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Bug 1057 - Fiji won't open .czi files created by Zeiss Zen2
Fiji won't open .czi files created by Zeiss Zen2
Status: RESOLVED INVALID
Product: Fiji
Classification: Unclassified
Component: Bio-Formats
unspecified
Macintosh Mac OS
: P5 blocker
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2015-04-21 04:10 CDT by amorbach
Modified: 2015-04-21 11:23 CDT
1 user (show)

See Also:
Description amorbach 2015-04-21 04:10:20 CDT 
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)
Comment 1 Curtis Rueden 2015-04-21 11:23:07 CDT 
Thanks for the bug report! However, we are trying to unify how Bio-Formats issues are tracked; please report this issue to the OME team as described here:
  http://openmicroscopy.org/site/support/bio-formats/about/bug-reporting.html

Or if you prefer GitHub Issues, you can also report it here:
  https://github.com/openmicroscopy/bioformats/issues