// This is a command line macro that processes
// all the ics images in a specified directory.
x = getNumber("remove slices from bottom:", 10);
y = getNumber("remove slices from top:", 10);
dir = getArgument();
if (dir=="")
dir = getDirectory("Select a Directory");
if (!(endsWith(dir, "/")||endsWith(dir, "\\")))
dir = dir + "/";
list = getFileList(dir);
run("Set Measurements...", "area mean display redirect=None decimal=3");
for (i=0; i<list.length; i++) {
if (endsWith(list[i], ".ics")) {
run("Open...", "path='"+dir+list[i]+"'");
print (nSlices);
w = (nSlices);
t = w - x +1;
run("Slice Remover", "first="+t+" last="+w+" increment=1");
run("Slice Remover", "first=1 last="+y+" increment=1");
run("Grouped ZProjector", "group=2 projection='Max Intensity'");
run("Enhance Contrast", "saturated=0.1 normalize normalize_all");
run("8-bit");
list2 = list[i] + ".tif";
run("Tiff...", "save='"+dir+list2+"'");
run("Close");
run("Close");
}
}