Materials scientists typically use solution-phase transmission electron microscopy (TEM) to reveal the unique physiochemical properties of three-dimensional (3-D) structures of nanocrystals. In a new report on Science Advances, Cyril F. Reboul and a research team at the Monash University, Australia, Seoul National University, South Korea, and the Lawrence Berkeley National Laboratory U.S., developed a single-particle Brownian 3-D reconstruction method. To accomplish this, they imaged ensembles of colloidal nanocrystals using graphene liquid cell transmission electron microscopy. The team obtained projection images of differently rotated nanocrystals using a direct electron detector to obtain an ensemble of 3-D reconstructions. In this work, they introduced computational methods to successfully reconstruct 3-D nanocrystals at atomic resolution and accomplished this by tracking individual particles throughout time, while subtracting the interfering background. The method could also identify/reject low-quality images to facilitate tailored strategies for 2-D/3-D alignment that differed from those in biological cryo-electron microscopy. The team made the developments available through an open-source software package known as SINGLE. The free software is available on GitHub.