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Cross-system biological image quality enhancement based on the generative adversarial network as a foundation for establishing a multi-institute microscopy cooperative network

arXiv

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arXiv 2024年

作者： Panek, Dominik Rząca, Carina Szczypior, Maksymilian Sorysz, Joanna Misztal, Krzysztof Baster, Zbigniew Rajfur, Zenon Doctoral School of Exact and Natural Sciences Jagiellonian University ul. Lojasiewicza 11 Kraków30-348 Poland Department of Molecular and Interfacial Biophysics Faculty of Physics Astronomy and Applied Computer Science Jagiellonian University ul. Lojasiewicza 11 Kraków30‑348 Poland Undergraduate Program in Biophysics Faculty of Physics Astronomy and Applied Computer Science Jagiellonian University ul. Lojasiewicza 11 Kraków30‑348 Poland Undergraduate program in Biomedical Engineering Faculty of Electrical Engineering Automatics Computer Science and Biomedical Engineering AGH University of Science and Technology Al. A. Mickiewicza 30 Building B-1 Kraków30-059 Poland Division of Computational Mathematics Faculty of Mathematics and Computer Science Jagiellonian University 6 Lojasiewicza St. Kraków Poland

High-quality fluorescence imaging of biological systems is limited by processes like photobleaching and phototoxicity, and also in many cases, by limited access to the latest generations of microscopes. Moreover, low temporal resolution can lead to a motion blur effect in living systems. Our work presents a deep learning (DL) generative-adversarial approach to the problem of obtaining high-quality (HQ) images based on their low-quality (LQ) equivalents. We propose a generative-adversarial network (GAN) for contrast transfer between two different separate microscopy systems: a confocal microscope (producing HQ images) and a wide-field fluorescence microscope (producing LQ images). Our model proves that such transfer is possible, allowing us to receive HQ-generated images characterized by low mean squared error (MSE) values, high structural similarity index (SSIM), and high peak signal-to-noise ratio (PSNR) values. For our best model in the case of comparing HQ-generated images and HQ-ground truth images, the median values of the metrics are 6·10-4, 0.9413, and 31.87, for MSE, SSIM, and PSNR, respectively. In contrast, in the case of comparison between LQ and HQ ground truth median values of the metrics are equal to 0.0071, 0.8304, and 21.48 for MSE, SSIM, and PSNR respectively. Therefore, we observe a significant increase ranging from 14% to 49% for SSIM and PSNR respectively. These results, together with other single-system cross-modality studies, provide proof of concept for further implementation of a cross-system biological image quality enhancement. © 2024, CC BY-SA.

关键词： Fluorescence imaging

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Spontaneous and Induced Oscillations in Confined Epithelia

arXiv

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arXiv 2024年

作者： Parmar, Toshi Dow, Liam P. Pruitt, Beth L. Cristina Marchetti, M. Department of Physics University of California Santa Barbara Santa BarbaraCA93106 United States Interdisciplinary Program in Quantitative Biosciences University of California Santa Barbara Santa BarbaraCA93106 United States Departments of Bioengineering and of Mechanical Engineering University of California Santa Barbara Santa BarbaraCA93106 United States

The feedback between mechanical and chemical signals plays a key role in controlling many biological processes and collective cell behavior. Here we focus on the emergence of spatiotemporal density waves in a one-dimensional"cell train." Combining a minimal theoretical model with in vitro experiments on MDCK epithelial cells confined to a linear pattern, we examine the spontaneous oscillations driven by feedback between myosin activation and mechanical deformations, as well as their effect on the response of the tissue to externally applied deformations. We show that the nature and frequency of spontaneous oscillations is controlled by the size of the cell train, with a transition from size-dependent standing waves to intrinsic spontaneous waves at the natural frequency of the tissue. The response to external boundary perturbations exhibit a resonance at this natural frequency, providing a possible venue for inferring the mechanochemical couplings that control the tissue behavior from rheological experiments. Copyright © 2024, The Authors. All rights reserved.

关键词： Tissue

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Frustrated metastable-to-equilibrium grain boundary structural transition in NbMoTaW due to segregation and chemical complexity

arXiv

引用

arXiv 2023年

作者： Geiger, Ian Apelian, Diran Pan, Xiaoqing Cao, Penghui Luo, Jian Rupert, Timothy J. Material and Manufacturing Technology University of California IrvineCA92697 United States Department of Materials Science and Engineering University of California IrvineCA92697 United States Department of Physics and Astronomy University of California IrvineCA92697 United States Department of Mechanical and Aerospace Engineering University of California IrvineCA92697 United States Department of NanoEngineering University of California San Diego La Jolla CA92093 United States Program in Materials Science and Engineering University of California San Diego La Jolla CA92093 United States

Grain boundary structural transitions can lead to significant changes in the properties and performance of materials. In multi-principal element alloys, understanding these transitions becomes complex due to phenomena such as local chemical ordering and multi-component segregation. Using atomistic simulations, we explore a metastable-to-equilibrium grain boundary structural transition in NbMoTaW. The transition, characterized by structural disordering and reduced free volume, shows high sensitivity to its local chemical environment. Most notably, the transition temperature range of the alloy is more than twice that of a pure metal. Differences in composition between coexisting metastable and equilibrium structures highlight the change in local site availability due to structural relaxation. Further examination of grain boundaries with fixed chemical states at varying temperatures reveals that the amount of segregation significantly influences the onset temperature yet has minimal effect on the transition width. These insights underscore the profound effect of chemical complexity and ordering on grain boundary transitions in complex concentrated alloys, marking a meaningful advancement in our understanding of grain boundary behavior at the atomic level. Copyright © 2023, The Authors. All rights reserved.

关键词： Grain boundaries

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BPS2025 - Mutagenesis of claudin-15 reveals structural basis for channel assembly and ion selectivity in tight junctions

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Biophysical Journal 2025年第3期124卷 546a-546a页

作者： Sarah McGuinness Samaneh Sajjadi Fatemeh Khalili-Araghi Department of Biomedical Engineering University of Illinois Chicago Chicago IL USA Department of Mechanical and Industrial Engineering University of Illinois Chicago Chicago IL USA Department of Physics University of Illinois Chicago Chicago IL USA

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Evaluate the Fidelity of Synthetic Tissues Used in Escharotomy Simulators 1

引用

SEM Annual Conference and Exposition on Experimental and Applied Mechanics, 2020

作者： Lee, Sangrock Rahul Hannay, Vanessa Gallagher, Samara Lee, Hanna Imtiaz, Aisha Turkseven, Melih Ryason, Adam Makled, Basiel Parsey, Conner Norfleet, Jack De, Suvranu Department of Mechanical Aerospace and Nuclear Engineering Rensselaer Polytechnic Institute TroyNY United States Center for Modeling Simulation and Imaging in Medicine Rensselaer Polytechnic Institute TroyNY United States Department of Biomedical Engineering Rensselaer Polytechnic Institute TroyNY United States U.S. Army Futures Command Combat Capabilities Development Command Soldier Center STTC OrlandoFL United States

ISBN: (数字)9783030597658

ISBN: (纸本)9783030597641

Patients with full thickness circumferential burns may require an urgent and relatively high-risk procedure known as an "escharotomy" to preserve limb perfusion and sometimes airway ventilation. The burned skin is incised down to the subcutaneous level, providing decompression through the incision sites. A delay in performing an escharotomy, or an inadequately performed escharotomy, may lead to true compartment syndrome endangering life and limb. With the Army’s emerging doctrine of prolonged field care, non-expert providers must be trained to perform escharotomies when indicated. However, existing physical simulations fall short of delivering the fidelity necessary to train the procedure by not providing adequate haptic and visual cues. To improve the fidelity of escharotomy simulations, gaps in performance between synthetic tissue and full thickness burned tissue must be measured. This work evaluates the fidelity of synthetic tissues used in escharotomy simulators with that of the full thickness burned tissues characterized using an ex vivo porcine model. Incision and cutting experiments are performed at the rates relevant to the escharotomy procedure. A statistical analysis shows a significant difference in the critical force to rupture synthetic tissues and burned porcine skin tissues. © The Society for Experimental Mechanics, Inc. 2021.

关键词： Statistical methods

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Real-Time Probabilistic Reachability Forecasting for Gliders in the Gulf of Mexico

Real-Time Probabilistic Reachability Forecasting for Gliders...

引用

OCEANS 2024 - Halifax, OCEANS 2024

作者： Mule, E.M. Haley, P.J. Mirabito, C. Dimarco, S.F. Mahmud, S. Dancer, A. Ge, X. Knap, A.H. Liu, Y. Nwankwo, U.C. Glenn, S. Miles, T.N. Aragon, D. Coleman, K. Smith, M. Leber, M. Ramos, R. Storie, J. Stuart, G. Marble, J. Barros, P. Chassignet, E.P. Bower, A. Furey, H.H. De La Cruz, B. Jaimes Shay, L.K. Tenreiro, M. Sanz, E. Pallas Sheinbaum, J. Perez-Brunius, P. Wilson, D. Van Smirren, J. Monreal-Jiménez, R. Salas-De-León, D.A. Tereza, V.K. Contreras Feldman, M. Khadka, M. Lermusiaux, P.F.J. Massachusetts Institute of Technology Department of Mechanical Engineering CambridgeMA United States Texas A&m University Department of Oceanography United States Rutgers University Department of Marine and Coastal Sciences United States Woods Hole Group Inc. United States Fugro Netherlands Department of Earth Ocean and Atmospheric Science Florida State University United States Physical Oceanography Woods Hole Oceanographic Institution United States Rosenstiel School of Marine Atmospheric and Earth Science University of Miami United States Cicese Department of Oceanography Mexico University of the Virgin Islands United States Virgin Islands Ocean Sierra United States Universidad Nacional Autónoma de Mexico Mexico Mexican Institute of Water Technology Mexico Gulf Research Program Nasem United States

ISBN: (纸本)9798331540081

As part of the Mini-Adaptive Sampling Test Run (MASTR) experiment in the Gulf of Mexico (GoM) region from February to April 2024, we demonstrated real-time deterministic and probabilistic reachability analysis and time-optimal path planning to guide a fleet of four ocean gliders. The governing differential equations for reachability analysis and time-optimal path planning were numerically integrated in real-time and forced by currents from our large-ensemble ocean forecasts. We illustrate the real-time deterministic and probabilistic forward reachability analyses, reachability and path planning for glider pickups, time-optimal path planning for gliders in distress, and planning of future glider deployments. Results show that the actual paths of gliders were contained within our reachable set forecasts and in accord with the dynamic reachability fronts. Our time-optimal headings and paths also predicted real glider motions, even for longer-range predictions of weeks to a month duration. Reachability and time-optimal path planning forecasts were successfully employed for glider recovery. They also enabled exploring options for future glider deployments. © 2024 IEEE.

关键词： Gliders

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A Prototype Coded Sensing SPECT designed for Ultra-high Sensitivity Imaging

A Prototype Coded Sensing SPECT designed for Ultra-high Sens...

引用

IEEE Symposium on Nuclear Science (NSS/MIC)

作者： L. Cai S. Aggarwal K. Enninful Y. Chen S. Komarov D. Thorek A. K. Jha Y.-C. Tai Imaging Science Phd Program Washington University in St. Louis Saint Louis Missouri United States of America Department of Biomedical Engineering Washington University in St. Louis Saint Louis Missouri United States of America Mallinckrodt Institute of Radiology Washington University in St. Louis Saint Louis Missouri United States of America

ISBN: (数字)9798350388152

ISBN: (纸本)9798350388169

In this work, we discuss the design and development of an ultra-high sensitivity imaging system, Coded Sensing SPECT (CS-SPECT), dedicated to guide and optimize application of alpha particle-emitting radiopharmaceutical therapy ($\alpha$RPT). Alpha particles are highly potent and unlike conventional external beam therapy, they can be used in metastatic settings. Currently, the lack of information of radionuclide distribution hinders estimated internal absorbed dose from $\alpha$RPT, which calls for ultrasensitive SPECT technologies that can report reliable activity distribution under ultra-low count rate imaging conditions. The proposed CS-SPECT is based on an innovative design that incorporates the geometry of both conventional pinhole collimator and coded aperture. Aimed to decouple the dependence of resolution and sensitivity, the heavy metal collimator is replaced by scintillator crystals to serve dual purposes of increasing detected events and providing spatial information. The proposed detector module consists of a 9×9 array of crystal elements. Each crystal presents an alternating pattern of GAGG scintillator and acrylic. The depth of interaction (DOI) information is obtained through dual-ended readout system. Our experimental results are based on a working prototype CS module that has 8x8 detector columns and is fully functional under a broad range of energy (70 keV – more than 511 keV), which is well-suited for alpha particle emitter imaging applications. Furthermore, we performed a preliminary imaging study of Tc99m point source. The number of detected events by the whole detector module is 11-fold higher than that from the bottom detectors resembling a conventional pinhole camera alone, demonstrating a tremendous improvement in system sensitivity.

关键词： Temperature sensors Collimators Sensitivity Scintillators Prototypes Medical treatment Crystals

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Amelioration of the brain structural connectivity is accompanied with changes of gut microbiota in a tuberous sclerosis complex mouse model

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Translational Psychiatry 2024年第1期14卷 68页

作者： Hsieh, Christine Chin-jung Lo, Yu-Chun Wang, Hsin-Hui Shen, Hsin-Ying Chen, You-Yin Lee, Yi-Chao Biomedical Translation Research Center Academia Sinica Taipei Taiwan Ph.D. Program in Medical Neuroscience College of Medical Science and Technology Taipei Medical University Taipei Taiwan Neuroscience Research Center Taipei Medical University Taipei Taiwan Department of Biomedical Engineering National Yang Ming Chiao Tung University Taipei Taiwan International Master Program in Medical Neuroscience College of Medical Science and Technology Taipei Medical University Taipei Taiwan

Tuberous sclerosis complex (TSC) is a genetic disease that causes benign tumors and dysfunctions in many organs, including the brain. Aside from the brain malformations, many individuals with TSC exhibit neuropsychiatric symptoms. Among these symptoms, autism spectrum disorder (ASD) is one of the most common co-morbidities, affecting up to 60% of the population. Past neuroimaging studies strongly suggested that the impairments in brain connectivity contribute to ASD, whether or not TSC-related. Specifically, the tract-based diffusion tensor imaging (DTI) analysis provides information on the fiber integrity and has been used to study the neuropathological changes in the white matter of TSC patients with ASD symptoms. In our previous study, curcumin, a diet-derived mTOR inhibitor has been shown to effectively mitigate learning and memory deficits and anxiety-like behavior in Tsc2 ^+/− mice via inhibiting astroglial proliferation. Recently, gut microbiota, which is greatly influenced by the diet, has been considered to play an important role in regulating several components of the central nervous system, including glial functions. In this study, we showed that the abnormal social behavior in the Tsc2 ^+/− mice can be ameliorated by the dietary curcumin treatment. Second, using tract-based DTI analysis, we found that the Tsc2 ^+/− mice exhibited altered fractional anisotropy, axial and radial diffusivities of axonal bundles connecting the prefrontal cortex, nucleus accumbens, hypothalamus, and amygdala, indicating a decreased brain network. Third, the dietary curcumin treatment improved the DTI metrics, in accordance with changes in the gut microbiota composition. At the bacterial phylum level, we showed that the abundances of Actinobacteria, Verrucomicrobia, and Tenericutes were significantly correlated with the DTI metrics FA, AD, and RD, respectively. Finally, we revealed that the expression of myelin-associated proteins, myelin bassic p

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GENERALIZING LLOYD'S ALGORITHM FOR GRAPH CLUSTERING

arXiv

引用

arXiv 2023年

作者： Zaman, Tareq Nytko, Nicolas Taghibakhshi, Ali Maclachlan, Scott Olson, Luke West, Matthew Interdisciplinary Program in Scientific Computing Memorial University of Newfoundland NL St. John's Canada Department of Computer Science University of Illinois Urbana-Champaign UrbanaIL61801 United States Department of Mechanical Science and Engineering University of Illinois Urbana-Champaign UrbanaIL61801 United States

Clustering is a commonplace problem in many areas of data science, with applications in biology and bioinformatics, understanding chemical structure, image segmentation, building recommender systems, and many more fields. While there are many different clustering variants (based on given distance or graph structure, probability distributions, or data density), we consider here the problem of clustering nodes in a graph, motivated by the problem of aggregating discrete degrees of freedom in multigrid and domain decomposition methods for solving sparse linear systems. Specifically, we consider the challenge of forming balanced clusters in the graph of a sparse matrix for use in algebraic multigrid, although the algorithm has general applicability. Based on an extension of the Bellman-Ford algorithm, we generalize Lloyd's algorithm for partitioning subsets of Rn to balance the number of nodes in each cluster;this is accompanied by a rebalancing algorithm that reduces the overall energy in the system. The algorithm provides control over the number of clusters and leads to "well centered" partitions of the graph. Theoretical results are provided to establish linear complexity and numerical results in the context of algebraic multigrid highlight the benefits of improved *** Codes 65F50, 65N55, 68R10 Copyright © 2023, The Authors. All rights reserved.

关键词： Domain decomposition methods

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Deep learning for Proportion Estimation of Target Radionuclides in Extreme Environment

Deep learning for Proportion Estimation of Target Radionucli...

引用

IEEE Symposium on Nuclear Science (NSS/MIC)

作者： M. Park J. Hwang J.-Y. Yeom C. Kim Department of Bioengineering Korea University Seoul Republic of Korea Korea University Interdisciplinary Program in Precision Public Health Seoul Republic of Korea Global Health-Tech Research Center Korea University Seoul Republic of Korea School of Biomedical Engineering Korea University Seoul Republic of Korea Korea Atomic Energy Research Institute Daejeon Republic of Korea

ISBN: (数字)9798350388152

ISBN: (纸本)9798350388169

We propose a deep learning-based approach utilizing a 1D Convolutional Neural Network to accurately estimate the proportions of target radionuclides, 137Cs and 133Ba, within mixed gamma-ray spectra, even under extreme conditions of high temperature and radiation. Our results demonstrated high precision, with Mean Absolute Error (MAE) values below 5% for each target radionuclide in standard testing conditions. Remarkably, even when 54Mn-a radionuclide not included in the training phase-was introduced as noise, the model’s performance remained robust, with error rates kept below 9%. This underscores the model’s capability to deliver accurate radionuclide quantification, despite the presence of unfamiliar spectral noise, affirming its substantial utility for nuclear safety in complex environments.

关键词： Training Semiconductor device modeling Microwave integrated circuits Semiconductor detectors Error analysis Noise Gamma-rays

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