Methods, systems, and apparatus, including computer programs encoded on a computer storage medium, for identifying the predicted type of one or more microorganisms. In one aspect, a system comprises a phase-contrast microscope and a microorganism classification system. The phase-contrast microscope is configured to generate a three-dimensional quantitative phase image of one or more microorganisms. The microorganism classification system is configured to process the three-dimensional quantitative phase image using a neural network to generate a neural network output characterizing the microorganisms, and thereafter identify the predicted type of the microorganisms using the neural network output.