Custom thresholding a stack

Posted by Sidnei Paciornik on May 22, 2014; 7:49pm
URL: http://imagej.273.s1.nabble.com/Custom-thresholding-a-stack-tp5007866.html

Dear All,

I have a stack of microtomography images which I need to segment to detect
some dark defects. As the average intensity and contrast of the slices
change along the stack, I cannot use a single threshold for all slices.

The natural solution would be to use an AutoThreshold option (let´s say
IJ_IsoData) and let it calculate a threshold for each slice. However, no
automatic method gives me a good threshold. I found out I can use
IJ_IsoData if I increase the upper threshold by a given factor.

So I wrote a macro that calls IJ_IsoData for each slice, gets the upper
threshold, multiplies this threshold by a factor, and then applies the new
upper threshold for each slice.

It seems OK until I try to convert each slice to binary. At this point the
program uses the upper threshold value of the LAST slice and applies it to
ALL other slices. Thus,  end up getting a fixed threshold for all slices,
which is what I wanted to avoid from the start.

What am I doing wrong?

Thank you!

Here is the simple macro code I use:
run("Duplicate...", "title=Binary duplicate");

mode = getString("Enter the background mode (bright/dark background)",
"bright");
if (mode == "bright") mode = "";
thmethod = "IJ_IsoData " + mode;

fator = getNumber("Enter the factor to increase the threshold", 1.15);

for (i=1; i<=nSlices; i++)
{
setSlice(i);
 setAutoThreshold(thmethod);
getThreshold(lower, upper);
if (mode =="dark")
 {
newlower = fator*lower;
setThreshold(newlower, upper);
 write(newlower, upper);
}
else
{
 newupper = fator*upper;
setThreshold(lower, newupper);
write(lower, newupper);
 }
}
run("Analyze Particles...", "show=Masks stack"); //I use this just to
create the binary mask
run("Invert LUT");
selectWindow("Binary");
close();

Prof. Sidnei Paciornik
Grupo de Análise de Imagens e Microscopia Digital
DEMa <http://www.dema.puc-rio.br/> - Departamento de Engenharia de Materiais
PUC-Rio <http://www.puc-rio.br/>
Rua Marquês de São Vicente 225
Prédio Leme, Sala 501L
Gávea - Rio de Janeiro - RJ
22451-900 - Brasil
tel: [phone]

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