Patch-clamp electrophysiology is the current gold-standard technique for obtaining high-resolution recordings of neuronal activity in vivo. However, robotic technologies recently developed to automate these labor-intensive and low-throughput experiments are limited to superficial regions of the brain or lack cell type specific-targeting (Kodandaramaiah et al., 2012; Suk et al., 2017; Annecchino et al., 2017) . In this work, a new approach for automatically navigating patch-clamp micropipette electrodes using fluorescence feedback collected at the electrode aperture was developed and validated in vitro. In future efforts, an internal excitation source will be integrated into the system to enable micropipette navigation at any electrode-accessible depth and the system will be tested in vivo using fluorescence feedback from cell type-specific labels.