Review
Chemistry, Analytical
Yucheng Sun, Zengnan Wu, Yuting Shang, Seong Ho Kang, Jin-Ming Lin
Summary: This article provides a brief overview of the technical development, applications, challenges, and future directions in single-cell analysis using single-molecule detection-based super-resolution microscopy (SMDSRM), aiming to guide researchers in promoting the methodological development and exploring the potential of SMDSRM for single-cell analysis.
TRAC-TRENDS IN ANALYTICAL CHEMISTRY
(2023)
Article
Biochemical Research Methods
Alon Saguy, Onit Alalouf, Nadav Opatovski, Soohyen Jang, Mike Heilemann, Yoav Shechtman
Summary: Single-molecule localization microscopy (SMLM) has significantly improved spatial resolution in biological imaging, but has limitations in observing dynamics at high temporal resolution. In this study, we introduce DBlink, a deep-learning-based method that reconstructs super spatiotemporal resolution videos from SMLM data. DBlink utilizes a convolutional neural network combined with a bidirectional long short-term memory network to capture long-term dependencies between different frames. Experimental results demonstrate the effectiveness of DBlink in various scenarios, including simulated structures and live-cell dynamic SMLM. This advancement in super-resolution imaging of dynamic processes in living cells is crucial.
Article
Optics
Prakash Joshi, Partha Pratim Mondal
Summary: Molecular assembly in cellular environments is crucial for understanding biological mechanisms. Biophysical parameters directly linked to cellular states require a multimodel approach for accurate estimation.
Article
Biology
Jigmi Basumatary, Neptune Baro, Prakash Joshi, Partha Pratim Mondal
Summary: Single-molecule localization microscopy (SMLM) is a powerful technique that improves spatial resolution beyond the diffraction limit and allows for the analysis of biological features at the nanoscale. This study introduces a single molecule-based scanning SMLM (scanSMLM) system that enables rapid volume imaging. By rapidly changing the aperture of an electrically-tunable lens, the system achieves selective imaging of the axial object plane, allowing for volume scanning. The technique is employed to visualize the architecture of actin-filaments, the distribution of Meos-Tom20 molecules on the mitochondrial membrane, and the clustering of Hemagglutinin (HA) protein single molecules for studying Influenza-A disease progression. The system enables 3D visualization of HA distribution, providing unprecedented insights into the disease progression at the single-molecule level.
COMMUNICATIONS BIOLOGY
(2023)
Review
Cell Biology
Mark Tingey, Steven J. Schnell, Wenlan Yu, Jason Saredy, Samuel Junod, Dhrumil Patel, Abdullah A. Alkurdi, Weidong Yang
Summary: The transient nature of RNA and temporal constraints within cells make it difficult to image RNA, especially endogenous RNA in transfected cells. However, recent advances have provided researchers with the tools to image endogenous RNA at the cellular and single-molecule level.
Review
Cell Biology
Jianquan Xu, Yang Liu
Summary: Chromatin organization plays a crucial role in gene regulation and genome maintenance. Disruption of chromatin structure is associated with various pathological processes and diseases. Recent advances in single molecule localization microscopy (SMLM) provide new opportunities to visualize chromatin architecture at nanometer resolution and improve our understanding of diseases.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Optics
Zhengyi Zhan, Chuankang Li, Xin Liu, Xiaofan Sun, Chenyin He, Cuifang Kuang, Xu Liu
Summary: This study presents a technique for simultaneously estimating the position and orientation of single molecules with ultra-high precision, which is suitable for tracking in living cells. Numerical simulations were conducted to explore the performance and potential applications. The results confirm that the proposed method can provide reasonable estimates even under weak signal conditions.
Article
Materials Science, Multidisciplinary
Zachary Hallenbeck, Esther A. Wertz
Summary: This work introduces a new technique that combines super-resolution microscopy with fluorescence lifetime imaging microscopy to study the enhancement of single-molecule decay rate by plasmonic nanoparticles. The technique provides high spatial resolution and temporal resolution, allowing for a better understanding of the mechanisms of plasmon-enhanced emission.
ADVANCED OPTICAL MATERIALS
(2022)
Article
Cell Biology
Mattia Marenda, Elena Lazarova, Sebastian van de Linde, Nick Gilbert, Davide Michieletto
Summary: Understanding biological function involves identifying and characterizing complex patterns of molecules, which can be quantitatively measured by single-molecule localization microscopy. Interconnected protein clusters are common within nuclear proteins, suggesting an important role in genome organization and function, while absent in ceramides located in the plasma membrane.
JOURNAL OF CELL BIOLOGY
(2021)
Review
Cell Biology
Evelyn Garlick, Steven G. Thomas, Dylan M. Owen
Summary: Immune cells consist of a diverse set of cells that undergo complex biological processes, with the cellular cytoskeleton playing a key role in regulating these processes. Optical microscopy is well-suited for imaging and quantitatively describing the structure and dynamics of the cytoskeleton. The latest methodology, hardware, and software for labeling and analyzing cytoskeletal structures are reviewed, with highlighted challenges and areas for future development.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Chemistry, Multidisciplinary
Vinit Sheth, Xuxin Chen, Evan M. Mettenbrink, Wen Yang, Meredith A. Jones, Ons M'Saad, Abigail G. Thomas, Rylee S. Newport, Emmy Francek, Lin Wang, Alex N. Frickenstein, Nathan D. Donahue, Alyssa Holden, Nathan F. Mjema, Dixy E. Green, Paul L. DeAngelis, Joerg Bewersdorf, Stefan Wilhelm
Summary: Super-resolution microscopy was used to visualize the distribution of nanoparticles inside mammalian cells. By exploiting the light scattering properties of nanoparticles, label-free imaging of intracellular nanoparticles was achieved. This technology can be widely used to study the intracellular fate of nanoparticles and inform the development of safer and more effective nanomedicines.
Article
Multidisciplinary Sciences
Yiming Li, Wei Shi, Sheng Liu, Ivana Cavka, Yu-Le Wu, Ulf Matti, Decheng Wu, Simone Koehler, Jonas Ries
Summary: Global fitting algorithm globLoc for multi-channel SMLM significantly improves localization precision and color assignment, by extracting maximum information from correlated signals in multi-channel data through flexible parameter sharing and modeling.
NATURE COMMUNICATIONS
(2022)
Article
Chemistry, Multidisciplinary
Teodora Andrian, Pietro Delcanale, Silvia Pujals, Lorenzo Albertazzi
Summary: The functionalization of nanoparticles with functional moieties is important for achieving cell targeting in nanomedicine. The correlation between size and ligand number in nanoparticles is crucial for understanding structure-activity relations. A new method combining super-resolution microscopy and transmission electron microscopy, called super-resCLEM, has been introduced to accurately measure these parameters and address the issue of heterogeneity in nanoparticle populations.
Article
Optics
Micaela Toscani, Oscar E. Martinez, Sandra Martinez
Summary: This work conducts a performance analysis of the SUPPOSe algorithm, a deconvolution method based on superposition of point sources of equal intensity. By testing with synthetic and experimental images, the accuracy, precision, and resolution of the method are determined under different signal/noise conditions.
OPTICS AND LASERS IN ENGINEERING
(2023)
Article
Biochemical Research Methods
Mengting Li, Qihang Song, Yinghao Xiao, Junnan Wu, Weibing Kuang, Yingjun Zhang, Zhen-Li Huang
Summary: Quantifying the resolution of super-resolution images is crucial for biologists using super-resolution microscopy. However, traditional FWHM resolution quantification methods are time-consuming, labor-intensive, and prone to errors. This paper investigates the influencing factors and introduces the LuckyProfiler plugin, providing biologists with a simple and effective way to quantify the resolution of super-resolution images.
BIOMEDICAL OPTICS EXPRESS
(2022)
Biographical-Item
Chemistry, Physical
Julie S. Biteen, Matthew D. Lew, Katherine A. Willets
JOURNAL OF PHYSICAL CHEMISTRY B
(2022)
Article
Chemistry, Multidisciplinary
Oumeng Zhang, Weiyan Zhou, Jin Lu, Tingting Wu, Matthew D. Lew
Summary: We present a radially and azimuthally polarized microscope that achieves high detection and estimation performance in single-molecule orientation-localization microscopy (SMOLM). This microscope allows us to measure the localization, orientation, and rotational wobble of Nile red (NR) within supported lipid bilayers (SLBs). The imaging results reveal the presence of randomly oriented binding pockets and cholesterol-rich nanodomains within the SLBs.
Article
Optics
Tingting Wu, Jin Lu, Matthew D. Lew
Summary: This article presents the pixOL algorithm, which optimizes the pixels within a phase mask to produce an engineered Green's function, enabling simultaneous measurement of the 3D orientation and location of a single molecule. The results demonstrate high precision in both experiments and simulations.
Article
Chemistry, Multidisciplinary
Meikun Shen, Tianben Ding, Che Tan, William H. Rackers, Dongyan Zhang, Matthew D. Lew, Bryce Sadtler
Summary: By controlling the surface-ligand redox chemistry on nanowires, the concentration of active sites on photocatalysts can be enhanced, leading to a significant improvement in photocatalytic water oxidation activity. This research result is of great significance for understanding the role of ligands in the catalytic process of nanocrystal catalysts.
Article
Optics
Tingting Wu, Peng Lu, Md Ashequr Rahman, Xiao LI, Matthew D. Lew
Summary: Dipole-spread function (DSF) engineering can reshape microscope images to maximize the sensitivity of measuring the 3D orientations of dipole-like emitters. However, Poisson shot noise, overlapping images, and fitting high-dimensional information pose challenges in image analysis for single-molecule orientation-localization microscopy (SMOLM). In this study, a deep-learning based estimator called Deep-SMOLM is introduced, which achieves superior precision in measuring 3D orientation and 2D position, approaching the theoretical limit. Deep-SMOLM also demonstrates excellent performance in estimating overlapping images of emitters.
Article
Optics
James M. Jusuf, Matthew D. Lew
Summary: This study introduces a simple heuristic for designing a point spread function (PSF) for precise measurement of the distance between two emitters and identifies two types of PSFs that achieve high performance in 3D emitter resolution.
Article
Optics
Oumeng Zhang, Zijian Guo, Yuanyuan He, Tingting Wu, Michael D. Vahey, Matthew D. Lew
Summary: Single-molecule orientation-localization microscopy is a powerful tool for studying biochemical processes, but the limited photon budget poses challenges for high-dimensional imaging. A raMVR microscope has been developed with isotropic 3D spatial resolution and precision in measuring molecular orientations, enabling detailed imaging of molecular dynamics within biological and chemical systems.
Article
Biochemical Research Methods
Mika Hayashi, Shinsuke Ohnuki, Yating Tsai, Naoko Kondo, Yuqi Zhou, Hongqian Zhang, Natsumi Tiffany Ishii, Tianben Ding, Maik Herbig, Akihiro Isozaki, Yoshikazu Ohya, Keisuke Goda
Summary: This study evaluates the necessity of using artificial intelligence in image-activated cell sorting (IACS) by comparing the performance of feature gating, classical machine learning, and deep learning with convolutional neural networks. The results show that deep learning with CNNs significantly improves enrichment capability while increasing processing time.
Meeting Abstract
Biophysics
Brian Sun, Weiyan Zhou, Tianben Ding, Tara S. Porter, Tingting Wu, Matthew D. Lew
BIOPHYSICAL JOURNAL
(2023)
Meeting Abstract
Biophysics
Tingting Wu, Matthew R. King, Mina Farag, Rohit V. Pappu, Matthew D. Lew
BIOPHYSICAL JOURNAL
(2023)
Meeting Abstract
Biophysics
Oumeng Zhang, Zijian Guo, Yuanyuan He, Tingting Wu, Michael Vahey, Matthew D. Lew
BIOPHYSICAL JOURNAL
(2023)
Meeting Abstract
Biophysics
Tianben Ding, Matthew D. Lew
BIOPHYSICAL JOURNAL
(2022)
Meeting Abstract
Biophysics
Tingting Wu, Jin Lu, Matthew R. King, Rohit V. Pappu, Matthew D. Lew
BIOPHYSICAL JOURNAL
(2022)
Meeting Abstract
Biophysics
Oumeng Zhang, Weiyan Zhou, Matthew D. Lew
BIOPHYSICAL JOURNAL
(2022)