// Select your first image of the stack
run("Bio-Formats Importer");
stk = getTitle(); 

// Avg IP to register to
run("Z Project...", "stop=20 projection=[Average Intensity]");
run("Enhance Contrast", "saturated=0.35");
avgip = getTitle(); 

// Set source = raw stack, target = avgip
// Rigid body registration, batch process
run("TurboReg ");

selectWindow("Registered"); 
reg = stk+"_reg";
rename(reg);