Normalising XY data by Z-direction in stacks

Posted by Thomson Neil (EAST KENT HOSPITALS UNIVERSITY NHS FOUNDATION TRUST) on
URL: http://imagej.273.s1.nabble.com/Normalising-XY-data-by-Z-direction-in-stacks-tp3685096p3685098.html

Hi James

I don't know your background, so forgive me if I'm way off the mark...

This should be a pretty trivial problem with some coding. If you haven't looked at the developer<http://rsbweb.nih.gov/ij/developer/index.html> section of he ImageJ website, have a look now. If you've never done any programming then writing a Java plugin might be a bit scary, but the macro language <http://rsbweb.nih.gov/ij/developer/macro/macros.html> should so the trick.

This macro-code snippet might give you an idea on normalisation:

// Make sure image accepts floating point values
run("32-bit");
// get image width x
// get image height y
// get image depth z
for (i=0; i < x; i++){
  for (j=0; i < y; j++){
    // Get max value in the x-y coord
    maxValue = 0;
    for (k=0; i < z; k++){
      setSlice(k);
      currValue = getPixel(x, y);
      if (currValue > maxValue){
        maxValue = currValue;
      }
    }
    // Set new value normalised to max value
    for (k=0; i < z; k++){
      setSlice(k);
      setValue(x, y, getPixel(x, y)/maxValue);
    }
  }
}

Neil

Neil Thomson,
Nuclear Medicine Physics Section,
Medical Physics,
Kent and Canterbury Hospital,
UK. CT1 3NG
[phone]

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