This application discloses a computing system implementing a mask synthesis system to generate synthetic image clips of design shapes and corresponding mask data for the synthetic image clips. The mask data can describe lithographic masks capable of being used to fabricate the design shapes on an integrated circuit. The mask synthesis system can utilize the synthetic image clips of the design shapes and the corresponding mask data to train a machine-learning system to determine pixelated output masks from portions of the layout design. The mask synthesis system can identify one or more pixelated output masks for portions of a layout design describing an electronic system using the trained machine-learning. The mask synthesis system can synthesize a mask layout design for the electronic system based, at least in part, on the layout design describing the electronic system and the one or more pixelated output masks for the layout design.