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Bug 913 - Fiji cannot open .jp2 (nikon microscope files)
Fiji cannot open .jp2 (nikon microscope files)
Status: RESOLVED MOVED
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
Macintosh Mac OS
: P4 normal
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2014-08-26 03:43 CDT by FijiHater01
Modified: 2014-08-26 07:46 CDT
2 users (show)

See Also:
Description FijiHater01 2014-08-26 03:43:12 CDT 
Fiji cannot open .jp2 (nikon microscope files)
Not via drag and drop and not via open command.
Tried with SCIFIO and without, both gave me this bug report:



(Fiji Is Just) ImageJ 2.0.0-rc-8/1.49c; Java 1.6.0_65 [64-bit]; Mac OS X 10.9.4; 26MB of 2611MB (1%)
 
java.lang.StringIndexOutOfBoundsException: String index out of range: -9011
	at java.lang.AbstractStringBuilder.substring(AbstractStringBuilder.java:881)
	at java.lang.StringBuffer.substring(StringBuffer.java:416)
	at loci.formats.in.NativeND2Reader.initFile(NativeND2Reader.java:1385)
	at loci.formats.FormatReader.setId(FormatReader.java:1315)
	at loci.formats.DelegateReader.setId(DelegateReader.java:253)
	at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:494)
	at loci.plugins.in.ImportProcess.execute(ImportProcess.java:144)
	at loci.plugins.in.Importer.showDialogs(Importer.java:141)
	at loci.plugins.in.Importer.run(Importer.java:79)
	at loci.plugins.LociImporter.run(LociImporter.java:81)
	at ij.IJ.runUserPlugIn(IJ.java:202)
	at ij.IJ.runPlugIn(IJ.java:166)
	at ij.IJ.runPlugIn(IJ.java:155)
	at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:421)
	at HandleExtraFileTypes.run(HandleExtraFileTypes.java:57)
	at ij.IJ.runUserPlugIn(IJ.java:202)
	at ij.IJ.runPlugIn(IJ.java:166)
	at ij.IJ.runPlugIn(IJ.java:155)
	at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:460)
	at ij.io.Opener.openImage(Opener.java:315)
	at ij.io.Opener.openImage(Opener.java:338)
	at ij.io.Opener.open(Opener.java:145)
	at ij.io.Opener.openAndAddToRecent(Opener.java:248)
	at ij.plugin.DragAndDrop.openFile(DragAndDrop.java:176)
	at ij.plugin.DragAndDrop.run(DragAndDrop.java:152)
	at java.lang.Thread.run(Thread.java:695)

Information about your version of Java:

  os.arch => x86_64
  os.name => Mac OS X
  os.version => 10.9.4
  java.version => 1.6.0_65
  java.vendor => Apple Inc.
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.6.0_65-b14-462-11M4609
  java.vm.name => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 20.65-b04-462
  java.vm.vendor => Apple Inc.
  java.vm.info => mixed mode
  java.awt.graphicsenv => apple.awt.CGraphicsEnvironment
  java.specification.name => Java Platform API Specification
  java.specification.version => 1.6
  sun.cpu.endian => little
  sun.desktop => null
  file.separator => /

The up-to-date check says: CHECK_TURNED_OFF

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: null
  imagej.dir => /Applications/Fiji.app

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20140709212330)
Fiji: http://fiji.sc/update/ (last check:20140709223742)
BioVoxxel: http://sites.imagej.net/BioVoxxel/ (last check:20140710145338)
IBMP: http://www-ibmp.u-strasbg.fr/fijiupdates/ (last check:20140526164644)
Jan's cool update site: http://www-public.rz.uni-duesseldorf.de/~eglinger/plugins/ (last check:20140424102012)

Files not up-to-date:
  7ecaf631 (OBSOLETE_UNINSTALLED) 20140604114338 jars/jruby-complete-1.7.11.jar
  24d47d70 (OBSOLETE_UNINSTALLED) 20130521235059 jars/junit-4.8.1.jar
  3ace1851 (LOCAL_ONLY) 20140331145334 plugins/Dot_Blot.txt
  0fb65ed4 (OBSOLETE_UNINSTALLED) 20140604114415 plugins/Filters/Adaptive_Filter.class
  7f2acd01 (OBSOLETE_UNINSTALLED) 20140604114416 plugins/Filters/Enhance_True_Color_Contrast.class
  448b2287 (OBSOLETE_UNINSTALLED) 20140604114415 plugins/Filters/Gaussian_Weighted_Median.class
  2c9ade75 (OBSOLETE_UNINSTALLED) 20140604114415 plugins/Filters/Limited_Mean.class
  1656d24d (OBSOLETE_UNINSTALLED) 20140604114415 plugins/Filters/Pseudo_flat_field_correction.class
  4c13cc04 (LOCAL_ONLY) 20121012113314 plugins/Liver_Analaysis/Analyze_pH3_Liver.ijm
  5026ebc3 (LOCAL_ONLY) 20120426114912 plugins/Liver_Analaysis/Area_AFP_Lyve1.ijm
  e5217bc7 (LOCAL_ONLY) 20120827140920 plugins/Liver_Analaysis/LiverLumenQuant.js
  8ddf00ed (LOCAL_ONLY) 20121012112539 plugins/Liver_Analaysis/Liver_pH3.js
  6d112716 (LOCAL_ONLY) 20120306141215 plugins/Liver_Analaysis/MacroGamma0.5JANImprovedAktuell.ijm
  1fe4769a (LOCAL_ONLY) 20121012095037 plugins/Liver_Analaysis/MacroGamma0.5JANImprovedmitZProject121012.ijm
  8f8b1049 (LOCAL_ONLY) 20120813154556 plugins/Liver_Analaysis/MeasureMaxPerParticle.js
  7ba658b6 (LOCAL_ONLY) 20120427114357 plugins/Liver_Analaysis/Quant_Beta1_in_EC.ijm
  065b6ff5 (LOCAL_ONLY) 20120813155153 plugins/Liver_Analaysis/Second_MaxPerParticle.js
  ca06e85f (LOCAL_ONLY) 20120503142710 plugins/Liver_Analaysis/Tiff.ijm
  3a3a000d (LOCAL_ONLY) 20120621093421 plugins/Liver_Analaysis/image.ijm
  9b53ff8e (LOCAL_ONLY) 20140331144658 plugins/MicroArray_Profile.jar
  d84cc2bb (LOCAL_ONLY) 20100922214634 plugins/Morphology/Add_Borders.class
  5cccefae (LOCAL_ONLY) 20100913095428 plugins/Morphology/AnnularClosing.txt
  763870ef (LOCAL_ONLY) 20100913095434 plugins/Morphology/AnnularDilation.txt
  5d777e5e (LOCAL_ONLY) 20100928170030 plugins/Morphology/BinaryConditionalDilate_.class
  6cfae168 (LOCAL_ONLY) 20060525192652 plugins/Morphology/BinaryConditionalErode_.class
  877be8e6 (LOCAL_ONLY) 20060525192958 plugins/Morphology/BinaryConnectivity_.class
  ebe4d9b0 (LOCAL_ONLY) 20111110085448 plugins/Morphology/BinaryDilateNoMerge4_.class
  65b35fcd (LOCAL_ONLY) 20111109155612 plugins/Morphology/BinaryDilateNoMerge8_.class
  da5dc033 (LOCAL_ONLY) 20081019152450 plugins/Morphology/BinaryDilateTest.txt
  fe9208a2 (LOCAL_ONLY) 20060525193012 plugins/Morphology/BinaryDilate_.class
  9f2b4ef9 (LOCAL_ONLY) 20081019152918 plugins/Morphology/BinaryErodeTest.txt
  b38e2aa0 (LOCAL_ONLY) 20060525193102 plugins/Morphology/BinaryErode_.class
  3f39caaf (LOCAL_ONLY) 20060525101716 plugins/Morphology/BinaryFilterReconstruct.txt
  76eb6799 (LOCAL_ONLY) 20090525193222 plugins/Morphology/BinaryFilterReconstruct_.class
  6a2c8b7a (LOCAL_ONLY) 20111109154430 plugins/Morphology/BinaryGeodesicDilateNoMerge8_.class
  14c67860 (LOCAL_ONLY) 20080602091844 plugins/Morphology/BinaryHitOrMiss_.class
  33b507c2 (LOCAL_ONLY) 20100418152848 plugins/Morphology/BinaryKillBorders_.class
  4204c1c6 (LOCAL_ONLY) 20101206082940 plugins/Morphology/BinaryLabel8_.class
  d3c84f8c (LOCAL_ONLY) 20070712112240 plugins/Morphology/BinaryLabelMacro.txt
  59e1afe9 (LOCAL_ONLY) 20100508085308 plugins/Morphology/BinaryLabel_.class
  36e4a042 (LOCAL_ONLY) 20060525101718 plugins/Morphology/BinaryPrune.txt
  c8c66f92 (LOCAL_ONLY) 20090526165400 plugins/Morphology/BinaryReconstruct_.class
  3ff298c7 (LOCAL_ONLY) 20060525193502 plugins/Morphology/BinaryThick2_.class
  b73f68f4 (LOCAL_ONLY) 20060525193450 plugins/Morphology/BinaryThick_.class
  2c4c813e (LOCAL_ONLY) 20060525193520 plugins/Morphology/BinaryThin2_.class
  d8a5d664 (LOCAL_ONLY) 20060525193512 plugins/Morphology/BinaryThin_.class
  3e83cc61 (LOCAL_ONLY) 20060525101718 plugins/Morphology/Boundary4.txt
  9d64440e (LOCAL_ONLY) 20060525101718 plugins/Morphology/Boundary8_.txt
  e9fc745d (LOCAL_ONLY) 20090602153322 plugins/Morphology/Catalogue_Particles.txt
  4d0095a2 (LOCAL_ONLY) 20070607090848 plugins/Morphology/Classify_Particles.class
  f53a898e (LOCAL_ONLY) 20090511083446 plugins/Morphology/CloseByReconstructionTopHat.txt
  2c7f38f5 (LOCAL_ONLY) 20101005103840 plugins/Morphology/CloseByReconstruction_.txt
  1c33105a (LOCAL_ONLY) 20060525101718 plugins/Morphology/ConvexHull1.txt
  7cb69fdf (LOCAL_ONLY) 20060525101718 plugins/Morphology/ConvexHull2.txt
  b19cb415 (LOCAL_ONLY) 20060525101718 plugins/Morphology/ConvexHull3.txt
  bd22187f (LOCAL_ONLY) 20060525101718 plugins/Morphology/Corners.txt
  55c709bf (LOCAL_ONLY) 20061116092256 plugins/Morphology/Correlate_Results.class
  d463ee86 (LOCAL_ONLY) 20081019163010 plugins/Morphology/Delete_ZeroArea.txt
  8df2eb76 (LOCAL_ONLY) 20060525101718 plugins/Morphology/Diagonal8to4.txt
  61193e21 (LOCAL_ONLY) 20100929125932 plugins/Morphology/Domes_.class
  e428a0f5 (LOCAL_ONLY) 20060525101718 plugins/Morphology/Domes_stack.txt
  1be944ae (LOCAL_ONLY) 20090506082436 plugins/Morphology/DoubleWaterfall.txt
  925d3d8c (LOCAL_ONLY) 20111208091210 plugins/Morphology/DrawBoundingBox.txt
  63c4cd27 (LOCAL_ONLY) 20111208091158 plugins/Morphology/DrawBoundingCircle.txt
  b97f945a (LOCAL_ONLY) 20111208091142 plugins/Morphology/DrawConvexHulls.txt
  2adcfe94 (LOCAL_ONLY) 20111208091226 plugins/Morphology/DrawFeret&Breadth.txt
  b60f4365 (LOCAL_ONLY) 20111208091236 plugins/Morphology/DrawMinR&MaxR.txt
  288ace7a (LOCAL_ONLY) 20100805124116 plugins/Morphology/EDM_16bits.txt
  71d10273 (LOCAL_ONLY) 20081019170232 plugins/Morphology/Euler.txt
  63757672 (LOCAL_ONLY) 20090511083446 plugins/Morphology/Extended_Maxima.txt
  285e4c16 (LOCAL_ONLY) 20090511083446 plugins/Morphology/Extended_Minima.txt
  2b80b381 (LOCAL_ONLY) 20100418175426 plugins/Morphology/FillHolesReconstruct.txt
  205b6052 (LOCAL_ONLY) 20060525130102 plugins/Morphology/Fill_Border_Holes.txt
  54d7ef21 (LOCAL_ONLY) 20090506082436 plugins/Morphology/Fill_Greyscale_Holes.txt
  75041650 (LOCAL_ONLY) 20101001143722 plugins/Morphology/GreyBlackTopHatByReconstruction_.txt
  6f716dcc (LOCAL_ONLY) 20101001143322 plugins/Morphology/GreyWhiteTopHatByReconstruction_.txt
  579b5383 (LOCAL_ONLY) 20090504142458 plugins/Morphology/GreyscaleCentreFilter.txt
  c4267b67 (LOCAL_ONLY) 20060525193602 plugins/Morphology/GreyscaleDilate_.class
  965f297a (LOCAL_ONLY) 20060525193612 plugins/Morphology/GreyscaleErode_.class
  0a50379d (LOCAL_ONLY) 20100920132950 plugins/Morphology/GreyscaleKillBorders.txt
  d3047959 (LOCAL_ONLY) 20090503182436 plugins/Morphology/GreyscaleProperAutomedian.txt
  b4d94111 (LOCAL_ONLY) 20090504122820 plugins/Morphology/GreyscaleProperClose.txt
  44d81a95 (LOCAL_ONLY) 20090504123000 plugins/Morphology/GreyscaleProperOpen.txt
  9aadbae0 (LOCAL_ONLY) 20090526165732 plugins/Morphology/GreyscaleReconstruct_.class
  4d7e6035 (LOCAL_ONLY) 20100908144402 plugins/Morphology/GreyscaleTopHat.txt
  cb2dc22a (LOCAL_ONLY) 20100908144826 plugins/Morphology/GreyscaleWell.txt
  282495a6 (LOCAL_ONLY) 20060525101718 plugins/Morphology/H-break.txt
  a73d2279 (LOCAL_ONLY) 20090511130552 plugins/Morphology/HMaxima_Transform.txt
  f1c1b630 (LOCAL_ONLY) 20090527092132 plugins/Morphology/HMinima_Transform.txt
  af3183b2 (LOCAL_ONLY) 20080605122624 plugins/Morphology/Hole_Counter.txt
  930ee9e1 (LOCAL_ONLY) 20090527171616 plugins/Morphology/HomotopicMarking.txt
  3429c4f3 (LOCAL_ONLY) 20060525101718 plugins/Morphology/Hysteresis.txt
  2511df4c (LOCAL_ONLY) 20090513103656 plugins/Morphology/Impose_Minimum.txt
  6be72748 (LOCAL_ONLY) 20060525101718 plugins/Morphology/Influence_Zones.txt
  5859277c (LOCAL_ONLY) 20060525101718 plugins/Morphology/KeepLargestParticle.txt
  559e475f (LOCAL_ONLY) 20080521222500 plugins/Morphology/KeepLargestParticlePixels_.txt
  4605ad0a (LOCAL_ONLY) 20080605144602 plugins/Morphology/KeepParticlesInRange.txt
  b46b2695 (LOCAL_ONLY) 20110415151004 plugins/Morphology/Lines8_.class
  43259a0b (LOCAL_ONLY) 20090519121520 plugins/Morphology/LocalMaxima.txt
  c0207001 (LOCAL_ONLY) 20090519122406 plugins/Morphology/LocalMinMax.txt
  b2139bd8 (LOCAL_ONLY) 20090519121444 plugins/Morphology/LocalMinima.txt
  05f0502d (LOCAL_ONLY) 20060525101718 plugins/Morphology/MCentroids.txt
  b3ea5e05 (LOCAL_ONLY) 20101007145910 plugins/Morphology/MinimaDynamic.txt
  57e4bbaa (LOCAL_ONLY) 20060525101718 plugins/Morphology/Morphological2Derivative1.txt
  35b51e7e (LOCAL_ONLY) 20060525101718 plugins/Morphology/Morphological2Derivative2.txt
  ef809632 (LOCAL_ONLY) 20060525101718 plugins/Morphology/Morphological2Derivative3.txt
  73902be6 (LOCAL_ONLY) 20100908144214 plugins/Morphology/MorphologicalContrastTopHat.txt
  86d43a13 (LOCAL_ONLY) 20100906132436 plugins/Morphology/MorphologicalExternalGradient.txt
  66d657f2 (LOCAL_ONLY) 20100908173708 plugins/Morphology/MorphologicalGradient3.txt
  2cd67873 (LOCAL_ONLY) 20100906132436 plugins/Morphology/MorphologicalGradientBeucher.txt
  b141cc35 (LOCAL_ONLY) 20100906132436 plugins/Morphology/MorphologicalInternalGradient.txt
  babf8d91 (LOCAL_ONLY) 20060525101718 plugins/Morphology/MorphologicalSharpGradient.txt
  7e05ec43 (LOCAL_ONLY) 20060525101718 plugins/Morphology/MorphologicalSmoothing1.txt
  df30c851 (LOCAL_ONLY) 20060525101718 plugins/Morphology/MorphologicalSmoothing2.txt
  b4232d82 (LOCAL_ONLY) 20100913095526 plugins/Morphology/Morphological_Clustering.txt
  c4024220 (LOCAL_ONLY) 20100922234422 plugins/Morphology/Morphological_PCA.txt
  44b58573 (LOCAL_ONLY) 20101005101848 plugins/Morphology/Morphological_SelfDualCentre.txt
  d20caeeb (LOCAL_ONLY) 20101005163722 plugins/Morphology/Morphological_contrast.txt
  c40dcb5d (LOCAL_ONLY) 20100908144252 plugins/Morphology/MultiscaleGradient.txt
  7fa60ae6 (LOCAL_ONLY) 20110425171914 plugins/Morphology/NumberParticles8_.txt
  cd6cf4de (LOCAL_ONLY) 20090511083446 plugins/Morphology/OpenByReconstructionTopHat.txt
  5f844fa9 (LOCAL_ONLY) 20101005103856 plugins/Morphology/OpenByReconstruction_.txt
  8fdf1b15 (LOCAL_ONLY) 20080521221818 plugins/Morphology/Parameter_Matrix.txt
  65c22a1e (LOCAL_ONLY) 20080529224340 plugins/Morphology/ParticleHoleArea.txt
  9a713d79 (LOCAL_ONLY) 20080529224456 plugins/Morphology/ParticleHoleNumber.txt
  9c0a7763 (LOCAL_ONLY) 20080529224152 plugins/Morphology/Particle_Data_Map.txt
  85b99ff0 (LOCAL_ONLY) 20100914150816 plugins/Morphology/Particles4_.class
  583118b2 (LOCAL_ONLY) 20100914150808 plugins/Morphology/Particles8_.class
  ac25812c (LOCAL_ONLY) 20080521215826 plugins/Morphology/Plot_BivariateGraphs.txt
  e8ea53cb (LOCAL_ONLY) 20080606114752 plugins/Morphology/Plot_Histograms.txt
  ce077644 (LOCAL_ONLY) 20060525101718 plugins/Morphology/Prune1.txt
  c4126534 (LOCAL_ONLY) 20060525101718 plugins/Morphology/PruneAll.txt
  916ac5a4 (LOCAL_ONLY) 20090511083446 plugins/Morphology/RegionalMinMax.txt
  3dcf6fa2 (LOCAL_ONLY) 20090511083446 plugins/Morphology/Regional_Maxima.txt
  bc61499e (LOCAL_ONLY) 20101001113926 plugins/Morphology/Regional_Minima.txt
  358d5270 (LOCAL_ONLY) 20100922235812 plugins/Morphology/SelfComplementaryTopHat.txt
  36e7e0b4 (LOCAL_ONLY) 20101005094120 plugins/Morphology/SelfDualReconstruction_.txt
  64886ac9 (LOCAL_ONLY) 20060525101718 plugins/Morphology/Skeleton1.txt
  64fa451e (LOCAL_ONLY) 20060525101718 plugins/Morphology/Skeleton2.txt
  809a6770 (LOCAL_ONLY) 20060525101718 plugins/Morphology/Skeleton3.txt
  16447730 (LOCAL_ONLY) 20090511121302 plugins/Morphology/Skeleton4.txt
  b2242712 (LOCAL_ONLY) 20100922212400 plugins/Morphology/SkeletonFiltering.txt
  5d0400a0 (LOCAL_ONLY) 20080521215352 plugins/Morphology/Summarize_Results.txt
  ab0b29c3 (LOCAL_ONLY) 20080603111018 plugins/Morphology/Thin_Results_Table.txt
  090f96c1 (LOCAL_ONLY) 20100621090218 plugins/Morphology/UnbiasedCounting.txt
  fecf6a46 (LOCAL_ONLY) 20080605121016 plugins/Morphology/UnbiasedParticleArea.txt
  19a9433c (LOCAL_ONLY) 20090330080642 plugins/Morphology/Viscous_Geodesic_Reconstruction.txt
  6d88799a (OBSOLETE_UNINSTALLED) 20140604114410 plugins/Script_Editor-2.0.0-SNAPSHOT.jar
  5e73d56b (MODIFIED) 20130912114206 plugins/TrackMate_-2.1.0.jar
Comment 1 Mark Hiner 2014-08-26 07:46:49 CDT 
As the failure is coming from a loci.formats class, this is a bug in Bio-Formats and not Fiji.

See http://www.openmicroscopy.org/site/support/bio-formats5/about/bug-reporting.html for instructions on reporting bugs to the OME team.

Thanks for the report.