Machine learning in scanning transmission electron microscopy
SV Kalinin, C Ophus, PM Voyles, R Erni… - Nature Reviews …, 2022 - nature.com
Scanning transmission electron microscopy (STEM) has emerged as a uniquely powerful
tool for structural and functional imaging of materials on the atomic level. Driven by …
tool for structural and functional imaging of materials on the atomic level. Driven by …
Volume electron microscopy
CJ Peddie, C Genoud, A Kreshuk, K Meechan… - Nature Reviews …, 2022 - nature.com
Life exists in three dimensions, but until the turn of the century most electron microscopy
methods provided only 2D image data. Recently, electron microscopy techniques capable of …
methods provided only 2D image data. Recently, electron microscopy techniques capable of …
New tools for automated cryo-EM single-particle analysis in RELION-4.0
D Kimanius, L Dong, G Sharov, T Nakane… - Biochemical …, 2021 - portlandpress.com
We describe new tools for the processing of electron cryo-microscopy (cryo-EM) images in
the fourth major release of the RELION software. In particular, we introduce VDAM, a …
the fourth major release of the RELION software. In particular, we introduce VDAM, a …
Search and sequence analysis tools services from EMBL-EBI in 2022
F Madeira, M Pearce, ARN Tivey… - Nucleic acids …, 2022 - academic.oup.com
The EMBL-EBI search and sequence analysis tools frameworks provide integrated access to
EMBL-EBI's data resources and core bioinformatics analytical tools. EBI Search …
EMBL-EBI's data resources and core bioinformatics analytical tools. EBI Search …
CryoDRGN: reconstruction of heterogeneous cryo-EM structures using neural networks
ED Zhong, T Bepler, B Berger, JH Davis - Nature methods, 2021 - nature.com
Cryo-electron microscopy (cryo-EM) single-particle analysis has proven powerful in
determining the structures of rigid macromolecules. However, many imaged protein …
determining the structures of rigid macromolecules. However, many imaged protein …
EMPIAR: the electron microscopy public image archive
A Iudin, PK Korir, S Somasundharam… - Nucleic Acids …, 2023 - academic.oup.com
Public archiving in structural biology is well established with the Protein Data Bank (PDB;
wwPDB. org) catering for atomic models and the Electron Microscopy Data Bank (EMDB; …
wwPDB. org) catering for atomic models and the Electron Microscopy Data Bank (EMDB; …
Estimation of high-order aberrations and anisotropic magnification from cryo-EM data sets in RELION-3.1
J Zivanov, T Nakane, SHW Scheres - IUCrJ, 2020 - journals.iucr.org
Methods are presented that detect three types of aberrations in single-particle cryo-EM data
sets: symmetrical and antisymmetrical optical aberrations and magnification anisotropy …
sets: symmetrical and antisymmetrical optical aberrations and magnification anisotropy …
New tools for automated high-resolution cryo-EM structure determination in RELION-3
J Zivanov, T Nakane, BO Forsberg, D Kimanius… - elife, 2018 - elifesciences.org
Here, we describe the third major release of RELION. CPU-based vector acceleration has
been added in addition to GPU support, which provides flexibility in use of resources and …
been added in addition to GPU support, which provides flexibility in use of resources and …
Isotropic reconstruction for electron tomography with deep learning
YT Liu, H Zhang, H Wang, CL Tao, GQ Bi… - Nature …, 2022 - nature.com
Cryogenic electron tomography (cryoET) allows visualization of cellular structures in situ.
However, anisotropic resolution arising from the intrinsic “missing-wedge” problem has …
However, anisotropic resolution arising from the intrinsic “missing-wedge” problem has …
Real-time cryo-electron microscopy data preprocessing with Warp
D Tegunov, P Cramer - Nature methods, 2019 - nature.com
The acquisition of cryo-electron microscopy (cryo-EM) data from biological specimens must
be tightly coupled to data preprocessing to ensure the best data quality and microscope …
be tightly coupled to data preprocessing to ensure the best data quality and microscope …