The auto focus works alone or in combination with:
Alone, just to focus the live preview image before capturing
•Before Extended Focus. This makes the need for very many z-slices less demanding.
•With Extended Field (Stitching)
•With XYZ- acquisition.
Two modes is available, center weighted image or region.
The mode is selected in the auto focus settings panel.
Tip: By Ctrl-Alt-Click on the 
button - the the actual region is indicated in fake color. This for testing purposes only.