Methods and apparatus that provide for precise and continuously-controlled generation of hyperfine polarizations and coherences in samples of laser cooled atoms. In one example, coherent population trapping induced by Raman pulses with preselected parameters (such as phase and duration) is employed as a mechanism for producing well-controlled atomic coherences and polarizations. In one example, these coherences and polarizations are used to provide precision polarization references for normalization of polarization readout measurements, and/or to provide precision phase references for phase storage or phase comparison.