[ImageJ-devel] Threshold command in IJ2

Aivar Grislis grislis at wisc.edu
Thu Jul 25 11:51:41 CDT 2013

In the Threshold command we should support threshold methods that 
automatically exclude both low and high values.

All of the current threshold methods separate figure from background by 
coming up with a single threshold value. The figure is then determined 
to be pixels with values from the minimum value to the threshold value 
and background threshold value to maximum value.  If the 'dark 
background' box is checked these ranges are swapped.  In the user 
interface and internal representation rather than having a single 
threshold value there is a minimum and maximum range that the user can 

As an example, for images that consist of data for each pixel that is 
expected to have a near-normal distribution, such as fitted lifetime 
images, it's useful to have statistics-based threshold methods that 
exclude outliers based on mean and standard deviation or else median and 
quartile ranges.  (I like to use Tukey's rule: 
http://www.edgarstat.com/tukeys_outliers_help.cfm )  Are there any other 
useful algorithms we could implement to exclude low and high values in 
ordinary images?


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