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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 - Trackmate XML output reports pixelated y displacement values but not x or z"
href="http://fiji.sc/bugzilla/show_bug.cgi?id=1165">1165</a>
</td>
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<th>Summary</th>
<td>Trackmate XML output reports pixelated y displacement values but not x or z
</td>
</tr>
<tr>
<th>Product</th>
<td>ImageJ
</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>
<tr>
<th>Status</th>
<td>NEW
</td>
</tr>
<tr>
<th>Severity</th>
<td>enhancement
</td>
</tr>
<tr>
<th>Priority</th>
<td>P5
</td>
</tr>
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<th>Component</th>
<td>Common
</td>
</tr>
<tr>
<th>Assignee</th>
<td>ctrueden@wisc.edu
</td>
</tr>
<tr>
<th>Reporter</th>
<td>leannao@stanford.edu
</td>
</tr>
<tr>
<th>CC</th>
<td>imagej-bugs@imagej.net
</td>
</tr></table>
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<pre>When using Trackmate to track fluorescent particles, the output results sent to
XML do not make sense, despite being checked over several raw fluorescence
datasets. The displacements between timepoints for the X and Z components of
the tracks appear approximately gaussian-distributed, as I would expect, but
the Y components are concentrated in small peaks centered on integral pixel
displacements. Is it possible to make sure that the particle detection and
output generation for these two components are the same?
My pixel dimensions are isotropic, I am using the LoG detector option (no
median filtering, subpixel localization=on), and the LAP tracker (no gap
closing).
I have run this with the same result on both processed and unprocessed image
stacks, so I know this is not an artifact of the image processing.
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\Leanna\Desktop\Fiji.app/java/win64/jdk1.6.0_24//jre
imagej.dir => C:\Users\Leanna\Desktop\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:20140916081414)
Fiji: <a href="http://fiji.sc/update/">http://fiji.sc/update/</a> (last check:20140925082044)
Files not up-to-date:
fdaccfea (LOCAL_ONLY) 20130528165028 macros/BatchMacro.ijm
d89be7db (LOCAL_ONLY) 20140914142458 plugins/Correct_3D_drift.txt
e8692561 (LOCAL_ONLY) 20140120155254 plugins/Iterative_Deconvolve_3D.class
19a2caaf (LOCAL_ONLY) 20140120153814
plugins/ParallelIterativeDeconvolution3D.txt
616e3252 (MODIFIED) 20130919195651 plugins/StackReg_.jar
240bc793 (LOCAL_ONLY) 20130919200249 plugins/turboRegDialog$15.class
48404114 (LOCAL_ONLY) 20130919200250 plugins/turboRegDialog$16.class</pre>
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