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
Multidisciplinary Sciences
Michael J. Wester, David J. Schodt, Hanieh Mazloom-Farsibaf, Mohamadreza Fazel, Sandeep Pallikkuth, Keith A. Lidke
Summary: In this study, a robust drift correction method is proposed for super-resolution methods based on single molecule localization, which combines 3D registration with a fast post-processing algorithm, ensuring stability and drift correction for an indefinite time period without specialized hardware.
SCIENTIFIC REPORTS
(2021)
Article
Optics
Mingtao Shang, Zhiwei Zhou, Weibing Kuang, Yujie Wang, Bo Xin, Zhen-Li Huang
Summary: Single molecule localization microscopy often suffers from sample drift due to long image acquisition time, but using DPC microscopy can improve image contrast and provide a more precise and robust 3D drift correction method.
Article
Optics
Mengnan Liu, Yu Han, Xiaoqi Xi, Linlin Zhu, Huijuan Fu, Siyu Tan, Xiangzhi Zhang, Lei Li, Jian Chen, Bin Yan
Summary: Nanocomputed tomography is an effective tool for observing 3D structures of nanomaterials, but it requires correction phantom to reduce artifacts. This study proposes a rough-to-refined correction framework based on global mixed evaluation for precise drift estimation.
Article
Computer Science, Information Systems
Wenqiang Xu, Liangxiao Jiang, Chaoqun Li
Summary: Crowdsourcing services offer a fast and cost-effective way to obtain labeled data, but label noise is commonly present. This study introduces a Cross-Entropy-based Noise Correction method that outperforms existing techniques in mitigating label noise in crowdsourced data.
INFORMATION SCIENCES
(2021)
Article
Optics
Mingtao Shang, Zhen-Li Huang, Yujie Wang
Summary: This paper investigates the relationship among drift correction precision, localization precision, and position estimation precision through theoretical analysis and simulation. It proposes the concept of relative localization precision to evaluate the impact of drift correction on imaging resolution. This is of great significance for selecting the appropriate drift correction method.
Article
Engineering, Multidisciplinary
Johannes Degenhardt, Rainer Tutsch, Gaoliang Dai
Summary: A method for correcting non-linear drift distortions in all three coordinate axes of atomic force microscope (AFM) images is presented. The method involves two measurements of the sample with two orthogonal fast scan axes, dividing the AFM images into segments, determining the shifts of the surface features, and calculating the drift. This method allows for correction of nonlinear drift and can be applied to existing images by measuring the sample again.
MEASUREMENT SCIENCE AND TECHNOLOGY
(2023)
Article
Multidisciplinary Sciences
Olivier Acher, Matheus Belisario de Abreu, Alexander Grigoriev, Philippe de Bettignies, Maxime Vilotta, Thanh-Liem Nguyen
Summary: This study investigates the in-plane positioning capabilities of microscopes using machine-readable encoded patterned scales. The scales contain absolute position information and adequate software accurately determines the in-plane position from the captured scale images. This approach simplifies and expedites in-plane positioning experiments and commercially available scales and software were used.
SCIENTIFIC REPORTS
(2023)
Article
Computer Science, Artificial Intelligence
Toshimitsu Aritake, Hideitsu Hino, Shigeyuki Namiki, Daisuke Asanuma, Kenzo Hirose, Noboru Murata
Summary: This study utilizes multifocal plane microscopy to address the 3D single-molecule localization problem, but small lateral drifts of camera positions can deteriorate the estimation accuracy. A deep neural network is applied to solve this problem accurately and efficiently, achieving an accuracy of 20 nm laterally and 50 nm axially without explicit drift correction.
Article
Automation & Control Systems
Ze-yin Dong, Zi-hang Yu
Summary: Baseline drift problem commonly exists in spectral analysis due to detector nonlinearities and temperature variations. To address this, we propose a novel and high-precise algorithm called baseline estimation using morphological and iterative local extremum (MILE). Our algorithm first obtains all local extrema of the measured spectrum and estimates a coarse baseline using the PCHIP interpolation method. It then iteratively updates the baseline by finding local extrema of the coarse baseline and their adjacent data. By subtracting the estimated baseline, the spectrum is corrected with high precision.
CHEMOMETRICS AND INTELLIGENT LABORATORY SYSTEMS
(2023)
Article
Nanoscience & Nanotechnology
Jiahui Wang, Jimmy Ching-Cheng Hsu, Ting-Jui Ben Chang, T. Tony Yang
Summary: This article proposes a simple approach to address the issue in single-molecule localization microscopy (SMLM) caused by overaccumulation of localizations from fluorophores. The proposed method successfully corrects localization artifacts and restores superresolution results of various cellular structures and organelles, allowing for precise interpretation of molecular clusters.
Article
Materials Science, Multidisciplinary
Yinan Wu, Yongchun Fang, Zhi Fan, Cunhuan Liu
Summary: This paper presents a novel and robust algorithm to correct image distortion caused by vertical drift and slope in AFM, improving imaging quality effectively.
MICROSCOPY AND MICROANALYSIS
(2021)
Article
Biochemical Research Methods
Christopher H. Bohrer, Xinxing Yang, Shreyasi Thakur, Xiaoli Weng, Brian Tenner, Ryan McQuillen, Brian Ross, Matthew Wooten, Xin Chen, Jin Zhang, Elijah Roberts, Melike Lakadamyali, Jie Xiao
Summary: Distance distribution correction (DDC) is a method that eliminates repeat localizations caused by fluorophore blinking without the need for calibrations. Use of DDC yields accurate and quantifiable single-molecule localization microscopy data.
Article
Instruments & Instrumentation
JiaHao Yao, Hongxuan Guo, Ziqing Yin, Chang Liu, Bo Da, Zheng Liu, Yajie Chu, Li Zhong, Litao Sun
Summary: In this study, an improved TEM image drift correction strategy is proposed that enhances accuracy without additional time consumption. The strategy involves the extraction of multiple feature points from the first image and utilizes the Lucas-Kanade optical flow algorithm to calculate the optical field of these feature points in subsequent images. A high-precision sub-pixel level correction strategy using linear interpolation is also developed. Experimental results demonstrate the superiority of this strategy compared to the cross correlation algorithm, and its insensitivity to image size. Additionally, a semantic segmentation neural network is provided for electron microscope image pre-processing, expanding the applicability of the methodology.
REVIEW OF SCIENTIFIC INSTRUMENTS
(2023)
Article
Computer Science, Artificial Intelligence
Rohgi Toshio Meneses Chikushi, Roberto Souto Maior de Barros, Marilu Gomes N. Monte da Silva, Bruno Iran Ferreira Maciel
Summary: Data stream mining involves extracting information from continuously evolving large amounts of data, where learning algorithms can combine a classifier and drift detector to identify changes in prediction error distribution. While many methods are based on error rate distribution, empirical studies have shown that error rate can be influenced by temporal dependence. New approaches, including using dynamical system tools, have been proposed for concept drift detection in unsupervised scenarios with temporal dependencies.
EXPERT SYSTEMS WITH APPLICATIONS
(2021)
Correction
Chemistry, Multidisciplinary
Laura Restrepo-Perez, Gang Huang, Peggy R. Bohlander, Nathalie Worp, Rienk Eelkema, Giovanni Maglia, Chirlmin Joo, Cees Dekker
Review
Biochemistry & Molecular Biology
Carolien Bastiaanssen, Chirlmin Joo
Summary: Tetrahymena uniquely deals with transposable elements by having separate somatic and germline genomes in a single cell. During sexual reproduction, a small RNA directed system compares the two genomes to identify and process transposable elements. The chromatin context in Tetrahymena allows for potential advantages in genome editing and gene therapy compared to the CRISPR-Cas9 system.
Article
Biochemistry & Molecular Biology
Hamza Balci, Viktorija Globyte, Chirlmin Joo
Summary: The structural characteristics of the complex formed by CRISPR-Cas9 and target DNA are influenced by the stability of GQ and the position of PQS, leading to variations in conformational states and dynamics. The presence of PQS in the target or nontarget strand results in different structural heterogeneity within the target dsDNA and the R-loop, impacting Cas9 activity.
ACS CHEMICAL BIOLOGY
(2021)
Article
Chemistry, Multidisciplinary
Mike Filius, Sung Hyun Kim, Ivo Severins, Chirlmin Joo
Summary: The research team introduced a new method that allows for determining multiple distances between FRET pairs in a single object by resolving the FRET efficiency of multiple fluorophore pairs through transient binding of short DNA strands. This FRET X technology is expected to be a tool for high-resolution analysis of biomolecules and nanostructures.
Review
Biology
Eitan Lerner, Anders Barth, Jelle Hendrix, Benjamin Ambrose, Victoria Birkedal, Scott C. Blanchard, Richard Boerner, Hoi Sung Chung, Thorben Cordes, Timothy D. Craggs, Ashok A. Deniz, Jiajia Diao, Jingyi Fei, Ruben L. Gonzalez, Irina Gopich, Taekjip Ha, Christian A. Hanke, Gilad Haran, Nikos S. Hatzakis, Sungchul Hohng, Seok-Cheol Hong, Thorsten Hugel, Antonino Ingargiola, Chirlmin Joo, Achillefs N. Kapanidis, Harold D. Kim, Ted Laurence, Nam Ki Lee, Tae-Hee Lee, Edward A. Lemke, Emmanuel Margeat, Jens Michaelis, Xavier Michalet, Sua Myong, Daniel Nettels, Thomas-Otavio Peulen, Evelyn Ploetz, Yair Razvag, Nicole C. Robb, Benjamin Schuler, Hamid Soleimaninejad, Chun Tang, Reza Vafabakhsh, Don C. Lamb, Claus A. M. Seidel, Shimon Weiss
Summary: Single-molecule FRET (smFRET) has become a mainstream technique for studying biomolecular structural dynamics, with significant progress being made in sample preparation, measurement procedures, data analysis, algorithms, and documentation. Efforts have been made to streamline experiments and analyze results for obtaining quantitative information. Open science practices are strongly encouraged for further progress in this field.
Article
Biophysics
Carlos Victor de Lannoy, Mike Filius, Sung Hyun Kim, Chirlmin Joo, Dick de Ridder
Summary: FRET is a useful phenomenon in biomolecular investigations for nanoscale measurements, and a semisupervised approach with the web tool FRETboard has been proposed to fit models more intuitively. This approach accurately reproduces ground truth FRET statistics in simulated scenarios and retrieves parameters in vitro data in a fraction of the time required for manual classification. Additionally, FRETboard is designed to easily adapt to future developments in FRET measurement and analysis by being extendable to other models.
BIOPHYSICAL JOURNAL
(2021)
Article
Biochemical Research Methods
Javier Antonio Alfaro, Peggy Bohlander, Mingjie Dai, Mike Filius, Cecil J. Howard, Xander F. van Kooten, Shilo Ohayon, Adam Pomorski, Sonja Schmid, Aleksei Aksimentiev, Eric V. Anslyn, Georges Bedran, Chan Cao, Mauro Chinappi, Etienne Coyaud, Cees Dekker, Gunnar Dittmar, Nicholas Drachman, Rienk Eelkema, David Goodlett, Sebastien Hentz, Umesh Kalathiya, Neil L. Kelleher, Ryan T. Kelly, Zvi Kelman, Sung Hyun Kim, Bernhard Kuster, David Rodriguez-Larrea, Stuart Lindsay, Giovanni Maglia, Edward M. Marcotte, John P. Marino, Christophe Masselon, Michael Mayer, Patroklos Samaras, Kumar Sarthak, Lusia Sepiashvili, Derek Stein, Meni Wanunu, Mathias Wilhelm, Peng Yin, Amit Meller, Chirlmin Joo
Summary: Single-cell profiling methods have greatly impacted the understanding of cellular heterogeneity, although proteome profiling at the single-cell level is still in the early stages. The development of new technologies, such as single-molecule protein sequencing and innovations in mass spectrometry, will eventually enable broad sequence coverage in single-cell proteomics, leading to new biological discoveries and opportunities for ultra-sensitive disease diagnostics.
Correction
Biochemistry & Molecular Biology
Suzan Ruijtenberg, Stijn Sonneveld, Tao Ju Cui, Ive Logister, Dion de Steenwinkel, Yao Xiao, Ian J. MacRae, Chirlmin Joo, Marvin E. Tanenbaum
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2021)
Review
Biochemistry & Molecular Biology
Raman van Wee, Mike Filius, Chirlmin Joo
Summary: Single-molecule localization microscopy (SMLM) is a powerful tool for examining biological systems with unprecedented resolution. DNA-based point accumulation for imaging in nanoscale topography (DNA-PAINT) has faced challenges such as low throughput, long acquisition time, and difficulty integrating with live-cell imaging, but recent advances are addressing these issues and expanding its applications. The current state of DNA-PAINT is reviewed in light of these advancements, with consideration for further developments needed to achieve live-cell imaging.
TRENDS IN BIOCHEMICAL SCIENCES
(2021)
Editorial Material
Multidisciplinary Sciences
Chirlmin Joo, Amit Meller
Article
Multidisciplinary Sciences
Carlos Victor de Lannoy, Mike Filius, Raman van Wee, Chirlmin Joo, Dick de Ridder
Summary: The study introduces a method called FRET X fingerprinting for single-molecule protein identification, which aims to create fingerprints for proteins. Through simulations and experimental validation, the effectiveness of the method was demonstrated, successfully identifying complex mixtures including multiple proteins, providing a new analysis tool for targeted proteomics.
Article
Engineering, Electrical & Electronic
Miri Seo, Eunseo Yang, Dong Hoon Shin, Yugyeong Je, Chirlmin Joo, Kookjin Lee, Sang Wook Lee
Summary: In this study, we successfully reduced noise interference and improved the accuracy of mass detection in suspended graphene-based nanomechanical resonators using machine learning techniques.
ACS APPLIED ELECTRONIC MATERIALS
(2022)
Article
Computer Science, Artificial Intelligence
Luuk Loeff, Jacob W. J. Kerssemakers, Chirlmin Joo, Cees Dekker
Summary: Single-molecule techniques allow visualization of molecular dynamics with high resolution. AutoStepfinder is a fast, automated, bias-free step detection method that can be used for a wide variety of experimental traces, providing a robust and user-friendly analysis procedure.
Article
Biochemistry & Molecular Biology
Benjamin Davis, Keri Backus, Georg Winter, Roberto Chica, Dan Li, Sang Yup Lee, Chuan He, Amy Weeks, Christopher Overall, Shinya Hagihara, Ben Thuronyi, Siddhesh Kamat, Ling-Ling Chen, Ramon Hurtado Guerrero, Shao Yao, Lara K. Mahal, Christopher Voigt, Christina Woo, Erick Strauss, Kazuya Kikuchi, Timothy Dore, Sheena Radford, Xiang David Li, Won Do Heo, Giulio Superti-Furga, Tara Deans, Vsevolod Belousov, Megan Matthews, Colin Jackson, Shiva Malek, Herbert Waldmann, Anna Rising, Michael Jewett, Dimitrios Stamou, Emily Parker, Mario Murakami, Karen Polizzi, Itaru Hamachi, Tobias Erb, Chirlmin Joo, Motonari Uesugi, Rab Prinjha, Gidi Rechavi, Roberto Solano, Brenda Schulman, Yael David, Rob Oslund
Summary: In the last five years, the most exciting research achievements or technological innovations in chemical biology have garnered attention from many chemical biologists.
NATURE CHEMICAL BIOLOGY
(2021)
