Czi files not opening with the bioformats importer

bio-formats
Tags: #<Tag:0x00007fb87e450dd8>

#1

Hi,
I am getting this error message.
can anybody help

(Fiji Is Just) ImageJ 2.0.0-rc-15/1.49k; Java 1.6.0_65 [64-bit]; Mac OS X 10.10; 39MB of 9983MB (<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:2144)
	at loci.formats.in.ZeissCZIReader.translateMetadata(ZeissCZIReader.java:1207)
	at loci.formats.in.ZeissCZIReader.initFile(ZeissCZIReader.java:689)
	at loci.formats.FormatReader.setId(FormatReader.java:1317)
	at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:494)
	at loci.plugins.in.ImportProcess.execute(ImportProcess.java:144)
	at loci.plugins.in.Importer.showDialogs(Importer.java:141)
	at loci.plugins.in.Importer.run(Importer.java:79)
	at loci.plugins.LociImporter.run(LociImporter.java:81)
	at ij.IJ.runUserPlugIn(IJ.java:202)
	at ij.IJ.runPlugIn(IJ.java:166)
	at ij.IJ.runPlugIn(IJ.java:155)
	at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:421)
	at HandleExtraFileTypes.run(HandleExtraFileTypes.java:57)
	at ij.IJ.runUserPlugIn(IJ.java:202)
	at ij.IJ.runPlugIn(IJ.java:166)
	at ij.IJ.runPlugIn(IJ.java:155)
	at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:460)
	at ij.io.Opener.openImage(Opener.java:315)
	at ij.io.Opener.openImage(Opener.java:338)
	at ij.io.Opener.open(Opener.java:145)
	at ij.io.Opener.openAndAddToRecent(Opener.java:248)
	at ij.plugin.DragAndDrop.openFile(DragAndDrop.java:176)
	at ij.plugin.DragAndDrop.run(DragAndDrop.java:152)
	at java.lang.Thread.run(Thread.java:695)

#2

Hi @embbmc,

thanks for the bug report. We have fixed a couple of similar issues over the last few months as part of recent Bio-Formats releases. Could you let us know which Bio-Formats version is running on your Fiji distribution (Help > About Plugins > Bio-Formats Plugins...)?

If this is not the latest (currently 5.5.1), could you try upgrading and see if that fixes the issue? Otherwise, you can send us a sample file at http://qa.openmicroscopy.org.uk/qa/upload/

Best,
Sebastien