When I try to open a czi file, I can only see channel 0 and channel 1 when using hyperstack, even though I did not acquire any blue channel (Ch0) during imaging.  
I can see the channel 2 (red) only if I tried to open as image 5D and only if I did not acquire green image (Ch1) of the original .czi file.  
Is this normal?  Because I can open the confocal sample image with both green and red channels, but the file was in tiff format?

My current way to get around is to save as new .czi file of individual channel and  color them differently in ImageJ before merge.  Is it better practice to export as tiff files? 

Any help is greatly appreciated.

Information about your version of Java:

  os.arch => amd64
  os.name => Windows 8.1
  os.version => 6.3
  java.version => 1.7.0_55
  java.vendor => Oracle Corporation
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.7.0_55-b13
  java.vm.name => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 24.55-b03
  java.vm.vendor => Oracle Corporation
  java.vm.info => mixed mode
  java.awt.graphicsenv => sun.awt.Win32GraphicsEnvironment
  java.specification.name => Java Platform API Specification
  java.specification.version => 1.7
  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: null
  imagej.dir => C:\Users\ZOEYNI~1\Desktop\FIJI-N~1\Fiji.app

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20150623225330)
Fiji: http://fiji.sc/update/ (last check:20150625052927)

Files not up-to-date:
  a755edd2 (MODIFIED) 20150629104217 jars/imagej-ops-0.14.0.jar
  b8e3cab7 (MODIFIED) 20150705225357 jars/imagej-ops-0.15.0.jar
  3be36100 (MODIFIED) 20150629104220 jars/imglib2-roi-0.3.1.jar
  2dc68041 (MODIFIED) 20150705225357 jars/imglib2-roi-0.3.2.jar
  d939c993 (MODIFIED) 20150629104336 jars/scijava-common-2.43.0.jar
  57f64454 (MODIFIED) 20150705225357 jars/scijava-common-2.44.0.jar
  c1877fe3 (LOCAL_ONLY) 20150705154828 plugins/zn_try1.ijm