Article
Biotechnology & Applied Microbiology
Weisong Zhao, Shiqun Zhao, Liuju Li, Xiaoshuai Huang, Shijia Xing, Yulin Zhang, Guohua Qiu, Zhenqian Han, Yingxu Shang, De-En Sun, Chunyan Shan, Runlong Wu, Lusheng Gu, Shuwen Zhang, Riwang Chen, Jian Xiao, Yanquan Mo, Jianyong Wang, Wei Ji, Xing Chen, Baoquan Ding, Yanmei Liu, Heng Mao, Bao-Liang Song, Jiubin Tan, Jian Liu, Haoyu Li, Liangyi Chen
Summary: Sparse structured illumination microscopy (Sparse-SIM) achieves nearly twofold resolution enhancement by utilizing sparse deconvolution algorithm, enabling the resolution of intricate biological structures such as small fusion pores, nuclear pores, and relative movements of inner and outer mitochondrial membranes.
NATURE BIOTECHNOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Michael Holtmannspoetter, Eike Wienbeuker, Timo Dellmann, Isabelle Watrinet, Ana J. Garcia-Saez, Kai Johnsson, Rainer Kurre, Jacob Piehler
Summary: Self-labeling enzymes (SLE) like the HaloTag are valuable tools in high and super-resolution fluorescence microscopy. New fluorogenic substrates for SLE allow imaging with excess dye. Two engineered variants of HaloTag7 with restored dehalogenase activity, reHaloTagS (approx. 0.006 s(-1)) and reHaloTagF (approx. 0.055 s(-1)), showed different turnover kinetics in vitro. Imaging with reHaloTag labeling demonstrated 3-5 times enhanced photostability, and single molecule imaging enabled controlled and stable labeling density over extended periods. Combination with structured illumination allowed simultaneous visualization of single molecule diffusion and organellar dynamics. These applications showcase the potential of reHaloTag labeling in advancing fluorescence microscopy techniques.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Neurosciences
Stefano Calovi, Federico N. Soria, Jan Tonnesen
Summary: STED microscopy is a super-resolution technique that allows imaging at higher spatial resolution than the diffraction limit of light, particularly well-suited for imaging inside live brain tissue. Over the past 20 years, STED microscopy has undergone extensive developments and facilitated remarkable neurophysiological discoveries.
NEUROBIOLOGY OF DISEASE
(2021)
Article
Multidisciplinary Sciences
Tianyan Liu, Till Stephan, Peng Chen, Jan Keller-Findeisen, Jingting Chen, Dietmar Riedel, Zhongtian Yang, Stefan Jakobs, Zhixing Chen
Summary: This study reports a mitochondrial inner membrane fluorescent marker, PK Mito Orange (PKMO), which features reduced phototoxicity and high stability, enabling super-resolution recordings of mitochondrial inner membrane dynamics. The PKMO dye is optically orthogonal with green and far-red markers, allowing multiplexed recordings. By using multi-color STED microscopy, interactions between mitochondria and other cellular components can be captured at sub-100 nm resolution.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Environmental Sciences
Xiuchao Yue, Xiaoxuan Chen, Wanxu Zhang, Hang Ma, Lin Wang, Jiayang Zhang, Mengwei Wang, Bo Jiang
Summary: A novel super-resolution method is proposed to reconstruct high-resolution remote sensing images, which outperforms state-of-the-art approaches in both quantitative indicators and visual qualities. The method utilizes preclassification, different SR networks, edge extraction, and loss functions to enhance the image reconstruction process.
Review
Computer Science, Hardware & Architecture
Shengyan Zhu, Caiqiu Zhou, Yongjian Wang
Summary: This paper proposes an infrared image super-resolution reconstruction algorithm based on pseudo texture transfer, which generates pseudo-infrared images using an image-to-image transfer learning framework and calculates the similarity of feature maps to reconstruct high-quality infrared images.
Article
Agricultural Engineering
Lorena Cardona, Catalina Arroyave, Adriana Aristiz
Summary: This work presents a new methodology for automatically measuring the morphological features of Spirulina filaments on microscopy images. A novel algorithm is presented that uses the variance of the distances between pixels on each half of the contour to identify filament ends. The proposed methodology can automatically and reliably estimate the morphological parameters of Spirulina filaments.
BIOSYSTEMS ENGINEERING
(2023)
Article
Environmental Sciences
Rudraksh Kapil, Guillermo Castilla, Seyed Mojtaba Marvasti-Zadeh, Devin Goodsman, Nadir Erbilgin, Nilanjan Ray
Summary: Operational forest monitoring often requires detailed information in the form of an orthomosaic created by stitching overlapping aerial images. However, using only RGB drone sensors for imaging results in reduced contrast and descriptive features. To address this, we propose a thermal orthomosaicking workflow that combines RGB and thermal images for higher quality and better alignment. Our technique achieves improved mutual information and preserves radiometric information from the original thermal imagery, making it suitable for downstream tasks such as tree crown detection. We provide an open-source tool to facilitate usage and further development.
Article
Biochemistry & Molecular Biology
Magalie Benard, Damien Schapman, Christophe Chamot, Fatemeh Dubois, Guenaelle Levallet, Hitoshi Komuro, Ludovic Galas
Summary: This study proposed a guide to optimize advanced light microscopy approaches by utilizing fluorescence lifetime of red/near-infrared dyes. The choice of appropriate imaging approach depends on fluorochrome number, characteristics, and STED compatibility. The combination of HyD's photon-counting mode and phasor plot analysis of fluorescence lifetimes enables flexible and fast imaging of multi-labeled living cells.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Environmental Sciences
Xin Zhao, Hui Li, Ping Wang, Linhai Jing
Summary: The proposed method improves the accuracy of matching features for multisource high-resolution remote sensing images by combining SIFT and ResNet features, demonstrating higher accuracies and more tie points compared to traditional feature-based methods.
Article
Chemistry, Multidisciplinary
Anselm F. L. Schneider, Laila S. Benz, Martin Lehmann, Christian P. R. Hackenberger
Summary: Super-resolution microscopy in living cells can be enhanced by the use of engineered cell-permeable and highly fluorescent nanobodies as intracellular targeting agents. These semi-synthetic nanobodies, with bright fluorescent signals achieved through intramolecular photostabilization, have a cleavable cell-penetrating peptide for efficient cellular entry. Their utility has been demonstrated in functional analysis through monitoring cell division and DNA replication via confocal and STED microscopy.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Nanoscience & Nanotechnology
Karolina Szafranska, Tanja Neuman, Zbigniew Baster, Zenon Rajfur, Oskar Szelest, Christopher Holte, Agata Kubisiak, Edyta Kus, Deanna L. Wolfson, Stefan Chlopicki, Balpreet S. Ahluwalia, Malgorzata Lekka, Marek Szymonski, Peter McCourt, Bartlomiej Zapotoczny
Summary: In this study, different types of microscopy techniques were compared to analyze fenestrations in liver sinusoidal endothelial cells (LSEC). Sample dehydration was found to alter fenestration diameters, and a combination of atomic force microscopy (AFM) with conventional microscopy was proposed to observe cell dynamics and obtain chemical information more effectively.
Article
Multidisciplinary Sciences
Kirti Prakash
Summary: This article discusses the performance of MINFLUX fluorescence microscopy technique, focusing on its spatial resolution, localization filtering, and imaging of biological samples. The analysis aims to provide guidance for future research directions and instrument investment.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Zhou Han-Qiu, Zhu Yin-Ru, Han Hong-Yi, Wang Lu-Wei, Yang Zhi-Gang, Yan Wei, Qu Jun-Le
Summary: Cells are the fundamental units of life with significant research implications in biology and medicine. Although the spatial structure of cells and organelles is well understood, their functions and interactions remain largely unknown. To address this gap, the study of subcellular organelles in vitro and in vivo has gained importance. Optical super-resolution imaging, specifically STED technology, has emerged as an effective tool for studying the nanoscale structure and function of subcellular organelles.
PROGRESS IN BIOCHEMISTRY AND BIOPHYSICS
(2023)
Article
Astronomy & Astrophysics
Paul Tiede, Avery E. E. Broderick, Daniel C. M. Palumbo, Andrew Chael
Summary: “The Event Horizon Telescope has provided the first image of the accretion environment of the supermassive black hole in the galaxy M87, revealing important details. The study investigates the sensitivity of the imaging parameters used in the analysis to ring ellipticity and measures the constraints on the ellipticity of M87*. It is found that the true ellipticity is biased low, preferring circular rings, even for simple geometric models. In order to place a constraint on the ellipticity, synthetic data sets from GRMHD simulations are analyzed, showing that intrinsic axis ratios of 2:1 are consistent with the observed ellipticity in the EHT image reconstructions.”
ASTROPHYSICAL JOURNAL
(2022)
Article
Biophysics
Mengyuan Sun, Kevin Hu, Joerg Bewersdorf, Thomas D. Pollard
Summary: PCFPs are widely used in super-resolution microscopy and studies of cellular dynamics, but our understanding of their photophysics is limited, hindering their quantitative application. Through experiments on formaldehyde fixation in fission yeast cells, it was found that fixation affects the photophysical properties of mEos3.2, but light fixation does not destroy the molecules. The study provides guidance on quantitatively comparing conditions for imaging mEos3.2-tagged molecules in yeast cells through a combination of imaging assays and mathematical models.
BIOPHYSICAL JOURNAL
(2021)
Article
Biochemical Research Methods
Jingyu Wang, Edward S. Allgeyer, George Sirinakis, Yongdeng Zhang, Kevin Hu, Mark D. Lessard, Yiming Li, Robin Diekmann, Michael A. Phillips, Ian M. Dobbie, Jonas Ries, Martin J. Booth, Joerg Bewersdorf
Summary: The development of single-molecule switching (SMS) fluorescence microscopy has allowed researchers to observe cell structures at unprecedented resolution. This protocol aims to guide interested researchers in establishing super-resolution microscopy in their laboratories. The process involves assembling the instrument, testing its performance, preparing test samples, acquiring images, and analyzing raw data to reconstruct 3D datasets.
Article
Optics
Nicholas Bender, Mengyuan Sun, Hasan Yilmaz, Joerg Bewersdorf, Hui Cao
Summary: This work demonstrates the design and creation of special speckle patterns for super-resolution microscopy, achieving a spatial resolution three times higher than the diffraction limit. The experimental results show that tailored speckles vastly outperform standard speckles, establishing customized speckles as a potent tool in parallelized super-resolution microscopy.
Article
Optics
Mary Grace M. Velasco, Mengyang Zhang, Jacopo Antonello, Peng Yuan, Edward S. Allgeyer, Dennis May, Ons M'Saad, Phylicia Kidd, Andrew E. S. Barentine, Valentina Greco, Jaime Grutzendler, Martin J. Booth, Joerg Bewersdorf
Summary: STED microscopy allows for three-dimensional visualization of dynamic nanoscale structures in living cells, but imaging deep inside biological tissue faces challenges. Researchers have developed a STED system that overcomes these challenges by combining various technologies to achieve deep aberration-corrected three-dimensional super-resolution imaging.
Article
Optics
Dong-Ryoung Lee, Joerg Bewersdorf
Summary: A concept was proposed to increase the imaging speed of super-resolution microscopy techniques by introducing highly flexible multifocal illumination and detection. The uniformity of the focus arrays was achieved by iteratively applying a weighted Gerchberg-Saxton phase retrieval algorithm. This approach is not only suitable for STED and isoSTED microscopes, but also applicable in confocal laser scanning microscopy.
Letter
Biochemical Research Methods
Zach Marin, Michael Graff, Andrew E. S. Barentine, Christian Soeller, Kenny Kwok Hin Chung, Lukas A. Fuentes, David Baddeley
Article
Biochemistry & Molecular Biology
Edward M. Courchaine, Andrew E. S. Barentine, Korinna Straube, Dong-Ryoung Lee, Joerg Bewersdorf, Karla M. Neugebauer
Summary: Biomolecular condensation plays a key role in cellular compartmentalization, with proteins like SMN promoting condensation through tudor domain-DMA interactions. The asymmetry or symmetry of DMA influences the organization of nuclear MLOs, as revealed by sub-diffraction microscopy.
Article
Biochemical Research Methods
Kenny K. H. Chung, Zhao Zhang, Phylicia Kidd, Yongdeng Zhang, Nathan D. Williams, Bennett Rollins, Yang Yang, Chenxiang Lin, David Baddeley, Joerg Bewersdorf
Summary: Two-color fluorogenic DNA-PAINT introduces self-quenching probes, improving imaging speed 26-fold without the need for optical sectioning.
Article
Biochemical Research Methods
Kevin M. Dean, Tonmoy Chakraborty, Stephan Daetwyler, Jinlong Lin, Gerard Garrelts, Ons M'Saad, Hannahmariam T. Mekbib, Fabian F. Voigt, Martina Schaettin, Esther T. Stoeckli, Fritjof Helmchen, Joerg Bewersdorf, Reto Fiolka
Summary: The protocol provides detailed instructions for assembling and operating a versatile variant of light-sheet fluorescence microscopy called axially swept light-sheet microscopy (ASLM), which offers an unparalleled combination of field of view, optical resolution, and optical sectioning. It includes information on the working principle, applications, practical tips, part lists, schematics, and software for instrument control of ASLM.
Editorial Material
Biochemistry & Molecular Biology
Florian Schueder, Joerg Bewersdorf
Summary: Spatial omics techniques provide comprehensive data about the identity and function of cells in tissues. Epigenetic multiplexing approaches like MERFISH allow researchers to study the epigenomic regulation of gene expression in tissue-specific regions.
Article
Cell Biology
Lukas A. Fuentes, Zach Marin, Jonathan Tyson, David Baddeley, Joerg Bewersdorf
Summary: This study demonstrates that Rtn4 forms linear-shaped oligomers that increase local curvature in the ER membrane. The research also reveals that the typical ER tubule possesses an elliptical cross-section with Rtn4 enriched at either end of the major axis.
JOURNAL OF CELL BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Mark E. Pownall, Liyun Miao, Charles E. Vejnar, Ons M'Saad, Alice Sherrard, Megan A. Frederick, Maria D. J. Benitez, Curtis W. Boswell, Kenneth S. Zaret, Joerg Bewersdorf, Antonio J. Giraldez
Summary: This study developed a new model called "kiss and kick" to explain gene regulation during zygotic genome activation. By using chromatin expansion microscopy, the researchers were able to visualize transcriptional elongation and the interaction between the pioneer factor Nanog and nucleosomes.
Article
Biochemical Research Methods
Seong J. An, Massimiliano Stagi, Travis J. Gould, Yumei Wu, Michael Mlodzianoski, Felix Rivera-Molina, Derek Toomre, Stephen M. Strittmatter, Pietro De Camilli, Joerg Bewersdorf, David Zenisek
Summary: A complete understanding of synaptic-vesicle recycling requires the use of multiple microscopy methods and probes that can be used with different techniques. This study presents a new single-vesicle probe based on the C2 domain of cPLA(2), which allows synaptic vesicles to be imaged at multiple levels of spatial and temporal resolution. This probe can also be used as a general endocytic marker for studying membrane recycling in various cell types.
CELL REPORTS METHODS
(2022)