1. A method for determining overlay between layers of a multilayer structure, the method comprising: obtaining a given image representative of the multilayer structure; obtaining expected images of layers of the multilayer structure; generating, based on the expected images, a combined expected image of the multilayer structure; registering the given image against the combined expected image; generating segmentation data for the given image; computing an overlay measurement between two layers of the multilayer structure; and correcting the segmentation data based on the computed overlay measurement.