// Converts a stack to binary  by thresholding each slice
// with the corresponding auto threshold value

for (i=1; i<=nSlices; i++) {
    run("Set Slice...", "slice="+i);
    run("Threshold", "slice");
 }

// This method is faster but the threshold value of 
// the first slice is applied to the entire stack.
// 
//run("Threshold", "stack");