Learning to automate cryo-electron microscopy data collection with Ptolemy

Over the past decade, cryogenic electron microscopy (cryo-EM) has emerged as a primary method for determining near-native, near-atomic resolution 3D structures of biological macromolecules. In order to meet increasing demand for cryo-EM, automated methods to improve throughput and efficiency while lowering costs are needed. Currently, all high-magnification cryo-EM data collection softwares require human input and manual tuning of parameters. Expert operators must navigate low- and medium-magnification images to find good high-magnification collection locations. Automating this is non-trivial: the images suffer from low signal-to-noise ratio and are affected by a range of experimental parameters that can differ for each collection session. Here, we use various computer vision algorithms, including mixture models, convolutional neural networks, and U-Nets to develop the first pipeline to automate low- and medium-magnification targeting. Learned models in this pipeline are trained on a large internal dataset of images from real world cryo-EM data collection sessions, labeled with locations that were selected by operators. Using these models, we show that we can effectively detect and classify regions of interest in low- and medium-magnification images, and can generalize to unseen sessions, as well as to images captured using different microscopes from external facilities. We expect our open-source pipeline, Ptolemy, will be both immediately useful as a tool for automation of cryo-EM data collection, and serve as a foundation for future advanced methods for efficient and automated cryo-EM microscopy.