[ImageJ-bugs] [Bug 1026] New: Problems opeining czi files

[bugzilla at fiji.sc]

http://fiji.sc/bugzilla/show_bug.cgi?id=1026

            Bug ID: 1026
           Summary: Problems opeining czi files
           Product: Fiji
           Version: unspecified
          Hardware: Macintosh
                OS: Mac OS
            Status: NEW
          Severity: normal
          Priority: P4
         Component: Plugins
          Assignee: imagej-bugs at imagej.net
          Reporter: j.m.fannon at warwick.ac.uk
                CC: j.m.fannon at warwick.ac.uk

I am unable to open .czi files using the Bio-Formats importer in Fiji or
ImageJ.

I am seeing this exception message when I try to open the files:

(Fiji Is Just) ImageJ 2.0.0-rc-23/1.49m; Java 1.6.0_65 [64-bit]; Mac OS X
10.8.5; 39MB of 2893MB (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.Executer.runCommand(Executer.java:131)
    at ij.Executer.run(Executer.java:64)
    at java.lang.Thread.run(Thread.java:695)


I have updated Java and attempted to update Fiji (following advice in bug 607
http://fiji.sc/bugzilla/show_bug.cgi?id=607)

I am unable to update Fiji, getting the following warnings. 
WARNING: The following files are set to read-only: 'jars/itext-2.1.5.jar,
jars/miglayout-3.7.4-swing.jar.....

Installer failed: java.io.IOException: No such file or directory.

I am sorry if this is an easy fix and I've wasted your time. 
Many thanks for your patience.

Information about your version of Java:

  os.arch => x86_64
  os.name => Mac OS X
  os.version => 10.8.5
  java.version => 1.6.0_65
  java.vendor => Apple Inc.
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.6.0_65-b14-462-11M4609
  java.vm.name => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 20.65-b04-462
  java.vm.vendor => Apple Inc.
  java.vm.info => mixed mode
  java.awt.graphicsenv => apple.awt.CGraphicsEnvironment
  java.specification.name => Java Platform API Specification
  java.specification.version => 1.6
  sun.cpu.endian => little
  sun.desktop => null
  file.separator => /

The up-to-date check says: READ_ONLY

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: null
  imagej.dir => /Volumes/Fiji/Fiji.app

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20150122044514)
Fiji: http://fiji.sc/update/ (last check:20150127132630)

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