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Bug 966 - threshold "red" display wrong /treshold upper/lower values not updated
threshold "red" display wrong /treshold upper/lower values not updated
Status: RESOLVED FIXED
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
PC Windows
: P4 normal
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2014-12-01 08:08 CST by felix.keber
Modified: 2015-04-21 11:40 CDT
3 users (show)

See Also:

Attachments
two stacks concateneted and resized (681.33 KB, image/tiff)
2014-12-03 03:27 CST, felix.keber

Description felix.keber 2014-12-01 08:08:01 CST 
Hello,

I was measuring areas limited to threshold on 16bit image stacks (to imagine the data: circular gradients, white on black), updated version today.  I realized that the measured area was far smaller than the one highlighted red in the image. 
I found out that the highest possible value of the min-max-sliders of the threshold-dialogue-box does not belong to the actual image (and also not to the actual stack). It changes to proper values only when i use "stack histogram" (or after that un-select "stack histogram" to get the values for the actual slice). Closing and re-opening the threshold-dialogue-box also does not help.
The values also are not actualized when setting a new minimum/maximum value via the sliders (using "set" updates them). However, changing the maximum slider (just by one step) updates the look-up table, so not the entire area is highlighted red.
The problem may  occur because of changing between different image stacks. (I was clicking around now a bit and it happens quite sometimes, but i couldn't find out when exactly.)
I don't mind the values stay the same, this is just inconvenient -updating the stack histogram fixes it. But i think it is a big problem that the red highlighted region is not the thresholded region. If the the wrong value is not too far from the true one, it is hard for the user to realize that not the dispayed region is evaluated.

Best regards & big thanks for developing this software,
Felix

Information about your version of Java:

  os.arch => amd64
  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) 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.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: D:\Fiji\Fiji.app/java/win64/jdk1.6.0_24//jre
  imagej.dir => D:\Fiji\Fiji.app

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20141126221327)
Fiji: http://fiji.sc/update/ (last check:20141125171145)

Files not up-to-date:
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Comment 1 Wayne Rasband 2014-12-02 20:56:40 CST 
Please use "Add an attachment" to upload a 16-bit image that we can use to reproduce this problem.
Comment 2 felix.keber 2014-12-03 03:27:34 CST 
Created attachment 222
two stacks concateneted and resized
Comment 3 felix.keber 2014-12-03 03:34:24 CST 
It seems that if the maximum slider in the threshold window is on the max, all values >=max are highlighted red. Thus if the max value is not updated (when changing between windows (?)) the highlighted area is not correct (if the max of the new window is bigger than the previous)
Comment 4 Wayne Rasband 2014-12-04 20:48:44 CST 
The "Threshold" widget in the latest ImageJ daily build (1.49n4) should work better with 16-bit stacks. To upgrade, use the Help>Update ImageJ command and select "daily build" from the drop down menu.