SINGLE: Atomic-resolution structure identification of nanocrystals by graphene liquid cell EM

Cyril F. Reboul, Junyoung Heo, Chiara Machello, Simon Kiesewetter, Byung Hyo Kim, Sungin Kim, Dominika Elmlund, Peter Ercius, Jungwon Park, Hans Elmlund

Research output: Contribution to journalArticleResearchpeer-review

11 Citations (Scopus)


Analysis of the three-dimensional (3D) structures of nanocrystals with solution-phase transmission electron microscopy is beginning to reveal their unique physiochemical properties. We developed a “one-particle Brownian 3D reconstruction method” based on imaging of ensembles of colloidal nanocrystals using graphene liquid cell electron microscopy. Projection images of differently rotated nanocrystals are acquired using a direct electron detector with high temporal (<2.5 ms) resolution and analyzed to obtain an ensemble of 3D reconstructions. Here, we introduce computational methods required for successful atomic-resolution 3D reconstruction: (i) tracking of the individual particles throughout the time series, (ii) subtraction of the interfering background of the graphene liquid cell, (iii) identification and rejection of low-quality images, and (iv) tailored strategies for 2D/3D alignment and averaging that differ from those used in biological cryo–electron microscopy. Our developments are made available through the open-source software package SINGLE.

Original languageEnglish
Article numbereabe6679
Number of pages9
JournalScience Advances
Issue number5
Publication statusPublished - 29 Jan 2021

Cite this