<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 - micromanager-recorded image sequence fails to open in fiji"
href="http://fiji.sc/bugzilla/show_bug.cgi?id=880">880</a>
</td>
</tr>
<tr>
<th>Summary</th>
<td>micromanager-recorded image sequence fails to open in fiji
</td>
</tr>
<tr>
<th>Product</th>
<td>Fiji
</td>
</tr>
<tr>
<th>Version</th>
<td>unspecified
</td>
</tr>
<tr>
<th>Hardware</th>
<td>PC
</td>
</tr>
<tr>
<th>OS</th>
<td>Windows
</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>a.tapacob@gmail.com
</td>
</tr>
<tr>
<th>CC</th>
<td>a.tapacob@gmail.com
</td>
</tr></table>
<p>
<div>
<pre>(Fiji Is Just) ImageJ 2.0.0-rc-9/1.49d; Java 1.6.0_24 [64-bit]; Windows 7 6.1;
1007MB of 6093MB (16%)
java.lang.NullPointerException
at
io.scif.formats.MicromanagerFormat$Reader.openPlane(MicromanagerFormat.java:781)
at
io.scif.formats.MicromanagerFormat$Reader.openPlane(MicromanagerFormat.java:740)
at io.scif.AbstractReader.openPlane(AbstractReader.java:167)
at io.scif.filters.ChannelFiller.openPlane(ChannelFiller.java:170)
at io.scif.filters.ChannelFiller.openPlane(ChannelFiller.java:151)
at io.scif.filters.PlaneSeparator.openPlane(PlaneSeparator.java:297)
at io.scif.filters.PlaneSeparator.openPlane(PlaneSeparator.java:208)
at
io.scif.filters.AbstractReaderFilter.openPlane(AbstractReaderFilter.java:225)
at
io.scif.filters.AbstractReaderFilter.openPlane(AbstractReaderFilter.java:191)
at io.scif.img.ImgOpener.read(ImgOpener.java:808)
at io.scif.img.ImgOpener.read(ImgOpener.java:793)
at io.scif.img.ImgOpener.read(ImgOpener.java:793)
at io.scif.img.ImgOpener.read(ImgOpener.java:793)
at io.scif.img.ImgOpener.read(ImgOpener.java:775)
at io.scif.img.ImgOpener.readPlanes(ImgOpener.java:761)
at io.scif.img.ImgOpener.openImgs(ImgOpener.java:362)
at io.scif.img.ImgOpener.openImgs(ImgOpener.java:257)
at io.scif.img.ImgOpener.openImgs(ImgOpener.java:145)
at net.imagej.DefaultDatasetService.open(DefaultDatasetService.java:266)
at net.imagej.DefaultDatasetService.open(DefaultDatasetService.java:250)
at net.imagej.io.DatasetIOPlugin.open(DatasetIOPlugin.java:78)
at net.imagej.io.DatasetIOPlugin.open(DatasetIOPlugin.java:50)
at
net.imagej.legacy.plugin.DefaultLegacyOpener.open(DefaultLegacyOpener.java:135)
at
net.imagej.legacy.DefaultLegacyHooks.interceptFileOpen(DefaultLegacyHooks.java:421)
at
net.imagej.legacy.DefaultLegacyHooks.interceptRunPlugIn(DefaultLegacyHooks.java:154)
at ij.IJ.runPlugIn(IJ.java)
at ij.Executer.runCommand(Executer.java:131)
at ij.Executer.run(Executer.java:64)
at java.lang.Thread.run(Thread.java:662)
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: UP_TO_DATE
Information relevant to JAVA_HOME related problems:
JAVA_HOME is set to: C:\FIJI\Fiji.app/java/win64/jdk1.6.0_24//jre
imagej.dir => C:\FIJI\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:20140802165300)
Fiji: <a href="http://fiji.sc/update/">http://fiji.sc/update/</a> (last check:20140730200634)
Files not up-to-date:
12663f8b (LOCAL_ONLY) 20140424013044 macros/FindStackMaxima.ijm
1447bd80 (LOCAL_ONLY) 20050408111420
plugins/3D_Deconvolution/DecCredits$1.class
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plugins/3D_Deconvolution/DecCredits.class
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plugins/3D_Deconvolution/DeconvolutionFFT.class
359a47eb (LOCAL_ONLY) 20050408093628
plugins/3D_Deconvolution/DeconvolutionSolution.class
bb1377de (LOCAL_ONLY) 20050408093628
plugins/3D_Deconvolution/DeconvolutionWavelets.class
e7854ddb (LOCAL_ONLY) 20050408111420
plugins/3D_Deconvolution/Deconvolution_.class
63533ca6 (LOCAL_ONLY) 20050408093628 plugins/3D_Deconvolution/FFT1D.class
49ea638f (LOCAL_ONLY) 20050408093628
plugins/3D_Deconvolution/FourierSpace.class
d4cfb1eb (LOCAL_ONLY) 20050408140536 plugins/3D_Deconvolution/GibsonPSF.class
330c6e0c (LOCAL_ONLY) 20050408140244
plugins/3D_Deconvolution/GibsonPSFF.class
f4e7f902 (LOCAL_ONLY) 20050408093628
plugins/3D_Deconvolution/ImageAccess.class
faa88a5f (LOCAL_ONLY) 20050408142652
plugins/3D_Deconvolution/OndCredits$1.class
72630389 (LOCAL_ONLY) 20050408140014
plugins/3D_Deconvolution/OndCredits.class
6e4486d6 (LOCAL_ONLY) 20050408140244
plugins/3D_Deconvolution/PSFCredits$1.class
848dad8b (LOCAL_ONLY) 20050408140244
plugins/3D_Deconvolution/PSFCredits.class
edf4dcb4 (LOCAL_ONLY) 20050408140536
plugins/3D_Deconvolution/PSFCreditsG$1.class
3beab6cf (LOCAL_ONLY) 20050408140536
plugins/3D_Deconvolution/PSFCreditsG.class
bf064d98 (LOCAL_ONLY) 20050408140536
plugins/3D_Deconvolution/PSF_Gibson_.class
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plugins/3D_Deconvolution/PSF_Simple_.class
d4342463 (LOCAL_ONLY) 20050408093628 plugins/3D_Deconvolution/WaveDaub4.class
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plugins/3D_Deconvolution/WaveDaub4Filter.class
3eee7451 (LOCAL_ONLY) 20050408142652
plugins/3D_Deconvolution/Wavelet_Deconvolution_.class
0a2a5833 (LOCAL_ONLY) 20130318171846
plugins/Analyze/Colocalization_Finder.jar
71331805 (LOCAL_ONLY) 20130318171801 plugins/Analyze/jacop_.jar
880cc61a (LOCAL_ONLY) 20130813112017 plugins/CairnImageAnalysis.jar
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plugins/DeconvolutionLab/DeconvolutionLab_.jar
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Analysis/Colocalisation_Threshold.class
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Analysis/ColocaliserWindow.class
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Analysis/Colocalization_Finder.class
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Analysis/Colocalization_Highligter.class
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Analysis/Intensity_Correlation_Analysis.class
c5238c99 (LOCAL_ONLY) 20090903084942 plugins/MBF/Colocalisation
Analysis/Manders_Coefficients.class
b76b8b75 (LOCAL_ONLY) 20090623094316 plugins/MBF/Colocalisation
Analysis/Manders_Coefficients_4D.class
b1954450 (LOCAL_ONLY) 20091207160738 plugins/MBF/Colocalisation
Analysis/Manders_ROI_Manager.class
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functions/Align_RGB_planes.class
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functions/Colour_Balance.class
6bbc7acd (LOCAL_ONLY) 20080104100640 plugins/MBF/Colour
functions/Colour_Composite_Merge.class
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functions/Colour_Correct.class
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functions/Colour_Deconvolution.class
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functions/Colour_ProfilePlot.class
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functions/Colour_merge.class
6fec1efe (LOCAL_ONLY) 20071216165326 plugins/MBF/Colour
functions/Composite_RGB_Merge.class
38b7d101 (LOCAL_ONLY) 20070214162148 plugins/MBF/Colour
functions/RGB_Gray_Merge.jar
34e573f1 (LOCAL_ONLY) 20090623091522 plugins/MBF/Colour
functions/RGB_Line_Profile.txt
3a5fcac1 (LOCAL_ONLY) 20060801112546 plugins/MBF/Colour
functions/RGB_Measure_Plus.class
a6ab4e82 (LOCAL_ONLY) 20040408181504 plugins/MBF/Colour
functions/RGB_Profiler.class
16a6bcd2 (LOCAL_ONLY) 20080623093956 plugins/MBF/Colour
functions/RGB_to_Montage.class
7d2f4af9 (LOCAL_ONLY) 20061011141404 plugins/MBF/Colour
functions/Recolor_RGB_to_MGB.txt
3a33950c (LOCAL_ONLY) 20050527160332 plugins/MBF/Colour
functions/Resize2Rotate_.txt
4739e1e0 (LOCAL_ONLY) 20071214171302 plugins/MBF/Colour
functions/Split_Composite.txt
15546ec8 (LOCAL_ONLY) 20090511154030 plugins/MBF/Colour
functions/Untitled2.txt
10854ad1 (LOCAL_ONLY) 20070126113526 plugins/MBF/Colour
functions/Whiten_background.class
7314f1c8 (LOCAL_ONLY) 20050509114822
plugins/MBF/Deconvolution/Diffraction_PSF_3D.class
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plugins/MBF/Deconvolution/Iterative_Deconvolve_3D.class
49b8aa90 (LOCAL_ONLY) 20080826172008
plugins/MBF/Deconvolution/ParallelSpectralDeconvolution_2D.txt
8bbf7ed2 (LOCAL_ONLY) 20080826172008
plugins/MBF/Deconvolution/ParallelSpectralDeconvolution_3D.txt
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plugins/MBF/Deconvolution/optimization.LICENSE.txt
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plugins/MBF/Deconvolution/optimization.jar
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plugins/MBF/Deconvolution/parallel_spectral_deconvolution-1.7.jar
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plugins/MBF/Deconvolution/parallel_spectral_deconvolution.LICENSE.txt
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plugins/MBF/Deconvolution/parallelcolt-0.5.jar
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plugins/MBF/Deconvolution/parallelcolt.LICENSE.txt
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plugins/MBF/FLIM/Batch_Convert_SDT_to_TIFF.txt
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plugins/MBF/FLIM/FLIM_Histogram$HistogramWindow.class
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837b4bcd (LOCAL_ONLY) 20071203124518 plugins/MBF/FLIM/FLIM_ROI_Manager.class
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4c61a47f (LOCAL_ONLY) 20081008092914 plugins/MBF/FLIM/Open_BH_export.txt
5600c6b2 (LOCAL_ONLY) 20091204154604 plugins/MBF/FLIM/Open_BH_export2.txt
229ef72b (LOCAL_ONLY) 20091207152514 plugins/MBF/FLIM/Open_LIFA_RAW.txt
e67d0211 (LOCAL_ONLY) 20091125104208
plugins/MBF/FLIM/Photon_weighted_FLIM.class
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32fdf502 (LOCAL_ONLY) 20031008133204 plugins/MBF/Transforms/TBasics.class
842730b0 (LOCAL_ONLY) 20031008133204 plugins/MBF/Transforms/Turn.class
df058b9b (LOCAL_ONLY) 20090204154230
plugins/MBF/Updates/ImageJ_Updater_.class
7c84e902 (LOCAL_ONLY) 20070524160224 plugins/MBF/Updates/MBF_Updates.class
26e5f686 (LOCAL_ONLY) 20030925164644 plugins/MBF/Utilities/FMath.class
d38f638d (LOCAL_ONLY) 20030925164644 plugins/MBF/Utilities/Messenger.class
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2eec921b (LOCAL_ONLY) 20030925164644 plugins/MBF/Utilities/Timer.class
4e06a4d7 (LOCAL_ONLY) 20030209140148 plugins/MBF/ij-plugins-toolkit.jar
d4b6f279 (LOCAL_ONLY) 20020424180028 plugins/MBF/lwf_jsdk2.6.jar
030038e3 (LOCAL_ONLY) 20070515142330 plugins/MBF/roiPushTool.jar
0e8ddb6d (LOCAL_ONLY) 20130411123556
plugins/ParallelHRRTDeconvolution/arpack-combo-0.1.jar
7bd78e6f (LOCAL_ONLY) 20130411123556
plugins/ParallelHRRTDeconvolution/core-lapack.jar
22a5a52c (LOCAL_ONLY) 20130411123556
plugins/ParallelHRRTDeconvolution/licenses/parallel_hrrt_deconvolution.LICENSE.txt
bb28d10f (LOCAL_ONLY) 20130411123556
plugins/ParallelHRRTDeconvolution/licenses/parallelcolt.LICENSE.txt
8ca827dd (LOCAL_ONLY) 20130411123556
plugins/ParallelHRRTDeconvolution/macros/ParallelHRRTDeconvolutionCGLS.txt
e4af5821 (LOCAL_ONLY) 20130411123556
plugins/ParallelHRRTDeconvolution/macros/ParallelHRRTDeconvolutionHyBR.txt
719a451a (LOCAL_ONLY) 20130411123556
plugins/ParallelHRRTDeconvolution/macros/ParallelHRRTDeconvolutionMRNSD.txt
bfff5e12 (LOCAL_ONLY) 20130411123556
plugins/ParallelHRRTDeconvolution/macros/ParallelHRRTDeconvolutionOSEM.txt
89cb5823 (LOCAL_ONLY) 20130411123556
plugins/ParallelHRRTDeconvolution/netlib-java-0.9.1.jar
f95a422c (LOCAL_ONLY) 20130411123556
plugins/ParallelHRRTDeconvolution/parallel_hrrt_deconvolution-1.5.jar
f40204ad (LOCAL_ONLY) 20130411123556
plugins/ParallelHRRTDeconvolution/parallelcolt-0.9.jar
55adb958 (LOCAL_ONLY) 20130411123544
plugins/ParallelIterativeDeconvolution/licenses/parallel_iterative_deconvolution.LICENSE.txt
dd8c3801 (LOCAL_ONLY) 20130411123544
plugins/ParallelIterativeDeconvolution/licenses/parallelcolt.LICENSE.txt
60508fb7 (LOCAL_ONLY) 20130411123544
plugins/ParallelIterativeDeconvolution/macros/ParallelIterativeDeconvolution2D.txt
20e21511 (LOCAL_ONLY) 20130411123544
plugins/ParallelIterativeDeconvolution/macros/ParallelIterativeDeconvolution3D.txt
2ca20125 (LOCAL_ONLY) 20130411123544
plugins/ParallelIterativeDeconvolution/parallel_iterative_deconvolution-1.11.jar
8fc126a3 (LOCAL_ONLY) 20130411123605
plugins/ParallelSpectralDeconvolution/licenses/parallel_spectral_deconvolution.LICENSE.txt
b3b247f9 (LOCAL_ONLY) 20130411123605
plugins/ParallelSpectralDeconvolution/licenses/parallelcolt.LICENSE.txt
26d68231 (LOCAL_ONLY) 20130411123605
plugins/ParallelSpectralDeconvolution/macros/ParallelSpectralDeconvolution2D.txt
ccb14fdc (LOCAL_ONLY) 20130411123605
plugins/ParallelSpectralDeconvolution/macros/ParallelSpectralDeconvolution3D.txt
cf3f0780 (LOCAL_ONLY) 20130411123605
plugins/ParallelSpectralDeconvolution/parallel_spectral_deconvolution-1.9.jar
85711b53 (LOCAL_ONLY) 20130411123605
plugins/ParallelSpectralDeconvolution/parallelcolt-0.7.2.jar
46cc7ddc (LOCAL_ONLY) 20130613003511 plugins/SaveAsMovie_win64.jar
1e9f9468 (LOCAL_ONLY) 20131210174603 plugins/Slice_Labeler.class
f459e42b (LOCAL_ONLY) 20131002140635 plugins/Slice_Remover.class
f9ba123d (MODIFIED) 20131002140819
plugins/Stack_Manipulation-2.0.0-SNAPSHOT.jar
27b4abe1 (LOCAL_ONLY) 20130613003344 plugins/Template_Matching.jar
cf445a74 (LOCAL_ONLY) 20131022125218 plugins/Time_Series_Analyzer.jar
c5e3987e (LOCAL_ONLY) 20131210174619 plugins/Time_Stamper.class
67674acb (LOCAL_ONLY) 20131023005729 plugins/Z_Profiler.class
25fc963e (LOCAL_ONLY) 20140522152842
plugins/differentials/differentials/Differentials_.class
b01b8b68 (LOCAL_ONLY) 20140407105610
plugins/differentials/differentials/Differentials_.jar
86bf5a23 (LOCAL_ONLY) 20140424140903 plugins/mcib3d-core2.71.jar
859549db (LOCAL_ONLY) 20140424135304 plugins/mcib3d_plugins2.71.jar
8cb8d89b (LOCAL_ONLY) 20140424140907 plugins/quickhull3d.jar</pre>
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