The altitude callout is usually given using the radio altimeter. The radio altimeter (Tx/Rx) is usually located in the forward fuselage and calibrated to tell the altitude of the main landing gear above the ground.
Location of Boeing 757 radio altimeter; image from flightdatacommunity.com
This patent gives details of a system used for calibration of the radio altimeter. From the document:
To ensure that a radio altimeter indicates zero altitude when the aircraft is on the ground, an on-ground calibration system utilizes a calibration switch to initiate a calibration radio altimeter signal from the radio altimeter's transmitter section which is reflected off of the ground and received by the altimeter's receiver section. The time delay between transmission and reception of the signal is measured and a value representing the delay is stored in the altimeter's microprocessor. This value corresponds to zero altitude and can be used as the relative zero point for calculating altitudes of the aircraft when it is in flight.
This gives the basics of operation of the altimeter. You can set the MLG altitude as the zero point for landing (of course once the aircraft is in hangar and the landing gear is compressed, it will show negative values).