**fScan Reference Manual, Chapter 1 (Topics): Thresholding**
===== Thresholding -- Using intensity thresholding =====

Displayed image intensity values can be clipped based on threshold settings.
Thresholding can be controlled interactively using the [[jvs:fscan:manual:chapter3:imagekeys:threshold|Threshold ('K')]] command. The Taskbar "Thresh" icons
provide a graphical interface for the 'K' command options.
Preset threshold values can also be stored as parameters in XML image header files if desired.
The <F7> keyboard key also provides a convenient way to set standard t-test threshold levels (Flag 4: +4.0 & -4.0).

**Overview**\\
For each image window there are 4 parameter values that control intensity thresholding:\\
  * Mode - controls whether intensity thresholding is active
  * Flag - controls how the Low and High threshold values are used
  * Low threshold - low intensity value (floating point number)
  * High threshold - high intensity value (floating point)

Mode options:\\
  * 0 - thresholding is off; all intensity values are displayed
  * 1 - thresholding is on; only display intensity values meeting the threshold condition

Flag options (threshold conditions):\\
  * 1 - show values >= low threshold
  * 2 - show values <= high threshold
  * 3 - show values >= low threshold AND <= high threshold (low<high)
  * 4 - show values >= low threshold OR  <= high threshold (low>high)
  * 8 - only show boundaries of thresholded regions
  * 16 - high threshold is a range; show values >= low AND <= low+high
  
 
**See Also:**\\
[[jvs:fscan:manual:chapter3:imagekeys:threshold|Threshold ('K')]] 

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