//This aligns the slices of each individual time point.
//This is useful to correct for movement artifact within a timepoint.
//May be useful to run this first, then Align Hyperstack.

stackregstr="StackReg ";
if(indexOf(getInfo("imagej.dir"),"Fiji")>-1) stackregstr="StackReg";

if(isOpen("1")) exit("Please close 1");
getDimensions(w,h,chs,sls,frms);
if(chs>1) run("Stack to RGB");
title=getTitle();

for(i=1;i<=frms;i++){
	selectWindow(title);
	run("Duplicate...", "title="+i+" duplicate frames="+i);
	run(stackregstr, "transformation=Affine");
	if(i!=1) run("Concatenate...", "stack1=1 stack2="+i+" title=1");
}
rename(title+"-tpza");
run("Stack to Hyperstack...", "order=xyczt(default) channels=1 slices="+sls+" frames="+frms);