Large-scale calcium imaging with a head-mounted axial scanning 3D fluorescence microscope

Summary Miniaturized fluorescence microscopes are becoming more important for deciphering the neural codes underlying various brain functions. With gradient index (GRIN) lenses, these devices enable recording neuronal activity in deep brain structures. However, to minimize any damage to brain tissues and local circuits, the diameter of the GRIN lens should be 0.5–1 mm, resulting in a small field of view. Volumetric imaging capability might increase the number of neurons imaged through the lenses considering the three-dimensional (3D) structure of neural circuits in the brain. To observe 3D calcium dynamics, we developed a miniaturized microscope with an electrically tunable lens and a novel CNMF-based neural signal extraction algorithm for wide-field 3D imaging data. By combining the hardware and software, approximately 1000 neurons were imaged from the cortices of freely behaving mice. Compared with the state-of-the-art 2D imaging technique, the proposed 3D method imaged 1.7–2.6 times more cells with a higher separation of cellular signals.