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Bug 290 - Auto threshold 'Try all' method give different results than individual method
Auto threshold 'Try all' method give different results than individual method
Status: RESOLVED WONTFIX
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
PC Windows
: P4 normal
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2011-02-21 20:15 CST by declan
Modified: 2011-02-23 12:22 CST
1 user (show)

See Also:

Description declan 2011-02-21 20:15:27 CST
When using Auto threshold 'Try all' selection the returned montage of results differs from the result obtained when a single method is selected.  I find this especially true when i use the triangle method.  Please let me know whether you can repeat this behaviour.  I am happy to provide my images if needed.  

Many thanks

Declan 

Information about your version of Java - this information is useful for the Fiji developers:

  os.arch => x86
  os.name => Windows XP
  os.version => 5.1
  java.version => 1.6.0_03
  java.vendor => Sun Microsystems Inc.
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.6.0_03-b05
  java.vm.name => Java HotSpot(TM) Client VM
  java.vm.version => 1.6.0_03-b05
  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: Up-to-date

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: C:\DOCUME~1\James\MYDOCU~1\FIJI-W~1\Fiji.app/java/win32/jdk1.6.0_03/jre
  fiji.dir => C:\DOCUME~1\James\MYDOCU~1\FIJI-W~1\Fiji.app

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Comment 1 Johannes Schindelin 2011-02-21 20:57:39 CST
Yes, it would be useful to have an example image. Please use Help>Upload Sample Image... Thanks!
Comment 2 G. Landini 2011-02-23 12:22:19 CST
Thanks for reporting this. This is not a bug, but the result of the re-implementation of the auto threshold methods in ImageJ.

I added a note in the plugin page in the Fiji Wiki  explaining this.

http://pacific.mpi-cbg.de/wiki/index.php/Auto_Threshold#Use

This plugin is accessed through the Image>Auto Threshold menu entry, however the thresholding methods were also partially implemented in ImageJ's thresholder applet accessible through the Image>Adjust>Threshold... menu entry. While the Auto Threshold plugin can use or ignore the extremes of the image histogram (Ignore black, Ignore white) the applet cannot: the 'default' method ignores the histogram extremes but the others methods do not. This means that applying the two plugins to the same image can produce apparently different results. In essence, the Auto Threshold plugin, with the correct settings, can reproduce the results of the applet, but not the way round.

There is nothing to fix in this plugin regarding the original bug report, at most ImageJ auto threshold applet could be modified to enable ignoring/not ignoring histogram extremes.