A method for using a synthetically trained neural network for tracking particle movement in video microscopy data includes receiving, as input, video microscopy data representing images of particles that move between video frames. The method includes using a synthetically trained neural network to track movement of the particles between the video frames, wherein the synthetically trained neural network comprises a neural network that is trained on a plurality of different simulated video microscopy data sets. The method further includes outputting, by the synthetically trained neural network, an indication of movement of the particles between the video frames.