Deep learning improves macromolecule identification in 3D cellular cryo-electron tomograms

Template-free detection and classification of membrane-bound complexes in cryo-electron tomograms

(2020) Antonio Martinez-Sanchez et al.   NATURE METHODS

Charting the native architecture of Chlamydomonas thylakoid membranes with single-molecule precision

(2020) Wojciech Wietrzynski et al.   eLife

SHREC’20 Benchmark: Classification in cryo-electron tomograms

(2020) Ilja Gubins et al.   COMPUTERS & GRAPHICS-UK

AutoCryoPicker: an unsupervised learning approach for fully automated single particle picking in Cryo-EM images

(2019) Adil Al-Azzawi et al.   BMC BIOINFORMATICS

Applications, promises, and pitfalls of deep learning for fluorescence image reconstruction

(2019) Chinmay Belthangady et al.   NATURE METHODS

Real-time cryo-electron microscopy data preprocessing with Warp

(2019) Dimitry Tegunov et al.   NATURE METHODS

Positive-unlabeled convolutional neural networks for particle picking in cryo-electron micrographs

(2019) Tristan Bepler et al.   NATURE METHODS

Direct visualization of degradation microcompartments at the ER membrane

(2019) Sahradha Albert et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Image processing techniques for high-resolution structure determination from badly ordered 2D crystals

(2018) Nikhil Biyani et al.   JOURNAL OF STRUCTURAL BIOLOGY

Improved deep learning-based macromolecules structure classification from electron cryo-tomograms

(2018) Chengqian Che et al.   MACHINE VISION AND APPLICATIONS

Deep learning massively accelerates super-resolution localization microscopy

(2018) Wei Ouyang et al.   NATURE BIOTECHNOLOGY

Content-aware image restoration: pushing the limits of fluorescence microscopy

(2018) Martin Weigert et al.   NATURE METHODS

U-Net: deep learning for cell counting, detection, and morphometry

(2018) Thorsten Falk et al.   NATURE METHODS

New tools for automated high-resolution cryo-EM structure determination in RELION-3

(2018) Jasenko Zivanov et al.   eLife

Deep Consensus, a deep learning-based approach for particle pruning in cryo-electron microscopy

(2018) Ruben Sanchez-Garcia et al.   IUCrJ

Optimized cryo-focused ion beam sample preparation aimed at in situ structural studies of membrane proteins

(2017) Miroslava Schaffer et al.   JOURNAL OF STRUCTURAL BIOLOGY

Convolutional neural networks for automated annotation of cellular cryo-electron tomograms

(2017) Muyuan Chen et al.   NATURE METHODS

Proteasomes tether to two distinct sites at the nuclear pore complex

(2017) Sahradha Albert et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

UCSF ChimeraX: Meeting modern challenges in visualization and analysis

(2017) Thomas D. Goddard et al.   PROTEIN SCIENCE

Dissecting the molecular organization of the translocon-associated protein complex

(2017) Stefan Pfeffer et al.   Nature Communications

ICON: 3D reconstruction with ‘missing-information’ restoration in biological electron tomography

(2016) Yuchen Deng et al.   JOURNAL OF STRUCTURAL BIOLOGY

Scipion: A software framework toward integration, reproducibility and validation in 3D electron microscopy

(2016) J.M. de la Rosa-Trevín et al.   JOURNAL OF STRUCTURAL BIOLOGY

DeepPicker: A deep learning approach for fully automated particle picking in cryo-EM

(2016) Feng Wang et al.   JOURNAL OF STRUCTURAL BIOLOGY

Resolving macromolecular structures from electron cryo-tomography data using subtomogram averaging in RELION

(2016) Tanmay A M Bharat et al.   Nature Protocols

Deep learning

(2015) Yann LeCun et al.   NATURE

Robust membrane detection based on tensor voting for electron tomography

(2014) Antonio Martinez-Sanchez et al.   JOURNAL OF STRUCTURAL BIOLOGY

Fast and accurate reference-free alignment of subtomograms

(2013) Yuxiang Chen et al.   JOURNAL OF STRUCTURAL BIOLOGY

Avoiding the pitfalls of single particle cryo-electron microscopy: Einstein from noise

(2013) R. Henderson   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High-resolution noise substitution to measure overfitting and validate resolution in 3D structure determination by single particle electron cryomicroscopy

(2013) Shaoxia Chen et al.   ULTRAMICROSCOPY

Single versus dual-axis cryo-electron tomography of microtubules assembled in vitro: Limits and perspectives

(2012) Audrey Guesdon et al.   JOURNAL OF STRUCTURAL BIOLOGY

PyTom: A python-based toolbox for localization of macromolecules in cryo-electron tomograms and subtomogram analysis

(2011) Thomas Hrabe et al.   JOURNAL OF STRUCTURAL BIOLOGY

Automatic recovery of missing amplitudes and phases in tilt-limited electron crystallography of two-dimensional crystals

(2011) Bryant R. Gipson et al.   PHYSICAL REVIEW E

Classification of cryo-electron sub-tomograms using constrained correlation

(2007) Friedrich Förster et al.   JOURNAL OF STRUCTURAL BIOLOGY