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+<code>
+// Autofocus hyperstack macro
+// Select the in focus frame from each slice of a hyperstack and create a new stack
+// of just the in focus frames
+// Based on algorithm F-11 "Normalized Variance"
+// In: Sun et al., 2004. MICROSCOPY RESEARCH AND TECHNIQUE 65, 139–149.
+// And the original macro by Andy Weller http://imagejdocu.tudor.lu/doku.php?id=macro:normalized_variance
+setBatchMode(true);
+//Get image type
+type = bitDepth();
+if (type==8) {type="8-bit";} else {if(type==16) {type="16-bit";} else{if(type==32) {type="32-bit";} else {if(type==24) {type="RGB";}}}}
+StackID=getTitle();
+Stack.getDimensions(width, height, channels, slices, frames);
+if (channels>1) {exit("The hyperstack has 2-channels please reduce dimensionality")} else{}
+for (k=1; k<=frames; k++) { Stack.setFrame(k);
+m=0;
+normVar = 0; // Set to 0 which is out of focus
+	for (l=1; l<=slices; l++){
+		selectWindow(StackID);
+		Stack.setSlice(l);
+getRawStatistics(nPixels, mean);
+W = getWidth();
+H = getHeight();
+b = 0;
+for (j=0; j<H; j++) {
+   for (i=0; i<W; i++) {
+      p = getPixel(i,j);
+      t = (p-mean)*(p-mean);
+      b += t;
+      }
+   }
+if ((b/(H*W*mean))>normVar) {normVar = (b/(H*W*mean)); m++;} else {normVar=normVar;}
+	}
+Stack.setSlice(m);
+run("Select All");
+run("Copy");
+if (isOpen("Output")){
+                selectWindow("Output");
+                run("Add Slice");
+            }
+            else{
+                newImage("Output", type, width, height, 1);
+            }
+run("Paste");
+selectWindow(StackID);
+Stack.setSlice(l);
+}
+setBatchMode("exit and display");
+//Richard Mort 27/09/2018
+</code>

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