Automated electron microscope tomography using robust prediction of specimen movements.

By David N. Mastronarde. 2005

5,184 citations recorded by the source corpus.

Subfields: Radiation, Structural Biology, Surfaces, Coatings and Films, Medical Imaging, ML Systems & Hardware

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Radiation

1. Sjors H. W. Scheres
2. Takanori Nakane
3. Dari Kimanius
4. W. Hagen
5. B. Nannenga
6. Tamir Gonen
7. M. Pilhofer
8. John A. G. Briggs

In Structural Biology

1. Sjors H. W. Scheres
2. Dari Kimanius
3. Takanori Nakane
4. Erik Lindahl
5. Yifan Cheng
6. Björn Forsberg
7. W. Hagen
8. Jasenko Zivanov

In Surfaces, Coatings and Films

1. Sjors H. W. Scheres
2. Dari Kimanius
3. Takanori Nakane
4. Yifan Cheng
5. W. Hagen
6. Erik Lindahl
7. Patrick Cramer
8. Björn Forsberg

In Medical Imaging

1. W. Hagen
2. Tamir Gonen
3. B. Nannenga
4. M. Pilhofer
5. Sjors H. W. Scheres
6. Takanori Nakane
7. Dari Kimanius
8. John A. G. Briggs

In ML Systems & Hardware

1. W. Hagen
2. Tamir Gonen
3. B. Nannenga
4. M. Pilhofer
5. Sjors H. W. Scheres
6. Takanori Nakane
7. Dari Kimanius
8. John A. G. Briggs

Citations in the corpus

• New tools for automated high-resolution cryo-EM structure determination in RELION-3 (2018, methodology): “The data were recorded using serialEM ( Mastronarde, 2005 ) in combination with a patch in the Thermo Fischer microscope software to perform active beam tilt compensation.”
• Real-time cryo–EM data pre-processing with Warp (2018, background): “Mechanical stage instabilities and imperfect eucentric height setting necessitate additional exposures for tracking and focusing 12 to correct the stage position between individual tilt images.”
• Construction, characterization, and immunization of nanoparticles that display a diverse array of influenza HA trimers (2020, methodology): “23 Å•pixel using SerialEM software [25], a -3 to -6 μm defocus range, and a total of 98 e•Å per tilt series.”
• Structure of the RNA-dependent RNA polymerase from COVID-19 virus (2020, methodology): “All images were automatically recorded using SerialEM (18).”
• Cryo-EM structures of human ZnT8 in both outward- and inward-facing conformations (2020, methodology): “Micrographs were acquired on a Titan Krios microscope (FEI) with a K3 Summit direct electron detector (Gatan) in the super-resolution counting mode, operated at 300 kV using the SerialEM software (Mastronarde, 2005).”
• Architecture of the ring formed by the tubulin homologue FtsZ in bacterial cell division (2014, methodology): “A Gatan Ultrascan 4000 CCD camera binned to 2k × 2k or a 4k × 4k K2 Summit direct electron detector was used for data acquisition with SerialEM software (Mastronarde, 2005).”
• Glycan-Masking Focuses Immune Responses to the HIV-1 CD4-Binding Site and Enhances Elicitation of VRC01-Class Precursor Antibodies (2018, neutral): “…Crooks et al., 2004 http://weblogo.berkeley.edu/logo.cgi NetNGlyc DTU Bioinformatics, Technical University of Denmark http://www.cbs.dtu.dk/services/NetNGlyc/ Glycosylate He and Zhu, 2015 N/A SerialEM Mastronarde, 2005 http://bio3d.colorado.edu/SerialEM/ EMAN2.”
• Structures of Human Antibodies Bound to SARS-CoV-2 Spike Reveal Common Epitopes and Recurrent Features of Antibodies (2020, positive): “For the C105-S trimer complex, micrographs were collected on a Titan Krios transmission electron microscope (Thermo Fisher) operating at 300 kV using SerialEM automated data collection software (Mastronarde, 2005).”
• Implementation of a cryo-electron tomography tilt-scheme optimized for high resolution subtomogram averaging (2017, methodology): “…neighbouring images in the tilt series, or allows estimation of the defocus based on the nominal focus (Schur et al., 2013) SerialEM was used for the development of the tilt-scheme as its macro language provides a convenient way to implement automated data collection routines (Mastronarde, 2005).”