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<base href="http://fiji.sc/bugzilla/" />
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<body><table border="1" cellspacing="0" cellpadding="8">
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<th>Bug ID</th>
<td><a class="bz_bug_link
bz_status_NEW "
title="NEW - Bioformats Plugin, problem opening .czi files"
href="http://fiji.sc/bugzilla/show_bug.cgi?id=950">950</a>
</td>
</tr>
<tr>
<th>Summary</th>
<td>Bioformats Plugin, problem opening .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>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>schmied@mpi-cbg.de
</td>
</tr>
<tr>
<th>CC</th>
<td>schmied@mpi-cbg.de
</td>
</tr></table>
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<pre>Hello,
I have a .czi dataset which is a 2 channel 2 illumination side single view
timeseries. The 2 illumination sides are not fused. Each dimension is saved as
an individual .czi file. Thus there are 4 files per time point with the
follwing order when they are saved by the microscope:
Time point 1; Channel 1; Right Illumination >> no index
Time point 1; Channel 2; Right Illumination >> index 1
Time point 1; Channel 1; Left Illumination >> index 2
Time point 1; Channel 2; Left Illumination >> index 3
Time point 2; Channel 1; Right Illumination >> index 4
etc...
For opening these files by dragging them into Fiji or selecting them via
Bio-Formats Importer I use the following settings: Hyperstack; Open Files
Individually; Color mode: Default; Autoscale; Specify range for each series.
This opens the Bio-formats Range option.
The range for the z slices are correct. In this dataset 155 slices. But the
Channels are incorrect.
For the first file of the dataset without index: C Begin = 1; C End = 4; 620
planes (4C x 155Z)
Interestingly if I give this file an index (such as 0) the behaviour is
different then it does not recoginze any channels.
The next file with index 1: C Begin = 1; C End = 2; 310 planes (2C x 155Z)
Index 2: C Begin = 1; C End = 2; 310 planes (2C x 155Z)
Index 3: C Begin = 1; C End = 4; 620 planes (4C x 155Z)
Index 4 (first file of new timepoint): no channels recognized.
This pattern is repeated within each following time point.
1. Problem: It does not open the selected file as individual file. It expects
multiple channels and tries to open them thus I need to set the range.
2. Problem: It recognizes the illumination sides as channels.
3. Problem: Both wrong guesses are not consistent within one time point. At
least the pattern is repeating so I was able to write a macro for now to
circumvent this.
I will provide an example dataset and share the link to my idisk via Email.
Thanks a lot!
Christopher
Information about your version of Java:
os.arch => amd64
os.name => Windows 7
os.version => 6.1
java.version => 1.6.0_24
java.vendor => Sun Microsystems Inc.
java.runtime.name => Java(TM) SE Runtime Environment
java.runtime.version => 1.6.0_24-b07
java.vm.name => Java HotSpot(TM) 64-Bit Server VM
java.vm.version => 19.1-b02
java.vm.vendor => Sun Microsystems Inc.
java.vm.info => mixed mode
java.awt.graphicsenv => sun.awt.Win32GraphicsEnvironment
java.specification.name => Java Platform API Specification
java.specification.version => 1.6
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:
C:\Users\Public\DOCUME~1\Fiji.app/java/win64/jdk1.6.0_24//jre
imagej.dir => C:\Users\Public\DOCUME~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:20141026020028)
Fiji: <a href="http://fiji.sc/update/">http://fiji.sc/update/</a> (last check:20141023165357)
BigDataViewer: <a href="http://sites.imagej.net/Pietzsch/">http://sites.imagej.net/Pietzsch/</a> (last check:20140930145441)
Bio-Formats: <a href="http://sites.imagej.net/Bio-Formats/">http://sites.imagej.net/Bio-Formats/</a> (last check:20141031022635)
Files not up-to-date:
c64b4276 (MODIFIED) 20141031124410 jars/ij-1.49j.jar
a2d4d92b (LOCAL_ONLY) 20140809134357 plugins/Read_Spim.jar</pre>
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