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]=13.951654 [g1]=23.660986 [b1]=19.173325 [r2]=7.737847 [g2]=7.301559 [b2]=9.771005 [r3]=144.38943 [g3]=112.913376 [b3]=85.59621");
//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(); 
}

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html