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Bug 676 - Issues in the VIB protocol
Issues in the VIB protocol
Status: NEW
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
PC Windows
: P4 normal
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2013-11-18 06:51 CST by Martin Benz
Modified: 2014-06-16 15:19 CDT
2 users (show)

See Also:
Description Martin Benz 2013-11-18 06:51:05 CST 
As a master student in the university of Fribourg in Switzerland in the lab of Simon Sprecher, I am working with the VIB protocol to establish a 3D standard model of the ant Cardiocondyla obscurior.

 I have several unsalvable problems using the VIB protocol in Fiji concerning the saving of the files. After I finished the segmentation part of different structures of the neuropile, often the saving did not occur. No saving in the working directory, except the image in stack. But no label saved. Once, it worked (without any special different prodecure), the label was saved and the second stack came in the window. But here again, after finishing the segmentation job, the saving did not occur.

 I tried several times, but I really have no clue for this issue. A guy and me tried to do exactly the same procedure in pairs : it worked for me and not for him.

If you could shed a light on this, it would be very kind. I don't know if it is possible that I missed an update or something like it. Is the VIB protocol still updated and available? Do you also have this kind of problem?

Thank you for your attention

Best

Martin Benz

Information about your version of Java:

  os.arch => amd64
  os.name => Windows NT (unknown)
  os.version => 6.2
  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: PROTECTED_LOCATION

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: C:\PROGRA~1\fiji\Fiji.app/java/win64/jdk1.6.0_24//jre
  ij.dir => C:\PROGRA~1\fiji\Fiji.app

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  28a6b42a 20130920071350 plugins/Trainable_Segmentation-2.0.0-SNAPSHOT.jar
  9193871e 20130920071350 plugins/TrakEM2_-1.0b-SNAPSHOT.jar
  8e7f3b79 20130920071350 plugins/TransformJ_-2.8.1-SNAPSHOT.jar
  c4e87a76 20130920071350 plugins/TurboReg_-2.0.0-SNAPSHOT.jar
  9558400d 20130920071350 plugins/UnwarpJ_.jar
  a32dfe46 20130920071350 plugins/Utilities/Close_All_Without_Saving.txt
  253c6df4 20130920071350 plugins/VIB_-2.0.0-SNAPSHOT.jar
  baa78901 20130920071350 plugins/Vaa3d_Reader-2.0.0-SNAPSHOT.jar
  81279d21 20130920071350 plugins/Video_Editing-2.0.0-SNAPSHOT.jar
  73396eef 20130920071352 plugins/View5D_-1.3.1-SNAPSHOT.jar
  980c0ed9 20130920071352 plugins/Volume_Calculator-1.0.1-SNAPSHOT.jar
  b332808b 20130920071352 plugins/Volume_Viewer-2.01.1-SNAPSHOT.jar
  2079ca32 20130920071352 plugins/bUnwarpJ_-2.6.1-SNAPSHOT.jar
  0307564a 20130920071352 plugins/blockmatching_-2.0.0-SNAPSHOT.jar
  659ad6a3 20130920071352 plugins/ij-ImageIO_.jar
  82f900ac 20130920071352 plugins/level_sets-1.0.1-SNAPSHOT.jar
  89866b35 20130920071352 plugins/loci_plugins-4.4.9-SNAPSHOT.jar
  df2af815 20130920071352 plugins/mpicbg_-0.6.1-SNAPSHOT.jar
  5e32d936 20130920071352 plugins/panorama_.jar
  96b34801 20130920071352 plugins/readme.txt
  7e27d804 20130920071352 plugins/register_virtual_stack_slices-2.0.0-SNAPSHOT.jar
  16012d5a 20130920071352 plugins/registration_3d-2.0.0-SNAPSHOT.jar
  34b7341d 20130920071356 retro/backport-util-concurrent-3.1.jar
  8759ba20 20130920071356 retro/retrotranslator-runtime-1.2.9.jar
  a6d5a3b2 20130920071356 retro/retrotranslator-transformer-1.2.9.jar
  d7160d38 20130920071356 scripts/InstallJava3D.m
  05a92a3c 20130920071356 scripts/IsJava3DInstalled.m
  ff34d026 20130920071356 scripts/Matlab3DViewerDemo_1.m
  25be149f 20130920071356 scripts/Matlab3DViewerDemo_2.m
  cb529b6c 20130920071356 scripts/Matlab3DViewerDemo_3.m
  53d2da73 20130920071356 scripts/Matlab3DViewerIntroduction.m
  4bb342fa 20130920071356 scripts/Miji.m
  868cd434 20130920071356 scripts/Miji_Test.m
  dc94c3a3 20130920071356 scripts/bfopen.m
  a77cab39 20130920071356 scripts/importTrackMateTracks.m
Comment 1 Curtis Rueden 2014-06-16 15:19:10 CDT 
We try to keep plugins like the VIB Protocol working, but its main author, Bene Schmid, has not been active in the Fiji community for a couple of years now.

The symptoms you are describing (where two people do the exact same thing with the exact same data and get different results) sound like a race condition, which would definitely be a bug in the code. However, without a small reproducible test case, it becomes very difficult to diagnose the issue and there is little we can do to assist.

If you find a way to reliably reproduce the problem, please follow up with more details. Otherwise, we'll probably have to close this issue without a fix.

There is one thing I notice: your update check says "PROTECTED_LOCATION" which means you have installed Fiji into "C:\Program Files" which is highly discouraged. I know: it's very unintuitive. But the fact is that Windows will not grant Fiji permission to update itself if it is installed into Program Files -- blame Microsoft.

So you could try with your Fiji installed to e.g. C:\Users\mbenz\Programs\Fiji.app (or wherever your user directory is), with a fully updated (or freshly downloaded) copy of Fiji, and see if you still have the same problems.