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Fluorescence Microscopy: a statistics-optics perspective

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arXiv 2023年

作者： Fazel, Mohamadreza Grussmayer, Kristin S. Ferdman, Boris Radenovic, Aleksandra Shechtman, Yoav Enderlein, Jörg Pressé, Steve Department of Physics Arizona State University TempeAZ United States Center for Biological Physics Arizona State University TempeAZ United States Department of Bionanoscience Faculty of Applied Science Kavli Institute for Nanoscience Delft University of Technology Delft Netherlands Russel Berrie Nanotechnology Institute Department of Biomedical Engineering Technion - Israel Institute of Technology Haifa Israel Lausanne Switzerland III. Institute of Physics - Biophysics Georg August University Göttingen Germany

Fundamental properties of light unavoidably impose features on images collected using fluorescence microscopes. Modeling these features is ever more important in quantitatively interpreting microscopy images collected at scales on par or smaller than light’s wavelength. Here we review the optics responsible for generating fluorescent images, fluorophore properties, microscopy modalities leveraging properties of both light and fluorophores, in addition to the necessarily probabilistic modeling tools imposed by the stochastic nature of light and measurement. © 2023, CC BY.

关键词： Fluorophores

Mechanistic insights of evaporation-induced actuation in supramolecular crystals (Sept, 10.1038/s41563-020-0799-0, 2020)

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NATURE MATERIALS 2021年第3期20卷 434-434页

作者： Piotrowska, Roxana Hesketh, Travis Wang, Haozhen Martin, Alan R. G. Bowering, Deborah Zhang, Chunqiu Hu, Chunhua T. McPhee, Scott A. Wang, Tong Park, Yaewon Singla, Pulkit McGlone, Thomas Florence, Alastair Tuttle, Tell Ulijn, Rein V. Chen, Xi Advanced Science Research Center (ASRC) at the Graduate Center of the City University of New York New York NY USA PhD Program in Chemistry The Graduate Center of the City University of New York New York NY USA PhD Program in Physics The Graduate Center of the City University of New York New York NY USA Department of Chemistry and Biochemistry Hunter College City University of New York New York NY USA Department of Chemical Engineering The City College of New York New York NY USA Department of Pure and Applied Chemistry University of Strathclyde Glasgow UK EPSRC Continuous Manufacturing and Crystallisation Future Research Hub c/o Strathclyde Institute of Pharmacy and Biomedical Sciences Technology Innovation Centre University of Strathclyde Glasgow UK Department of Chemistry New York University New York NY USA

A Correction to this paper has been published: https://***/10.1038/s41563-021-00950-3.

关键词： Hydrogen bonds

Quantum aspects of hydrodynamic transport from weak electron-impurity scattering

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Physical Review B 2020年第12期101卷 121107(R)-121107(R)页

作者： Aaron Hui Samuel Lederer Vadim Oganesyan Eun-Ah Kim School of Applied & Engineering Physics Cornell University Ithaca New York 14853 USA Department of Physics Cornell University Ithaca New York 14853 USA Department of Physics and Astronomy College of Staten Island CUNY Staten Island New York 10314 USA Physics Program and Initiative for the Theoretical Sciences The Graduate Center CUNY New York New York 10016 USA

Recent experimental observations of apparently hydrodynamic electronic transport have generated much excitement. However, the understanding of the observed nonlocal transport (whirlpool) effects and parabolic (Poiseuille-like) current profiles has largely been motivated by a phenomenological analogy to classical fluids. This is due to difficulty in incorporating strong correlations in quantum mechanical calculation of transport, which has been the primary angle for interpreting the apparently hydrodynamic transport. Here we demonstrate that even free-fermion systems, in the presence of (inevitable) disorder, exhibit nonlocal conductivity effects such as those observed in experiments because of the fermionic system's long-range entangled nature. On the basis of explicit calculations of the conductivity at finite wave vector, σ(q), for selected weakly disordered free-fermion systems, we propose experimental strategies for demonstrating distinctive quantum effects in nonlocal transport at odds with the expectations of classical kinetic theory. Our results imply that the observation of whirlpools or other “hydrodynamic” effects does not guarantee the dominance of electron-electron scattering over electron-impurity scattering.

关键词： Electrical conductivity Quantum field theory Disordered systems Hydrodynamics

Statistical behavior of nonequilibrium and living biological systems subjected to active and thermal fluctuations

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Physical Review E 2022年第1期105卷 014415-014415页

作者： Ashesh Ghosh Andrew J. Spakowitz Department of Chemical Engineering Stanford University Stanford California 94305 USA Department of Materials Science Stanford University Stanford California 94305 USA Department of Chemistry Stanford University Stanford California 94305 USA Department of Applied Physics Stanford University Stanford California 94305 USA Biophysics Program Stanford University Stanford California 94305 USA

We present a path-integral formulation of the motion of a particle subjected to fluctuating active and thermal forces. This general framework predicts the statistical behavior associated with the stochastic trajectories of the particle, accounting for all possible realizations of Brownian and active forces, over an arbitrary potential landscape. Temporal correlations in the active forces result in non-Markovian statistics, necessitating the inclusion of a fixed active-force value at specified times within the statistical treatment. We specialize our theory to that of exponentially correlated active forces for a particle in a harmonic potential. We find the exact results for the statistical distributions for the initial position of the particle, accounting for the impact of the correlated active forces at all times prior to the initial time. Our theory is then used to find the two-point distribution for the active Brownian particle, which governs the joint probability that a particle begins and ends at specified locations. Analyses of the active Brownian statistics demonstrate that the impact of active forces can be interpreted through a time-dependent temperature whose influence depends on the competition of timescales of the active-force correlation and the relaxation time of the particle in the harmonic potential. The general results presented in this work are transferable to a broad range of nonequilibrium systems with active and Brownian motion, and the time-dependent temperature serves as a governing principle to describe the competition of timescales associated with active forces and internal relaxation processes.

关键词： Nonequilibrium fluctuations Nonequilibrium statistical mechanics Active brownian particles Active matter Nonequilibrium systems

Direct Visualization of a Disorder Driven Electronic Smectic Phase in Dirac Nodal Line Semimetal GdSbTe

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arXiv 2024年

作者： Venkatesan, Balaji Guan, Syu-You Chang, Jen-Te Chiu, Shiang-Bin Yang, Po-Yuan Su, Chih-Chuan Chang, Tay-Rong Raju, Kalaivanan Sankar, Raman Fongchaiya, Somboon Chu, Ming-Wen Chang, Chia-Seng Chang, Guoqing Lin, Hsin Del Maestro, Adrian Kao, Ying-Jer Chuang, Tien-Ming Department of Physics National Taiwan University Taipei10617 Taiwan Nano Science and Technology Program Taiwan International Graduate Program Academia Sinica National Taiwan University Taipei11529 Taiwan Institute of Physics Academia Sinica Taipei11529 Taiwan Department of Physics National Cheng-Kung University Tainan701 Taiwan Center for Condensed Matter Sciences National Taiwan University Taipei10617 Taiwan Molecular Science and Technology Program Taiwan International Graduate Program Academia Sinica Taipei11529 Taiwan Division of Physics and Applied Physics School of Physical and Mathematical Sciences Nanyang Technological University 21 Nanyang Link 637371 Singapore Department of Physics and Astronomy University of Tennessee KnoxvilleTN37996 United States Institute for Advanced Materials & Manufacturing University of Tennessee KnoxvilleTN37996 United States Min H. Kao Department of Electrical Engineering and Computer Science University of Tennessee KnoxvilleTN37996 United States Center for Quantum Science and Technology National Taiwan University Taipei10607 Taiwan

Electronic liquid crystal (ELC) phases are spontaneous symmetry breaking states believed to arise from strong electron correlation in quantum materials such as cuprates and iron pnictides. Here, we report a direct observation of a smectic phase in a weakly correlated Dirac nodal line (DNL) semimetal GdSbxTe2-x. Incommensurate smectic charge modulation and intense local unidirectional nanostructure are visualized by using spectroscopic imaging - scanning tunneling microscopy. As topological materials with symmetry protected Dirac or Weyl fermions are mostly weakly correlated, the discovery of such an ELC phase are anomalous and raise questions on the origin of their emergence. Specifically, we demonstrate how chemical substitution generates these symmetry breaking phases before the system undergoes a charge density wave (CDW) - orthorhombic structural transition. Our results highlight the importance of impurities in realizing ELC phases and present a new material platform for exploring the interplay among quenched disorder, topology and electron correlation. Copyright © 2024, The Authors. All rights reserved.

关键词： Charge density waves

Rapid and efficient characterization of cervical collagen orientation using linearly polarized colposcopic images

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Journal of Innovative Optical Health Sciences 2023年第5期16卷 21-31页

作者： Cat Phan Ngoc Khuong Dung Nguyen Huu Quang Hai Pham Thanh Long Nguyen Quynh Nguyen Ngoc Duc Le Huynh Tien Tran Van Tu Ly Anh Department of Applied Physics Ho Chi Minh City University of Technology 268 Ly Thuong Kiet Street District 10 Ho Chi Minh City 700000Vietnam Quality Management Department Tu Du Hospital 284 Cong QuynhDistrict 1 Ho Chi Minh City 700000Vietnam Department of Biomedical Engineering Nguyen Tat Thanh University 300A Nguyen Tat Thanh District 4Ho Chi Minh City 700000Vietnam Faculty of Science and Technology Jean Monnet University 11 Rue du Docteur Annino Saint Etienne 42000France

Collagen provides tissue strength and structural *** fication of the orientated dispersion of collagen fibers is an important factor when studying the mechanical properties of the *** this study,for the first time,a new method for rapid characterization of the collagen fiber orientations of the cervix using linearly polarized light colposcopy is presented.A total of 24 colposcopic images were captured using a cross-polarized imaging system with white LED light *** the preprocessing stage,the Red channel of the RGB image was chosen,which contains no information of the blood vessels because of the low-absorption of blood cells in the red ***,which is an ImageJ plug-in,was used to estimate the local orientation of the collagen *** result shows that in the nonpregnant cervix,the middle zone(Zone 2)has circumferentially aligned collagen fibers while the inner zone(Zone 1)has randomly *** collagen fiber dispersion in Zone 2 is much smaller than that in Zone 1 at all four quadrants region(anterior,posterior,left,and right quadrant).This new analysis technique could potentially combine with diagnostic tools to provide a quantitative platform of collagen fibers in the clinic.

关键词： Cervix collagen fibers collagen orientation coherency cross-polarized imaging colposcopy

Experimental verification of the treatment of time-dependent flux in circuit quantization

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arXiv 2022年

作者： Bryon, Jacob Weiss, D.K. You, Xinyuan Sussman, Sara Croot, Xanthe Huang, Ziwen Koch, Jens Houck, Andrew Department of Electrical Engineering Princeton University PrincetonNJ08540 United States Department of Physics and Astronomy Northwestern University EvanstonIL60208 United States Graduate Program in Applied Physics Northwestern University EvanstonIL60208 United States Department of Physics Princeton University PrincetonNJ08540 United States Center for Applied Physics and Superconducting Technologies Northwestern University EvanstonIL60208 United States

Recent theoretical work has highlighted that quantizing a superconducting circuit in the presence of time-dependent flux Φ(t) generally produces Hamiltonian terms proportional to dΦ/dt unless a special allocation of the flux across inductive terms is chosen. Here, we present an experiment probing the effects of a fast flux ramp applied to a heavy-fluxonium circuit. The experiment confirms that naïve omission of the dΦ/dt term leads to theoretical predictions inconsistent with experimental data. Experimental data are fully consistent with recent theory that includes the derivative term or equivalently uses "irrotational variables" that uniquely allocate the flux to properly eliminate the dΦ/dt term. Copyright © 2022, The Authors. All rights reserved.

关键词： Timing circuits

Emulating Complex Synapses Using Interlinked Proton Conductors

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arXiv 2024年

作者： Zhang, Lifu Li, Ji-An Hu, Yang Jiang, Jie Lai, Rongjie Benna, Marcus K. Shi, Jian Department of Materials Science and Engineering Rensselaer Polytechnic Institute TroyNY12180 United States Neurosciences Graduate Program University of California San Diego La Jolla CA92093 United States Department of Mathematics Purdue University West LafayetteIN47907 United States Department of Neurobiology School of Biological Sciences University of California at San Diego La Jolla CA92093 United States Department of Physics Applied Physics and Astronomy Rensselaer Polytechnic Institute TroyNY12180 United States

In terms of energy efficiency and computational speed, neuromorphic electronics based on non-volatile memory devices is expected to be one of most promising hardware candidates for future artificial intelligence (AI). However, catastrophic forgetting, networks rapidly overwriting previously learned weights when learning new tasks, remains as a pivotal hurdle in either digital or analog AI chips for unleashing the true power of brain-like computing. To address catastrophic forgetting in the context of online memory storage, a complex synapse model (the Benna-Fusi model) has been proposed recently[1], whose synaptic weight and internal variables evolve following a diffusion dynamics. In this work, by designing a proton transistor with a series of charge-diffusion-controlled storage components, we have experimentally realized the Benna-Fusi artificial complex synapse. The memory consolidation from coupled storage components is revealed by both numerical simulations and experimental observations. Different memory timescales for the complex synapse are engineered by the diffusion length of charge carriers, the capacity and number of coupled storage components. The advantage of the demonstrated complex synapse in both memory capacity and memory consolidation is revealed by neural network simulations of face familiarity detection. Our experimental realization of the complex synapse suggests a promising approach to enhance memory capacity and to enable continual learning. Copyright © 2024, The Authors. All rights reserved.

关键词： Computational efficiency

Small metal artifact detection and inpainting in cardiac CT images

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arXiv 2024年

作者： McKeown, Trevor Michael Gach, H. Hao, Yao An, Hongyu Robinson, Clifford G. Cuculich, Phillip S. Yang, Deshan Medical Physics Program Duke University United States Department of Radiation Oncology Duke University United States Department of Radiation Oncology School of Medicine Washington University in Saint Louis United States Department of Radiology School of Medicine Washington University in Saint Louis United States Department of Biomedical Engineering Washington University in Saint Louis United States Department of Cardiology School of Medicine Washington University in Saint Louis United States

Background: Quantification of cardiac motion on pre-treatment CT imaging for stereotactic arrhythmia radiotherapy patients is difficult due to the presence of image artifacts caused by metal leads of implantable cardioverter-defibrillators (ICDs). The CT scanners’ onboard metal artifact reduction tool does not sufficiently reduce these artifacts. More advanced artifact reduction techniques require the raw CT projection data and thus are not applicable to already reconstructed CT images. New methods are needed to accurately reduce the metal artifacts in already reconstructed CTs to recover the otherwise lost anatomical information. Purpose: To develop a methodology to automatically detect metal artifacts in cardiac CT scans and inpaint the affected volume with anatomically consistent structures and values. Methods: Breath-hold ECG-gated 4DCT scans of 12 patients who underwent cardiac radiation therapy for treating ventricular tachycardia were collected. The metal artifacts in the images caused by the ICD leads were manually contoured. A 2D U-Net deep learning (DL) model was developed to segment the metal artifacts automatically using eight patients for training, two for validation, and two for testing. A dataset of 592 synthetic CTs was prepared by adding segmented metal artifacts from the patient 4DCT images to artifact-free cardiac CTs of 148 patients. A 3D image inpainting DL model was trained to refill the metal artifact portion in the synthetic images with realistic image contents that approached the ground truth artifact-free images. The trained inpainting model was evaluated by analyzing the automated segmentation results of the four heart chambers with and without artifacts on the synthetic dataset. Additionally, the raw cardiac patient images with metal artifacts were processed using the inpainting model and the results of metal artifact reduction were qualitatively inspected. Results: The artifact detection model worked well and produced a Dice score of 0.9

关键词： Computerized tomography