Review
Biology
Michela Relucenti, Giuseppe Familiari, Orlando Donfrancesco, Maurizio Taurino, Xiaobo Li, Rui Chen, Marco Artini, Rosanna Papa, Laura Selan
Summary: Bacterial biofilms cause infections that are often resistant to antibiotics, necessitating detailed imaging techniques for research. Scanning electron microscopy with customized protocols is preferred for ultrastructural characterization of biofilm matrix and bacterial cells in drug treatment studies, providing unparalleled image quality and resolution. Various imaging methodologies, including traditional and innovative scanning electron microscopy techniques, have been used in biofilm studies to deepen understanding of their structure.
Article
Engineering, Multidisciplinary
Patrycja Wyszkowska, Robert Duchnowski
Summary: Terrestrial laser scanning provides a point cloud with hundreds or thousands of points, some of which may be mismeasured. Modern statistical methods, such as M-split estimation, are required to process the non-homogeneous observation set. This paper proposes new robust variants of M-split estimation that are twice as accurate as existing methods and can tolerate up to 50% outliers, exceeding the capabilities of traditional robust methods.
Article
Anatomy & Morphology
Naglaa F. Madkour, Mohamed M. A. Abumandour, Raafat El-Bakary, Ashraf Karkoura, Samir El-Gendy, Mohamed Alsafy
Summary: The present study characterized the ultrastructural roof of the oral cavity in juvenile and adult Epinephelus aeneus using SEM. The results showed the presence of five tooth bands, an upper valve, and a palatine region in both age groups. This study provides important data for aquaculture in Egypt.
MICROSCOPY RESEARCH AND TECHNIQUE
(2022)
Article
Chemistry, Multidisciplinary
Frederic Joucken, Cristina Bena, Zhehao Ge, Eberth Quezada-Lopez, Sarah Pinon, Vardan Kaladzhyan, Takashi Taniguchi, Kenji Watanabe, Aires Ferreira, Jairo J. R. Velasco
Summary: Graphite commonly used for preparing graphene devices contains a significant amount of native defects, impacting the electronic properties of Bernal-stacked bilayer graphene. The distribution of scattering vectors shows a clear carrier density dependence. The dilute native defects identified in the study are found to be an important extrinsic source of scattering, influencing charge carrier mobility at low temperatures.
Article
Anatomy & Morphology
Hoon-Seok Jang, Guhnoo Yun, Husna Mutahira, Mannan Saeed Muhammad
Summary: A new focus measure operator based on the adaptive sum of weighted modified Laplacian is proposed in this research, which uses GLV to select window size and assigns appropriate weights to Modified Laplacian values based on pixel distances, with experimental results demonstrating its effectiveness.
MICROSCOPY RESEARCH AND TECHNIQUE
(2021)
Article
Multidisciplinary Sciences
J. C. Stinville, J. M. Hestroffer, M. A. Charpagne, A. T. Polonsky, M. P. Echlin, C. J. Torbet, V. Valle, K. E. Nygren, M. P. Miller, O. Klaas, A. Loghin, I. J. Beyerlein, T. M. Pollock
Summary: The development of high-fidelity mechanical property prediction models relies on large volumes of microstructural feature data. However, spatially correlated measurements of 3D microstructure and deformation fields have been rare. This study presents a unique multi-modal dataset that combines state-of-the-art experimental techniques for 3D tomography and high-resolution deformation field measurements.
Article
Geosciences, Multidisciplinary
Z. Pastore, P. Lelievre, S. A. McEnroe, N. S. Church
Summary: Scanning Magnetic Microscopy (SMM) is an important magnetometry technique that helps us understand the origin of rock behavior. In this study, 3D magnetic vector inversion was used to quantify the remanent magnetization in a norite sample and it was found that the main source of magnetization is pyroxenes.
GEOPHYSICAL RESEARCH LETTERS
(2022)
Article
Chemistry, Multidisciplinary
Yuhiro Segawa, Kenji Yamazaki, Jun Yamasaki, Kazutoshi Gohara
Summary: A new method for measuring the 3D atomic structure of free-standing graphene ripples using TEM is proposed and experimentally validated. The specimen in the experiment was found to be moving upward, and the ripple was approximated as a composite of sinusoidal waves while measuring the time dependence of its height and lateral size.
Proceedings Paper
Optics
Hernando Altamar-Mercado, Alberto Patino-Vanegas, Andres G. Marrugo
Summary: White Light Scanning Interferential Microscopy is a technique used to determine the 3D topography of surfaces with nanometer resolution. This study determined an adequate axial range for averaging and estimating the intensity of EFI images, with the highest SNR and UQI values being 44.332 and 0.9997, respectively.
DIMENSIONAL OPTICAL METROLOGY AND INSPECTION FOR PRACTICAL APPLICATIONS XI
(2022)
Article
Plant Sciences
Keith E. Duncan, Kirk J. Czymmek, Ni Jiang, August C. Thies, Christopher N. Topp
Summary: This study presents technical advances in using lab-based X-ray microscopy for high-resolution 3D imaging of plant samples at multiple scales. Serial imaging and improved sample preparation methods allow for the generation of sub-micron 3D volumes co-registered with lower magnification scans, providing explicit contextual reference. This method bridges the imaging gap between light and electron microscopy and can be applied to various economically and scientifically important plant systems.
Article
Chemistry, Multidisciplinary
Chong Chen, Pengcheng C. Ding, Zhuo Li, Guoqiang Q. Shi, Ye Sun, Lev N. Kantorovich, Flemming Besenbacher, Miao Yu
Summary: This study reports the super-robust complexes formed by xanthine and sodium and demonstrates their high thermal stability in a high-temperature environment. These findings support the theory of life originating from hydrothermal environments and reveal the robustness of the complexes and their ability to induce electron transfer in harsh conditions.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Optics
Yingying Qin, Ankit Butola, Krishna Agarwal
Summary: A rigorous forward model solver for conventional coherent microscope is developed based on Maxwell's equations, considering vectorial waves and multiple-scattering effect. The scattered field can be calculated with given refractive index distribution, and bright field images can be obtained through combining scattered field and reflected illumination. The model is applicable to other forms of label-free coherent microscopes as well.
Article
Engineering, Environmental
David Wertheim, Lisa Miyashita, Gary Foley, Ian Gill, Richard Giddens, Gavin Gillmore, Ruaraidh Dobson, Sean Semple, Ana Rule, Jonathan Grigg
Summary: Using confocal microscopy, this study examined the three-dimensional appearances and elemental characteristics of particulate matter found in the air at roadside and underground railway stations. The results showed that some particles have sharp surfaces, and the particles at the railway station primarily consist of iron, calcium, and silicon.
ENVIRONMENTAL SCIENCE & TECHNOLOGY LETTERS
(2023)
Article
Multidisciplinary Sciences
Priya Paulachan, Jorg Siegert, Ingo Wiesler, Roland Brunner
Summary: In this paper, a fully automated and high-efficient end-to-end convolutional neural network model is developed to classify and locate thousands of through silicon vias (TSVs) and provide statistical information. The model uses scanning acoustic microscopy (SAM) imaging to generate interference patterns of the TSVs, and scanning electron microscopy (SEM) is used to validate and identify the patterns. Compared to semi-automated machine learning approaches, the model shows outstanding performance with 100% localization accuracy and over 96% classification accuracy. This approach is not limited to SAM-image data and is an important step towards zero defect strategies.
SCIENTIFIC REPORTS
(2023)
Article
Engineering, Electrical & Electronic
Thibaut Eloy, Etienne Baudrier, Marine Laporte, Virginie Hamel, Paul Guichard, Denis Fortun
Summary: Single particle reconstruction is a powerful technique in 3D fluorescence microscopy, which improves the axial resolution and fluorescence labeling degree by reconstructing the average volume of a biological particle from multiple views with unknown poses. This paper proposes a dedicated single particle reconstruction method for convolutional models, overcoming issues such as template bias, restriction to 2D data, high computational cost, and lack of robustness to low fluorescent labeling. The method achieves better resolution and reconstruction error with low computational cost, as demonstrated on synthetic data and real datasets of centrioles.
IEEE TRANSACTIONS ON COMPUTATIONAL IMAGING
(2023)
Article
Optics
Andres G. Marrugo, Raul Vargas, Lenny A. Romero, Song Zhang
Summary: The proposed method aims to increase the overall accuracy of a large-scale structured light system by multi-stage calibration, calibrating intrinsic and extrinsic parameters separately and establishing pixel-wise phase-to-coordinate relationships using polynomial functions to achieve sub-millimeter high precision within a large volume.
Article
Optics
Jhacson Meza, Sonia H. Contreras-Ortiz, Lenny A. Romero, Andres G. Marrugo
Summary: The proposed 3D multimodal medical imaging system integrates freehand ultrasound and structured light 3D reconstruction, showing high accuracy and reproducibility without the need for registration.
OPTICAL ENGINEERING
(2021)
Article
Optics
Lenny A. Romero, Andres G. Marrugo, Maria S. Millan
Summary: This article explores the possibility of extending the depth of focus of an imaging lens using an asymmetric quartic phase-mask, while keeping aberration within a relatively low level. The proposed method is suitable for ophthalmic applications, relying on the patient's neural adaptation to their own aberrations for clear imaging. The numerical and experimental results are validated.
Editorial Material
Optics
Maria S. Millan, Andres G. Marrugo
Article
Optics
Raul Vargas, Lenny A. Romero, Song Zhang, Andres G. Marrugo
Summary: This Letter presents a novel structured light system model that takes into account local lens distortion by pixel-wise rational functions. The authors utilize a stereo method for initial calibration and then estimate the rational model for each pixel. The proposed model achieves high measurement accuracy within and outside the calibration volume, demonstrating its robustness and accuracy.
Article
Biochemical Research Methods
Juan S. Sierra, Jesus Pineda, Daniela Rueda, Alejandro Tello, Angelica M. Prada, Virgilio Galvis, Giovanni Volpe, Maria S. Millan, Lenny A. Romero, Andres G. Marrugo
Summary: This paper proposes a UNet-based segmentation approach for assessing the human corneal endothelium (CE) in Fuchs' dystrophy, which achieves reliable CE morphometric assessment and guttae identification.
BIOMEDICAL OPTICS EXPRESS
(2023)
Proceedings Paper
Computer Science, Artificial Intelligence
Caleb D. Romero-Mercado, Sonia H. Contreras-Ortiz, Andres G. Marrugo
Summary: This study investigates the impact of different speckle filtering methods on the performance of convolutional neural networks (CNNs) in ultrasound image segmentation. The results show that the SRAD filter performs the best even in low quality data, and the lowest values for standard deviation and variance indicate lower data dispersion, better repeatability, and increased confidence in accuracy.
APPLIED COMPUTER SCIENCES IN ENGINEERING, WEA 2022
(2022)
Proceedings Paper
Optics
Raul Vargas, Lenny A. Romero, Song Zhang, Andres G. Marrugo
Summary: This article introduces a hybrid calibration procedure based on the standard stereo-vision method, which can improve the measurement accuracy of structured-light systems. Experimental results demonstrate that even with simple linear models and mapping functions, the measurement accuracy can be significantly improved. Further improvement can be achieved by using nonlinear models, without the need for elaborate calibration procedures or sophisticated ancillary equipment.
DIMENSIONAL OPTICAL METROLOGY AND INSPECTION FOR PRACTICAL APPLICATIONS XI
(2022)
Proceedings Paper
Optics
Hernando Altamar-Mercado, Alberto Patino-Vanegas, Andres G. Marrugo
Summary: White Light Scanning Interferential Microscopy is a technique used to determine the 3D topography of surfaces with nanometer resolution. This study determined an adequate axial range for averaging and estimating the intensity of EFI images, with the highest SNR and UQI values being 44.332 and 0.9997, respectively.
DIMENSIONAL OPTICAL METROLOGY AND INSPECTION FOR PRACTICAL APPLICATIONS XI
(2022)
Article
Optics
Andres G. Marrugo, Atilio Bustos-Gonzalez, Edgar Rueda
Summary: This study evaluated the state of optics research in Colombia based on international journal publications. The research output has increased significantly over the past two decades, with a majority of the articles published in high-impact journals. Over 25 higher education institutions actively contribute to this research, collaborating both nationally and internationally. Colombian optics research is ranked second in Latin America, with a normalized citation impact close to the world average.
OPTICA PURA Y APLICADA
(2022)
Proceedings Paper
Computer Science, Artificial Intelligence
Eberto Benjumea, Juan S. Sierra, Jhacson Meza, Andres G. Marrugo
Summary: Pose estimation of surgical instruments is a common issue in medical science, with marker occlusion posing a challenge. An adaptable multi-target attachment with ArUco markers is proposed as a solution to occlusion issues, enabling precise and redundant real-time pose estimation. Encouraging results suggest the multi-target device could be beneficial in clinical settings.
PATTERN RECOGNITION (MCPR 2021)
(2021)
Proceedings Paper
Computer Science, Artificial Intelligence
Jhacson Meza, Lenny A. Romero, Andres G. Marrugo
Summary: MarkerPose is a system for automatic pose estimation based on three circular target and stereo vision system, aiming to provide high-accuracy pose estimation. It utilizes deep neural networks for marker point detection and achieves robust target point detection under low lighting and motion blur conditions. It outperforms classical computer vision techniques in terms of accuracy and demonstrates suitability for applications requiring highly accurate pose estimation.
2021 IEEE/CVF CONFERENCE ON COMPUTER VISION AND PATTERN RECOGNITION WORKSHOPS, CVPRW 2021
(2021)
Proceedings Paper
Engineering, Electrical & Electronic
Jesus Pineda, Hernando Altamar-Mercado, Lenny A. Romero, Andres G. Marrugo
DIMENSIONAL OPTICAL METROLOGY AND INSPECTION FOR PRACTICAL APPLICATIONS IX
(2020)
Proceedings Paper
Computer Science, Artificial Intelligence
Juan S. Sierra, Jesus Pineda, Eduardo Viteri, Daniela Rueda, Beatriz Tibaduiza, Ruben D. Berrospi, Alejandro Tello, Virgilio Galvis, Giovanni Volpe, Maria S. Millan, Lenny A. Romero, Andres G. Marrugo
APPLICATIONS OF MACHINE LEARNING 2020
(2020)
Proceedings Paper
Engineering, Electrical & Electronic
Jhacson Meza, Raul Vargas, Lenny A. Romero, Song Zhang, Andres G. Marrugo
DIMENSIONAL OPTICAL METROLOGY AND INSPECTION FOR PRACTICAL APPLICATIONS IX
(2020)