Compensation of physiological motion enables high-yield whole-cell recording in vivo

•Gigaseal formation shows a strong dependence on pipette-cell distance.•Tissue motion can be predicted and compensated with a feed-forward control system.•Compensation for tissue motion improves whole-cell success rates in the thalamus. Whole-cell patch-clamp recording in vivo is the gold-standard method for measuring subthreshold electrophysiology from single cells during behavioural tasks, sensory stimulations, and optogenetic manipulation. However, these recordings require a tight, gigaohm resistance, seal between a glass pipette electrode's aperture and a cell's membrane. These seals are difficult to form, especially in vivo, in part because of a strong dependence on the distance between the pipette aperture and cell membrane. We elucidate and utilize this dependency to develop an autonomous method for placement and synchronization of pipette's tip aperture to the membrane of a nearby, moving neuron, which enables high-yield seal formation and subsequent recordings deep in the brain of the living mouse. This synchronization procedure nearly doubles the reported gigaseal yield in the thalamus (>3 mm below the pial surface) from 26 % (n = 17/64) to 48 % (n = 32/66). Whole-cell recording yield improved from 10 % (n = 9/88) to 24 % (n = 18/76) when motion compensation was used during the gigaseal formation. As an example of its application, we utilized this system to investigate the role of the sensory environment and ventral posterior medial region (VPM) projection synchrony on intracellular dynamics in the barrel cortex. Current methods of in vivo whole-cell patch clamping do not synchronize the position of the pipette to motion of the cell. This method results in substantially greater subcortical whole-cell recording yield than previously reported and thus makes pan-brain whole-cell electrophysiology practical in the living mouse brain.