Advanced Electron Microscopy Techniques and Applications

Multi-species cryoEM calibration and workflow verification standard

The paper introduces a multi-species cryoEM calibration sample to validate instrument performance and image processing workflows.

Localization of Albumin with Correlative Super Resolution Light- and Electron Microscopy in the Kidney

This study localizes albumin in kidney tissue using correlative super-resolution light and electron microscopy to map its distribution and quantify concentration gradients across the filtration barrier.

Ice thickness control and measurement in the VitroJet for time-efficient single particle structure determination

The paper develops a method to measure and control ice thickness in the VitroJet for cryo-EM, improving efficiency in single particle structure determination.

An approach for coherent periodogram averaging of tilt-series data for improved CTF estimation

The paper introduces an algorithm to improve CTF estimation in cryo-ET tilt-series data by using tilt-series alignment parameters to account for specimen geometry, enhancing resolution of subtomogram averages.

In situ crystalline structure of the Eosinophil major basic protein-1

This study determines the in-situ crystalline structure of MBP-1 in eosinophil secretory granules and shows activation-dependent crystal expansion and extrusion.

Roodmus: A toolkit for benchmarking heterogeneous electron cryo-microscopy reconstructions

The paper introduces Roodmus, a toolkit for benchmarking heterogeneous cryo-EM reconstructions using synthetic data with known ground truth.

Automated model-free analysis of cryo-EM volume ensembles with SIREn

This paper introduces SIREn, a tool for automated analysis of cryo-EM volume ensembles to identify structural states and quantify their occupancies.

VirtualIce: Half-synthetic CryoEM Micrograph Generator

VirtualIce generates half-synthetic cryoEM micrographs to address the lack of realistic ground-truth datasets for training and evaluating cryoEM machine learning models.

OPUS-DSD2: Disentangling Dynamics and Compositional Heterogeneity for Cryo-EM/ET

OPUS-DSD2 disentangles structural heterogeneity in cryo-EM and cryo-ET data by separating rigid-body dynamics from other variations, improving analysis of macromolecular structures.

Camera Paths, Modeling, and Image Processing Tools for ArtiaX

The paper introduces an updated plugin, ArtiaX, for cryo-electron tomography analysis, offering tools for particle selection, camera path definition, and image processing.

CryoVesNet: A Dedicated Framework for Synaptic Vesicle Segmentation in Cryo Electron Tomograms

The paper introduces CryoVesNet, a framework for automated synaptic vesicle segmentation in cryo-ET data, improving accuracy and efficiency compared to manual methods.

Mesoscale Explorer - Visual Exploration of Large-Scale Molecular Models

Mesoscale Explorer provides a web-based tool for interactive 3D visualization of large molecular models using GPU rendering and web technologies.

Biological volume EM with focused Ga ion beam depends on formation of radiation-resistant Ga-rich layer at block face

This study investigates how FIB-SEM achieves high resolution in biological volume EM by forming a radiation-resistant Ga-rich layer at the block face, preventing specimen collapse and damage.

High-fidelity Image Restoration of Large 3D Electron Microscopy Volume

The paper develops an image-processing pipeline to restore VEM images with high fidelity while preserving relative contrast, tested on Microwasp head datasets.

Ultrastructural analysis of the brain endothelium by electron tomography

The paper explains how electron tomography (ET) can be used to study the ultrastructure of brain endothelial cells in three dimensions.

Structural analysis of S-ring composed of FliFG fusion proteins in marine Vibrio polar flagellar motors

The paper reports the near-atomic structure of the S-ring from Vibrio alginolyticus flagellar motor using cryo-EM, revealing structural differences compared to Salmonella.

Subnanometer structure of medusavirus capsid during maturation using cryo-electron microscopy

The paper uses cryo-EM to reveal structural changes in medusavirus capsids during maturation, identifying dynamic rearrangements of minor capsid proteins and penton proteins.

Novel cell-to-cell interactions revealed by cryotomography of a DPANN coculture system

This study uses cryo-ET to reveal intercellular nanotubes between a DPANN archaeon and its host, providing insights into host-DPANN communication and proteomic changes during symbiosis.

An image processing pipeline for electron cryo-tomography in RELION-5

The paper introduces an image processing pipeline for electron cryo-tomography in RELION-5, enabling automated atomic model building from tomographic data.

Fast imaging of millimeter-scale areas with beam deflection transmission electron microscopy

This paper improves TEM imaging speed by using beam deflection to capture multiple image tiles, increasing efficiency for millimeter-scale brain tissue imaging.

Overcoming cryo-EM map anisotropy reveals ALK-cytokine assemblies with distinct stoichiometries

The paper reanalyzes cryo-EM data to reveal a 2:1 stoichiometry of ALK-ALKAL2 complexes, resolving discrepancies with previous structural studies.

SPOT-RASTR - a cryo-EM specimen preparation technique that overcomes problems with preferred orientation and the air/water interface

The paper introduces SPOT-RASTR, a cryo-EM technique using lipid nanotubes to overcome air-water interface and preferred orientation issues, enabling automated data collection and near-atomic resolution.

Likelihood-based interactive local docking into cryo-EM maps in ChimeraX

The paper introduces a likelihood-based local docking method for cryo-EM maps, improving speed and sensitivity when component locations are known, implemented in ChimeraX.

Accurate model and ensemble refinement using cryo-electron microscopy maps and Bayesian inference

This paper introduces EMMIVox, a Bayesian method for refining cryo-EM maps into high-quality structural models and ensembles, balancing data fit with physico-chemical accuracy.

DeepOrientation: Deep Orientation Estimation of Macromolecules in Cryo-electron tomography

This paper introduces a deep learning model for orientation estimation of macromolecules in cryo-ET images using synthetic data and shows promising results.

Refinement of Cryo-EM 3D Maps with Self-Supervised Denoising Model: crefDenoiser

The paper introduces crefDenoiser, a self-supervised denoising model that improves the quality of 3D cryo-EM maps by amplifying signals and reducing noise.

CryoJAM: Automating Protein Homolog Fitting in Medium Resolution Cryo-EM Density Maps

CryoJAM automates fitting homologous protein structures into medium-resolution cryo-EM density maps, reducing RMSE in most test cases.

Towards Interpretable Cryo-EM: Disentangling Latent Spaces of Molecular Conformations

This paper frames the challenge of interpreting cryo-EM latent spaces as an Independent Component Analysis problem, aiming to develop identifiable models for conformational landscapes.

iTome Volumetric Serial Sectioning Apparatus for TEM

The paper describes an automated ultra-microtome for TEM sectioning, achieving high success rates in cutting and picking up sections from various biological samples.

OPUS-TOMO: Towards Resolving Dynamics and Compositional Heterogeneities of Biomolecules with Cryo-Electron Tomography

OPUS-TOMO improves resolution and resolves structural heterogeneity in cryo-ET data for biomolecules like ATP synthase and ribosomes.