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<base href="http://fiji.sc/bugzilla/" />
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<body><table border="1" cellspacing="0" cellpadding="8">
<tr>
<th>Bug ID</th>
<td><a class="bz_bug_link
bz_status_NEW "
title="NEW - Problems opeining czi files"
href="http://fiji.sc/bugzilla/show_bug.cgi?id=1026">1026</a>
</td>
</tr>
<tr>
<th>Summary</th>
<td>Problems opeining czi files
</td>
</tr>
<tr>
<th>Product</th>
<td>Fiji
</td>
</tr>
<tr>
<th>Version</th>
<td>unspecified
</td>
</tr>
<tr>
<th>Hardware</th>
<td>Macintosh
</td>
</tr>
<tr>
<th>OS</th>
<td>Mac OS
</td>
</tr>
<tr>
<th>Status</th>
<td>NEW
</td>
</tr>
<tr>
<th>Severity</th>
<td>normal
</td>
</tr>
<tr>
<th>Priority</th>
<td>P4
</td>
</tr>
<tr>
<th>Component</th>
<td>Plugins
</td>
</tr>
<tr>
<th>Assignee</th>
<td>imagej-bugs@imagej.net
</td>
</tr>
<tr>
<th>Reporter</th>
<td>j.m.fannon@warwick.ac.uk
</td>
</tr>
<tr>
<th>CC</th>
<td>j.m.fannon@warwick.ac.uk
</td>
</tr></table>
<p>
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<pre>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 <a class="bz_bug_link
bz_status_RESOLVED bz_closed"
title="RESOLVED DUPLICATE - opening czi files with Fiji"
href="show_bug.cgi?id=607">bug 607</a>
<a class="bz_bug_link
bz_status_RESOLVED bz_closed"
title="RESOLVED DUPLICATE - opening czi files with Fiji"
href="show_bug.cgi?id=607">http://fiji.sc/bugzilla/show_bug.cgi?id=607</a>)
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: <a href="http://update.imagej.net/">http://update.imagej.net/</a> (last check:20150122044514)
Fiji: <a href="http://fiji.sc/update/">http://fiji.sc/update/</a> (last check:20150127132630)</pre>
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</p>
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<ul>
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