NOTICE! This is a static HTML version of a legacy Fiji BugZilla bug.

The Fiji project now uses GitHub Issues for issue tracking.

Please file all new issues there.

Bug 208 - LUT not applicable on stacks of images in .dv files
LUT not applicable on stacks of images in .dv files
Status: RESOLVED FIXED
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
Macintosh Mac OS
: P4 normal
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2010-08-06 17:33 CDT by Martin Machyna
Modified: 2010-09-16 20:44 CDT
1 user (show)

See Also:

Description Martin Machyna 2010-08-06 17:33:51 CDT
[Enter details of the problem or bug and how to reproduce it here.]
LUT cannot be changed for stack of images in deltavision file.
Assigning custom color in open dialog or directly changing LUT from menu sets the LUT only temporarily.
After moving slider to another timepoint or z-stack image LUT changes back to grays.


Information about your version of Java - this information is useful for the Fiji developers:
  os.arch => x86_64
  os.name => Mac OS X
  os.version => 10.5.8
  java.version => 1.6.0_07
  java.vendor => Apple Inc.
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.6.0_07-b06-153
  java.vm.name => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 1.6.0_07-b06-57
  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 => /
Comment 1 Curtis Rueden 2010-08-06 18:06:04 CDT
Thanks for reporting this. It is a bug with the Bio-Formats virtual stack support. For now you can work around it by unchecking the "Use virtual stack" option. The Bio-Formats team will investigate how to fix the problem.
Comment 2 Curtis Rueden 2010-08-13 19:57:53 CDT
As of r6792, LUTs should be preserved when using virtual stacks:
http://www.loci.wisc.edu/trac/java/changeset/6792
Comment 3 Johannes Schindelin 2010-08-13 21:20:29 CDT
Question: so far I tracked svn/4.2 with Fiji. Would you prefer I track trunk? (r6792 is on trunk...)
Comment 4 Curtis Rueden 2010-08-13 22:53:10 CDT
(In reply to comment #3)
> Question: so far I tracked svn/4.2 with Fiji. Would you prefer I track trunk?
> (r6792 is on trunk...)

4.2 is probably still safer. I backported the fix to the 4.2 branch now; thanks for reminding me.
Comment 5 Johannes Schindelin 2010-08-14 04:32:24 CDT
Thanks! I uploaded a new version built from svn/4.2.
Comment 6 Martin Machyna 2010-09-02 17:10:08 CDT
LUT now stays permanent but it has a side effect that it changes the LUT for all channels in hyperstack.
One should be able to change LUT for each channel separately as it works for e.g. in zeiss .lsm files.
Comment 7 Curtis Rueden 2010-09-11 00:45:37 CDT
Thanks Martin, I was able to duplicate the bug with one of our datasets. We'll investigate and reply back to the ticket when the problem is resolved.
Comment 8 Curtis Rueden 2010-09-16 20:44:12 CDT
The LUT bug with virtual stacks should be fixed again with the latest Bio-Formats trunk build, as well as on the 4.2 branch.