A macro to determine image focal quality image-wide (not ROI-wide).

Note (2011): please note that this macro is not really necessary as ImageJ already supports computation of the standard deviation via the same command used to obtain the mean image value:

run("Set Measurements...", "  mean standard redirect=None decimal=5");

The variance is the squared value of the standard deviation.

// A macro to determine image focal quality image-wide (not ROI-wide)
// Based on algorithm F-10 "Variance"
// In: Sun et al., 2004. MICROSCOPY RESEARCH AND TECHNIQUE 65, 139–149.
// 
// Version: 0.1
// Date: 14/07/2006
// Author: Andy Weller
 
macro "Variance_" {
run("Clear Results");
run("Set Measurements...", "  mean redirect=None decimal=5");
run("Measure");
mean = getResult("Mean");
selectWindow("Results");
run("Close");
W = getWidth();
H = getHeight();
b = 0;
Var = 0; // Set to 0 which is out of focus
for (j=0; j<H; j++) {
   for (i=0; i<W; i++) {
      p = getPixel(i,j);
      t = (p-mean)*(p-mean);
      b += t;
      }
   }
Var = b/(H*W); // Maximum value is best-focused, decreasing as defocus increases
print(Var); // This can also (should) be changed to return(Var)
}

by Andy Weller — last modified 2006-07-14 20:44