<html>
<head>
<base href="http://fiji.sc/bugzilla/" />
</head>
<body><table border="1" cellspacing="0" cellpadding="8">
<tr>
<th>Bug ID</th>
<td><a class="bz_bug_link
bz_status_NEW "
title="NEW - Wrong tranformed image when using the Rigid registration plugin"
href="http://fiji.sc/bugzilla/show_bug.cgi?id=915">915</a>
</td>
</tr>
<tr>
<th>Summary</th>
<td>Wrong tranformed image when using the Rigid registration plugin
</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>
<tr>
<th>OS</th>
<td>Windows
</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>claudio.collinet@univ-amu.fr
</td>
</tr>
<tr>
<th>CC</th>
<td>claudio.collinet@univ-amu.fr
</td>
</tr></table>
<p>
<div>
<pre>Dear Johannes and everyone else,
I’m trying to use the rigid registration plugin you developed to register
(translation + rotation) images of the same sample acquired with different
cameras on the same microscope. More specifically, I have a stack of images of
multi-color beads that I would like to use as reference to calculate the shift
matrix and then apply it to the real image stack of my sample. Your plugin
seems perfectly suited for the purpose, however, I’m having troubles because
the plug-in produces mistakes when outputting the transformed image stack.
While the first image of the transformed stack looks good the following ones
are a stitch of the subsequent images in the stack (e.g. slice 2 would be a
stitch of slice 1 and 2, slice 3 a stitch of slices 2 and 3 and so on). The
problem seems to be not systematic as for example I have it if I try to
transform stack-1 to match stack-2 but not viceversa. Moreover, the stitched
transformed stack looks different using different parameters (i.e. the stitched
regions change). This looks like a bug in the plugin If you need I can send you
an example of the wrong transformed output along with the source image stacks.
Please let me know how I can help you with this.
Thanks a lot in advance for your help. Claudio
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:\Fiji.app/java/win64/jdk1.6.0_24//jre
imagej.dir => C:\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:20140822175924)
Fiji: <a href="http://fiji.sc/update/">http://fiji.sc/update/</a> (last check:20140821133247)
Files not up-to-date:
cead9d98 (LOCAL_ONLY) 20120529201719 macros/Automatic image translator.ijm
fbe02b83 (LOCAL_ONLY) 20120411122453 macros/Bleach corrector_EMBL.ijm
25a1c1c1 (LOCAL_ONLY) 20131118203904 macros/CS-CR bundler and measurer +
centroids_ALL AUTOMATIC.ijm
e7bc6b1d (LOCAL_ONLY) 20111007102539 macros/Measure background.ijm
42858716 (LOCAL_ONLY) 20120111152135 macros/NaN substituter.ijm
bce4257d (LOCAL_ONLY) 20120413120931 macros/NaN substituter_V2.ijm
7af3841b (LOCAL_ONLY) 20111205170940 macros/PickROIcompositeONEcolor.ijm
2a34a48f (LOCAL_ONLY) 20111205171003 macros/PickROIcompositeONEcolor_CC.ijm
b49fd7cd (LOCAL_ONLY) 20111205170907 macros/PickROIonestackONEcolor_CC.ijm
fad49d1f (LOCAL_ONLY) 20111006121145
macros/PickpointcoordinateSinglecolor.txt
8b4e9b20 (LOCAL_ONLY) 20111124170338
macros/PickpointcoordinateSinglecolor_CC.ijm
e26d4a95 (LOCAL_ONLY) 20111209145342
macros/PickpointcoordinateSinglecolor_withTEXT_CC.ijm
5fd889d5 (LOCAL_ONLY) 20120315221407
macros/PickpointcoordinateSinglecolor_withTEXT_HOLD_CC.ijm
334652b7 (LOCAL_ONLY) 20120112145951 macros/Residual background
substracter.ijm
a56bcfbf (LOCAL_ONLY) 20120417164401 macros/Value substituter_V2.ijm
50249564 (LOCAL_ONLY) 20111205155346 macros/loadtxtimageJ-1
junction-1colour-minus_vertex+2vertices_CC.ijm
c71f2154 (LOCAL_ONLY) 20111205154208 macros/loadtxtimageJ-1
junction-1colour-minus_vertex_CC.ijm
bdac72d2 (LOCAL_ONLY) 20111205153039
macros/loadtxtimageJ-1junction-1colour_CC.txt.ijm
1ca3422f (LOCAL_ONLY) 20120417205741
macros/loadtxtimageJ-1junction-1colour_automatic_CC.txt.ijm
92cbc5e6 (LOCAL_ONLY) 20111208193319
macros/loadtxtimageJ-1junction_straightener_CC.t.ijm
aee188c5 (LOCAL_ONLY) 20111208195131 macros/loadtxtimageJ-2ROI based on
junction-1colour_CC.txt.ijm
160ce66a (LOCAL_ONLY) 20120213134325 macros/loadtxtimageJ-2ROI central cell
based on junction-1colour_CC.txt.ijm
e69b835d (LOCAL_ONLY) 20111208234102 macros/loadtxtimageJ-2ROI perpendicular
based on junction-1colour_CC.txt.ijm
5f0f1a55 (LOCAL_ONLY) 20120214124007 macros/loadtxtimageJ-2ROI_along
junction_based on junction-1colour_CC.ijm
03b4fc77 (LOCAL_ONLY) 20120307172622 macros/loadtxtimageJ-2circles at
vertexes_CC.txt.ijm
31a549d1 (LOCAL_ONLY) 20120110193834
macros/loadtxtimageJ-Angle-1colour_CC.ijm
33df74b8 (LOCAL_ONLY) 20111006121053 macros/loadtxtimageoneJunction.txt
f51b3492 (MODIFIED) 20131025185130 plugins/Extended_Depth_Field.jar
077159f3 (LOCAL_ONLY) 20120229180236 plugins/Image_Stabilizer.class
0acd6f4f (LOCAL_ONLY) 20120229180242
plugins/Image_Stabilizer_Log_Applier.class
3589dfdf (LOCAL_ONLY) 20120301134956 plugins/MultiStackReg1.45_.jar
d74e90b9 (LOCAL_ONLY) 20111104115337 plugins/PerkinElmer_Reader.class
b8888137 (LOCAL_ONLY) 20111104115916 plugins/Perkin_ElmerPan1_2_2.jar
0e98bded (LOCAL_ONLY) 20111006123126
plugins/PickpointcoordinateSinglecolor.txt
fb8e6753 (LOCAL_ONLY) 20130910153405
plugins/PickpointcoordinateSinglecolor_withTEXT_low res_CC.ijm
d31ed141 (LOCAL_ONLY) 20131025141413 plugins/Stack_Focuser_.class
4e8762e7 (LOCAL_ONLY) 20140503183317
plugins/Tissue_Analyzer/TAPrefs/TAPrefs.txt
f9a5a806 (LOCAL_ONLY) 20140401160552
plugins/Tissue_Analyzer/TA_additions/TA_plugins/Cortex.jar
df9d5e5c (LOCAL_ONLY) 20140401160552
plugins/Tissue_Analyzer/TA_additions/TA_plugins/FlowPlugin.jar
4646ca0d (LOCAL_ONLY) 20140401160524
plugins/Tissue_Analyzer/TA_additions/TA_plugins/OptimizedZProjectionPlugin.jar
19fe9de6 (LOCAL_ONLY) 20140401160524
plugins/Tissue_Analyzer/TA_additions/TA_plugins/TA_prefs/-5016441619325897676.txt
d33234ed (LOCAL_ONLY) 20140401160524
plugins/Tissue_Analyzer/TA_additions/TA_plugins/TA_prefs/-9017831500860737827.txt
25565151 (LOCAL_ONLY) 20140401160524
plugins/Tissue_Analyzer/TA_additions/TA_plugins/TA_prefs/-9017831500860737828.txt
ed266808 (LOCAL_ONLY) 20140401160524
plugins/Tissue_Analyzer/TA_additions/TA_plugins/TA_prefs/-9017831500860737829.txt
88bda428 (LOCAL_ONLY) 20140401160524
plugins/Tissue_Analyzer/TA_additions/TA_plugins/TA_prefs/1485007076864121860.txt
2988ede2 (LOCAL_ONLY) 20140401160524
plugins/Tissue_Analyzer/TA_additions/TA_plugins/TA_prefs/1686600116616992404.txt
02d84def (LOCAL_ONLY) 20140401160524
plugins/Tissue_Analyzer/TA_additions/TA_plugins/TA_prefs/3067474680756133309.txt
da3bcc9e (LOCAL_ONLY) 20140401160524
plugins/Tissue_Analyzer/TA_additions/TA_plugins/TA_prefs/3075613455810560214.txt
cfacf28b (LOCAL_ONLY) 20140401160552
plugins/Tissue_Analyzer/TA_additions/TA_plugins/additionalCloneTools.jar
b874bdaf (LOCAL_ONLY) 20140401160552
plugins/Tissue_Analyzer/TA_additions/TA_plugins/cloneRoughness.jar
2f84c617 (LOCAL_ONLY) 20140430161547
plugins/Tissue_Analyzer/TA_prefs/-1630055098717882576.txt
4c5ad27e (LOCAL_ONLY) 20140503175935
plugins/Tissue_Analyzer/TA_prefs/-2237172708600457378.txt
51dbbe4e (LOCAL_ONLY) 20140430114021
plugins/Tissue_Analyzer/TA_prefs/1340415277717500058.txt
1ef92d98 (LOCAL_ONLY) 20140411202430
plugins/Tissue_Analyzer/TA_prefs/2736396125801632005.txt
3a928fd4 (LOCAL_ONLY) 20140503170950
plugins/Tissue_Analyzer/TA_prefs/3041661471071799889.txt
0e4aeb1b (LOCAL_ONLY) 20140411210106
plugins/Tissue_Analyzer/TA_prefs/3046661476071799889.txt
0f73b997 (LOCAL_ONLY) 20140401160552
plugins/Tissue_Analyzer/Tissue_Analyzer.jar
a1beec46 (LOCAL_ONLY) 20140401160520 plugins/Tissue_Analyzer/changes.txt
548ba66b (LOCAL_ONLY) 20140401160524
plugins/Tissue_Analyzer/compilationDate.txt
7d5d1123 (LOCAL_ONLY) 20140401160520 plugins/Tissue_Analyzer/launcher.jar
bdddbf0c (LOCAL_ONLY) 20140401160522 plugins/Tissue_Analyzer/lib/IJ.jar
6f3fdc0d (LOCAL_ONLY) 20140401160522 plugins/Tissue_Analyzer/lib/Icons.jar
53bc4ebb (LOCAL_ONLY) 20140401160522 plugins/Tissue_Analyzer/lib/IconsPA.jar
c3cdf2d0 (LOCAL_ONLY) 20140401160522 plugins/Tissue_Analyzer/lib/REngine.jar
6ba3fcd5 (LOCAL_ONLY) 20140401160522 plugins/Tissue_Analyzer/lib/Rserve.jar
269cc20e (LOCAL_ONLY) 20140401160522 plugins/Tissue_Analyzer/lib/Rsession.jar
9b7b3d20 (LOCAL_ONLY) 20140401160522
plugins/Tissue_Analyzer/lib/batik-all-1.7.jar
694bbee3 (LOCAL_ONLY) 20140401160522
plugins/Tissue_Analyzer/lib/sqlite-jdbc-3.7.2.jar
e822575d (LOCAL_ONLY) 20140401160522
plugins/Tissue_Analyzer/lib/xml-apis-ext.jar
245f5a10 (LOCAL_ONLY) 20140401160520 plugins/Tissue_Analyzer/license.txt
397bab67 (LOCAL_ONLY) 20140401160524
plugins/Tissue_Analyzer/otherLicenses/licenseIcons.txt
0f96dbd0 (LOCAL_ONLY) 20140401160524
plugins/Tissue_Analyzer/otherLicenses/licenseRsession.txt
d3260180 (LOCAL_ONLY) 20110920162328 scripts/Record_Desktop.py
0ea7f8fc (LOCAL_ONLY) 20110920162328 scripts/Record_Window.py</pre>
</div>
</p>
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