The ROME (Refinement and Optimization via Machine lEarning for cryo-EM) software package is a parallel computing software system dedicated for high-resolution cryo-EM structure determination and data analysis, which implements advanced machine learning approaches in modern computer sciences and runs natively in an HPC environment. The ROME 1.0 introduces SML (statistical manifold learning)-based deep classification following MAP-based image alignment. It also implemented traditional unsupervised MAP-based classification and includes several useful tools, such as 2D class averaging with CTF (contrast transfer function) correction and a convenient GUI for curation, inspection and verification of single-particle classes. The ROME system has be optimized on both Intel® Xeon multi-core CPUs and Intel® Xeon Phi many-core coprocessors.
