Elucidating the neural mechanisms governing changes in individual animal behavior is a key goal in neuroscience. Such research has important implications for behavioral pharmacology and could lead to the development of treatments for psychiatric and neurological disorders. Given that the brain likely represents vast amounts of information through the combined activity of multiple neurons, studying these mechanisms requires the simultaneous recording of many neurons. Recent years have seen significant advancements in techniques for multi-cellular activity recording. Calcium imaging utilizing fluorescent sensors has emerged as a powerful method, enabling the concurrent acquisition of spatial arrangements and temporal activity changes in neuronal populations. This article focuses on deep brain imaging using GRIN lenses, particularly deep brain calcium imaging in freely behaving animals with miniaturized head-mounted microscopes. We compare the strengths and limitations of this approach to other calcium imaging methods, electrophysiological techniques, and fiber photometry. Finally, we discuss future developments in this field, including two-photon microscopy for imaging beyond cell bodies, membrane potential imaging using voltage sensors, and single-cell resolution manipulation of neural activity by integrating spatial light modulators and electrically tunable lenses.