Advanced Electron Microscopy Techniques and Applications

Scaling data analyses in cellular cryoET using comprehensive segmentation

The paper presents a comprehensive segmentation strategy for cryoET data using convolutional neural networks, enabling efficient analysis of large datasets and improving particle picking and template matching.

CryoNeRF: reconstruction of homogeneous and heterogeneous cryo-EM structures using neural radiance field

CryoNeRF improves cryo-EM structure reconstruction by handling both homogeneous and heterogeneous data, achieving better performance than existing methods.

Obtaining high-resolution cryo-EM structures using a common LaB6, 120-keV electron microscope equipped with a sub 200-keV optimised direct electron detector.

This paper demonstrates that a standard 120-keV TEM with a direct electron detector can achieve high-resolution cryo-EM reconstructions of various proteins.

Cryo-EM Structure of AAA + ATPase Thorase Reveals Novel Helical Filament Formation

The paper determines the cryo-EM structure of Thorase filaments, showing how ATP binding drives filament formation and provides insights into its role in disassembling mTORC1 complexes.

Radiation damage behavior of soft matter in ultrafast cryo-electron microscopy (cryo-UEM)

This study investigates whether pulsed-electron imaging in ultrafast cryo-EM mitigates radiation damage, finding no significant mitigation effect despite varying experimental conditions.

Time-resolved cryo-EM (TRCEM) sample preparation using a PDMS-based microfluidic chip assembly

This paper introduces a PDMS-based microfluidic chip for time-resolved cryo-EM sample preparation, enabling structural and kinetic studies of biomolecular reactions in the 10-1000 ms time range.

A Labeled Dataset for AI-based Cryo-EM Map Enhancement

The paper introduces a labeled dataset for AI-based cryo-EM map denoising, including experimental maps and three types of generated label maps for benchmarking.

Accurate and fast segmentation of filaments and membranes in micrographs and tomograms with TARDIS

TARDIS is a deep learning framework that rapidly and accurately segments membranes and filaments in electron microscopy data, enabling large-scale biophysical analysis.

Direct cryo-ET detection of native SNARE and Munc13 protein bridges using AI classification and preprocessing

The paper uses AI classification and preprocessing to detect native SNARE and Munc13 protein bridges in cryo-ET data, revealing their role in synaptic vesicle tethering.

High-Resolution Cryo-EM Structure Determination of α-Synuclein - A Prototypical Amyloid Fibril

This paper provides a protocol for high-resolution cryo-EM structure determination of α-synuclein fibrils, resulting in a 2.04 Å structure with new density features.

New Statistical Metric for Robust Target Detection in Cryo-EM Using 2DTM

This paper introduces a new statistical metric, 2DTM p-value, to improve target detection in cryo-EM by combining SNR and z-score, showing better performance for complex targets.

The 8-nm spaghetti: well-structured glycans coating linear tetrapeptide repeats discovered from freshwater with CryoSeek

The paper discovers a new glycofibril structure using CryoSeek, revealing its 8-nm diameter and unique glycan-coated tetrapeptide repeats.

Identification and cryoEM structure determination of Escherichia phage YDC107 tail found in a bacteria-contaminated buffer

The paper identifies a contaminant phage from a cryoEM grid and determines its tail structure using ML-based methods without prior sequence knowledge.

Bayesian Perspective for Orientation Determination in Cryo-EM with Application to Structural Heterogeneity Analysis

This paper introduces a Bayesian framework for orientation estimation in cryo-EM, showing it improves reconstruction accuracy and structural heterogeneity analysis.

Unveiling the Structural Proteome of an Alzheimer's Disease Rat Brain Model

This study uses cryo-EM and BaR to analyze protein complexes in an Alzheimer's rat brain model, revealing structural insights relevant to multiple diseases.

Semi-automated navigation for efficient targeting of electron tomography to regions of interest in volume correlative light and electron microscopy

The paper introduces a software workflow for correlating optical and electron microscopy data to target specific regions of interest for electron tomography analysis.

Revisiting Sodium Phosphotungstate and Ammonium Molybdate as non-radioactive negative staining agents for single particle analysis

This paper demonstrates that sodium phosphotungstate and ammonium molybdate can replace uranyl-based stains in negative staining electron microscopy for single particle analysis, offering non-radioactive, cost-effective alternatives.

Reconstruction and identification of the native PLP synthase complex from Methanosarcina acetivorans lysate

This study uses cryoID to reconstruct the native PLP synthase complex from Methanosarcina acetivorans lysate, revealing a homo-dodecamer structure and absence of a previously proposed supracomplex.

De novo identification of protein domains in cryo-electron tomography maps from AlphaFold2 models

DomainSeeker identifies protein domains in cryo-ET maps using AlphaFold2 structures and Bayesian inference, improving accuracy and resolution robustness.

Overcoming the preferred orientation problem in cryoEM with self-supervised deep-learning

This paper introduces spIsoNet, a deep-learning tool that improves 3D reconstruction isotropy and particle alignment in cryoEM by addressing the preferred orientation problem without altering specimen preparation.

Improved model building for cryo-EM maps using local attention and 3D rotary position embedding

CryFold improves de novo model building for cryo-EM maps using local attention and 3D rotary position embedding, producing more complete models and reducing resolution requirements.

Cryo-EM phase-plate images reveal unexpected levels of apparent specimen damage

The paper shows that laser phase-plate images of apoF and rubisco reveal unexpected structural heterogeneity, suggesting that specimen damage may be more prevalent than previously thought.

TOMOMAN: a software package for large scale cryo-electron tomography data preprocessing, community data sharing, and collaborative computing

TOMOMAN streamlines cryo-ET data processing by integrating tools for interoperability, metadata management, and collaborative data sharing.

TomoScore: A Neural Network Approach for Quality Assessment of Cellular cryo-ET

TomoScore assesses cryo-ET tomogram quality for cellular annotation using a deep learning model, identifying optimal electron dose ranges to improve data processing efficiency.

Open-source Tools for CryoET Particle Picking Machine Learning Competitions

The paper introduces open-source tools for a machine learning competition focused on particle picking in cryo-electron tomography data.

Annotating CryoET Volumes: A Machine Learning Challenge

The paper introduces a phantom sample and annotated 3D volumes for a machine learning challenge to improve cryoET volume annotation.

Optical Interference for the Guidance of Cryogenic Focused Ion Beam Milling Beyond the Axial Diffraction Limit

The paper demonstrates using optical interference in a cryogenic FIB-SEM-LM system to target lamella production beyond the diffraction limit for capturing virions in host cells.

cryoMDM; Molecular simulation Driven structural Matching Approach to Estimate Variety of Atomic Three-dimensional Model Based on Noisy cryoEM Single Particle Images.

The paper introduces cryoMDM, a method that estimates 3D atomic models from single cryoEM particle images by matching them to simulated structural models, revealing intermediate structures of the SARS-CoV-2 spike protein.

REPIC -- an ensemble learning methodology for cryo-EM particle picking

REPIC uses ensemble learning to identify high-quality cryo-EM particles by consensus, reducing manual effort and improving consistency across different pickers.

Vesicle Picker: A tool for efficient identification of membrane protein complexes in vesicles

Vesicle Picker automatically identifies vesicles and selects particle locations in cryo-EM micrographs, improving efficiency for membrane protein complex analysis.