The interrogation of the atoms by microwaves will either cause an atom to make a transition to another state, or it will leave it alone. The probability of the transition occurring depends on the frequency of the microwaves as compared to the Cesium atoms' natural transition frequency.
As the microwave frequency is scanned and the resulting population of atomic states is probed, we generate an interference pattern. If the microwaves oscillate exactly the same number of times as the Cesium atoms, or they are different by an integral number, then the atoms are left in one atomic state and we see a signal maximum. If the oscillations differ by one-half of an oscillation, the atoms are left in the other atomic state and we see a signal minimum.
If we know that we are on the central fringe (near zero detuning between the microwaves and the atoms) then the signal size indicates what the frequency difference is between the microwaves and the atoms.
Shown above is the result of a scan of the microwave frequency near the resonance of the Cesium atoms. The fringe period is about 2 Hz, a direct result of tossing the atoms above the microwave region for about one-half of a second. This is best seen in the inset graph, which shows the central fringes.