<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 - Fiji cannot open .jp2 (nikon microscope files)"
href="http://fiji.sc/bugzilla/show_bug.cgi?id=913">913</a>
</td>
</tr>
<tr>
<th>Summary</th>
<td>Fiji cannot open .jp2 (nikon microscope files)
</td>
</tr>
<tr>
<th>Product</th>
<td>Fiji
</td>
</tr>
<tr>
<th>Version</th>
<td>unspecified
</td>
</tr>
<tr>
<th>Hardware</th>
<td>Macintosh
</td>
</tr>
<tr>
<th>OS</th>
<td>Mac OS
</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>tobias.buschmann@hhu.de
</td>
</tr>
<tr>
<th>CC</th>
<td>tobias.buschmann@hhu.de
</td>
</tr></table>
<p>
<div>
<pre>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: <a href="http://update.imagej.net/">http://update.imagej.net/</a> (last check:20140709212330)
Fiji: <a href="http://fiji.sc/update/">http://fiji.sc/update/</a> (last check:20140709223742)
BioVoxxel: <a href="http://sites.imagej.net/BioVoxxel/">http://sites.imagej.net/BioVoxxel/</a> (last check:20140710145338)
IBMP: <a href="http://www-ibmp.u-strasbg.fr/fijiupdates/">http://www-ibmp.u-strasbg.fr/fijiupdates/</a> (last check:20140526164644)
Jan's cool update site:
<a href="http://www-public.rz.uni-duesseldorf.de/~eglinger/plugins/">http://www-public.rz.uni-duesseldorf.de/~eglinger/plugins/</a> (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</pre>
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