Miniature single-photon microscopes have been widely used to image neuronal assemblies in the brain of freely moving animals over the last decade. However, these systems have important limitations for imaging in-depth fine neuronal structures. We present a subcellular imaging single-photon device that uses an electrically tunable liquid crystal lens to enable a motion-free depth scan in the search of such structures. Our miniaturized microscope is compact ($10\mathrm{mm}\times 17\mathrm{mm}\times 12\mathrm{mm}$) and lightweight ($\approx 1.4\mathrm{g}$), with a fast acquisition rate (30–50 frames per second), high magnification ($8.7\times$), and high resolution (1.4 μm) that allow imaging of calcium activity of fine neuronal processes in deep brain regions during a wide range of behavioral tasks of freely moving mice.