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Bug 915 - Wrong tranformed image when using the Rigid registration plugin
Wrong tranformed image when using the Rigid registration plugin
Status: NEW
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
PC Windows
: P4 normal
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2014-08-26 10:14 CDT by claudio.collinet
Modified: 2014-08-26 10:14 CDT
1 user (show)

See Also:
Description claudio.collinet 2014-08-26 10:14:38 CDT 
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: http://update.imagej.net/ (last check:20140822175924)
Fiji: http://fiji.sc/update/ (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
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  42858716 (LOCAL_ONLY) 20120111152135 macros/NaN substituter.ijm
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  7af3841b (LOCAL_ONLY) 20111205170940 macros/PickROIcompositeONEcolor.ijm
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  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
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  53bc4ebb (LOCAL_ONLY) 20140401160522 plugins/Tissue_Analyzer/lib/IconsPA.jar
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  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