Methods and systems for generating a simulated image from an input image are provided. One system includes one or more computer subsystems and one or more components executed by the one or more computer subsystems. The one or more components include a neural network that includes two or more encoder layers configured for determining features of an image for a specimen. The neural network also includes two or more decoder layers configured for generating one or more simulated images from the determined features. The neural network does not include a fully connected layer thereby eliminating constraints on size of the image input to the two or more encoder layers.