There is provided a system and method of generating a training set for training a Deep Neural Network usable for examination of a specimen. The method includes: for each given training image in a group: i) generating a first batch of training patches, including cropping the given training image into a first plurality of original patches; and augmenting at least part of the first plurality of original patches in order to simulate variations caused by a physical process of the specimen; and ii) generating a second batch of training patches, including: shifting the plurality of first positions on the given training image to obtain a second plurality of original patches, and repeating the augmenting to the second plurality of original patches to generate a second plurality of augmented patches; and including at least the first second batches of training patches corresponding to each given training image in the training set.