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Bug 638 - trouble opening three channel zvi stack with loci
trouble opening three channel zvi stack with loci
Status: RESOLVED FIXED
Product: Fiji
Classification: Unclassified
Component: Bio-Formats
unspecified
PC Windows
: P4 normal
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2013-07-22 12:19 CDT by Dave Schneider
Modified: 2014-06-16 14:39 CDT
2 users (show)

See Also:
Description Dave Schneider 2013-07-22 12:19:23 CDT 
When opening zvi file of a three channel stack, only the first window is correct (correct lut and stack). Two other windows are opened but the middle one is just a copy of the first stack with no lut applied (have to apply a lut in order to see anything). The third window is the true second channel with correct lut applied. True third channel is not opened at all. I have tried reinstalling Fiji, tried different LOCI settings, and tried first download onto a new computer. All behave the same. I can open these files correctly in Axiovision. I have no trouble opening a single-plane RGB file with LOCI; only stack images are not opening correctly anymore. I've tried to upload a sample file "5-msa-gfp-0004.zvi".

THank you for any help.

Information about your version of Java:

  os.arch => x86
  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) Client 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\das\Desktop\FIJI-W~1\Fiji.app/java/win32/jdk1.6.0_24//jre
  ij.dir => C:\Users\das\Desktop\FIJI-W~1\Fiji.app

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Comment 1 Curtis Rueden 2013-07-22 12:42:21 CDT 
I confirm that I can reproduce this Bio-Formats bug with the latest Fiji.
Comment 2 Curtis Rueden 2014-06-16 14:39:55 CDT 
With an up-to-date Fiji from today, I can no longer reproduce this problem using one of our test datasets ('sebastian/test.zvi' which has SizeC=3, SizeZ=46). Unfortunately, I didn't note which file I used to reproduce a year ago, so I could not use that exact same file in today's test.

Anyway, I'm closing this bug as fixed, since Bio-Formats has seen many improvements over the past year. Please reopen if the problem still occurs for you with a fully updated Fiji -- and if so, upload a sample non-working dataset using Help > Upload Sample Image. Thanks!