Fully Integrated Time-Gated 3D Fluorescence Imager for Deep Neural Imaging Jaebin Choi, Adriaan J. Taal, William L. Meng, Eric H. Pollmann, John W. Stanton [Student Member, IEEE], Changhyuk Lee, Sajjad Moazeni [Member, IEEE], Laurent C. Moreaux, Michael L. Roukes, Kenneth L. Shepard [Fellow, IEEE] Abstract This paper presents a device for time-gated fluorescence imaging in the deep brain, consisting of two on-chip laser diodes and 512 single-photon avalanche diodes (SPADs). The edge-emitting laser diodes deliver fluorescence excitation above the SPAD array, parallel to the imager. In the time domain, laser diode illumination is pulsed and the SPAD is time-gated, allowing a fluorescence excitation rejection up to O.D. 3 at 1 ns of time-gate delay. Each SPAD pixel is masked with Talbot gratings to enable the mapping of 2D array photon counts into a 3D image. The 3D image achieves a resolution of 40, 35, and 73 in the x, y, z directions, respectively, in a noiseless environment, with a maximum frame rate of 50 kilo-frames-per-second. We present measurement results of the spatial and temporal profiles of the dual-pulsed laser diode illumination and of the photon detection characteristics of the SPAD array. Finally, we show the imager’s ability to resolve a glass micropipette filled with red fluorescent microspheres. The system’s 420 μm-wide cross section allows it to be inserted at arbitrary depths of the brain while achieving a field of view four times larger than fiber endoscopes of equal diameter. Keywords Single photon avalanche diode; time-gated fluorescence imaging; neural imaging; computational imaging 1. INTRODUCTION While the superficial brain has been extensively studied with the development of modem neural imaging techniques, the deep brain largely remains an elusive area of investigation. Deep-brain imaging with conventional free-space optics is challenged by the scattering and absorption of photons in tissue, which appears opaque in the visible spectrum. Scattering events, which occur with mean free paths of ~50 μm for visible light in grey matter [1], cause photons to quickly lose directionality with depth in tissue. Ongoing developments in multiphoton microscopy [2, 3] and super-resolution microscopy [4] have enabled near single-cell resolution at depths of up to two millimeters in the mouse brain, but imaging depths are not expected to improve significantly beyond this. One way to acquire an image at greater depths is to guide photons through a non-scattering medium. In particular, imagers with graded index rod lenses (1.8 mm diameter) [5] and multimode fiber endoscopes (50 μm core diameter) [6, 7] have successfully imaged neural HHS Public Access Author manuscript IEEE Trans Biomed Circuits Syst. Author manuscript; available in PMC 2021 August 01. Published in final edited form as: IEEE Trans Biomed Circuits Syst. 2020 August ; 14(4): 636–645. doi:10.1109/TBCAS.2020.3008513. Author Manuscript Author Manuscript Author Manuscript Author Manuscript