====== Standard Deviation-Based Correlation ======

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

<code java> 

// A macro to determine image focal quality image-wide (not ROI-wide)
// Based on algorithm F-13 "Standard Deviation-Based Correlation"
// In: Sun et al., 2004. MICROSCOPY RESEARCH AND TECHNIQUE 65, 139–149.
// 
// Version: 0.1
// Date: 14/07/2006
// Author: Andy Weller

macro "Corr_Stddev" {
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 = H*W*(mean*mean);
StddevCorr = 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);
      p1 = getPixel(i+1,j);
      t = p*p1;
      StddevCorr += (p*p1)-b; // Maximum value is best-focused, decreasing as defocus increases
      }
   }
print(StddevCorr); // This can also (should) be changed to return(StddevCorr)
}

</code>

by Andy Weller — last modified 2006-07-14 20:37