The emergence of fluorescent reporters has enabled neuroscientists to image neurons in action in live mice. Conventional imaging setups, however, cannot interrogate structures below the surface of the brain, and the animal must be restrained. This work advances fiber photometry, a simple method to monitor the average activity of a population of cells, to enable experiments in freely-moving mice and in deep brain structures. By targeting a small-diameter probe to the structure of interest, single fiber optoelectronic systems may be designed that monitor changes in calcium-mediated fluorescence intensity. The systems are optimized for an application in a CRH-Cre transgenic mouse, with the calcium reporter GCaMP6s, for minimal damage to tissue. This thesis covers: (a) optoelectronic system design, characterization, and refinement (b) application and results in awake and freely-moving mice, (c) investigation into potential artifacts and (d) method and results of an improved targeting protocol.