Re: A question about ImageJ's threshold values

Posted by Avital Steinberg on Jun 16, 2015; 2:51pm
URL: http://imagej.273.s1.nabble.com/A-question-about-ImageJ-s-threshold-values-tp5013177p5013183.html

Thanks - I get the same answer when I use the macro you wrote and the macro
I found in this link:

http://imagej.1557.x6.nabble.com/Threshold-as-a-percentage-of-image-histogram-td3695671.html

But when I choose adjust, threshold and manually adjust the sliding bar, I
get a different result.

Why would this be?

Thanks,

Avital


On Tue, Jun 16, 2015 at 4:10 PM, Michael Schmid <[hidden email]>
wrote:

> Hi Avital,
>
> yes, the small number below the histogram in the Threshold panel is the
> percentage of pixels within the histogram bounds selected by the threshold.
> Here is a macro that sets the threshold such that roughly 80% of the
> pixels are included:
>
>
> percentage = 80;
> nBins = 256;
> resetMinAndMax();
> getHistogram(values, counts, nBins);
> // find culmulative sum
> nPixels = 0;
> for (i = 0; i<counts.length; i++)
>   nPixels += counts[i];
> nBelowThreshold = nPixels * percentage / 100;
> sum = 0;
> for (i = 0; i<counts.length; i++) {
>   sum = sum + counts[i];
>   if (sum >= nBelowThreshold) {
>     setThreshold(values[0], values[i]);
>     print(values[0]+"-"+values[i]+": "+sum/nPixels*100+"%");
>     i = 99999999;//break
>   }
> }
>
> For 16-bit and floating-point images, there will be a small difference
> between the exact number of pixels actually selected and the number printed
> by the macro. That's because the macro uses only an 8-bit histogram (256
> values). When using an 8-bit histogram, for 16-bit and 32-bit images it
> would be usually better to include one more histogram bin.
>
> Michael
> ________________________________________________________________
> Michael Schmid                    email: [hidden email]
> Institut für Angewandte Physik, Technische Universität Wien
> Wiedner Hauptstr. 8-10/E134, A 1040 Wien, Austria
> Tel. [phone] or -13453, Fax [phone]
> ________________________________________________________________
>
> On Jun 16, 2015, at 14:36, Avital Steinberg wrote:
>
> > Hi,
> > When I choose any auto thresholding method in ImageJ, I get a histogram.
> I
> > can change the threshold values using a slide bar and I see percent
> values.
> > Are these percent cumulative frequencies for the histogram, or something
> > else?
> >
> > I would like to write a macro which, when given a percent value from this
> > slide bar, would give me a threshold value. I tried doing this with the
> > following macro:
> >
> >
> http://imagej.1557.x6.nabble.com/Threshold-as-a-percentage-of-image-histogram-td3695671.html
> >
> > but the values it gave were different from what I expected.
> >
> > Also, there must be something that I don't understand, because the
> > percentile auto thresholding method shows a value of 70.17% percent on
> the
> > slide bar. I thought it would give me 50%.
> >
> > I'm confused and would appreciate your help.
> >
> > Thanks,
> >
> > Avital
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
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> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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