[ImageJ-bugs] [Bug 1073] New: bioformat virtual stacks don't merge channel Z slices!

[bugzilla at fiji.sc]

http://fiji.sc/bugzilla/show_bug.cgi?id=1073

            Bug ID: 1073
           Summary: bioformat virtual stacks don't merge channel Z slices!
           Product: Fiji
           Version: unspecified
          Hardware: PC
                OS: Windows
            Status: NEW
          Severity: normal
          Priority: P4
         Component: Plugins
          Assignee: imagej-bugs at imagej.net
          Reporter: vbindoka at bsd.uchicago.edu
                CC: vbindoka at bsd.uchicago.edu

..it used to work, but not today.
I open 4 Zstacks as virtual using bioformats importer, then use "merge
channels". The images become what looks correct [4Ch+Z slider], but all Z
slices are the same as z=1.
Doing same with non-virtual stacks still works as expected. 

best regards,

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: E:\DEC201~1/java/win64/jdk1.6.0_24//jre
  imagej.dir => E:\DEC201~1

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20150501134914)
Fiji: http://fiji.sc/update/ (last check:20150520024906)
3D ImageJ Suite: http://sites.imagej.net/Tboudier/ (last check:20150520045130)
FFMPEG: http://fiji.sc/~schindelin/ffmpeg-plugins/ (last check:20130606102449)
GDSC-SMLM: http://sites.imagej.net/GDSC-SMLM/ (last check:20150327072750)
HDF5: http://sites.imagej.net/Ronneber/ (last check:20150214064119)
IJPB-plugins: http://sites.imagej.net/IJPB-plugins/ (last check:20150323044329)
Morphology: http://sites.imagej.net/Landini/ (last check:20140723095558)
MIST: http://sites.imagej.net/NIST-ISG-MIST/ (last check:20150416125920)
OpenSPIM: http://openspim.org/update/ (last check:20150512090259)
BigDataViewer: http://sites.imagej.net/Pietzsch/ (last check:20141221090506)
Micro-Manager-dev: http://sites.imagej.net/Micro-Manager-dev/ (last
check:20150501012722)

Files not up-to-date:
  1ad3be0d (LOCAL_ONLY) 20141222042830 jars/jpedalSTD.jar
  3b282216 (LOCAL_ONLY) 20150430163144
mm/win32/OlympusIX3Control/OlympusIX3Control.old.exe
  956e4529 (LOCAL_ONLY) 20150430163144
mm/win64/OlympusIX3Control/OlympusIX3Control.old.exe
  6d337b7a (LOCAL_ONLY) 20140730142734 plugins/Accurate_Gaussian_Blur.class
  6e9d50db (LOCAL_ONLY) 20140320051924 plugins/Adjustable_Watershed.class
  12ec0761 (LOCAL_ONLY) 20120224100622 plugins/Align_RGB_planes.class
  0c575fd1 (LOCAL_ONLY) 20141209160514 plugins/BioVoxxel_Plugins.jar
  52ff6766 (LOCAL_ONLY) 20150115075008 plugins/Create_Template.jar
  55de57f2 (LOCAL_ONLY) 20050408121420 plugins/DecCredits$1.class
  66a64476 (LOCAL_ONLY) 20050408121420 plugins/DecCredits.class
  fd4ce3cd (LOCAL_ONLY) 20050408103628 plugins/DeconvolutionFFT.class
  b0398adb (LOCAL_ONLY) 20141028073350
plugins/DeconvolutionLab/DeconvolutionLab_.jar
  8866a3cd (LOCAL_ONLY) 20050408103628 plugins/DeconvolutionSolution.class
  ce989b93 (LOCAL_ONLY) 20050408103628 plugins/DeconvolutionWavelets.class
  13072662 (LOCAL_ONLY) 20050408121420 plugins/Deconvolution_.class
  11326750 (LOCAL_ONLY) 20050408103628 plugins/FFT1D.class
  18f23277 (LOCAL_ONLY) 20050408103628 plugins/FourierSpace.class
  44693e65 (LOCAL_ONLY) 20150325121214 plugins/Frac_Lac.jar
  348da731 (LOCAL_ONLY) 20141126044659 plugins/GHT_.jar
  15a0aac2 (LOCAL_ONLY) 20050408150536 plugins/GibsonPSF.class
  52861b7c (LOCAL_ONLY) 20050408150244 plugins/GibsonPSFF.class
  f481dc68 (LOCAL_ONLY) 20120817074900 plugins/Hybrid_2D_Filters.class
  6b2de3e5 (LOCAL_ONLY) 20120817084143 plugins/Hybrid_3D_Filters.class
  e9cb6eb7 (LOCAL_ONLY) 20150115083713 plugins/Image_CorrelationJ_1o.class
  d6bc39b9 (LOCAL_ONLY) 20141023044548 plugins/Jay_Plugins.jar
  04b38ca7 (LOCAL_ONLY) 20141023044548 plugins/Jay_Plugins2.jar
  71ae5c42 (LOCAL_ONLY) 20140509130342 plugins/KalmanOpenStackFilter_.class
  44f1acfa (LOCAL_ONLY) 20121128135145 plugins/Mexican_Hat_Filter.class
  53c5c1ad (LOCAL_ONLY) 20141103073745 plugins/NL_Means_.jar
  4ed208ff (LOCAL_ONLY) 20140929064046 plugins/NanoTrackJ_.jar
  21927175 (LOCAL_ONLY) 20140808090713 plugins/PIV_.jar
  b3b13b1f (LOCAL_ONLY) 20050408150244 plugins/PSFCredits$1.class
  cb99705d (LOCAL_ONLY) 20050408150244 plugins/PSFCredits.class
  de90b917 (LOCAL_ONLY) 20050408150536 plugins/PSFCreditsG$1.class
  e33950eb (LOCAL_ONLY) 20050408150536 plugins/PSFCreditsG.class
  9f2412ff (LOCAL_ONLY) 20141028082626 plugins/PSF_Generator.jar
  5a3abd78 (LOCAL_ONLY) 20050408150536 plugins/PSF_Gibson_.class
  65b190f7 (LOCAL_ONLY) 20121002063426 plugins/PSF_Simple_.class
  0c89ccf5 (LOCAL_ONLY) 20140507100709 plugins/PoissonNMF_.jar
  12289f6e (LOCAL_ONLY) 20110916093010 plugins/PureDenoise_.jar
  33ca5f87 (LOCAL_ONLY) 20141215122204 plugins/Thunder_STORM.jar
  69b16199 (LOCAL_ONLY) 20050408103628 plugins/WaveDaub4.class
  f0990b22 (LOCAL_ONLY) 20050408103628 plugins/WaveDaub4Filter.class
  27901023 (LOCAL_ONLY) 20050408152652 plugins/Wavelet_Deconvolution_.class
  71331805 (LOCAL_ONLY) 20140314082430 plugins/jacop_.jar
  9bbfb280 (LOCAL_ONLY) 20140225135257 plugins/octane2_.jar

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