Article
Optics
Chengxin Zhou, Xianxin Han, Zhenqian Wang, Ran Sun, Wanqing Zhong, Giancarlo Pedrini, Liyun Zhong, Xiaoxu Lu
Summary: In this paper, a differential phase measurement method based on synchronous phase shift determination is proposed. The method achieves a phase measurement accuracy higher than 0.007 rad and exhibits advantages in error compensation, anti-interference, and noise suppression.
Article
Optics
Chengxin Zhou, Tao Huang, Zhenghui Wang, Shengde Liu, Liyun Zhong, Giancarlo Pendrini, Caojin Yuan, Xiaoxu Lu
Summary: The study introduces a quantitative differential interference contrast microscopy system that utilizes a liquid crystal shearing assembly, allowing for DIC imaging with arbitrary shearing amount and direction. By compensating for errors using a quarter-wave plate and a mirror, the system demonstrates high practical value in quantitative phase measurement.
OPTICS AND LASERS IN ENGINEERING
(2021)
Article
Optics
Jiaming Lyu, Jiaming Qian, Kailong Xu, Yuxia Huang, Chao Zuo
Summary: Structured illumination microscopy (SIM) is a significant super-resolution technique in bio-science for observing live-cell dynamics. This Letter proposes a robust motion-resistant SIM algorithm based on principal component analysis (mrPCA-SIM), which can efficiently compensate for nonuniform pixel shifts and phase errors in each raw illumination image. Experiments demonstrate that mrPCA-SIM achieves more robust imaging quality in complex, unstable conditions compared with conventional methods, promising a more compatible and flexible imaging tool for live cells.
Article
Biochemical Research Methods
Yu-Chun Lin, Yuan Luo, Ying-Ju Chen, Huei-Wen Chen, Tai-Horng Young, Hsuan-Ming Huang
Summary: This study presents a single-shot quantitative differential phase-contrast (DPC) imaging method based on deep learning (DL) and color-encoded illumination. The DL-based model is trained to generate an isotropic quantitative phase image directly from a single-shot intensity measurement. The results show that the DL-based phase images are visually similar to the ground-truth phase images and have a high structural similarity index. This study demonstrates the feasibility of using DL to generate quantitative phase imaging from a single-shot intensity measurement.
BIOMEDICAL OPTICS EXPRESS
(2023)
Article
Geochemistry & Geophysics
Weijie Chen, Zhenhong Jia, Jie Yang, Nikola K. Kasabov
Summary: A method of multispectral image enhancement based on improved WPCA and IFD filtering is proposed in this paper. By selecting appropriate bands, compensating each band, introducing a mask, and adjusting brightness values, the method achieves enhancement of multispectral images, and experimental results demonstrate its superiority.
IEEE GEOSCIENCE AND REMOTE SENSING LETTERS
(2022)
Article
Optics
Kiarash Tajbakhsh, Samira Ebrahimi, Masoomeh Dashtdar
Summary: This paper presents a quantitative differential phase-contrast microscopy based on Talbot interferometry. The system uses a low temporal coherence light source and reconstructs differential phase-contrast images of transparent samples using a phase-shifting algorithm. The method eliminates speckle noise and undesirable interferences to obtain high-quality images. The spatial phase stability of the system is compared to other common-path interferometers.
Article
Optics
Ying Ma, Yang Wang, Lin Ma, Juanjuan Zheng, Min Liu, Peng Gao
Summary: This paper proposes a reflective quantitative phase-contrast microscopy based on annular epi-illumination of light-emitting diodes, which enables high-resolution imaging. By phase-retarding the unscattered wave from the sample, finer structures or three-dimensional tomography of reflective samples can be obtained, making it significant for imaging of industrial devices and biomedical dynamics.
Article
Food Science & Technology
Morad Mousazadeh, Mohammad Mousavi, Zahra Emam-Djomeh, Salar Ali Ahmed, Mehri Hadinezhad, Hamed Hassanzadeh
Summary: Principal component analysis (PCA) was used to investigate the effects of different ingredients on the sensory descriptors of a spread based on pistachio oil. PCA revealed that adhesiveness, hardness, oiliness, and fluidness were the most significant factors. The power law model was found to be more accurate in fitting the samples. The optimum combination of variables (15% pistachio oil, 7.5% cocoa butter, 0.3% xanthan gum, and 1% distilled monoglyceride) produced desirable spreads that mimic commercial spreads.
FOOD SCIENCE & NUTRITION
(2023)
Article
Biochemical Research Methods
Xiaomin Lai, Sheng Xiao, Chen Xu, Shanhui Fan, Kaihua Wei
Summary: Digital holographic microscopy is commonly used to obtain quantitative phase information of transparent cells, but the presence of aberrations can affect the accuracy of the results. A technique utilizing derivative-based principal component analysis (dPCA) has been proposed to achieve aberration-free phase imaging efficiently and effectively by extracting and compensating for almost all aberrations.
JOURNAL OF BIOMEDICAL OPTICS
(2021)
Article
Optics
Chiara Bonati, Damien Loterie, Timothe Laforest, Christophe Moser
Summary: A lock-in method is introduced to enhance the phase contrast in incoherent differential phase contrast (DPC) imaging. By analog removal of the background, this method improves the phase sensitivity. Experimental results show an 8-fold increase in sensitivity and a 70-fold reduction in data collection compared to standard DPC measurements. The method achieves a single-shot sensitivity of 0.7 mrad at a frame rate of 1400 frames per second. This approach opens up possibilities for the use of incoherent phase microscopy in biological applications requiring high phase sensitivity and millisecond response time.
PHOTONICS RESEARCH
(2022)
Article
Biochemical Research Methods
Kuangnan Fang, Rui Ren, Qingzhao Zhang, Shuangge Ma
Summary: Dimension reduction techniques like PCA, PLS, and CCA are extensively used in the analysis of high-dimensional omics data. Integrative analysis, which outperforms meta-analysis and individual-data analysis, has been developed for multiple datasets with compatible designs. We developed the R package iSFun to facilitate integrative dimension reduction analysis, offering comprehensive analysis options under different models and penalties.
Article
Computer Science, Information Systems
Ang Li, Jingqi Fu, Huaming Shen, Sizhou Sun
Summary: An indoor positioning algorithm based on principal component analysis (PCA) and adaptive hierarchical clustering has been proposed to improve positioning accuracy by aggregating reference points and conducting cluster-based PCA feature extraction. Experimental results show that this algorithm can increase positioning accuracy by 9.3% compared to traditional fingerprint algorithms.
IEEE INTERNET OF THINGS JOURNAL
(2021)
Article
Computer Science, Interdisciplinary Applications
An-Cin Li, Sunil Vyas, Yu-Hsiang Lin, Yi-You Huang, Hsuan-Ming Huang, Yuan Luo
Summary: The proposed DL-based method utilizes U-net architecture to generate isotropic qDPC microscopy images from the least number of measurements. Training the model with a patch-wise approach improves phase uniformity and retrieves missing spatial frequencies in 1-axis reconstructed images. Results show higher PSNR and SSIM values compared to other methods, indicating the advantage of using the U-net model for isotropic qDPC microscopy in high-resolution quantitative studies for cell biology.
IEEE TRANSACTIONS ON MEDICAL IMAGING
(2021)
Article
Optics
Ignacio Iglesias
Summary: This non-interferometric technique offers a simple way to achieve quantitative phase microscopy by rotating a mask to detect wavefront gradient. The method also includes calibrating the sensor and processing signals for phase extraction. Three-dimensional images of polystyrene microspheres immersed in index-matching liquid were successfully obtained using this technique.
OPTICS AND LASER TECHNOLOGY
(2021)
Article
Physiology
Marie Piriou, Corinne Lorenzo, Isabelle Raymond-Letron, Sophie Coronas-Dupuis, Laetitia Pieruccioni, Jacques Rouquette, Christophe Guissard, Jade Chaumont, Louis Casteilla, Valerie Planat-Benard, Philippe Kemoun, Paul Monsarrat
Summary: The study developed a framework based on multi-fluorescence imaging and spectral Principal Component Analysis for thick section microscopy, allowing accurate preservation and delineation of different anatomical/morphological features of complex tooth-supporting tissues, providing an effective method for histopathological investigation.
FRONTIERS IN PHYSIOLOGY
(2022)
Article
Physics, Applied
Rong Lin, Xiaoliang He, Zhilong Jiang, Cheng Liu, Shouyu Wang, Yan Kong
Summary: The study introduces a dual-layer graphene THz absorber with high absorption rate in a wide THz frequency range and insensitivity to incident angle and polarization.
JOURNAL OF PHYSICS D-APPLIED PHYSICS
(2021)
Article
Optics
Miao Yu, Yuanjie Gu, Zhilong Jiang, Xiaoliang He, Yan Kong, Cheng Liu, Lingyu Ai, Shouyu Wang
Summary: Traditional 2D images lose details of targets out of depth-of-focus, while all-in-focus images can focus on targets in an extended depth-of-view by fusing multi-focus images. REPAID, using deep neural networks, achieves high-quality all-in-focus imaging suitable for dynamic targets in large depth-of-view.
Article
Dentistry, Oral Surgery & Medicine
Maxime Rousseau, Javier Vargas, Frank Rauch, Juliana Marulanda, Jean-Marc Retrouvey
Summary: This study quantitatively assessed the morphological characteristics of osteogenesis imperfecta (OI) patients, identifying significant differences in facial features among different types of patients. The researchers successfully trained a PCALog model to automatically detect OI patients based on facial landmarks.
ORTHODONTICS & CRANIOFACIAL RESEARCH
(2021)
Article
Biology
Ruben Sanchez-Garcia, Josue Gomez-Blanco, Ana Cuervo, Jose Maria Carazo, Carlos Oscar S. Sorzano, Javier Vargas
Summary: Sanchez-Garcia et al. introduce DeepEMhancer, a deep learning-based method for automatic post-processing of raw cryo-electron microscopy density maps. It globally improves local quality of density maps and shows potential as a useful tool for structures without readily available PDB models.
COMMUNICATIONS BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
David Strelak, Amaya Jimenez-Moreno, Jose L. Vilas, Erney Ramirez-Aportela, Ruben Sanchez-Garcia, David Maluenda, Javier Vargas, David Herreros, Estrella Fernandez-Gimenez, Federico P. de Isidro-Gomez, Jan Horacek, David Myska, Martin Horacek, Pablo Conesa, Yunior C. Fonseca-Reyna, Jorge Jimenez, Marta Martinez, Mohamad Harastani, Slavica Jonic, Jiri Filipovic, Roberto Marabini, Jose M. Carazo, Carlos O. S. Sorzano
Summary: Xmipp is an open-source software package developed by the Biocomputing Unit of the Spanish National Center for Biotechnology, consisting of multiple programs for processing data from electron microscopy and electron tomography. Despite numerous publications on new programs and functionalities added to Xmipp, there has been no single publication on Xmipp as a package since 2013. This article provides an overview of the changes and new work done on Xmipp since then, as well as an insight into the technologies and future developments of the package.
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
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
Qiang Lu, Fake Lu, Xiaoliang He, Zhilong Jiang, Hongyan Lu, Fan Zhu, Cheng Liu, Shouyu Wang, Yan Kong
Summary: A numerical model for multipulse laser drilling is constructed, and it is found that temperature accumulation, thermal stress, and crater morphology change induced by previous laser pulses promote subsequent pulse laser drilling.
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
Nanoscience & Nanotechnology
Xiaoliang He, Suhas P. Veetil, Zhilong Jiang, Yan Kong, Shouyu Wang, Cheng Liu, Jianqiang Zhu
Summary: Ptychography is a lensless imaging technique that reconstructs an object and illumination simultaneously. It has become a powerful tool in high resolution imaging and optical metrology. This study presents a detailed theoretical analysis, numerical simulations and experimental results on the relationship between reconstructed images and object-detector distance error.
Article
Optics
Shuaichao Wang, Xiali Gao, Pengfei Zhu, Xiaoliang He, Zhilong Jiang, Yan Kong, Shouyu Wang, Cheng Liu
Summary: A three-wavelength photoelasticity method is proposed to simplify the optical setup and speed up data acquisition. By recording six intensity images with circularly polarized illuminations of three close wavelengths, accurate computation of phase retardation and inner stress can be achieved. The method avoids the mechanical rotations required by classic photoelasticity techniques, enabling speedy data acquisition and measurement of dynamic samples using a simple and compact optical setup. The feasibility of this suggested three-wavelength digital photoelasticity method is confirmed through theoretical analyses, numerical simulations, and experimental evidence.
Article
Optics
Xiaoli Ji, Xiaoliang He, Zhilong Jiang, Yan Kong, Shouyu Wang, Cheng Liu
Summary: By deducing a formula and conducting analytical analysis, the relationship among the highest achievable resolution of ptychographic iterative engine (PIE), its illumination angle, and its collection angle was discussed. Curved illumination was proposed to enhance the resolution for PIE, and a corresponding computing algorithm was proposed to avoid undersampling effect without increasing the size of the computing matrix, thus enabling high-resolution PIE imaging with a simple experimental setup. The feasibility of this proposed method was verified both numerically and experimentally.
Article
Optics
Lin Zhu, Zhibo Xiao, Chao Chen, Aihui Sun, Xiaoliang He, Zhilong Jiang, Yan Kong, Liang Xue, Cheng Liu, Shouyu Wang
Summary: sPhaseStation is a label-free whole slide quantitative phase imaging system based on transport of intensity phase microscopy, which can capture high-resolution digital images of microscope slides and provide accurate phase retrieval.
Article
Optics
Zhilong Jiang, Suhas P. Veetil, Xiaoliang He, Aihui Sun, Yan Kong, Cheng Liu, Jianqiang Zhu
Summary: Depth resolved imaging is achieved by displacing the sample laterally in a standard digital holographic setup. Holograms are recorded in the reflection geometry while the sample is moved, and an algorithm is developed to reconstruct the complex amplitude of the sample at specific focal depths. The recommended method significantly reduces the amount of information required for reconstruction. Experimental findings using a basic holographic setup suggest that this approach is suitable for three-dimensional imaging applications, particularly for high transmittance materials.
Meeting Abstract
Biophysics
Shintaroh Kubo, Ahmad Khalifa, Muneyoshi Ichikawa, Daniel Dai, Corbin S. Black, Katya Peri, Shun Kai Yang, Javier Vargas, Khanh Huy Bui
BIOPHYSICAL JOURNAL
(2021)
