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Nat Methods. 2019 Jun;16(6):471-477. doi: 10.1038/s41592-019-0396-9. Epub 2019 May 13.

Software tools for automated transmission electron microscopy.

Author information

1
Electron Microscopy Core Facility, EMBL, Heidelberg, Germany. martin.schorb@embl.de.
2
Department of Hematology, Oncology and Rheumatology, University Hospital Heidelberg, Heidelberg Research Center for Molecular Medicine, EMBL, Heidelberg, Germany.
3
Cell Biology and Biophysics Unit, EMBL, Heidelberg, Germany.
4
Structural and Computational Biology Unit and Cryo-Electron Microscopy Service Platform, EMBL, Heidelberg, Germany.
5
Electron Microscopy Core Facility, EMBL, Heidelberg, Germany.
6
Department of Molecular, Cellular & Developmental Biology, University of Colorado, Boulder, CO, USA. mast@colorado.edu.

Abstract

The demand for high-throughput data collection in electron microscopy is increasing for applications in structural and cellular biology. Here we present a combination of software tools that enable automated acquisition guided by image analysis for a variety of transmission electron microscopy acquisition schemes. SerialEM controls microscopes and detectors and can trigger automated tasks at multiple positions with high flexibility. Py-EM interfaces with SerialEM to enact specimen-specific image-analysis pipelines that enable feedback microscopy. As example applications, we demonstrate dose reduction in cryo-electron microscopy experiments, fully automated acquisition of every cell in a plastic section and automated targeting on serial sections for 3D volume imaging across multiple grids.

PMID:
31086343
DOI:
10.1038/s41592-019-0396-9
[Indexed for MEDLINE]

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