dir1 = getDirectory("Choose Source Directory ");
dir2 = getDirectory("Choose Destination Directory ");
list = getFileList(dir1);
setBatchMode(true);
for (i=0; i<list.length; i++) {
showProgress(i+1, list.length);
open(dir1+list[i]);
imgName=getTitle(); 
run("Colour Deconvolution", "vectors=[User values] show [r1]=60.27969 [g1]=15.12007 [b1]=14.169498 [r2]=53.738953 [g2]=114.16744 [b2]=106.36251 [r3]=1.4947393 [g3]=7.050659 [b3]=12.738025");
//close windows we don't need 
selectWindow(imgName + "-(Colour_3)"); 
close(); 
selectWindow(imgName +"-(Colour_1)"); 
title = getTitle(); 
saveAs("TIFF", dir2 + title);
close(); 
selectWindow(imgName + "-(Colour_2)"); 
title = getTitle(); 
saveAs("TIFF", dir2 + title);
close(); 
}

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