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<base href="http://fiji.sc/bugzilla/" />
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<th>Bug ID</th>
<td><a class="bz_bug_link
bz_status_NEW "
title="NEW - I can only see two channels when open a czi file as a hyperstack"
href="http://fiji.sc/bugzilla/show_bug.cgi?id=1106">1106</a>
</td>
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<tr>
<th>Summary</th>
<td>I can only see two channels when open a czi file as a hyperstack
</td>
</tr>
<tr>
<th>Product</th>
<td>Fiji
</td>
</tr>
<tr>
<th>Version</th>
<td>unspecified
</td>
</tr>
<tr>
<th>Hardware</th>
<td>PC
</td>
</tr>
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<th>OS</th>
<td>Windows
</td>
</tr>
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<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>zni@agavebio.com
</td>
</tr>
<tr>
<th>CC</th>
<td>zni@agavebio.com
</td>
</tr></table>
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<pre>When I try to open a czi file, I can only see channel 0 and channel 1 when
using hyperstack, even though I did not acquire any blue channel (Ch0) during
imaging.
I can see the channel 2 (red) only if I tried to open as image 5D and only if I
did not acquire green image (Ch1) of the original .czi file.
Is this normal? Because I can open the confocal sample image with both green
and red channels, but the file was in tiff format?
My current way to get around is to save as new .czi file of individual channel
and color them differently in ImageJ before merge. Is it better practice to
export as tiff files?
Any help is greatly appreciated.
Information about your version of Java:
os.arch => amd64
os.name => Windows 8.1
os.version => 6.3
java.version => 1.7.0_55
java.vendor => Oracle Corporation
java.runtime.name => Java(TM) SE Runtime Environment
java.runtime.version => 1.7.0_55-b13
java.vm.name => Java HotSpot(TM) 64-Bit Server VM
java.vm.version => 24.55-b03
java.vm.vendor => Oracle Corporation
java.vm.info => mixed mode
java.awt.graphicsenv => sun.awt.Win32GraphicsEnvironment
java.specification.name => Java Platform API Specification
java.specification.version => 1.7
sun.cpu.endian => little
sun.desktop => windows
file.separator => \
The up-to-date check says: REMIND_LATER
Information relevant to JAVA_HOME related problems:
JAVA_HOME is set to: null
imagej.dir => C:\Users\ZOEYNI~1\Desktop\FIJI-N~1\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:20150623225330)
Fiji: <a href="http://fiji.sc/update/">http://fiji.sc/update/</a> (last check:20150625052927)
Files not up-to-date:
a755edd2 (MODIFIED) 20150629104217 jars/imagej-ops-0.14.0.jar
b8e3cab7 (MODIFIED) 20150705225357 jars/imagej-ops-0.15.0.jar
3be36100 (MODIFIED) 20150629104220 jars/imglib2-roi-0.3.1.jar
2dc68041 (MODIFIED) 20150705225357 jars/imglib2-roi-0.3.2.jar
d939c993 (MODIFIED) 20150629104336 jars/scijava-common-2.43.0.jar
57f64454 (MODIFIED) 20150705225357 jars/scijava-common-2.44.0.jar
c1877fe3 (LOCAL_ONLY) 20150705154828 plugins/zn_try1.ijm</pre>
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</p>
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