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Bug 542 - Fiji cannot open images acquired by NIS 4.10
Fiji cannot open images acquired by NIS 4.10
Status: RESOLVED FIXED
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
PC Windows
: P4 normal
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2013-01-03 12:46 CST by sylvie le guyader
Modified: 2013-01-04 17:13 CST
3 users (show)

See Also:
Description sylvie le guyader 2013-01-03 12:46:46 CST 
Fiji cannot open images acquired by NIS 4.10

Information about your version of Java - this information is useful for the Fiji developers:

  os.arch => x86
  os.name => Windows XP
  os.version => 5.1
  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) Client 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: UP_TO_DATE

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: C:\DOCUME~1\syle.AD\MYDOCU~1\Fiji.app/java/win32/jdk1.6.0_24/jre/
  ij.dir => C:\DOCUME~1\syle.AD\MYDOCU~1\Fiji.app

Information about the version of each plugin:

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  a32dfe463fa2c8814cb0caf9079478ff4e1c44bf 20120912165713 plugins/Utilities/Close_All_Without_Saving.txt
  ad9dcb2776203a1e4bf6704e12d48f098445ff7d 20121109163411 plugins/Utilities/figurej/LSM_Reader.jar
  69bc16a5e4bd171219877cb5bf5f387f3c7ec344 20121109163409 plugins/Utilities/figurej/figure_j.jar
  0dfa50708bfce0235311900fe7d70525f6cbdf83 20121109163409 plugins/Utilities/figurej/imagescience.jar
  f691331fa9e309be56419191bb75118ad9b5d842 20121109163411 plugins/Utilities/figurej/loci_tools.jar
  61cc86131f0c7f2c21a9373bcc490d7a0efed712 20120912170441 plugins/VIB_.jar
  dbea7327d27dac86777079759676492a6c20d509 20121120172617 plugins/Vaa3d_Reader-2.0.0-SNAPSHOT.jar
  d6cf9638dc212f49fc3d2d4e99ca7aedc78956a2 20120926101946 plugins/Video_Editing.jar
  f658bff40fb04112a21da67873fbc1e73953f7c5 20120912170441 plugins/View5D_.jar
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  df64e95348d93d638a66bcbcd8de782d1d0956a9 20120926170928 plugins/bUnwarpJ_.jar
  e7c1c98c51a7a6cc24bdc2591b67b1cf20a6db1b 20120912170502 plugins/blockmatching_.jar
  69bc16a5e4bd171219877cb5bf5f387f3c7ec344 20121109163605 plugins/figure_j.jar
  659ad6a335b4947eef8758b1b0cf050779430b78 20120912165712 plugins/ij-ImageIO_.jar
  1398b098bf9d094f2dbabe8e7c6ce6fdca8c05ae 20120912170441 plugins/level_sets.jar
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  5a50a9eb8531ebf052814bb0a0026b662edd4072 20121212104220 plugins/mpicbg_-0.6.0-SNAPSHOT.jar
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  e6e0879f5d50afa8d0dd213b4b66e396a39a47b7 20120912165758 retro/backport-util-concurrent-3.1.jar
  e250f0c40b768e90ed7d3910d9869075f3e438cd 20120912165758 retro/retrotranslator-runtime-1.2.7.jar
  eea1390da8fac38763ed4c03f1acb3342b942717 20120912165758 retro/retrotranslator-transformer-1.2.7.jar
  d7160d38a0b805381cb0c0dcedd60e197e247897 20120912170455 scripts/InstallJava3D.m
  05a92a3c3f518ec50976326bf16a8a8858af2183 20120912170455 scripts/IsJava3DInstalled.m
  ff34d026692414ecd743ba34e828780c8614ea8d 20120912170456 scripts/Matlab3DViewerDemo_1.m
  25be149fecd1f6551b9b0ad53946642db65d5a4e 20120912170456 scripts/Matlab3DViewerDemo_2.m
  cb529b6c4fb0505e6e58f8d18fa8f81fc86ebe82 20120912170458 scripts/Matlab3DViewerDemo_3.m
  53d2da73a4a560c41f3c4493d1377c56fe84106c 20120912170456 scripts/Matlab3DViewerIntroduction.m
  4bb342fa00a9d96bda9fd36c8e7df515bbfa8b60 20120912170454 scripts/Miji.m
  868cd43462fefc57c310656d4b35a028f0bda4f4 20120912170454 scripts/Miji_Test.m
  d326018044a582f5106efc6fc90ad09f98a6a822 20120912165722 scripts/Record_Desktop.py
  0ea7f8fc6683e74065ae7fd82c1b92676e069526 20120912165721 scripts/Record_Window.py
  dc94c3a32b5edb3106ad7f2c7c68a852d064089a 20120912170454 scripts/bfopen.m
Comment 1 Melissa Linkert 2013-01-03 16:45:38 CST 
Do you see an error message when opening these files (I assume they are .nd2 files)?  If so, could you please paste the complete message into this bug report?
Comment 2 sylvie le guyader 2013-01-04 14:52:29 CST 
Hi Melissa

Here is the error message:

java.lang.NoSuchMethodError: loci.common.IniTable.get(Ljava/lang/Object;)Ljava/lang/String;
            at loci.plugins.prefs.OptionsList.<init>(OptionsList.java:72)
            at loci.plugins.prefs.OptionsList.<init>(OptionsList.java:66)
            at loci.plugins.in.ImporterOptions.<init>(ImporterOptions.java:158)
            at loci.plugins.in.Importer.parseOptions(Importer.java:114)
            at loci.plugins.in.Importer.run(Importer.java:73)
            at loci.plugins.LociImporter.run(LociImporter.java:81)
            at ij.IJ.runUserPlugIn(IJ.java:184)
            at ij.IJ.runPlugIn(IJ.java:151)
            at ij.IJ.runPlugIn(IJ.java:140)
            at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:405)
            at HandleExtraFileTypes.run(HandleExtraFileTypes.java:57)
            at ij.IJ.runUserPlugIn(IJ.java:184)
            at ij.IJ.runPlugIn(IJ.java:151)
            at ij.IJ.runPlugIn(IJ.java:140)
            at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:430)
            at ij.io.Opener.openImage(Opener.java:304)
            at ij.io.Opener.openImage(Opener.java:325)
            at ij.io.Opener.open(Opener.java:140)
            at ij.io.Opener.openAndAddToRecent(Opener.java:240)
            at ij.plugin.DragAndDrop.openFile(DragAndDrop.java:176)
            at ij.plugin.DragAndDrop.run(DragAndDrop.java:152)
            at java.lang.Thread.run(Thread.java:662)
Sylvie
Comment 3 Melissa Linkert 2013-01-04 16:09:20 CST 
Thank you for adding the error message.  That sort of error typically means that there are multiple conflicting versions of Bio-Formats installed in Fiji.

I noticed that in addition to the standard installation of Bio-Formats, there is a loci_tools.jar file installed in plugins/Utilities/figurej/.  If you move plugins/Utilities/figurej/loci_tools.jar somewhere outside of your Fiji installation, does that solve the problem?  If so, it is probably something that should be fixed in FigureJ.
Comment 4 sylvie le guyader 2013-01-04 16:47:10 CST 
Hi Melissa

Yes it does solve it. Thanks! :)
Sylvie
Comment 5 Johannes Schindelin 2013-01-04 17:13:41 CST 
Since this is such a common problem, I will work on a nicer and more informative error message.

As to FigureJ: if only my advice to make an update site would be heard ;-)