Real-time 3D analysis during electron tomography using tomviz

Jonathan Schwartz; Chris Harris; Jacob Pietryga; Huihuo Zheng; Prashant Kumar; Anastasiia Visheratina; Nicholas A Kotov; Brianna Major; Patrick Avery; Peter Ercius; Utkarsh Ayachit; Berk Geveci; David A Muller; Alessandro Genova; Yi Jiang; Marcus Hanwell; Robert Hovden

doi:10.1038/s41467-022-32046-0

Real-time 3D analysis during electron tomography using tomviz

Nat Commun. 2022 Aug 1;13(1):4458. doi: 10.1038/s41467-022-32046-0.

Authors

Jonathan Schwartz¹, Chris Harris², Jacob Pietryga¹, Huihuo Zheng³, Prashant Kumar⁴, Anastasiia Visheratina⁴, Nicholas A Kotov⁴, Brianna Major², Patrick Avery², Peter Ercius⁵, Utkarsh Ayachit², Berk Geveci², David A Muller⁶, Alessandro Genova², Yi Jiang⁷, Marcus Hanwell^{2

8}, Robert Hovden^{9

10}

Affiliations

¹ Department of Material Science and Engineering, University of Michigan, Ann Arbor, MI, USA.
² Kitware Inc, Clifton Park, NY, USA.
³ Argonne Leadership Computing Facility, Argonne National Laboratory, Lemont, IL, USA.
⁴ Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, USA.
⁵ The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
⁶ School of Applied and Engineering Physics, Cornell University, Ithaca, NY, USA.
⁷ Advanced Photon Source, Argonne National Laboratory, Lemont, IL, USA.
⁸ National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY, USA.
⁹ Department of Material Science and Engineering, University of Michigan, Ann Arbor, MI, USA. hovden@umich.edu.
¹⁰ Applied Physics Program, University of Michigan, Ann Arbor, MI, USA. hovden@umich.edu.

Abstract

The demand for high-throughput electron tomography is rapidly increasing in biological and material sciences. However, this 3D imaging technique is computationally bottlenecked by alignment and reconstruction which runs from hours to days. We demonstrate real-time tomography with dynamic 3D tomographic visualization to enable rapid interpretation of specimen structure immediately as data is collected on an electron microscope. Using geometrically complex chiral nanoparticles, we show volumetric interpretation can begin in less than 10 minutes and a high-quality tomogram is available within 30 minutes. Real-time tomography is integrated into tomviz, an open-source and cross-platform 3D data analysis tool that contains intuitive graphical user interfaces (GUI), to enable any scientist to characterize biological and material structure in 3D.

Publication types

Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Electron Microscope Tomography* / methods
Image Processing, Computer-Assisted / methods
Imaging, Three-Dimensional* / methods
Tomography
Tomography, X-Ray Computed