Advanced Electron Microscopy Techniques and Applications

CryoARC: Atomic-resolution conformational landscapes of protein assemblies from cryo-EM single particles with evolutionary priors

CryoARC reconstructs atomic-resolution conformational landscapes of protein assemblies from cryo-EM data using evolutionary sequence priors and deep learning.

AreTomoLive: Automated reconstruction of comprehensively-corrected and denoised cryo-electron tomograms in real-time and at high throughput

AreTomo3 and DenoisET form an automated GPU pipeline that reconstructs cryo-electron tomograms with tile-based contrast transfer function correction, screens their quality, and denoises them during acquisition.

Visual exoproteomics of Clostridium thermocellum during anaerobic biomass-degradation identifies functional spirosomes

The paper uses visual proteomics to identify functional spirosomes in Clostridium thermocellum during biomass degradation.

Characterization Standard for In-situ Cryo-electron Tomography

The paper introduces PP7 virus-like particles as a standardized benchmark for cryo-electron tomography, enabling rapid validation and resolution assessment of tomographic pipelines.

Structures of Multiple Peptide Resistance Factor from Pseudomonas aeruginosa

This study presents cryoEM structures of PaMprF from Pseudomonas aeruginosa, revealing its dimeric architecture and dynamic elements involved in lipid modification.

Easymode: general pretrained networks for cellular cryo-ET enable flexible approaches to subtomogram averaging

Easymode provides pretrained networks for cryo-ET segmentation, enabling efficient subtomogram averaging and cellular context analysis without per-dataset training.

Cryo-FIB Lift-out and Electron Tomography Workflow for Bacteria-Nanopillar Interface Imaging Under Native Conditions: Investigating Dragonfly Inspired Bactericidal Titanium Surfaces

This paper develops a cryo-FIB lift-out and electron tomography workflow to image bacteria-nanostructure interfaces under native hydrated conditions.

Atomic resolution cryo-EM at 200 keV

The paper demonstrates atomic resolution cryo-EM at 200 kV using upgraded hardware, achieving 1.24 Å resolution comparable to 300 kV systems.

In situ molecular architecture of the mammalian sperm nuclear vacuole

The paper identifies components of mammalian sperm nuclear vacuoles using cryo-ET and AlphaFold docking, revealing proteasomes, PA200, and ferritin, and their structural roles.

StructAgent: Orchestrating Cryo-EM Model Building and Refinement with a Multi-Agent LLM System

StructAgent automates cryo-EM model building and refinement with a multi-agent system, enabling auditable workflows while preserving expert control.

EMReady2: improvement of cryo-EM and cryo-ET maps by local quality-aware deep learning with Mamba

EMReady2 improves cryo-EM and cryo-ET maps using a Mamba-based deep learning model, enhancing quality and interpretability while reducing computational cost.

In-situ structure of the flagellar export apparatus in Borrelia burgdorferi

This study uses cryo-EM to determine the structure of the flagellar export apparatus in Borrelia burgdorferi, revealing its assembly mechanism and role in substrate translocation.

Automated LN2 refill device for uninterrupted cryoFIB-SEM operations.

This paper introduces an automated LN2 refill system for cryoFIB-SEM to enable uninterrupted long-term operations.

Heterogeneous reconstruction algorithms for cryoEM achieve limited particle classification accuracy on real benchmark datasets

This study evaluates heterogeneous reconstruction algorithms in cryoEM using benchmark datasets with ground-truth labels, finding limited accuracy in particle classification despite resolving structural heterogeneity.

ParSeek: Accurate cryo-EM particle picking with a deep learning model trained on synthetic data

ParSeek is a deep learning model for cryo-EM particle picking trained on synthetic data, achieving high accuracy and outperforming existing methods on multiple datasets.

Cryo-electron microscopy ensemble optimization using individual particles and physical constraints

This paper introduces a Bayesian optimization method for cryo-EM ensemble optimization, directly inferring structures and population weights from particle images and physical constraints.

Measurement of atomic scattering factors by cryo-electron microscopy

This paper introduces a Bayesian method to estimate atomic scattering factors from cryo-EM data, improving accuracy by incorporating molecular environment effects.

Engineered Cas9 complexes establish an experimentally grounded benchmark for heterogeneous cryoEM reconstruction methods

The paper develops an experimentally grounded benchmark dataset for heterogeneous cryoEM reconstruction using engineered Cas9 complexes with defined DNA extensions.

Architecture of the type II secretion system

The paper uses AlphaFold and cryo-EM to reveal the structure of the type II secretion system's pilus assembly platform and its organization across membranes.

Helical Reconstruction of Amyloids in cryoSPARC

This paper provides processing guidelines for helical reconstruction of amyloids using cryoSPARC, highlighting current capabilities and limitations while advocating for amyloid-specific parameter optimization.

A 37-million-particle dataset from over 250 experiments to accelerate data-driven cryo-EM analysis

The paper introduces a large annotated cryo-EM particle dataset and validates it through reconstruction and model training.

MissAlignment Teaches Itself Better Cryo-ET Tilt-Series Alignment by Making It Worse

MissAlignment improves cryo-ET tilt-series alignment by training a neural network to recognize misalignment without requiring well-aligned ground truth.

Unbend: Correction of local beam-induced sample motion in cryo-EM images using a 3D spline model

Unbend improves cryo-EM image correction by addressing localized sample motion with a 3D spline model, enhancing signal-to-noise ratio and particle detection.

Three-dimensional quantitative characterization of Coxiella burnetii infection using focused ion beam-scanning electron microscopy

This paper uses FIB-SEM and machine learning to study Coxiella burnetii infection, revealing 3D structure variations in bacteria and CCVs and showing that a mutant's vacuole defect does not affect its developmental cycle.

Multiscale volume electron microscopy of the human liver maps vascular-cellular architecture, organelle dynamics and inter-organelle communication

The paper maps the multiscale structure of human liver tissue using electron microscopy and deep learning, revealing vascular, cellular, and organelle organization and dynamics.

Interleaved multi-magnification cryo-electron tomography bridges cellular and structural biology

This paper introduces a multi-magnification cryo-ET technique that combines low- and high-resolution data to study cellular structures across scales.

A cryo-EM processing pipeline for microtubules using CryoSPARC

The paper introduces MiCSPARC, a cryo-EM pipeline for microtubule structure determination, achieving high-resolution reconstructions of decorated and undecorated microtubules.

View Tomo: Context-aware targeting and analysis in electron cryo-tomography

View Tomo improves cryoET by enabling 3D analysis and targeting through low-dose, rapid tomogram acquisition and automated processing.

A simplified High-Pressure Freezing Workflow in Autogrids

This paper introduces a simplified high-pressure freezing workflow using optimized planchettes for cryo-ET, improving vitrification and reducing handling for diverse specimens.

TomoSwin3D: a Swin3D Transformer for the Identification and Classification of Macromolecules in 3D Cryo-ET Tomograms

TomoSwin3D improves automated macromolecule detection in 3D cryo-ET tomograms by using a Swin Transformer-based U-Net with enhanced input features and occupancy-preserving supervision.