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Bug 794 - ImageJ 1.x color table comments not supported
ImageJ 1.x color table comments not supported
Status: CLOSED FIXED
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
PC Linux
: P4 normal
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2014-06-16 09:35 CDT by Benoit Aigouy
Modified: 2014-06-19 02:18 CDT
2 users (show)

See Also:

Attachments
test image (54.23 KB, image/tiff)
2014-06-16 09:35 CDT, Benoit Aigouy

Description Benoit Aigouy 2014-06-16 09:35:02 CDT 
error reading LUT of composite image

best,

benoit

Information about your version of Java:

  os.arch => amd64
  os.name => Linux
  os.version => 3.13.0-29-generic
  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.X11GraphicsEnvironment
  java.specification.name => Java Platform API Specification
  java.specification.version => 1.6
  sun.cpu.endian => little
  sun.desktop => gnome
  file.separator => /

The up-to-date check says: REMIND_LATER

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: /home/benoit/Fiji.app/java/linux-amd64/jdk1.6.0_24//jre
  imagej.dir => /home/benoit/Fiji.app

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20140616153006)
Fiji: http://fiji.sc/update/ (last check:20140612230314)
IBMP-CNRS: http://www-ibmp.u-strasbg.fr/fijiupdates/ (last check:20140526164644)
ScientiFig: http://sites.imagej.net/Aigouy/ (last check:20140516135525)

Files not up-to-date:
  a5d02cb7 (LOCAL_ONLY) 20131005162326 plugins/Kymo_graph1001.jar
  b5819511 (LOCAL_ONLY) 20140616133353 plugins/projection_/Projection_.jar
  7872d78f (LOCAL_ONLY) 20140616133353 plugins/projection_/lib/AbsoluteLayout.jar
  e71fc299 (LOCAL_ONLY) 20140616133353 plugins/projection_/lib/Common.jar
  bdddbf0c (LOCAL_ONLY) 20140616133353 plugins/projection_/lib/IJ.jar
  6f3fdc0d (LOCAL_ONLY) 20140616133353 plugins/projection_/lib/Icons.jar
  c3cdf2d0 (LOCAL_ONLY) 20140616133353 plugins/projection_/lib/REngine.jar
  6ba3fcd5 (LOCAL_ONLY) 20140616133353 plugins/projection_/lib/Rserve.jar
  269cc20e (LOCAL_ONLY) 20140616133353 plugins/projection_/lib/Rsession.jar
  2adf1436 (LOCAL_ONLY) 20140616133353 plugins/projection_/lib/ScientiFig_.jar
  9b7b3d20 (LOCAL_ONLY) 20140616133353 plugins/projection_/lib/batik-all-1.7.jar
  e822575d (LOCAL_ONLY) 20140616133353 plugins/projection_/lib/xml-apis-ext.jar
Comment 1 Benoit Aigouy 2014-06-16 09:35:55 CDT 
Created attachment 161
test image
Comment 2 Mark Hiner 2014-06-17 11:33:45 CDT 
I updated the summary of this ticket.

To clarify, the problem here is that we have an ImageJ 1.x TIFF with a G-R-B color table. When opened by SCIFIO, it displays as R-G-B.

Note that when opened via the Bio-Formats importer we get a grayscale image (still RGB if changed to composite or color mode via the Channels Tool).

The problem is that the color tables embedded in the ImageJ comment are not parsed properly: https://github.com/scifio/scifio/issues/202
Comment 3 Mark Hiner 2014-06-18 15:01:34 CDT 
This should be fixed in the latest Fiji.
Comment 4 Benoit Aigouy 2014-06-19 02:18:39 CDT 
works perfectly. Great job!

best,

benoit