Article
Engineering, Electrical & Electronic
Qiang Liu, Zhenguo Jing, Ang Li, Yueying Liu, Zhenjie Xia, Wei Peng
Summary: This work proposes a novel frequency-scanned parallel phase-shifting interferometry for simultaneous detection of high-frequency dynamic parameters and low-frequency quasi-static parameters. A MI and a 3 x 3 coupler are used for high-frequency vibration measurement, with a frequency swept laser source and modified phase shifting algorithm significantly improving the sampling rate of the dynamic MI. It can directly measure the asymmetric parameters of non-ideal couplers and perform spectral demodulation of multiple quasi-static parameters.
JOURNAL OF LIGHTWAVE TECHNOLOGY
(2021)
Article
Optics
Julio C. Estrada, Victor H. Flores, Javier Vargas
Summary: This paper introduces a two-step phase-shifting fringe pattern demodulation method using VU factorization, which is robust to non-constant background illuminations and modulating terms. The method can recover the phase without known phase shifts, normalized fringe patterns, or any special non-linear preprocessing. Tests with diverse interferograms demonstrate the feasibility of this method.
OPTICS AND LASERS IN ENGINEERING
(2021)
Article
Optics
Lin Chang, Bing Li, Yulan Wei, Yingjie Yu
Summary: An local spectral intensifying method using the Chirp-Z transform is introduced to implement efficient multi-surface phase demodulation. The proposed algorithm's robustness to common measurement errors is analyzed and demonstrated using Zernike polynomials. Experimental results confirm the effectiveness of the proposed method by measuring two transparent plates with different thicknesses.
OPTICS AND LASERS IN ENGINEERING
(2023)
Article
Optics
Kashmira Nakhoda, Lei Huang, Tianyi Wang, Dennis Kuhne, Joseph Porter, Mourad Idir, Charles Joenathan
Summary: This paper presents the in-lab development of an angular sensor based on a single reflection compact Sagnac interferometer using instantaneous phase shifting. The results show high repeatability and sensitivity over a range of 100 angles.
OPTICS AND LASER TECHNOLOGY
(2022)
Article
Optics
Gustavo A. Gomez-Mendez, Amalia Martinez-Garcia, David I. Serrano-Garcia, Juan Antonio Rayas-Alvarez, Areli Montes Perez, Juan M. Islas-Islas, Noel Ivan Toto-Arellano
Summary: This study proposes combining electronic speckle pattern interferometry with polarizing phase-shifting techniques to measure in-plane displacement fields, and demonstrates the effectiveness of the proposal through experimental validation.
OPTICS COMMUNICATIONS
(2021)
Article
Engineering, Electrical & Electronic
Qiang Liu, Zhenguo Jing, Yueying Liu, Ang Li, Zhenjie Xia, Wei Peng
Summary: A novel laser frequency modulated phase-shifting white-light interferometry (PS-WLI) is proposed to absolutely demodulate the cavity length of dynamic low-finesse Fabry-Perot sensor. By combining the advantages of frequency-switched two-step phase shifting interferometry and scanning WLI, the method can achieve absolute measurement with high sampling rate, effectively demodulating vibration signals between 0.5 to 20 kHz.
JOURNAL OF LIGHTWAVE TECHNOLOGY
(2021)
Article
Optics
Qinnan Zhang, Shengyu Lu, Jiaosheng Li, Dong Li, Xiaoxu Lu, Liyun Zhong, Jindong Tian
Summary: This paper proposes a method using deep learning framework to generate multiple phase-shifting interferograms equivalent to multiple images, by training the model to map a single frame interferogram to three phase-shifting interferograms. This approach achieves high-precision dynamic phase measurement with similar accuracy to traditional methods and better generalization ability.
OPTICS COMMUNICATIONS
(2021)
Article
Optics
Chenhui Hu, Lei Chen, Donghui Zheng, Yuntao Wang, Zhiyao Ma, Zhe Zhang, Jianxin Li
Summary: This article discusses the phase error caused by parameter mismatch in simultaneous phase-shifting interferometry and proposes a phase-extraction method to solve these problems.
OPTICS AND LASERS IN ENGINEERING
(2022)
Article
Engineering, Multidisciplinary
Lin Chang, Yingjie Yu
Summary: The difficulty in measuring transparent flats lies in the fact that the measured surfaces contribute corresponding sub-signals to the captured interferograms. The accuracy of the frequency solution in traditional algorithms is not satisfactory due to frequency leakage. A Fourier transform-based frequency correction algorithm has been proposed to address this issue, showing significant improvements.
Review
Green & Sustainable Science & Technology
Sungtae Kim, Jurim Jeon, Yangjin Kim, Naohiko Sugita, Mamoru Mitsuishi
Summary: This review introduces the design and assessment of phase-shifting algorithms in the Fizeau interferometer for precision measurement of surface shape and optical thickness of silicon wafers and glass plates in the semiconductor industry. Different phase-shifting algorithms are categorized based on their error compensation ability. The optical setup and principle of phase extraction using phase-shifting interferometry are explained, and design methods for error source elimination are introduced. The error compensation abilities of the designed algorithms are estimated.
INTERNATIONAL JOURNAL OF PRECISION ENGINEERING AND MANUFACTURING-GREEN TECHNOLOGY
(2023)
Article
Optics
Dong Yang, Yanfeng Zhang, Zhongming Yang
Summary: We proposed a novel optical surface shapes measurement method based on conformal mapping-angular phase -shifting interferometry (APSI). The method involves rotating a Q-plate in the reference light path to introduce a 90-degree phase shift. By utilizing the mathematical tool of conformal mapping, high-precision surface shape demodulation is achieved. The removal of the helical phase in the compound phase resulted in surface shape deviations of 3.33 nm (PV) and 0.26 nm (RMS). This work establishes a foundation for surface shape measurement and compound phase demodulation using vortex beams.
OPTICS AND LASERS IN ENGINEERING
(2023)
Review
Optics
Fuzhong Bai, Jiwei Lang, Xiaojuan Gao, Yang Zhang, Jiahai Cai, Jianxin Wang
Summary: Simultaneous phase-shifting interferometry (SPSI) allows for the simultaneous acquisition of multiple phase-shifted interferograms and enables dynamic wavefront measurement using a phase-shifting algorithm. This article classifies and summarizes research progress on spatial phase shifting approaches for SPSI systems, focusing on beam-splitting techniques and phase shift achievement. The key problem affecting SPSI technology is discussed, along with a review of methods for accurate position registration of multi-channel phase-shifted interferograms. This review aims to stimulate further research in the field of phase-shifting interferometry.
Article
Engineering, Electrical & Electronic
Yan Zhao, Ke Hu, Fengwei Liu
Summary: In this letter, a Multi-Stage phase-shifting network (MSPS-Net) is proposed for one-shot phase retrieval interferometry based on Multi-Stage Progressive Image Restoration. This network excellently generates three interferograms with specific phase shifts from interferograms recorded in a single frame, and metrics such as PSNR and SSIM indicate high similarity to the real one. The proposed method retrieves error maps with higher accuracy than the latest phase-shifting network built by Encoder and Decoder, based on the analysis of different types of aberrations. All experimental results demonstrate that this solution is applicable for high-accuracy dynamic phase measurement and exhibits excellent generalization ability.
IEEE PHOTONICS TECHNOLOGY LETTERS
(2023)
Article
Optics
Tatsuki Tahara, Yuichi Kozawa, Ayumi Ishii, Koki Wakunami, Yasuyuki Ichihashi, Ryutaro Oi
Summary: A new phase-shifting interferometry technique is proposed in this study, using only two in-line phase-shifted self-interference holograms without the need for additional recording or estimation. The effectiveness of the technique is demonstrated through experiments on incoherent digital holographic microscopy and color-multiplexed fluorescence digital holography. The study also achieves two-color-multiplexed four-step phase-shifting incoherent digital holography for the first time.
Article
Optics
Shanta Hardas Patil, Rishikesh Kulkarni
Summary: A computationally efficient phase shift estimation algorithm is proposed for two-step phase-shifting interferometry based on a cost function minimization technique. The proposed method accurately estimates the phase shift over a wide range, resulting in reliable phase estimation. It has a higher computational efficiency than existing state-of-the-art methods due to its analytical solution.
Article
Optics
Javier Vargas, Jose A. Gomez-Pedrero, J. Antonio Quiroga, Jose Alonso
Summary: The study introduces an approach to enhance cryo-electron microscopy (cryo-EM) postprocessed maps using a multiscale tubular filter. By analyzing the eigenvalues of the Hessian matrix, the method enhances elongated structures and attenuates blob-like and plate-like structures, improving the interpretability and analysis of the maps.
Article
Optics
Jose A. Gomez-Pedrero, Julio C. Estrada, Jose Alonso, Juan A. Quiroga, Javier Vargas
Summary: This work proposes a new algorithm for demodulating fringe patterns using principal component analysis. The algorithm incrementally processes interferograms using singular value decomposition, and determines the minimum number of images required for accurate demodulation through a phase quality parameter.
Article
Biochemical Research Methods
James Michael Krieger, Carlos Oscar S Sorzano, Jose Maria Carazo, Ivet Bahar
Summary: Cryo-electron microscopy (cryoEM) is an important technique for studying the structure and dynamics of large and dynamic supramolecular complexes. Due to the unique characteristics of these molecular systems, traditional approaches are not suitable for structural modeling and molecular dynamics simulations, necessitating the development of new computational methods and models. Elastic network models, normal mode analysis, and ensemble analyses have played a significant role in this field.
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
(2022)
Review
Chemistry, Multidisciplinary
Jose Luis Vilas, Jose Maria Carazo, Carlos Oscar S. Sorzano
Summary: This article reviews the main contributions of image processing to the current reconstruction workflow of single particle analysis (SPA) in cryo-electron microscopy (CryoEM), emphasizing the time evolution of algorithms across different steps.
Article
Chemistry, Multidisciplinary
Erney Ramirez-Aportela, Jose M. Carazo, Carlos Oscar S. Sorzano
Summary: Single-particle cryo-electron microscopy is a powerful technique for determining the 3D structure of biological molecules. This article explores the use of deepEMhancer, a deep-learning approach, as a regularizer in the refinement process. The combination of deepEMhancer with RELION improves image quality and is particularly useful for studying membrane proteins.
Article
Biochemistry & Molecular Biology
C. O. S. Sorzano, J. M. Carazo
Summary: Cryo-Electron Microscopy (CryoEM) is a well-established method to determine the three-dimensional structure of biological macro-molecules. Continuous advancements in technology and methodology have contributed to its success in sample preparation, image processing, and map interpretation. This paper analyzes trends in over 1,000 methodological papers, highlighting the growth of Single Particle Analysis (SPA) and the potential impact of Electron Tomography. It also emphasizes the importance of best practices in methods reporting and the evolving field of atomic modeling.
JOURNAL OF STRUCTURAL BIOLOGY
(2022)
Article
Optics
Manuel Servin, Moises Padilla, Gonzalo Paez, Guillermo Garnica
Summary: This article proposes a non-iterative, universal phase-shifting algorithm (UPSA) for phase-demodulation, regardless of the characteristics of the phase steps. Additionally, a null-testing criterion is introduced to verify the accuracy of the demodulated phase.
OPTICS AND LASERS IN ENGINEERING
(2022)
Article
Biochemistry & Molecular Biology
Arkadiusz W. Kulczyk, Carlos Oscar S. Sorzano, Przemyslaw Grela, Marek Tchorzewski, Nilgun E. Tumer, Xiao-Ping Li
Summary: This study uses cryo-EM to determine the structure of Shiga toxin 2a (Stx2a) complexed with the ribosomal P-stalk. The findings reveal the dynamics of the Stx2a-P-stalk interaction and suggest that the binding interface between Stx2a and the P-stalk could be a potential target for drug discovery.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Tristan Bepler, Andrew J. Borst, Jonathan Bouvette, Giuseppe Cannone, Songye Chen, Anchi Cheng, Ao Cheng, Quanfu Fan, Fanis Grollios, Harshit Gupt, Meghna Gupta, Theo Humphreys, Paul T. Kim, Huihui Kuang, Yilai Li, Alex J. Noble, Ali Punjani, William J. Rice, Carlos Oscar S. Sorzano, Scott M. Stagg, Joshua Strauss, Lingbo Yu, Bridget Carragher, Clinton S. Potter
Summary: This report provides an overview of the discussions, presentations, and consensus thinking from the Workshop on Smart Data Collection for CryoEM. The workshop aimed to address next generation data collection strategies that integrate machine learning and real-time processing into the workflow to reduce or eliminate the need for operator intervention.
JOURNAL OF STRUCTURAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
J. Garcia Condado, A. Munoz-Barrutia, C. O. S. Sorzano
Summary: Single-Particle Analysis by Cryo-Electron Microscopy is a technique used to determine the 3D structure of biological macromolecules. This article introduces HaPi, a method that automatically determines the handedness of macromolecule electron density maps solved by CryoEM. HaPi utilizes convolutional neural networks and a consensus strategy to determine the hand of the maps.
JOURNAL OF STRUCTURAL BIOLOGY
(2022)
Article
Chemistry, Multidisciplinary
C. O. S. Sorzano, M. A. Perez-de-la-Cruz Moreno, J. L. Vilas
Summary: This article investigates the absorption models of drugs in the body, including carrier mediated transport and saturable absorption. By studying the exact solutions of different absorption models, the differences between these models can be illustrated.
PHARMACEUTICAL RESEARCH
(2023)
Article
Multidisciplinary Sciences
D. Herreros, R. R. Lederman, J. M. Krieger, A. Jimenez-Moreno, M. Martinez, D. Myska, D. Strelak, J. Filipovic, C. O. S. Sorzano, J. M. Carazo
Summary: The advancements in Cryo-EM Single Particle Analysis play a vital role in understanding the relationship between macromolecular structure and function in biological processes. Traditional approaches have limitations in fully characterizing the conformational landscape due to the small number of accurately reconstructed states. To overcome this, we propose an extension of the Zernike3D method that can extract continuous flexibility information directly from particle datasets. Additionally, the introduced ZART reconstruction algorithm minimizes blurring induced by molecular motions.
NATURE COMMUNICATIONS
(2023)
Article
Optics
Ricardo Legarda-Saenz, Jorge L. Flores, Manuel Servin, Anabel Martin-gonzalez
Summary: One challenge in phase measuring deflectometry is to recover the wavefront from objects with discontinuities or non-differentiable gradient fields. We propose integrating such gradient fields by solving an LP-norm minimization problem, resulting in a nonlinear partial differential equation. This equation can be efficiently solved using a well-known numerical method without external parameters. Numerical reconstructions on synthetic and experimental data demonstrate the effectiveness of our proposed method.
Article
Biochemistry & Molecular Biology
D. Herreros, J. Kiska, E. Ramirez-Aportela, J. Filipovic, J. M. Carazo, C. O. S. Sorzano
Summary: The main purpose of CryoEM Single Particle Analysis is to reconstruct the three-dimensional structure of a macromolecule. ZART is a new Algebraic Reconstruction Technique that can include continuous flexibility information to improve resolution and reduce motion blurring.
JOURNAL OF MOLECULAR BIOLOGY
(2023)
Article
Chemistry, Analytical
David Strelak, Daniel Marchan, Jose Maria Carazo, Carlos O. S. Sorzano
Summary: This article conducts a comparative analysis of the quality and performance of commonly used software for movie alignment in Cryo-EM. The tested software includes FlexAlign, MotionCor2, Relion MotionCor, Warp, and CryoSPARC. The alignment precision, power spectra density, and performance scaling were compared using generated phantom data and real datasets.
