Advanced Electron Microscopy Techniques and Applications

De Novo Atomic Protein Structure Modeling for Cryo-EMDensity Maps Using 3D Transformer and Hidden MarkovModel

Cryo2Struct improves de novo atomic protein structure modeling from cryo-EM density maps using a 3D transformer and HMM, outperforming Phenix on multiple metrics.

Structure of Aquifex aeolicus Lumazine Synthase by Cryo-Electron Microscopy to 1.42 Angstrom Resolution

The paper uses Cryo-EM to determine the structure of Aquifex aeolicus lumazine synthase at 1.42 Angstrom resolution, revealing hydrogen atoms and confirming near-atomic resolution for protein complexes.

CryoViT: Efficient Segmentation of Cryogenic Electron Tomograms with Vision Foundation Models

CryoViT improves segmentation of large subcellular structures in cryoET data using vision transformers, outperforming U-Net-based methods with limited training data.

Cryo-electron tomographic investigation of native hippocampal glutamatergic synapses

The paper develops methods to image glutamatergic synapses in hippocampal tissue using cryo-electron tomography, enabling high-resolution visualization of synaptic structures.

cryoSPHERE: Single-particle heterogeneous reconstruction from cryo EM

The paper introduces cryoSPHERE, a deep learning method for heterogeneous cryo-EM reconstruction, improving upon state-of-the-art methods in three examples.

Scalable electron tomography for connectomics

This paper demonstrates limited-tilt serial section electron tomography for high-resolution 3D mapping of brain circuits and evaluates imaging parameters for connectomic-scale projects.

FilamentID reveals the composition and function of metabolic enzyme polymers during gametogenesis

The paper introduces FilamentID, a workflow to identify filament composition in cells, finding Ald4ALDH2 and Acs1ACSS2 form filaments in mitochondria and nucleus during meiosis, aiding cell recovery from stress.

The cage effect of electron beam irradiation damage in cryo-electron microscopy

This study uses simulations to show that frozen water cages dissociated fragments, supporting the cage effect hypothesis in cryo-EM.

Surforama: interactive exploration of volumetric data by leveraging 3D surfaces

Surforama enables interactive visualization and analysis of membrane proteins in cryo-ET data by rendering local densities on segmented surfaces and exporting results for further analysis.

Mean Shift Clustering as a Loss Function for Accurate and Segmentation-aware Localization of Macromolecules in Cryo-electron Tomography

This paper introduces a Mean Shift loss function for more accurate protein localization in cryo-electron tomography using scoremap-guided clustering and random point sampling.

Accurate cryo-EM protein particle picking by integrating the foundational AI image segmentation model and specialized U-Net

The paper introduces CryoSegNet, a method combining a specialized U-Net and SAM for cryo-EM particle picking, achieving higher accuracy than existing methods.

Missing Wedge Completion via Unsupervised Learning with Coordinate Networks

This paper introduces an unsupervised learning approach using coordinate networks to address the missing wedge problem in cryoET, improving reconstruction quality and reducing runtime.

High-confidence 3D template matching for cryo-electron tomography

This paper introduces a high-confidence 3D template matching method for CryoET, enabling accurate localization of cellular structures with improved statistical confidence.

Simulating the cellular context in synthetic datasets for cryo-electron tomography

This paper introduces synthetic datasets for cryo-electron tomography to train deep learning algorithms by simulating cellular structures and geometries.

Single particle cryo-electron microscopy with an enhanced 200 kV cryo-TEM configuration achieves near-atomic resolution

This study shows that a 200 kV cryo-TEM with advanced detectors can achieve near-atomic resolution for single particle cryo-EM, comparable to 300 kV systems.

Cryo2StructData: A Large Labeled Cryo-EM Density Map Dataset for AI-based Modeling of Protein Structures

The paper introduces Cryo2StructData, a large labeled cryo-EM density map dataset for training AI models to build atomic protein structures, showing it is larger and higher quality than existing datasets.

Tuning ice thickness using the chameleon for high-quality cryoEM data collection

This paper describes the use of the chameleon device for tuning ice thickness to improve cryoEM grid quality and image quality.

Heterogeneous local structures of the microtubule lattice revealed by cryo-ET and non-averaging analysis

The paper uses cryo-ET and non-averaging analysis to reveal heterogeneous local structures of microtubules, showing polymerizing and depolymerizing ends share similar lattice spacing but differ in twisting.

Ultrastructural Dynamics of Dopaminergic Presynaptic Release Sites revealed by Cryo-correlative Light and Electron Microscopy

This study uses cryo-correlative light and electron microscopy to investigate the ultrastructure and dynamics of dopaminergic presynaptic release sites and identifies protein complexes and modulatory effects of pharmacological treatments.

STOPGAP, an open-source package for template matching, subtomogram alignment, and classification

STOPGAP is an open-source tool for subtomogram averaging in cryo-ET data to identify, localize, and classify molecular structures.

Ais: streamlining segmentation of cryo-electron tomography datasets

Ais provides a user-friendly, high-performance tool for cryo-electron tomography segmentation, accelerating particle picking and cellular architecture analysis.

Cryo-EM map anisotropy can be attenuated by map post-processing and a new method for its estimation

The paper identifies a limitation in existing cryo-EM map anisotropy measurement methods and shows that post-processing can reduce anisotropy.

Learning structural heterogeneity from cryo-electron sub-tomograms with tomoDRGN

This paper introduces tomoDRGN, a deep learning tool for analyzing cryo-ET sub-tomograms, revealing structural heterogeneity in macromolecules like ribosomes.

DeepETPicker: Fast and accurate 3D particle picking for cryo-electron tomography using weakly supervised deep learning

DeepETPicker improves 3D particle picking in cryo-electron tomography with weakly supervised deep learning, achieving higher accuracy and speed than existing methods.

DUAL: deep unsupervised simultaneous simulation and denoising for cryo-electron tomography

DUAL improves cryo-electron tomography by simultaneously denoising and simulating data without labeled training data, enhancing structural detection and annotation.

GAUSS-EM: Guided accumulation of ultrathin serial sections with a static magnetic field for volume electron microscopy

GAUSS-EM is a high-throughput method for serial sectioning electron microscopy that efficiently collects and packs thousands of ultrathin sections onto silicon wafers, enabling large 3D EM volumes with high resolution and low cost.

Indirect Correlative Light and Electron Microscopy (iCLEM): A Novel Pipeline for Multiscale Quantification of Structure from Molecules to Organs

The paper introduces iCLEM, a pipeline that correlates multiscale structural data from different imaging modalities using intrinsic fiducials, enabling structure-function relationship discovery.

Automated model building and protein identification in cryo-EM maps

ModelAngelo combines convolutional and graph neural networks with protein language model embeddings and hidden Markov model searches to automate atomic model building and identify unknown proteins in cryo-EM maps.

Sample preparation methods for volume electron microscopy in mollusc Berghia stephanieae

The paper introduces sample preparation methods for volume electron microscopy in the gastropod mollusc Berghia stephanieae, addressing challenges in cryopreservation and processing time.

CryoTransformer: A Transformer Model for Picking Protein Particles from Cryo-EM Micrographs

CryoTransformer improves protein particle picking in cryo-EM micrographs using a transformer model, achieving better resolution and F1-score than existing methods.