System and method for geometric correction of OCT data representing a scan obtained by means of optical coherence tomography imaging of a sample. First scan morphological data relating to a morphology of the sample in the scan are obtained. Then reference morphological data relating to a reference morphology of the sample are obtained. For each of one or more scans of OCT data scan morphological data are compared with the reference morphological data to determine a relative geometric transformation of the morphology of the scan with respect to the reference morphology. Corrected scan is generated by performing on the OCT data representing the scan a transform that relates to the determined relative geometric transformation.
