In an automated methodology for in vivo image-guided cell patch clamping, a cell patch clamping device is moved into position and targeted to a specific cell using automated image-guided techniques. Cell contact is determined by analyzing the temporal series of measured resistance levels at the clamping device as it is moved. The difference between successive resistance levels is compared to a threshold, which must be exceeded before cell contact is assumed. Pneumatic control methods are used to achieve gigaseal formation and cell break-in, leading to whole-cell patch clamp formation. An automated robotic system capable of performing this methodology automatically performs patch clamping in vivo, automatically locating cells through image guidance and by analyzing the temporal sequence of electrode impedance changes. By continuously monitoring the patching process and rapidly executing actions triggered by specific measurements, the robot can rapidly find target cells in vivo and establish patch-clamp recordings.