http://imagej.273.s1.nabble.com/How-to-find-percentiles-of-intensity-tp5011293p5011301.html
Thanks, Michael - that was very helpful. I succeeded in using the commands
> Hi Avital,
>
> use Plugins>Macros>Record in 'Java' mode and try what it says when you do
> it manually.
>
> You can also type 'L' (Plugins>Utilies>Find Command') to find out that
> "Enhance Contrast" uses the ij.plugin.ContrastEnhancer class, ant have a
> look at that class. You will see that it has two public methods that look
> promising:
>
> public void stretchHistogram(ImagePlus imp, double saturated)
> public void stretchHistogram(ImageProcessor ip, double saturated)
>
> Michael
> ________________________________________________________________
> On Jan 20, 2015, at 11:51, Avital Steinberg wrote:
>
> > Thanks - I am writing a java plugin. How would I do what you describe in
> > Java?
> >
> > Avital
> >
> > On Tue, Jan 20, 2015 at 11:30 AM, Michael Schmid <
>
[hidden email]>
> > wrote:
> >
> >> Hi Avital,
> >>
> >> did you have a look at Process>Enhance contrast? There you can specify
> the
> >> percentage of saturated pixels. If you specify 1%, it will be 0.5% dark
> >> pixels becoming saturated black and 0.5% bright pixels becoming
> saturated
> >> white.
> >>
> >>
http://rsb.info.nih.gov/ij/docs/guide/146-29.html#toc-Subsection-29.5> >>
> >> For grayscale images, this only changes the lookup table. In the
> >> Brightness&Contrast panel, you can recover the original display with
> >> 'Reset' or make it a permanent change with 'Apply' (the latter only for
> >> 8-bit and color images).
> >>
> >> Michael
> >> ________________________________________________________________
> >> On Jan 20, 2015, at 07:41, Avital Steinberg wrote:
> >>
> >>> Hi,
> >>> I would like to perform contrast stretching for an 8-bit image. When I
> >> use
> >>> set min and max, it gives me 0-255. (which does absolutely nothing in
> >> terms
> >>> of contrast stretching) When I check in ImageJ what values are used, it
> >>> looks like it takes 0 as min and 105 as max for a specific image that I
> >>> examined.
> >>>
> >>> So my question is:
> >>>
> >>> Is it possible to get less extreme values of the intensity values in
> >> order
> >>> to ignore the outliers, say the 5th and 95th percentiles of the
> intensity
> >>> values? If so - how?
> >>>
> >>> Thank you,
> >>> Avital
> >>
> >> --
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http://imagej.nih.gov/ij/list.html> >>
> >
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