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Bug 233 - lookup table issues in recent updates
lookup table issues in recent updates
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: 2010-09-16 19:46 CDT by Bryan Crawford
Modified: 2011-03-23 15:24 CDT
1 user (show)

See Also:
Description Bryan Crawford 2010-09-16 19:46:18 CDT 
Hello Fijians.

I've been very happily using Fiji for quite a while, and ImageJ for many years before that.  But during the past few weeks (I'm afraid I didn't notice at what version this started happening), I've been encountering either some bugs with lookup tables, or a change in how these are defined that I don't know how to deal with.

Firstly, if I open a 16-bit confocal stack (Leica SP2... opened via the .lei file), it inevitably displays all focal planes as black, with an indication in the title bar of the window that it is using an inverted LUT.  I can go to Image->Lookup Tables and select greys and everything is fine, but I can't figure out how to stop it from doing this... it never used to.

Secondly, and even more problematically, in the current version of Fiji, if I open a stack and run Image->Stacks->3D project the resulting rotation is completely munged.  Again, it switches to and inverted lut, but because it's putting the projections on a black background I can't just switch the LUT to fix it.  Fortunately, I have an older version of Fiji on another computer (which uses ImageJ 1.44a) and these problems don't manifest on it.

Let me know if (and how) you want me to send example stacks.

Thanks for your help!


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 => 10.6.4
  java.version => 1.6.0_20
  java.vendor => Apple Inc.
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.6.0_20-b02-279-10M3065
  java.vm.name => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 16.3-b01-279
  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 => /

The up-to-date check says: Up-to-date

Information about the version of each plugin:

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Comment 1 Bryan Crawford 2010-09-16 19:50:59 CDT 
I don't want to remove this bug report, but I've found a solution.  I didn't notice that after updating Fiji, it had switched to using ImageJA.  I ran the update of ImageJ (which brings the version to 1.44f) and the problem is gone.
Comment 2 Curtis Rueden 2010-09-24 18:06:03 CDT 
Thanks for the bug report, Bryan.

To be clear, when you updated from ImageJA to ImageJ v1.44f, you did not update any of the plugins, right? I ask because it sounds like you are using the Bio-Formats Importer plugin to read your LEI files, and we recently made substantial changes to how the Importer works, especially with regard to color lookup tables.

If you can verify that the problem is definitely resolved between versions of ImageJ itself, that would be very helpful.
Comment 3 Johannes Schindelin 2011-03-23 15:24:39 CDT 
Assuming that this has been fixed, I close the bug. If this is not correct, please reopen it with more information.