Advanced Electron Microscopy Techniques and Applications

ColabSeg: An interactive tool for editing, processing, and visualizing membrane segmentations from cryo-ET data

ColabSeg is a tool for processing and visualizing membrane segmentations from cryo-ET data, enabling high-throughput segmentation and training of CNNs.

DeepSLICEM: Clustering CryoEM particles using deep image and similarity graph representations

DeepSLICEM improves clustering of cryo-EM 2D projections by combining image and graph features, achieving better accuracy than previous methods on synthetic and experimental datasets.

PyTME (Python Template Matching Engine): A fast, flexible, and multi-purpose template matching library for cryogenic electron microscopy data

The paper introduces pyTME, a Python library for template matching in cryo-EM data that improves efficiency and scalability for large datasets.

CryoCycle your grids: Plunge vitrifying and reusing clipped grids to advance cryoEM democratization

This paper introduces CryoCycle, a method for blotting, vitrifying, and reusing clipped cryoEM grids to reduce costs and improve access to cryoEM.

DiffModeler: Large Macromolecular Structure Modeling in Low-Resolution Cryo-EM Maps Using Diffusion Model

DiffModeler uses diffusion models to accurately model protein complex structures from low-resolution cryo-EM maps, achieving high TM-Scores across various resolutions.

Development of immobilized antibody-based affinity grid strategy and application in on-grid purification of target proteins for high-resolution cryo-EM

The paper develops an immobilized antibody-based affinity grid strategy to improve cryo-EM sample preparation by enabling on-grid purification of target proteins and overcoming orientation issues.

Genome organization in double-stranded DNA viruses observed by cryoET

This study uses cryoET to observe the 3D organization of dsDNA in viral particles, revealing a conserved 'rod-and-coil' structure and proposing a packaging mechanism.

SegmA: Residue Segmentation of cryo-EM density maps

SegmA is a deep learning model that segments cryo-EM density maps into residue types, achieving 80% accuracy for nucleotides and improved amino acid detection after removing low-confidence regions.

blik: an extensible napari plugin for cryo-ET data visualisation, annotation and analysis

blik is an open-source napari plugin for visualizing, annotating, and analyzing cryo-ET data with extensibility and modularity.

Imaging intracellular components in situ using super-resolution cryo-correlative light and electron microscopy

This paper outlines a workflow for SRcryoCLEM, demonstrating its application using Vimentin and showing how it enables targeted imaging of intracellular components in situ.

Highly amine-reactive graphene-oxide EM grids for biochemical surface modification in aqueous buffer

This paper describes a chemical method to modify graphene oxide surfaces with amine-reactive groups for biochemical interactions in aqueous buffer.

Rapid in-EPON CLEM for everyone: Combining fast and efficient labeling of self-labeling enzyme tags with EM resistant Janelia Fluor dyes

The paper compares Janelia Fluor dyes and TMR for fluorescence preservation in EM-compatible in-resin CLEM, identifying JFX549 and JFX554 as optimal for signal intensity and background ratio.

Super-resolution fluorescence imaging of cryosamples does not limit achievable resolution in cryoEM

The paper investigates whether super-resolution fluorescence imaging before cryoEM affects resolution, finding no detrimental effect.

EMDB - The Electron Microscopy Data Bank

The paper provides an overview of the EMDB archive, its current holdings, recent updates, and future plans.

Integrated Protocol of Protein Structure Modeling for Cryo-EM with Deep Learning and Structure Prediction

The paper introduces a method combining deep learning for density tracing with AlphaFold2 to improve protein structure modeling from cryo-EM maps and accurately assign chain identities in homo-multimers.

ATUM-Tomo: A multi-scale approach to cellular ultrastructure by combined volume scanning electron microscopy and electron tomography

The paper introduces ATUM-Tomo, a hybrid method combining SEM and electron tomography for multi-scale ultrastructural analysis of cellular structures.

Finding Antibodies in Cryo-EM densities with CrAI

This paper introduces CrAI, a fully automatic method for detecting antibodies in cryo-EM densities, achieving faster and more accurate results than existing methods.

A Scalable Staining Strategy for Whole-Brain Connectomics

The paper introduces a 12-step protocol called ODeCO to infiltrate osmium in whole mouse brains, preserving ultrastructure for connectome mapping.

Integrating AlphaFold and deep learning for atomistic interpretation of cryo-EM maps

This work integrates AlphaFold with a deep learning tool, CryoFEM, to improve the accuracy of 3-D atomic models built from cryo-EM maps.

A robust normalized local filter to estimate compositionalheterogeneity directly from cryo-EM maps

This paper introduces a normalized local filter to estimate compositional heterogeneity in cryo-EM maps and demonstrates its utility for interpretation and signal subtraction.

Photoemission electron microscopy for connectomics

This paper introduces photoemission electron microscopy (PEEM) as a new method for connectomics, offering synaptic resolution and faster imaging compared to traditional TEM and SEM.

Exploring the Conformational Landscape of Cryo-EM Using Energy-Aware Pathfinding Algorithm

This study introduces an energy-aware pathfinding algorithm to identify preferred conformational transition paths in high-dimensional cryo-EM data.

Smart Leginon enables cryoEM screening automation across multiple grids

This paper introduces Smart Leginon Autoscreen, an automated cryoEM grid screening system that reduces operator time from 6 hours to 10 minutes for 12 grids using machine learning and computer vision.

Rehydration of freeze substituted brain tissue for preembedding immuno-electron microscopy

This paper introduces a method for rehydrating freeze-substituted brain tissue to enable immunolabeling while preserving ultrastructure for electron microscopy.

CryoPPP: A Large Expert-Labelled Cryo-EM Image Dataset for Machine Learning Protein Particle Picking

doubleHelix: nucleic acid sequence identification, assignment and validation tool for cryo-EM and crystal structure models

doubleHelix identifies and validates nucleic acid sequences in cryo-EM and crystal structures, improving accuracy at lower resolutions and detecting errors missed by existing methods.

Toward single particle reconstruction without particle picking: Breaking the detection limit

This paper proposes a method to reconstruct 3D structures from cryo-EM micrographs without detecting individual particles, aiming to improve detection of small molecules.

Selecting optimal support grids for super-resolution cryogenic correlated light and electron microscopy

The paper investigates how support grid design in cryo-TEM affects fluorescence microscopy illumination and demonstrates improvements in super-resolution image quality through optimal grid selection.

Multiplexed volumetric CLEM enabled by antibody derivatives provides new insights into the cytology of the mouse cerebellar cortex

The paper introduces a vCLEM method using fluorescent scFvs to combine molecular labeling with ssEM, revealing new cell types and subcellular features in mouse cerebellar cortex.

Structure of Anabaena flos-aquae gas vesicles revealed by cryo-ET

This study uses cryo-electron tomography to reveal the structure of Anabaena flos-aquae gas vesicles, showing how GvpA subunits form the shell and how GvpC provides structural reinforcement.