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Editorial Material
Multidisciplinary Sciences
Michael Eisenstein
Article
Biochemical Research Methods
Irene de Teresa-Trueba et al.
Summary: DeePiCt is a deep learning framework for supervised segmentation and localization of subcellular organelles and biomolecular complexes in cryo-electron tomography. It shows unique ability to identify low-abundance and low-density complexes and has been successfully applied in studying cellular ribosomes and their association with mitochondria and endoplasmic reticulum. DeePiCt achieves high-quality predictions in unseen datasets from different biological species in a matter of minutes.
Article
Biochemistry & Molecular Biology
Andrii Iudin et al.
Summary: Public archiving in structural biology has been well established with the Protein Data Bank (PDB) and the Electron Microscopy Data Bank (EMDB). EMPIAR, as a public archive, has become an important resource for storing cryo-EM image data and 3D reconstructions, meeting the increasing demand for archiving such data from cryo-EM experiments, as well as from volume EM and X-ray tomography experiments.
NUCLEIC ACIDS RESEARCH
(2023)
Review
Biochemical Research Methods
Casper Berger et al.
Summary: Cryogenic electron tomography (cryo-ET) on focused ion beam lamellae allows for the study of cellular structures in near-native state and has greatly advanced in recent years. This technology benefits from developments in electron microscopes, detectors, and data processing, enabling the acquisition of more in situ structures at higher resolutions. The future of cryo-ET lies in further method development and expanding its biological applications.
Article
Microscopy
V. Gonzalez-Ruiz et al.
Summary: FIB-SEM is an imaging technique that allows 3D ultra-structural analysis of cells and tissues at the nanoscale. Our study developed a new approach to structure-preserving noise reduction, which combines the simplicity of Gaussian filtering with the adaptability to biological structures. The results showed that our denoising approach outperforms standard Gaussian filtering and is competitive with state-of-the-art methods in terms of noise reduction and preservation of structure sharpness.
Article
Computer Science, Interdisciplinary Applications
V. Gonzalez-Ruiz et al.
Summary: In this study, an Optical Flow (OF)-driven interpolation strategy was developed to address the significant changes between consecutive images in FIB-SEM stacks. The approach compensated for variations by aligning the spatial regions of the biological structures using OF, resulting in sharp interpolated images. The OF-driven interpolation outperformed classical interpolation methods and produced isotropic resolution in anisotropic data.
COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE
(2022)
Editorial Material
Cell Biology
Brenda Andrews et al.
Summary: Imaging technologies play a crucial role in driving discoveries in cell biology, with innovations in microscopy hardware, imaging methods, and computational analysis of complex datasets enhancing imaging resolution and clarity, as well as expanding our understanding of new biological processes. Experts in the field are excited about the potential of microscopy in cell biology, but acknowledge the need to overcome certain challenges.
NATURE CELL BIOLOGY
(2022)
Article
Computer Science, Interdisciplinary Applications
Jose -Jesus Fernandez et al.
COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE
(2022)
Article
Multidisciplinary Sciences
Christopher J. Peddie et al.
Summary: Volume electron microscopy (vEM) is an emerging technique that allows deep imaging of cellular and tissue structures. This article provides an introduction to the different vEM imaging modalities, specialized sample processing, and image analysis pipelines, showcasing key applications in the biosciences.
NATURE REVIEWS METHODS PRIMERS
(2022)
Article
Biochemical Research Methods
Jose-Jesus Fernandez et al.
Article
Biology
Wojciech Wietrzynski et al.
Article
Biology
Yury S. Bykov et al.
Review
Microscopy
Jose-Jesus Fernandez
