The invention generally relates to methods for manually calibrating imaging systems such as optical coherence tomography systems. In certain aspects, an imaging system displays an image showing a target and a reference item. A user looks at the image and indicates a point within the image near the reference item. A processor detects an actual location of the reference item within an area around the indicated point. The processor can use an expected location of the reference item with the detected actual location to calculate a calibration value and provide a calibrated image. In this way, a user can identify the actual location of the reference point and a processing algorithm can give precision to the actual location.