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Bug 1024 - Stitching does not load file - nothing happens
Stitching does not load file - nothing happens
Status: RESOLVED WONTFIX
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
PC Windows
: P4 normal
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2015-03-12 05:47 CDT by Sebastian Rhode
Modified: 2015-03-12 09:12 CDT
2 users (show)

See Also:

Attachments
Output from starting Fiji in debug mode (150.84 KB, text/plain)
2015-03-12 08:17 CDT, Sebastian Rhode

Description Sebastian Rhode 2015-03-12 05:47:29 CDT 
I just tried to use the Stitchinh Plugin with the newest Fiji version (updated 2015_03_12). As usual I started the plugin, selected the options and pressed ok. The task was to read the required metadata from an CZI file (this used to work fine so far) and fuse the ouput.

But after pressing OK just nothing ever happens. No messages in the Log window. It just says Internal Stitchcing 1.2.1 - usially one could follwo the progress of loading the data etc. Any idea what the prblem could be?

Sebi

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: REMIND_LATER

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: C:\Users\Public\DOCUME~1\Fiji/java/win64/jdk1.6.0_24//jre
  imagej.dir => C:\Users\Public\DOCUME~1\Fiji

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20150309141004)
Fiji: http://fiji.sc/update/ (last check:20150310172923)
3D ImageJ Suite: http://sites.imagej.net/Tboudier/ (last check:20141208085245)
BAR: http://sites.imagej.net/Tiago/ (last check:20150302230332)
BigDataViewer: http://sites.imagej.net/Pietzsch/ (last check:20141221160506)
Bio-Formats: http://sites.imagej.net/Bio-Formats/ (last check:20150312022650)
BioVoxxel: http://sites.imagej.net/BioVoxxel/ (last check:20150307222524)
Cookbook: http://sites.imagej.net/Cookbook/ (last check:20150302230629)
CMCI-EMBL: http://sites.imagej.net/Miura/ (last check:20140718160940)
HDF5: http://sites.imagej.net/Ronneber/ (last check:20150214134119)
IBMP-CNRS: http://www-ibmp.u-strasbg.fr/fijiupdates/ (last check:20150127110748)
IJPB-plugins: http://sites.imagej.net/IJPB-plugins/ (last check:20150219113515)
IMCF Uni Basel: http://sites.imagej.net/UniBas-IMCF/ (last check:20150210233144)
MaMuT: http://sites.imagej.net/MaMuT/ (last check:20150216141428)
Morphology: http://sites.imagej.net/Landini/ (last check:20140723165558)
MOSAIC ToolSuite: http://mosaic.mpi-cbg.de/Downloads/update/Fiji/MosaicToolsuite/ (last check:20150227200151)
PHANTAST: http://sites.imagej.net/Nicjac/ (last check:20141204185001)
PTBIOP: http://biop.epfl.ch/Fiji-Update/ (last check:20150311160704)
ScientiFig: http://sites.imagej.net/Aigouy/ (last check:20150114185212)
Stowers: http://research.stowers.org/imagejplugins/updates/ (last check:20150224211959)

Files not up-to-date:
  1ad3be0d (LOCAL_ONLY) 20141126151630 jars/jpedalSTD.jar
  213d7341 (LOCAL_ONLY) 20150115182208 macros/ Update reports/15-1-2015 at 18.22.7.txt
  90cce723 (LOCAL_ONLY) 20140218172622 macros/3Dflight.txt
  8b307943 (LOCAL_ONLY) 20140218172622 macros/AA_ReadMe.txt
  d02a7ece (LOCAL_ONLY) 20140218172622 macros/AddCheckboxGroupDemo.txt
  be050d24 (LOCAL_ONLY) 20140218172622 macros/AddNamesToImportedStack.txt
  76dbe8bf (LOCAL_ONLY) 20140218172624 macros/AlignmentMacros.txt
  a765a5ef (LOCAL_ONLY) 20150115182131 macros/Alpha_Shape.txt
  3a1f2128 (LOCAL_ONLY) 20140218172624 macros/AnimatedGaussianBlur.txt
  8bfdfef8 (LOCAL_ONLY) 20140218172624 macros/AnimatedText.txt
  66e9f473 (LOCAL_ONLY) 20140218172624 macros/AnimationMacros.txt
  1f0a233a (LOCAL_ONLY) 20140218172626 macros/ApplyDicomRescaleSlope.txt
  a52d1ec7 (LOCAL_ONLY) 20140218172626 macros/ApplyFunctionToImage.txt
  c8fc77b7 (LOCAL_ONLY) 20140218172626 macros/Apply_3D_Mask_to_4D_Study.txt
  d4226e88 (LOCAL_ONLY) 20140218172626 macros/ArgumentPassingDemo.txt
  c0d8d781 (LOCAL_ONLY) 20140218172628 macros/Array_Functions.txt
  50b63fed (LOCAL_ONLY) 20140218172628 macros/Arrays.txt
  eba9a3b6 (LOCAL_ONLY) 20140218172628 macros/Artillery.txt
  19ac1727 (LOCAL_ONLY) 20140602121406 macros/AutoRun/AutoRun_Sebi.ijm
  da10d289 (LOCAL_ONLY) 20140218172628 macros/AutoThresholdAndSegment.txt
  cfa3e810 (LOCAL_ONLY) 20140218172628 macros/AzimuthalProfile.txt
  f37a07a5 (LOCAL_ONLY) 20140218172630 macros/BackgroundCorrectedDensity.txt
  b180cd35 (LOCAL_ONLY) 20140218172630 macros/BatchConvert.txt
  7d3e2a9d (LOCAL_ONLY) 20140218172630 macros/BatchConvertToBinary.txt
  f043d208 (LOCAL_ONLY) 20140218172630 macros/BatchConvertToJPEG.txt
  8d5ba370 (LOCAL_ONLY) 20140218172632 macros/BatchMeasure.txt
  185de5a6 (LOCAL_ONLY) 20140218172632 macros/BatchModeCalculator.txt
  a9a55fd8 (LOCAL_ONLY) 20140218172632 macros/BatchModeCompositeSelection.txt
  0e7afeff (LOCAL_ONLY) 20140218172632 macros/BatchModeTest.txt
  beafeb19 (LOCAL_ONLY) 20140218172632 macros/BatchProcessFolders.txt
  9bd8c963 (LOCAL_ONLY) 20140218172634 macros/BatchRGBMeasure.txt
  b3a0724e (LOCAL_ONLY) 20140218172634 macros/BatchSetScale.txt
  085bff79 (LOCAL_ONLY) 20140218172634 macros/Batch_GLCM_Measure.txt
  58fc5699 (LOCAL_ONLY) 20150115182132 macros/Batch_Gamma_Adjustment.txt
  010f5642 (LOCAL_ONLY) 20140218172634 macros/Batch_RGB_Merge.txt
  fbf9eda4 (LOCAL_ONLY) 20150115182132 macros/Batch_RG_Merge.txt
  6bea9547 (LOCAL_ONLY) 20140218172636 macros/Benchmark.txt
  3a121895 (LOCAL_ONLY) 20140218172636 macros/BlanketTransform.txt
  1f2a0ce6 (LOCAL_ONLY) 20140218172636 macros/BouncingBar.txt
  04bf76da (LOCAL_ONLY) 20150115182132 macros/BrushToolMacros.txt
  fcbbef7d (LOCAL_ONLY) 20140218172638 macros/BuiltinFunctions.txt
  58070be7 (LOCAL_ONLY) 20140218172638 macros/BullsEye.txt
  4a476481 (LOCAL_ONLY) 20140218172638 macros/CalculateMean.txt
  7c30a14d (LOCAL_ONLY) 20140218172638 macros/Calculate_Black_to_White_Ratio.txt
  952471f0 (LOCAL_ONLY) 20140218172640 macros/Calculations.txt
  f5e373cd (LOCAL_ONLY) 20140218172642 macros/CalibrationBarMacros.txt
  bc39f3d4 (LOCAL_ONLY) 20140218172642 macros/CallJavaDemo.txt
  2ea9c719 (LOCAL_ONLY) 20140218172642 macros/CellSegmentation.txt
  a1a6b981 (LOCAL_ONLY) 20140218172642 macros/Cellcounter3D.txt
  d6f3e95c (LOCAL_ONLY) 20140218172644 macros/ChangeColors.txt
  f55e4fb7 (LOCAL_ONLY) 20140218172644 macros/Channels_Montage.txt
  c546da4a (LOCAL_ONLY) 20140218172644 macros/CheckDICOMSlicePositions.txt
  196f2955 (LOCAL_ONLY) 20140218172644 macros/CircularParticles.txt
  4e3a5986 (LOCAL_ONLY) 20140218172646 macros/Clock.txt
  7503076f (LOCAL_ONLY) 20140218172646 macros/CloseAllWindows.txt
  71005bbe (LOCAL_ONLY) 20140218172646 macros/Close_All_Windows.txt
  9511365b (LOCAL_ONLY) 20140218172646 macros/Color_Transform_Stack.txt
  0fe6f084 (LOCAL_ONLY) 20140218172648 macros/Colorize.txt
  2c9bb8cb (LOCAL_ONLY) 20150115182133 macros/ColorizedRotation.txt
  4f2827bc (LOCAL_ONLY) 20140218172648 macros/CommandLine.txt
  8b6022a0 (LOCAL_ONLY) 20140218172648 macros/CompositeSelections.txt
  bde0aed3 (LOCAL_ONLY) 20140218172648 macros/ConvertDicomDictionary.txt
  26e7333e (LOCAL_ONLY) 20140218172650 macros/ConvertImageToStack.txt
  4355f7ed (LOCAL_ONLY) 20140218172650 macros/ConvertMaskToCompositeROI.txt
  6a0711b9 (LOCAL_ONLY) 20140218172650 macros/ConvertOverlayToIcon.txt
  3caf98b6 (LOCAL_ONLY) 20140218172650 macros/ConvertOverlayToIcon2.txt
  cf49e807 (LOCAL_ONLY) 20140218172652 macros/ConvertSigned16BitToUnsigned.txt
  456989bc (LOCAL_ONLY) 20140218172652 macros/ConvertStackToBinary.txt
  916b6901 (LOCAL_ONLY) 20140218172652 macros/ConvexHull.txt
  eb049c47 (LOCAL_ONLY) 20140218172652 macros/ConvexitySolidarity.txt
  f576fbed (LOCAL_ONLY) 20140218172652 macros/CopyResultsToClipboard.txt
  1fce3e00 (LOCAL_ONLY) 20140218172654 macros/CountAndMarkCells.txt
  0d4a85b7 (LOCAL_ONLY) 20140218172654 macros/Create3DSpectrums.txt
  9e7e2806 (LOCAL_ONLY) 20140218172654 macros/CreateImageFromFunction.txt
  901768ba (LOCAL_ONLY) 20140218172656 macros/Cumulative_Histogram.txt
  f6f8fdf1 (LOCAL_ONLY) 20140218172656 macros/CustomHistogram.txt
  28da825e (LOCAL_ONLY) 20140218172656 macros/CustomPopupMenu.txt
  a133e9aa (LOCAL_ONLY) 20150115182133 macros/CustomStackThreshold.txt
  3a08287e (LOCAL_ONLY) 20140218172656 macros/CustomTabStatFromResults.txt
  a35757e3 (LOCAL_ONLY) 20140218172658 macros/Custom_Profile_Plot.txt
  1899f37c (LOCAL_ONLY) 20150115182134 macros/Cycloid_grid.txt
  d53ad6b3 (LOCAL_ONLY) 20140218172658 macros/DXM_jpg_acquisition_Mode.txt
  02262316 (LOCAL_ONLY) 20140218172658 macros/DeconvolutionDemo.txt
  69148073 (LOCAL_ONLY) 20140218172658 macros/DeleteEdgeRois.txt
  578fd568 (LOCAL_ONLY) 20140218172658 macros/DeleteResultsByLabel.txt
  b91845b7 (LOCAL_ONLY) 20140218172700 macros/DialogDemo.txt
  a2134853 (LOCAL_ONLY) 20140218172700 macros/Dicom_Sorter.txt
  fa4a4904 (LOCAL_ONLY) 20140218172700 macros/DirectionalFilterWindow.txt
  11b543b1 (LOCAL_ONLY) 20140218172700 macros/DisplayJavaProperties.txt
  8de72b0a (LOCAL_ONLY) 20140218172702 macros/DisplayRangeMacros.txt
  dc8853fe (LOCAL_ONLY) 20140218172702 macros/DisplayTiffInfo.txt
  7c2fe4e8 (LOCAL_ONLY) 20140218172702 macros/DisplayWindowTitles.txt
  2ef33a50 (LOCAL_ONLY) 20140218172702 macros/Display_Pixel_Values.txt
  1932864d (LOCAL_ONLY) 20140218172704 macros/Dithering_.txt
  21d6e26e (LOCAL_ONLY) 20140218172704 macros/DivideCircularRoi.txt
  7b54bb2d (LOCAL_ONLY) 20140218172704 macros/DoWandDemo.txt
  15ee26f4 (LOCAL_ONLY) 20140218172704 macros/DodgeBurnAndSmooth.txt
  1dae5c1e (LOCAL_ONLY) 20140218172704 macros/DrawBestFitEllipse.txt
  f1302ddb (LOCAL_ONLY) 20140218172706 macros/DrawEllipse.txt
  56bf2797 (LOCAL_ONLY) 20140218172706 macros/DrawFeretDiameter.txt
  0c4717a1 (LOCAL_ONLY) 20140218172706 macros/DrawFeretsDiameter.txt
  046c483a (LOCAL_ONLY) 20140218182708 macros/DrawGradientLine.txt
  6bd69c45 (LOCAL_ONLY) 20140218172708 macros/DrawRandomDots.txt
  62808a66 (LOCAL_ONLY) 20140218172708 macros/DrawSliceLabels.txt
  45feda2e (LOCAL_ONLY) 20140218172708 macros/Draw_Scale_Bar.txt
  feae57cb (LOCAL_ONLY) 20140218172708 macros/EDM_16bits.txt
  0729923f (LOCAL_ONLY) 20140218172710 macros/EXIF_Batch_Reader.txt
  1dfa3b99 (LOCAL_ONLY) 20140218172710 macros/EllipseCalibration.txt
  d9b7272d (LOCAL_ONLY) 20140218172710 macros/Ellipsoid_Builder.txt
  89680ace (LOCAL_ONLY) 20140218172710 macros/ErodeToSinglePixel.txt
  36ec1f26 (LOCAL_ONLY) 20140218172712 macros/EvalDemo.txt
  e08f993a (LOCAL_ONLY) 20140218172712 macros/ExamplePlots.txt
  92519cec (LOCAL_ONLY) 20140218172712 macros/ExecExamples.txt
  b950d0a8 (LOCAL_ONLY) 20140218172712 macros/ExifDateAndTime.txt
  e9c6307a (LOCAL_ONLY) 20140218172714 macros/ExtractRGBChannels.txt
  0ce006cd (LOCAL_ONLY) 20140218172714 macros/FFTCustomFilterDemo.txt
  77255121 (LOCAL_ONLY) 20140218172714 macros/FFTRemoveStreaks.txt
  60b2318f (LOCAL_ONLY) 20140218172714 macros/Factorials.txt
  6d3eb1b0 (LOCAL_ONLY) 20140218172716 macros/FeretsDiameter.txt
  8624bb98 (LOCAL_ONLY) 20140218172716 macros/FileDemo.txt
  f03df029 (LOCAL_ONLY) 20140218172716 macros/FileSequences.txt
  690db285 (LOCAL_ONLY) 20140218172716 macros/Filename_Randomizer.txt
  e7686d48 (LOCAL_ONLY) 20140218172718 macros/FilterTester.txt
  60da0538 (LOCAL_ONLY) 20140218172718 macros/FilterTesterTasklist.txt
  7500743a (LOCAL_ONLY) 20140218172718 macros/Find.txt
  56359a56 (LOCAL_ONLY) 20140218172718 macros/FindMaxPixelLocation.txt
  5ae22159 (LOCAL_ONLY) 20140218172720 macros/FindMaxima1D.txt
  72e9c2ee (LOCAL_ONLY) 20140218172720 macros/FindSelectionLimits.txt
  8f19a25e (LOCAL_ONLY) 20140218172720 macros/FindSelectionPeak.txt
  fe92a253 (LOCAL_ONLY) 20140218172720 macros/FindStackMaxima.txt
  7831904c (LOCAL_ONLY) 20140218172722 macros/FindTopPixel.txt
  1c0227cf (LOCAL_ONLY) 20140218172722 macros/First10Bytes.txt
  b1cf13db (LOCAL_ONLY) 20140218172722 macros/FixLineEndings.txt
  22a8568c (LOCAL_ONLY) 20140218172722 macros/FixNIHImageTiffs.txt
  92d2b6f4 (LOCAL_ONLY) 20140218172722 macros/Fixed16BitTo8BitConversion.txt
  af749002 (LOCAL_ONLY) 20140218172724 macros/FlipSelection.txt
  f1636023 (LOCAL_ONLY) 20140218172724 macros/Fonts.txt
  4851d1de (LOCAL_ONLY) 20140218172724 macros/FractalEDM.txt
  d7a0f1db (LOCAL_ONLY) 20140218172724 macros/FullRange16BitInvert.txt
  71813cd7 (LOCAL_ONLY) 20140218172726 macros/FullTelomerecounter.txt
  0d6e4e4a (LOCAL_ONLY) 20140218172726 macros/Gamma.txt
  bfee945b (LOCAL_ONLY) 20140218172726 macros/Gamma_LUT.txt
  c81db86f (LOCAL_ONLY) 20140218172726 macros/GarbageCollectionTest.txt
  73aff9a6 (LOCAL_ONLY) 20140218172726 macros/GaussianConvolution.txt
  fd4c432a (LOCAL_ONLY) 20140218172728 macros/GenerateColorMap.txt
  2c73e2bb (LOCAL_ONLY) 20140218172728 macros/GetCurrentPasteMode.txt
  49c26300 (LOCAL_ONLY) 20140218172728 macros/GetCursorLocDemo.txt
  9d66737f (LOCAL_ONLY) 20140218172728 macros/GetDateAndTime.txt
  fda65c70 (LOCAL_ONLY) 20140218172730 macros/GetDirectoryDemo.txt
  eb419cad (LOCAL_ONLY) 20140218172730 macros/GetLineDemo.txt
  ad668f7d (LOCAL_ONLY) 20140218172730 macros/GetProfileExample.txt
  57a7f3ee (LOCAL_ONLY) 20140218172730 macros/GetRGBPixelCount.txt
  7d349284 (LOCAL_ONLY) 20140218172732 macros/GetTextFromClipboard.txt
  4f0b3e65 (LOCAL_ONLY) 20140218172732 macros/HSB_Histogram.txt
  5955e59a (LOCAL_ONLY) 20140218172732 macros/HalfCircleSelections.txt
  cb58358c (LOCAL_ONLY) 20140218172732 macros/HanningWindow.txt
  3068f1f8 (LOCAL_ONLY) 20140218172732 macros/HistogramLister.txt
  f9ffec33 (LOCAL_ONLY) 20140218172734 macros/HistogramOfResultsValues.txt
  d854f2fd (LOCAL_ONLY) 20140218172734 macros/HistogramPlotter.txt
  ddb895c0 (LOCAL_ONLY) 20140218172734 macros/HtmlDialogDemo.txt
  0c8f9e62 (LOCAL_ONLY) 20140218172734 macros/HueRotation.txt
  844c0fbf (LOCAL_ONLY) 20140218172736 macros/HyperStackDemo.txt
  dff74cda (LOCAL_ONLY) 20140218172736 macros/HyperVolume_Maker.txt
  5b62e0c5 (LOCAL_ONLY) 20140218172736 macros/Image5dMacros.txt
  c0f592bf (LOCAL_ONLY) 20140218172736 macros/ImageCalculatorDemo.txt
  7628e561 (LOCAL_ONLY) 20140218172738 macros/ImageCreationTest.txt
  e47b856e (LOCAL_ONLY) 20140218172738 macros/ImageJ-dm3-Batch-Convert.txt
  f6b7324e (LOCAL_ONLY) 20140218172738 macros/ImageRotator.txt
  77242879 (LOCAL_ONLY) 20140218172740 macros/Image_Montage.txt
  69e1362f (LOCAL_ONLY) 20150115182134 macros/ImportHexDataAsImage.txt
  620987df (LOCAL_ONLY) 20140218172740 macros/ImportTextImageSequence.txt
  d2a4729a (LOCAL_ONLY) 20140218172740 macros/Import_Results_Table.txt
  904a14c6 (LOCAL_ONLY) 20140218172740 macros/Init.txt
  c7aa97a2 (LOCAL_ONLY) 20140218172742 macros/InvertImage.txt
  bebb0f7f (LOCAL_ONLY) 20140218172742 macros/Kaleidoscope.txt
  b092aaf3 (LOCAL_ONLY) 20140218172742 macros/KeyboardShortcuts.txt
  062fbbd0 (LOCAL_ONLY) 20140218172742 macros/LSM_Batch_With_Colors.txt
  0ac2f679 (LOCAL_ONLY) 20140218172744 macros/LabelParticlesWithArea.txt
  40c57d43 (LOCAL_ONLY) 20140218172744 macros/LineCounter.txt
  6b98acc6 (LOCAL_ONLY) 20140218172744 macros/LineStatistics.txt
  0fafe37a (LOCAL_ONLY) 20140218172744 macros/ListDemo.txt
  7ebbf763 (LOCAL_ONLY) 20140218172744 macros/ListDicomTags.txt
  b1a12a76 (LOCAL_ONLY) 20140218172746 macros/ListFilesRecursively.txt
  1f69fc28 (LOCAL_ONLY) 20140218172746 macros/ListRGBHistogramCounts.txt
  3d97a8fd (LOCAL_ONLY) 20140218172746 macros/ListSelectionCoordinates.txt
  7d59ed47 (LOCAL_ONLY) 20140218172746 macros/List_Online_Macros.txt
  d1c3f6c3 (LOCAL_ONLY) 20140218172748 macros/LogWindowTricks.txt
  3688091d (LOCAL_ONLY) 20140218172748 macros/LookupTables.txt
  ea924aaa (LOCAL_ONLY) 20140218172748 macros/LoopStack.txt
  597e00eb (LOCAL_ONLY) 20140218172748 macros/MacroExtensions.txt
  10a274de (LOCAL_ONLY) 20140218172750 macros/MacroSet.txt
  54b06f94 (LOCAL_ONLY) 20140218172750 macros/MakeImageJLogo.txt
  5b190856 (LOCAL_ONLY) 20140218172750 macros/MakeMontage.txt
  ba5bfc0d (LOCAL_ONLY) 20140218172750 macros/MakeSelectionDemo.txt
  14bb537d (LOCAL_ONLY) 20140218172750 macros/MakeSliceBinary.txt
  1f91bd33 (LOCAL_ONLY) 20140218172752 macros/Mandelbrot.txt
  762eb69e (LOCAL_ONLY) 20140218172752 macros/MarkCentroids.txt
  e94ea4c2 (LOCAL_ONLY) 20140218172752 macros/Max_Value_Segmentation.txt
  743af0f9 (LOCAL_ONLY) 20140218172752 macros/Measure3Lengths.txt
  62053169 (LOCAL_ONLY) 20140218172754 macros/MeasureAndLabelXYZ.txt
  16ffaa0e (LOCAL_ONLY) 20140218172754 macros/MeasureAndSetLabel.txt
  649797ca (LOCAL_ONLY) 20140218172754 macros/MeasureAreaFraction.txt
  68c51797 (LOCAL_ONLY) 20140218172754 macros/MeasureCumulativeDistances.txt
  4d3e82bf (LOCAL_ONLY) 20140218172756 macros/MeasureEdgePixels.txt
  799615f8 (LOCAL_ONLY) 20140218172756 macros/MeasurePointSpacing.txt
  3db4c3bc (LOCAL_ONLY) 20140218172756 macros/MeasureRGB.txt
  00045511 (LOCAL_ONLY) 20140218172756 macros/MeasureRedirected.txt
  bcc6bc7e (LOCAL_ONLY) 20140218172756 macros/MeasureStack.txt
  3285da65 (LOCAL_ONLY) 20140218172758 macros/Measure_And_Label.txt
  2f05f4d4 (LOCAL_ONLY) 20140218172758 macros/Measure_And_Set_Label.txt
  4133d7af (LOCAL_ONLY) 20140218172758 macros/Measure_Angle_And_Length.txt
  97fa1b30 (LOCAL_ONLY) 20140218172758 macros/Measure_Hyperstack.txt
  75de8b0d (LOCAL_ONLY) 20150115182134 macros/Measure_Stack.txt
  4c3d384c (LOCAL_ONLY) 20140218172800 macros/Merz_grid.txt
  402a5e63 (LOCAL_ONLY) 20140218172800 macros/MotionBlurRemoval.txt
  c24760e7 (LOCAL_ONLY) 20140218172800 macros/MoveSelection.txt
  7a0a6254 (LOCAL_ONLY) 20140218172802 macros/Mulitple_Thresholds.txt
  a9634cf5 (LOCAL_ONLY) 20140218172802 macros/MultipleColourAnalysis.txt
  5b211427 (LOCAL_ONLY) 20140218172802 macros/MultipleColourBackgrounds.txt
  0cc3cbe7 (LOCAL_ONLY) 20140218172804 macros/Multiple_Circles_grid.txt
  2838d754 (LOCAL_ONLY) 20140218172804 macros/Multipurpose_grid.txt
  540902a3 (LOCAL_ONLY) 20140218172804 macros/Normalize_Stack_Means.txt
  9c2157d9 (LOCAL_ONLY) 20140218172804 macros/Object_Color_Sorting.txt
  f22c24ae (LOCAL_ONLY) 20140218172806 macros/Offline_Macro_Help.txt
  6a5941eb (LOCAL_ONLY) 20140218172806 macros/OpenDialogDemo.txt
  691e5cb4 (LOCAL_ONLY) 20140218172806 macros/OpenImagesFromList.txt
  fc433d94 (LOCAL_ONLY) 20140218172806 macros/OpenMacIPLab.txt
  de1ceba0 (LOCAL_ONLY) 20140218172806 macros/OpenPoints.txt
  f6026307 (LOCAL_ONLY) 20140218172808 macros/OpenSeriesUsingFilter.txt
  9ee1e735 (LOCAL_ONLY) 20140218172808 macros/OpenStackUsingURLs.txt
  61b38fd8 (LOCAL_ONLY) 20140218172808 macros/ParseFloatIntExamples.txt
  219ddb43 (LOCAL_ONLY) 20140218172808 macros/ParticleClusterAnalysis.txt
  41cbb94f (LOCAL_ONLY) 20140218172810 macros/ParticleLabelingExample.txt
  19edc327 (LOCAL_ONLY) 20140218172810 macros/ParticleOutlines.txt
  cd6ffeac (LOCAL_ONLY) 20140218172810 macros/ParticleRotator.txt
  a5a1025e (LOCAL_ONLY) 20140218172812 macros/PasteControlDemo.txt
  5a18a536 (LOCAL_ONLY) 20150115182135 macros/Percent_Green.txt
  8502b566 (LOCAL_ONLY) 20140218172812 macros/PerimeterAndCircularityTest.txt
  7d350c9e (LOCAL_ONLY) 20140218172814 macros/Perspective_Stack_View.txt
  18631c5e (LOCAL_ONLY) 20140218172814 macros/PhAct.txt
  a7ad7d61 (LOCAL_ONLY) 20140218172814 macros/PlateMontage.txt
  e47f9945 (LOCAL_ONLY) 20140218172816 macros/Plot3DPoints.txt
  dc3444f1 (LOCAL_ONLY) 20140218172816 macros/PlotColumnPixelCounts.txt
  2136d7aa (LOCAL_ONLY) 20140218172816 macros/PlotOceanOpticsSpectrumFiles.txt
  f85b157e (LOCAL_ONLY) 20140218172816 macros/PlotProfileWithSD.txt
  c80c66e4 (LOCAL_ONLY) 20140218172818 macros/PlotRadialMeanVersusAngle.txt
  48fbb148 (LOCAL_ONLY) 20140218172818 macros/PlotStack.txt
  f303f251 (LOCAL_ONLY) 20140218172818 macros/Plot_Multicolor.txt
  5d02c924 (LOCAL_ONLY) 20140218172818 macros/PointsToStack.txt
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Comment 1 Sebastian Rhode 2015-03-12 05:56:52 CDT 
The CZI data set can be downloaded here:

https://dl.dropboxusercontent.com/u/623476/Overview_10X_DAPI.czi

It has 208 Tiles and can be loaded via BioFormtas as a stack of 208 images.
Also the Stitch Tiles option inside the BioFormats Import Options works fine.
Comment 2 Mark Hiner 2015-03-12 07:45:49 CDT 
Hi Sebastian,

 You can try launching in debug mode[1] - by launching from the command line you will see many more error messages that would otherwise be lost.

 You can also turn the ImageJ debug mode on[2] which should allow more error messages to show up in the log.

Hopefully these options will at least allow you to identify the error message.

[1] http://imagej.net/Debugging#Launching_ImageJ_in_debug_mode

[2] http://imagej.net/Debugging#Switching_on_ImageJ.27s_debug_mode
Comment 3 Sebastian Rhode 2015-03-12 08:17:14 CDT 
Created attachment 239
Output from starting Fiji in debug mode
Comment 4 Sebastian Rhode 2015-03-12 08:18:11 CDT 
The output was created by starting Fiji and trying to run the Stitching plugin with the CZI file mentioned above.

Sebi
Comment 5 Mark Hiner 2015-03-12 08:55:06 CDT 
Hi Sebastian,

The IMCF update site deploys a custom Stitching plugin, which clashes with the plugin provided by the Bio-Formats update site.

By default, Fiji ships Bio-Formats 5.0.x. The Bio-Formats update site provides Bio-Formats 5.1 which has breaking API changes that affect the Stitching plugin. Thus the Bio-Formats update site also provides a 5.1-compatible Stitching plugin.

Enabling IMCF overwrites the Bio-Formats update site's Stitching plugin with a 5.0 version, which then breaks because of 5.1 and 5.0 incompatibility.

To fix your installation, I would suggest uninstalling both Bio-Formats and IMCF update sites ONE AT A TIME.

Then just enable one of the two based on your current needs (e.g. Bio-Formats if you need 5.1).

I am also going to file a bug report for the updater, as I could not find a way to have both update sites installed but have the Bio-Formats Stitching.jar "win".
Comment 6 Mark Hiner 2015-03-12 09:12:22 CDT 
You can have the two update sites enabled if you do the following:

1. Uninstall both update sites
2. Install the Bio-Formats update site
3. Enable the IMCF update site, but select the Stitching.jar and choose "Keep as-is". Then continue the installation.

This will avoid overwriting the 5.1-compatible Stitching.jar