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Bug 922 - bio-formats broke
bio-formats broke
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: 2014-08-29 09:09 CDT by Aryeh Weiss
Modified: 2014-08-29 13:15 CDT
2 users (show)

See Also:
Description Aryeh Weiss 2014-08-29 09:09:25 CDT 
Bio-formatds no longer properly reads nd2 multifield files. I just noticed it today.

I will try to upload an example. Bsically, ir gets the frames, z-size, etc wrong.
I tried both the version distributed with Fiji, and the cersion I get when I select the bio-formats update site.
I hae not founda way to fall bakc to previous versions of bio-formats to see where things changed, I am abroad so Ido not have access to backups.
I will try to upload an image.

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: REMIND_LATER

Information relevant to JAVA_HOME related problems:

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

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20140827132801)
Fiji: http://fiji.sc/update/ (last check:20140829035108)
3D ImageJ Suite: http://sites.imagej.net/Tboudier/ (last check:20140604010506)
Bio-Formats: http://sites.imagej.net/Bio-Formats/ (last check:20140828202636)
BioVoxxel: http://sites.imagej.net/BioVoxxel/ (last check:20140819150502)
Cookbook: http://sites.imagej.net/Cookbook/ (last check:20131220171857)
CMCI-EMBL: http://sites.imagej.net/Miura/ (last check:20140718090940)
ImageJ Latex: http://sites.imagej.net/Yul.liuyu/ (last check:20130816175011)
LOCI: http://sites.imagej.net/LOCI/ (last check:20140401135514)
Morphology: http://sites.imagej.net/Landini/ (last check:20140723095558)
ScientiFig: http://sites.imagej.net/Aigouy/ (last check:20140821115917)

Files not up-to-date:
  6604b5ad (MODIFIED) 20140827142124 jars/ij-1.49d.jar
  d79f9ea6 (LOCAL_ONLY) 20131229034506 luts/ND1-6-11-23 despecal.lut
  9194f1b2 (LOCAL_ONLY) 20131229035601 luts/hadasLUT.lut
  f2b7e781 (LOCAL_ONLY) 20131229033201 luts/lifetime.lut
  e5b59c01 (LOCAL_ONLY) 20131207121339 macros/AutoRun/Register_Jay_Reader.ijm
  2f19e4ec (LOCAL_ONLY) 20110616035254 macros/BatchMacro.ijm
  7ac59f8a (LOCAL_ONLY) 20110205131055 macros/Mark_objects.ijm
  2bed7e59 (LOCAL_ONLY) 20110205131252 macros/Mark_patterns.ijm
  c630043e (LOCAL_ONLY) 20111116123833 macros/OpenFileList.txt
  5f405e9f (LOCAL_ONLY) 20100118020436 macros/PSA_dev.txt
  d4f8abbe (LOCAL_ONLY) 20100118020420 macros/PSA_r12.txt
  e991a157 (LOCAL_ONLY) 20140703075151 macros/Particle_Classifier.ijm
  abb807be (LOCAL_ONLY) 20130623063925 macros/Particle_Classifier.txt
  545e8639 (LOCAL_ONLY) 20140827212548 macros/RunAtStartup.ijm
  6508f387 (LOCAL_ONLY) 20130319052944 macros/StartupMacros.txt
  cce6f4e1 (LOCAL_ONLY) 20101128090151 macros/amw_macro.ijm
  cb3df91c (LOCAL_ONLY) 20130319001610 macros/cicleGrid.ijm
  6f74d729 (LOCAL_ONLY) 20110822073016 macros/claheStack.ijm
  6f901fd0 (LOCAL_ONLY) 20120418051404 macros/corr_bleach050405.txt
  a1475486 (LOCAL_ONLY) 20100614124806 macros/creatingimage.ijm
  1ee9355a (LOCAL_ONLY) 20110818061014 macros/damon_thresholds.ijm
  c90cbd09 (LOCAL_ONLY) 20140510124133 macros/deleteROI.ijm
  a71f6a6b (LOCAL_ONLY) 20140512052921 macros/deleteROIa.ijm
  1873a274 (LOCAL_ONLY) 20090709114926 macros/dima_amw.txt
  d62aa133 (LOCAL_ONLY) 20090816151515 macros/focus_macro_2.txt
  43a15391 (LOCAL_ONLY) 20140510142831 macros/gridTool.ijm
  88d4bd3e (LOCAL_ONLY) 20080127132656 macros/henis-1a.txt
  32108318 (LOCAL_ONLY) 20120124091147 macros/landini_startup.ijm
  b6eda886 (LOCAL_ONLY) 20080917030344 macros/naomi_fix_filenumbers.txt
  b1ce3fba (LOCAL_ONLY) 20090803022549 macros/nrg0091_amw.txt
  28276e43 (LOCAL_ONLY) 20090914040859 macros/nrg010.txt
  bcf0803e (LOCAL_ONLY) 20090914033101 macros/nrg010_amw.txt
  bc690cb9 (LOCAL_ONLY) 20091015032920 macros/nrg016_amw.txt
  8aa156f2 (LOCAL_ONLY) 20091028025405 macros/nrg022.txt
  10c27176 (LOCAL_ONLY) 20130319001527 macros/randomLines.ijm
  a4351c75 (LOCAL_ONLY) 20130419005326 macros/recursiveDirSearch.ijm
  63598ced (LOCAL_ONLY) 20100720061138 macros/red_to_magenta.txt
  30324b71 (LOCAL_ONLY) 20110818061531 macros/resizeROIs.ijm
  1a4001e2 (LOCAL_ONLY) 20090927035412 macros/time_stamp.txt
  3da9830a (LOCAL_ONLY) 20130301080716 macros/toolsets/MiToBo_Runner.txt
  4794b9ba (LOCAL_ONLY) 20131215230147 macros/toolsets/ROI Manager Tools.txt
  9a9b8420 (LOCAL_ONLY) 20140209061104 mmautofocus/MMAutofocus.jar
  8a993e35 (LOCAL_ONLY) 20131207121338 mmautofocus/MMAutofocusDuo.jar
  0524fa64 (LOCAL_ONLY) 20140209061104 mmautofocus/MMAutofocusTB.jar
  ef6fd981 (LOCAL_ONLY) 20140209061104 mmautofocus/MMOughtaFocus.jar
  e02925cd (LOCAL_ONLY) 20140209061100 mmplugins/SPIMAcquisition.jar
  81368c3d (LOCAL_ONLY) 20090519161428 plugins/3D/3d-oc_.jar
  dd0089ce (LOCAL_ONLY) 20090519035018 plugins/3D/Object_Counter3D.class
  5a02e888 (LOCAL_ONLY) 20120717060527 plugins/3D/VoltIJ_.jar
  d75ceaf3 (LOCAL_ONLY) 20090723033800 plugins/3D/WatershedCounting3D_Instructions.txt
  81f10d1d (LOCAL_ONLY) 20090723033752 plugins/3D/WatershedCounting_3D.jar
  2d117ad9 (LOCAL_ONLY) 20100701003659 plugins/AccPbFRET_Plugin.class
  af1bd32b (LOCAL_ONLY) 20100701003659 plugins/AcceptorCTCorrDialog.class
  51cf8d93 (LOCAL_ONLY) 20100701003659 plugins/AcceptorPPCorrDialog.class
  42d1a127 (LOCAL_ONLY) 20130604103909 plugins/ActionBar/Shared Bars/BIOP_HRM_Manager.ijm
  bd7bc5d1 (LOCAL_ONLY) 20140605074244 plugins/ActionBar/Shared Bars/BIOP_MultiManualSelect.ijm
  c271b415 (LOCAL_ONLY) 20140605074244 plugins/ActionBar/Shared Bars/BIOP_PSF_Quality.ijm
  e9bf0b0f (LOCAL_ONLY) 20130624225921 plugins/ActionBar/Shared Bars/BIOP_SIMAssess.ijm
  08afb731 (LOCAL_ONLY) 20140310075147 plugins/ActionBar/Shared Bars/BIOP_VSI_Reader.ijm
  4edb1d6f (LOCAL_ONLY) 20140605074245 plugins/ActionBar/Shared Bars/Common_Tools.ijm
  db280c9c (LOCAL_ONLY) 20140315161112 plugins/ActionBar/Shared Bars/JaCoP_Tools.ijm
  fc766719 (LOCAL_ONLY) 20090804223824 plugins/Adrian_FWHM.jar
  2076fd3d (LOCAL_ONLY) 20110509101247 plugins/Analyze/Auto_Corr.class
  0faf81bc (LOCAL_ONLY) 20110509101134 plugins/Analyze/Auto_Corr_AW.class
  b7c33b97 (LOCAL_ONLY) 20091223012558 plugins/Analyze/Cell_Outliner$1.class
  ed0770b8 (LOCAL_ONLY) 20091223012558 plugins/Analyze/Cell_Outliner$2.class
  df5364aa (LOCAL_ONLY) 20091223012558 plugins/Analyze/Cell_Outliner$3.class
  649faa7f (LOCAL_ONLY) 20091223012558 plugins/Analyze/Cell_Outliner$4.class
  ad4ad3b7 (LOCAL_ONLY) 20091223012558 plugins/Analyze/Cell_Outliner$5.class
  e5892834 (LOCAL_ONLY) 20091223012558 plugins/Analyze/Cell_Outliner$6.class
  ea85a145 (LOCAL_ONLY) 20091223012558 plugins/Analyze/Cell_Outliner$7.class
  64fb05a7 (LOCAL_ONLY) 20091223012558 plugins/Analyze/Cell_Outliner$8.class
  2f965736 (LOCAL_ONLY) 20091223012558 plugins/Analyze/Cell_Outliner$SliceMover.class
  28b7646e (LOCAL_ONLY) 20091223012558 plugins/Analyze/Cell_Outliner$SliceSetter.class
  798d5b01 (LOCAL_ONLY) 20091223012558 plugins/Analyze/Cell_Outliner.class
  07f433a4 (LOCAL_ONLY) 20091209045709 plugins/Analyze/Hough_Circles.class
  757c47ea (LOCAL_ONLY) 20110202041422 plugins/Analyze/IntraCell_v1.class
  265de9a4 (LOCAL_ONLY) 20091125020519 plugins/Analyze/Multi_Cell_Outliner$1.class
  052c8fa8 (LOCAL_ONLY) 20091125020519 plugins/Analyze/Multi_Cell_Outliner$2.class
  0f0f3ebf (LOCAL_ONLY) 20091125020519 plugins/Analyze/Multi_Cell_Outliner$3.class
  d174ffd1 (LOCAL_ONLY) 20091125020519 plugins/Analyze/Multi_Cell_Outliner$4.class
  05b04d7f (LOCAL_ONLY) 20091125020519 plugins/Analyze/Multi_Cell_Outliner$5.class
  8e8c9c1f (LOCAL_ONLY) 20091125020519 plugins/Analyze/Multi_Cell_Outliner$6.class
  d70f7c92 (LOCAL_ONLY) 20091125020519 plugins/Analyze/Multi_Cell_Outliner$7.class
  91d9e8b3 (LOCAL_ONLY) 20091125020519 plugins/Analyze/Multi_Cell_Outliner$8.class
  a1baffb2 (LOCAL_ONLY) 20091125020519 plugins/Analyze/Multi_Cell_Outliner$SliceMover.class
  1a5b7df4 (LOCAL_ONLY) 20091125020519 plugins/Analyze/Multi_Cell_Outliner$SliceSetter.class
  7da88be3 (LOCAL_ONLY) 20091125020519 plugins/Analyze/Multi_Cell_Outliner$WandMM.class
  66ebe0b3 (LOCAL_ONLY) 20091125020519 plugins/Analyze/Multi_Cell_Outliner.class
  435937fb (LOCAL_ONLY) 20130817231157 plugins/Analyze/Nnd_.class
  ebeb645f (LOCAL_ONLY) 20091223012558 plugins/Analyze/WandMM.class
  f9f617b5 (LOCAL_ONLY) 20131104021336 plugins/Analyze/analyze_stripes_v2.4.1.ijm
  b41e0913 (LOCAL_ONLY) 20110429084014 plugins/Analyze/stack_counter.jar
  287c3f2c (LOCAL_ONLY) 20100822150259 plugins/AnalyzeSkeleton$1.class
  4dd99988 (LOCAL_ONLY) 20100822150259 plugins/AnalyzeSkeleton.class
  69d17271 (LOCAL_ONLY) 20100701003659 plugins/ApplyMaskDialog.class
  324f928d (LOCAL_ONLY) 20111031025200 plugins/Auto_Align_1.jar
  c0e551d1 (LOCAL_ONLY) 20140604133911 plugins/BIOP_Common_Tools.jar
  c6c24a8e (LOCAL_ONLY) 20140604133910 plugins/BIOP_VSI_reader.jar
  82418c28 (LOCAL_ONLY) 20130529010002 plugins/BioVoxxel_Toolbox.ijm
  606743ae (LOCAL_ONLY) 20130824145122 plugins/Blend_Images.class
  7f6d6194 (LOCAL_ONLY) 20120225105825 plugins/Blob_Prob.jar
  59a303cc (LOCAL_ONLY) 20120429032745 plugins/BoneJ_.jar
  6ddd37a8 (LOCAL_ONLY) 20130327214546 plugins/CUDA_Deconvolution.jar
  7eee9a1d (LOCAL_ONLY) 20100701003659 plugins/CalculateImgRatioDialog.class
  65ab9874 (LOCAL_ONLY) 20100511233356 plugins/Colony_Counter.jar
  bfdf66c3 (LOCAL_ONLY) 20100714123838 plugins/Colour functions/Align_RGB_planes.class
  4da741fc (LOCAL_ONLY) 20120723225825 plugins/Colour functions/ColorSegmentation_.jar
  0a5c1981 (LOCAL_ONLY) 20080220073008 plugins/Colour functions/Color_Profiler.jar
  63cef19d (LOCAL_ONLY) 20121105111335 plugins/Colour functions/Color_Space_Converter$ColorSpaceConverter.class
  933620c3 (LOCAL_ONLY) 20121105111335 plugins/Colour functions/Color_Space_Converter.class
  ed9a6168 (LOCAL_ONLY) 20070416091000 plugins/Colour functions/Colour_Balance.class
  05883551 (LOCAL_ONLY) 20050512094136 plugins/Colour functions/Colour_Correct.class
  365af84e (LOCAL_ONLY) 20050201093722 plugins/Colour functions/Colour_merge.class
  4a5615b5 (LOCAL_ONLY) 20070626125056 plugins/Colour functions/HSV_Stack.class
  d24cd2d1 (LOCAL_ONLY) 20070626125118 plugins/Colour functions/Lab_Stack.class
  199930f3 (LOCAL_ONLY) 20070626125128 plugins/Colour functions/Luv_Stack.class
  af44f592 (LOCAL_ONLY) 20070620025212 plugins/Colour functions/RGB_Gray_Merge.class
  e9928b83 (LOCAL_ONLY) 20050512090626 plugins/Colour functions/RGB_Measure.class
  ed01e3ec (LOCAL_ONLY) 20130419010306 plugins/Colour functions/RGB_Measure_Plus.class
  7cf305a0 (LOCAL_ONLY) 20040408101504 plugins/Colour functions/RGB_Profiler.class
  f26d321b (LOCAL_ONLY) 20050106085130 plugins/Colour functions/RGB_recolor .txt
  12af1bda (LOCAL_ONLY) 20070214063600 plugins/Colour functions/RGB_to_Montage.class
  6ad1190e (LOCAL_ONLY) 20061011081400 plugins/Colour functions/Recolor_RGB_to_MGB.txt
  67914d0c (LOCAL_ONLY) 20050527100332 plugins/Colour functions/Resize2Rotate_.txt
  109660fc (LOCAL_ONLY) 20100708085138 plugins/Colour functions/Retinex_.class
  5b673829 (LOCAL_ONLY) 20110528215137 plugins/Colour functions/SmartCapture_Lite.jar
  3273d22c (LOCAL_ONLY) 20070126043500 plugins/Colour functions/Whiten_background.class
  f0854dbd (LOCAL_ONLY) 20130319045246 plugins/Common_Toolbar_amw.class
  52ff6766 (LOCAL_ONLY) 20100211110655 plugins/Create_Template.jar
  8d9bdfa0 (LOCAL_ONLY) 20090703072912 plugins/DeconvolutionLab/DeconvolutionLab_.jar
  d14a7cbc (LOCAL_ONLY) 20090625091804 plugins/Depth_from_focus.class
  6a87ed7d (LOCAL_ONLY) 20100701003659 plugins/DonorBlCorrDialog.class
  dec56900 (LOCAL_ONLY) 20081202081412 plugins/EDF/Demo.class
  52b4532b (LOCAL_ONLY) 20081202081546 plugins/EDF/EDF-demo.txt
  fc7d947e (LOCAL_ONLY) 20081202081412 plugins/EDF/EDF_Easy_$1.class
  460c8107 (LOCAL_ONLY) 20081202081412 plugins/EDF/EDF_Easy_.class
  b87549d6 (LOCAL_ONLY) 20081202081412 plugins/EDF/EDF_Expert_$1.class
  eecd3775 (LOCAL_ONLY) 20081202081412 plugins/EDF/EDF_Expert_.class
  bb4d8598 (LOCAL_ONLY) 20081202081412 plugins/EDF/EDF_Viewer3D_$MainDialog.class
  1f8adba2 (LOCAL_ONLY) 20081202081412 plugins/EDF/EDF_Viewer3D_.class
  402b90b1 (LOCAL_ONLY) 20081202081412 plugins/EDF/edf/AbstractEdfAlgorithm.class
  f3d26126 (LOCAL_ONLY) 20081202081412 plugins/EDF/edf/Color2BW.class
  e4704d0c (LOCAL_ONLY) 20081202081412 plugins/EDF/edf/EdfComplexWavelets.class
  ef475177 (LOCAL_ONLY) 20081202081412 plugins/EDF/edf/EdfRealWavelets.class
  7510215e (LOCAL_ONLY) 20081202081412 plugins/EDF/edf/EdfSobel.class
  c5aae14a (LOCAL_ONLY) 20081202081412 plugins/EDF/edf/EdfVariance.class
  65434783 (LOCAL_ONLY) 20081202081412 plugins/EDF/edf/EdfWaveletMaximumModulus.class
  2f0e80f0 (LOCAL_ONLY) 20081202081412 plugins/EDF/edf/LogSingleton.class
  0ffe4e0d (LOCAL_ONLY) 20081202081412 plugins/EDF/edf/MorphologicalOperators.class
  f434f107 (LOCAL_ONLY) 20081202081412 plugins/EDF/edf/PostProcessing.class
  9441e9e6 (LOCAL_ONLY) 20081202081412 plugins/EDF/edf/ProcessTopology.class
  0187d9a9 (LOCAL_ONLY) 20081202081412 plugins/EDF/edf/Sobel.class
  c653047b (LOCAL_ONLY) 20081202081412 plugins/EDF/edf/Tools.class
  cce5515a (LOCAL_ONLY) 20081202081412 plugins/EDF/edf/Variance.class
  56f0b03f (LOCAL_ONLY) 20081202081412 plugins/EDF/edfgui/AboutDialog.class
  46e2be67 (LOCAL_ONLY) 20081202081412 plugins/EDF/edfgui/AbstractDialog$TimerListener.class
  794d8ccb (LOCAL_ONLY) 20081202081412 plugins/EDF/edfgui/AbstractDialog.class
  cdb53d41 (LOCAL_ONLY) 20081202081412 plugins/EDF/edfgui/AdvancedDialog$MyVerifier.class
  0fdfdf3d (LOCAL_ONLY) 20081202081412 plugins/EDF/edfgui/AdvancedDialog.class
  5bed4a73 (LOCAL_ONLY) 20081202081412 plugins/EDF/edfgui/BasicDialog.class
  dcb35ca5 (LOCAL_ONLY) 20081202081412 plugins/EDF/edfgui/ExtendedDepthOfField.class
  5af8f029 (LOCAL_ONLY) 20081202081412 plugins/EDF/edfgui/LogPane.class
  2a3ab5f0 (LOCAL_ONLY) 20081202081412 plugins/EDF/edfgui/MySlider.class
  ad85c9b5 (LOCAL_ONLY) 20081202081412 plugins/EDF/edfgui/MyTableRenderer.class
  44d641d2 (LOCAL_ONLY) 20081202081412 plugins/EDF/edfgui/Parameters.class
  417bbbb0 (LOCAL_ONLY) 20081202081412 plugins/EDF/edfgui/SimpleTableModel.class
  dc4cd10b (LOCAL_ONLY) 20081202081412 plugins/EDF/edfgui/ThreadEdf.class
  fc5d4c0d (LOCAL_ONLY) 20081202081412 plugins/EDF/edfgui/ThreadTopoProc.class
  b77b5da8 (LOCAL_ONLY) 20081202081412 plugins/EDF/imageware/Access.class
  895118eb (LOCAL_ONLY) 20081202081412 plugins/EDF/imageware/Buffer.class
  8f404b54 (LOCAL_ONLY) 20081202081412 plugins/EDF/imageware/Builder.class
  17439d9c (LOCAL_ONLY) 20081202081412 plugins/EDF/imageware/ByteAccess.class
  f773aa9e (LOCAL_ONLY) 20081202081412 plugins/EDF/imageware/ByteBuffer.class
  6035dc3e (LOCAL_ONLY) 20081202081412 plugins/EDF/imageware/BytePointwise.class
  6ce255b2 (LOCAL_ONLY) 20081202081412 plugins/EDF/imageware/ByteProcess.class
  f91ef099 (LOCAL_ONLY) 20081202081412 plugins/EDF/imageware/ByteSet.class
  10ade4a4 (LOCAL_ONLY) 20081202081412 plugins/EDF/imageware/Convolver.class
  79469ee7 (LOCAL_ONLY) 20081202081412 plugins/EDF/imageware/Display.class
  05be9179 (LOCAL_ONLY) 20081202081412 plugins/EDF/imageware/DoubleAccess.class
  3bb456d7 (LOCAL_ONLY) 20081202081412 plugins/EDF/imageware/DoubleBuffer.class
  b17dc16f (LOCAL_ONLY) 20081202081412 plugins/EDF/imageware/DoublePointwise.class
  b4a3c6e6 (LOCAL_ONLY) 20081202081412 plugins/EDF/imageware/DoubleProcess.class
  f7d47d5d (LOCAL_ONLY) 20081202081412 plugins/EDF/imageware/DoubleSet.class
  3c98dbe0 (LOCAL_ONLY) 20081202081412 plugins/EDF/imageware/FMath.class
  84d13c91 (LOCAL_ONLY) 20081202081412 plugins/EDF/imageware/FloatAccess.class
  752ca783 (LOCAL_ONLY) 20081202081412 plugins/EDF/imageware/FloatBuffer.class
  49437fea (LOCAL_ONLY) 20081202081412 plugins/EDF/imageware/FloatPointwise.class
  cb6b1fd7 (LOCAL_ONLY) 20081202081412 plugins/EDF/imageware/FloatProcess.class
  cbb54e2a (LOCAL_ONLY) 20081202081412 plugins/EDF/imageware/FloatSet.class
  bc7be688 (LOCAL_ONLY) 20081202081412 plugins/EDF/imageware/ImageAccess.class
  a3cb9815 (LOCAL_ONLY) 20081202081412 plugins/EDF/imageware/ImageWare.class
  3b5db209 (LOCAL_ONLY) 20081202081412 plugins/EDF/imageware/Pointwise.class
  bab794cb (LOCAL_ONLY) 20081202081412 plugins/EDF/imageware/Process.class
  3aaf16b5 (LOCAL_ONLY) 20081202081412 plugins/EDF/imageware/ShortAccess.class
  589b6994 (LOCAL_ONLY) 20081202081412 plugins/EDF/imageware/ShortBuffer.class
  401574fa (LOCAL_ONLY) 20081202081412 plugins/EDF/imageware/ShortPointwise.class
  cf524c2d (LOCAL_ONLY) 20081202081412 plugins/EDF/imageware/ShortProcess.class
  9edb2a7c (LOCAL_ONLY) 20081202081412 plugins/EDF/imageware/ShortSet.class
  8961c58e (LOCAL_ONLY) 20081202081412 plugins/EDF/surfacemap/SurfaceMap3D$1.class
  1bb5f6bf (LOCAL_ONLY) 20081202081412 plugins/EDF/surfacemap/SurfaceMap3D$2.class
  bfcba439 (LOCAL_ONLY) 20081202081412 plugins/EDF/surfacemap/SurfaceMap3D$Cube.class
  ef435d1d (LOCAL_ONLY) 20081202081412 plugins/EDF/surfacemap/SurfaceMap3D$CustomWindow$1.class
  b42c62d0 (LOCAL_ONLY) 20081202081412 plugins/EDF/surfacemap/SurfaceMap3D$CustomWindow.class
  f4abafd9 (LOCAL_ONLY) 20081202081412 plugins/EDF/surfacemap/SurfaceMap3D$ImageRegion.class
  cae6b66c (LOCAL_ONLY) 20081202081412 plugins/EDF/surfacemap/SurfaceMap3D$Lines.class
  5d974d9c (LOCAL_ONLY) 20081202081412 plugins/EDF/surfacemap/SurfaceMap3D$Lut.class
  05950138 (LOCAL_ONLY) 20081202081412 plugins/EDF/surfacemap/SurfaceMap3D$Misc.class
  6233cdce (LOCAL_ONLY) 20081202081412 plugins/EDF/surfacemap/SurfaceMap3D$Picture.class
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  d0b39e39 (LOCAL_ONLY) 20081202081412 plugins/EDF/surfacemap/SurfaceMap3D$Transform.class
  daeb1ff1 (LOCAL_ONLY) 20081202081412 plugins/EDF/surfacemap/SurfaceMap3D.class
  6d6af260 (LOCAL_ONLY) 20081202081412 plugins/EDF/wavelets/ComplexWaveFilter.class
  69bbb302 (LOCAL_ONLY) 20081202081412 plugins/EDF/wavelets/ComplexWavelet.class
  28e0c7d6 (LOCAL_ONLY) 20081202081412 plugins/EDF/wavelets/ImageAccess.class
  fe5d7760 (LOCAL_ONLY) 20081202081412 plugins/EDF/wavelets/WaveSpline.class
  f469ca9f (LOCAL_ONLY) 20081202081412 plugins/EDF/wavelets/WaveSplineFilter.class
  3f57d09c (LOCAL_ONLY) 20111228064830 plugins/Examples/Erode_Demo.class
  88f402c4 (LOCAL_ONLY) 20130525125227 plugins/Exif_Reader.jar
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  918c7ebf (LOCAL_ONLY) 20020221063130 plugins/FFTJ/deconvolutionj/ComplexNum2.class
  5fca0f50 (LOCAL_ONLY) 20020221063130 plugins/FFTJ/deconvolutionj/ComplexNumPrecision2.class
  235df616 (LOCAL_ONLY) 20020221063130 plugins/FFTJ/deconvolutionj/ComplexValueType2.class
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Comment 1 Curtis Rueden 2014-08-29 09:49:23 CDT 
You can fall back to an older version of Bio-Formats by downloading one of the "Life-Line" versions of Fiji from the Downloads page.

The 2013-July version comes with Bio-Formats circa 4.4.9.
The 2014-June version comes with Bio-Formats 5.0.2.

In any case, please report this bug on the OME Users mailing list, which is the best place to report Bio-Formats issues.

http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users/

Sample files less than ~500MB can be uploaded to the OME QA system:

http://qa.openmicroscopy.org.uk/qa/upload/
Comment 2 Aryeh Weiss 2014-08-29 12:26:51 CDT 
My file is almost 2GB . I uploaded it using the Fiji Help>Upload Sample Image...
Comment 3 Curtis Rueden 2014-08-29 12:36:01 CDT 
Thanks Aryeh, if you mention that you uploaded data via the "Upload Sample Image", as well as what the filename is, when you send your mail to OME Users, the OME team will be able to access the data.
Comment 4 Aryeh Weiss 2014-08-29 13:15:12 CDT 
ok -- I verified the following:

1. A fresh download of the newest Fiji reproduces the problem
2. The June 2014 lifeline version works
3. pasting the Jars/Bio=formats directory from lifeline to latest fixes the problem.

I have to run now, but I will report to the other list when I return.