As long as you're scanning over a perfectly flat, if tilted (relative to the microscope's focus plane) 2d plane, you don't need to autofocus much. Just measure

As long as you're scanning over a perfectly flat, if tilted (relative to the microscope's focus plane) 2d plane, you don't need to autofocus much. Just measure the focus at a few points and fit the plane, then run the scan and apply the focus parameters from the fit.