thread.java:695)

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