A method includes obtaining at least one 2-D image dataset of semiconductor structures formed on a wafer including one or more defects during a wafer run of a wafer using a predefined fabrication process. The method also includes determining, based on at least one machine-learning algorithm trained on prior knowledge of the fabrication process and based on the at least one 2-D image dataset, one or more process deviations of the wafer run from the predefined fabrication process as a root cause of the one or more defects. A 3-D image dataset may be determined as a hidden variable.