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BigNeuron: a resource to benchmark and predict performance of algorithms for automated tracing of neurons in light microscopy datasets

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Nature methods 2023年第6期20卷 824-835页

作者： Linus Manubens-Gil Zhi Zhou Hanbo Chen Arvind Ramanathan Xiaoxiao Liu Yufeng Liu Alessandro Bria Todd Gillette Zongcai Ruan Jian Yang Miroslav Radojević Ting Zhao Li Cheng Lei Qu Siqi Liu Kristofer E Bouchard Lin Gu Weidong Cai Shuiwang Ji Badrinath Roysam Ching-Wei Wang Hongchuan Yu Amos Sironi Daniel Maxim Iascone Jie Zhou Erhan Bas Eduardo Conde-Sousa Paulo Aguiar Xiang Li Yujie Li Sumit Nanda Yuan Wang Leila Muresan Pascal Fua Bing Ye Hai-Yan He Jochen F Staiger Manuel Peter Daniel N Cox Michel Simonneau Marcel Oberlaender Gregory Jefferis Kei Ito Paloma Gonzalez-Bellido Jinhyun Kim Edwin Rubel Hollis T Cline Hongkui Zeng Aljoscha Nern Ann-Shyn Chiang Jianhua Yao Jane Roskams Rick Livesey Janine Stevens Tianming Liu Chinh Dang Yike Guo Ning Zhong Georgia Tourassi Sean Hill Michael Hawrylycz Christof Koch Erik Meijering Giorgio A Ascoli Hanchuan Peng Institute for Brain and Intelligence Southeast University Nanjing China. Microsoft Corporation Redmond WA USA. Tencent AI Lab Bellevue WA USA. Computing Environment and Life Sciences Directorate Argonne National Laboratory Lemont IL USA. Kaya Medical Seattle WA USA. University of Cassino and Southern Lazio Cassino Italy. Center for Neural Informatics Structures and Plasticity Krasnow Institute for Advanced Study George Mason University Fairfax VA USA. Faculty of Information Technology Beijing University of Technology Beijing China. Beijing International Collaboration Base on Brain Informatics and Wisdom Services Beijing China. Nuctech Netherlands Rotterdam the Netherlands. Janelia Research Campus Howard Hughes Medical Institute Ashburn VA USA. Department of Electrical and Computer Engineering University of Alberta Edmonton Alberta Canada. Ministry of Education Key Laboratory of Intelligent Computation and Signal Processing Anhui University Hefei China. Paige AI New York NY USA. Scientific Data Division and Biological Systems and Engineering Division Lawrence Berkeley National Lab Berkeley CA USA. Helen Wills Neuroscience Institute and Redwood Center for Theoretical Neuroscience UC Berkeley Berkeley CA USA. RIKEN AIP Tokyo Japan. Research Center for Advanced Science and Technology (RCAST) The University of Tokyo Tokyo Japan. School of Computer Science University of Sydney Sydney New South Wales Australia. Texas A&M University College Station TX USA. Cullen College of Engineering University of Houston Houston TX USA. Graduate Institute of Biomedical Engineering National Taiwan University of Science and Technology Taipei Taiwan. National Centre for Computer Animation Bournemouth University Poole UK. PROPHESEE Paris France. Department of Neuroscience Columbia University New York NY USA. Mortimer B. Zuckerman Mind Brain Behavior Institute Columbia University New York NY USA. Department of Computer Science Northern Illinois Universit

BigNeuron is an open community bench-testing platform with the goal of setting open standards for accurate and fast automatic neuron tracing. We gathered a diverse set of image volumes across several species that is representative of the data obtained in many neuroscience laboratories interested in neuron tracing. Here, we report generated gold standard manual annotations for a subset of the available imaging datasets and quantified tracing quality for 35 automatic tracing algorithms. The goal of generating such a hand-curated diverse dataset is to advance the development of tracing algorithms and enable generalizable benchmarking. Together with image quality features, we pooled the data in an interactive web application that enables users and developers to perform principal component analysis, t-distributed stochastic neighbor embedding, correlation and clustering, visualization of imaging and tracing data, and benchmarking of automatic tracing algorithms in user-defined data subsets. The image quality metrics explain most of the variance in the data, followed by neuromorphological features related to neuron size. We observed that diverse algorithms can provide complementary information to obtain accurate results and developed a method to iteratively combine methods and generate consensus reconstructions. The consensus trees obtained provide estimates of the neuron structure ground truth that typically outperform single algorithms in noisy datasets. However, specific algorithms may outperform the consensus tree strategy in specific imaging conditions. Finally, to aid users in predicting the most accurate automatic tracing results without manual annotations for comparison, we used support vector machine regression to predict reconstruction quality given an image volume and a set of automatic tracings.

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Optomechanically Induced Birefringence and Optomechanically Induced Faraday Effect

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Physical Review Letters 2019年第2期123卷 023602-023602页

作者： Robert Duggan Javier del Pino Ewold Verhagen Andrea Alù Department of Electrical and Computer Engineering The University of Texas at Austin Austin Texas 78712 USA Center for Nanophotonics AMOLF Science Park 104 1098 XG Amsterdam The Netherlands Photonics Initiative Advanced Science Research Center City University of New York New York 10031 USA Physics Program Graduate Center City University of New York New York 10016 USA Department of Electrical Engineering City College of The City University of New York New York 10031 USA

We demonstrate an optomechanical platform where optical mode conversion mediated by mechanical motion enables the arbitrary tailoring of polarization states of propagating light fields. Optomechanical interactions are realized in a Fabry-Pérot resonator, which naturally supports two polarization-degenerate states while an optical control field induces rotational symmetry breaking. Applying such principles, the entire Poincaré sphere is spanned by just optical control of the driving field, realizing reciprocal and nonreciprocal optomechanically induced birefringence for linearly polarized and circularly polarized control driving. A straightforward extension of this setup also enables all-optical tunable isolation and circulation. Our findings open new avenues to exploit optomechanics for the arbitrary manipulation of light polarization.

关键词： Nonlinear optics Optomechanics

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Nonreciprocal hyperbolic propagation over moving metasurfaces

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Physical Review B 2019年第4期99卷 045407-045407页

作者： Yarden Mazor Andrea Alù Department of Electrical and Computer Engineering The University of Texas at Austin Austin Texas 78712 USA Photonics Initiative Advanced Science Research Center City University of New York New York New York 10031 USA Physics Program Graduate Center City University of New York New York New York 10026 USA Department of Electrical Engineering City College of New York New York New York 10031 USA

Hyperbolic propagation offers exciting opportunities in nanophotonics, from subdiffraction imaging to enhanced local density of states. This transport regime is typically induced by strong modulation of conductivity, i.e., with alternating metallic and dielectric material properties. Here, we analyze a moving impedance surface, showing that suitably tailored homogeneous metasurfaces can support one-way hyperbolic propagation when in motion, adding nonreciprocity to hyperbolic propagation phenomena, and without suffering from nonlocal effects stemming from discretization or finite granularity of the surface.

关键词： Electromagnetism Metamaterials Photonics

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Independent histological validation of MR-derived radio-pathomic maps of tumor cell density using image-guided biopsies in human brain tumors

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Journal of neuro-oncology 2025年 1-12页

作者： Gianluca Nocera Francesco Sanvito Jingwen Yao Sonoko Oshima Samuel A Bobholz Ashley Teraishi Catalina Raymond Kunal Patel Richard G Everson Linda M Liau Jennifer Connelly Antonella Castellano Pietro Mortini Noriko Salamon Timothy F Cloughesy Peter S LaViolette Benjamin M Ellingson UCLA Brain Tumor Imaging Laboratory (BTIL) Center for Computer Vision and Imaging Biomarkers University of California Los Angeles Los Angeles CA USA. Department of Radiological Sciences David Geffen School of Medicine University of California Los Angeles Los Angeles CA USA. University Vita-Salute San Raffaele Milan Italy. Neuroradiology Unit and CERMAC IRCCS Ospedale San Raffaele Milan Italy. Department of Neurosurgery and Gamma Knife Radiosurgery IRCCS Ospedale San Raffaele Milan Italy. Department of Diagnostic Imaging and Nuclear Medicine Graduate School of Medicine Kyoto University Kyoto Japan. Department of Radiology Medical College of Wisconsin Milwaukee WI USA. Department of Neurosurgery David Geffen School of Medicine University of California Los Angeles CA USA. Department of Neurology Medical College of Wisconsin Milwaukee WI USA. Department of Neurology Ronald Reagan UCLA Medical Center University of California Los Angeles CA USA. David Geffen School of Medicine UCLA Neuro-Oncology Program University of California Los Angeles CA USA. Department of Biomedical Engineering Medical College of Wisconsin Milwaukee WI USA. UCLA Brain Tumor Imaging Laboratory (BTIL) Center for Computer Vision and Imaging Biomarkers University of California Los Angeles Los Angeles CA USA. bellingson@mednet.ucla.edu. Department of Radiological Sciences David Geffen School of Medicine University of California Los Angeles Los Angeles CA USA. bellingson@mednet.ucla.edu. Department of Neurosurgery David Geffen School of Medicine University of California Los Angeles CA USA. bellingson@mednet.ucla.edu. Department of Bioengineering Henry Samueli School of Engineering and Applied Science University of California Los Angeles Los Angeles CA USA. bellingson@mednet.ucla.edu. Department of Psychiatry and Biobehavioral Sciences David Geffen School of Medicine University of California Los Angeles CA USA. bellingson@mednet.ucla.edu. UCLA Radiology UCLA Brain Tumor Imaging

PURPOSE:In brain gliomas, non-invasive biomarkers reflecting tumor cellularity would be useful to guide supramarginal resections and to plan stereotactic biopsies. We aim to validate a previously-trained machine learning algorithm that generates cellularity prediction maps (CPM) from multiparametric MRI data to an independent, retrospective external cohort of gliomas undergoing image-guided biopsies, and to compare the performance of CPM and diffusion MRI apparent diffusion coefficient (ADC) in predicting cellularity. METHODS:A cohort of patients with treatment-naïve or recurrent gliomas were prospectively studied. All patients underwent pre-surgical MRI according to the standardized brain tumor imaging protocol. The surgical sampling site was planned based on image-guided biopsy targets and tissue was stained with hematoxylin-eosin for cell density count. The correlation between MRI-derived CPM values and histological cellularity, and between ADC and histological cellularity, was evaluated both assuming independent observations and accounting for non-independent observations. RESULTS:Sixty-six samples from twenty-seven patients were collected. Thirteen patients had treatment-naïve tumors and fourteen had recurrent lesions. CPM value accurately predicted histological cellularity in treatment-naïve patients (b = 1.4, R = 0.2, p = 0.009, rho = 0.41, p = 0.016, RMSE = 1503 cell/mm), but not in the recurrent sub-cohort. Similarly, ADC values showed a significant association with histological cellularity only in treatment-naive patients (b = 1.3, R = 0.22, p = 0.007; rho = -0.37, p = 0.03), not statistically different from the CPM correlation. These findings were confirmed with statistical tests accounting for non-independent observations. CONCLUSION:MRI-derived machine learning generated cellularity prediction maps (CPM) enabled a non-invasive evaluation of tumor cellularity in treatment-naïve glioma patients, although CPM did not clearly outperform ADC alone in this co

关键词： Artificial intelligence Diffusion imaging Glioma Histological validation Imaging biomarker

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Angular-momentum selectivity and asymmetry in highly confined wave propagation along sheath-helical metasurface tubes

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Physical Review B 2019年第15期99卷 155425-155425页

Highly confined surface waves present unique opportunities to enhance light interactions with localized emitters or molecules. Hyperbolic dispersion in metasurfaces allows us to tailor and manipulate surface waves, enhancing the local density of states over broad bandwidths. So far, propagation on this platform was mainly studied in planar geometries, which facilitates the analysis but somehow limits the realm of possibilities. Here we show that “wrapping” hyperbolic metasurfaces into tubes may greatly enrich the wave propagation dynamics along their axis. This system shows strong interaction with fields and sources carrying optical angular momentum and pronounced field asymmetries, and opens pathways to valley-specific excitation and routing. In addition, we demonstrate that various parameter regimes enable strong spin/helicity momentum locking.

关键词： Angular momentum of light Hyperbolic metamaterials Light-matter interaction Surface plasmons Surfaces

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Hyperbolic Sound Propagation over Nonlocal Acoustic Metasurfaces

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Physical Review Letters 2019年第24期123卷 244303-244303页

作者： Li Quan Andrea Alù Department of Electrical and Computer Engineering The University of Texas at Austin Austin Texas 78712 USA Photonics Initiative Advanced Science Research Center City University of New York New York New York 10031 USA Physics Program Graduate Center City University of New York New York New York 10016 USA Department of Electrical Engineering City College of The City University of New York New York 10031 USA

Hyperbolic metasurfaces, supporting extreme anisotropy of the surface impedance tensor, have recently been explored in nanophotonic systems for robust diffractionless propagation over a surface, offering interesting opportunities for subdiffraction imaging and enhanced Purcell emission. In acoustics, due to the longitudinal nature of sound transport in fluids, these phenomena are forbidden by symmetry, requiring the acoustic surface impedance to be inherently isotropic. Here we show that nonlocalities produced by strong coupling between neighboring impedance elements enable extreme anisotropic responses for sound traveling over a surface, supporting negative phase and energy velocities, as well as hyperbolic propagation for acoustic surface waves.

关键词： Acoustics Hyperbolic metamaterials Metamaterials

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Passive Acoustic Metasurface with Unitary Reflection Based on Nonlocality

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Physical Review applied 2019年第5期11卷 054077-054077页

作者： Li Quan Andrea Alù Department of Electrical and Computer Engineering The University of Texas at Austin Austin Texas 78712 USA Photonics Initiative Advanced Science Research Center City University of New York New York New York 10031 USA Physics Program Graduate Center City University of New York New York New York 10026 USA Department of Electrical Engineering City College of New York New York New York 10031 USA

Metasurfaces have introduced large flexibility in manipulating the impinging wavefront for light and sound by locally engineering the reflection and transmission coefficients based on generalized Snell’s laws. Local phenomena in each unit cell, however, are fundamentally limited in the level of efficiency with which anomalous wavefront transformations can be achieved. Here, we explore acoustic metasurfaces with suitably engineered nonlocality, obtained by coupling neighboring cells. We demonstrate that nonlocal passive metastructures can overcome the limitations of local designs, and mimic balanced gain and loss distributions, enabling unitary efficiency for extreme beam steering.

关键词： Acoustic metamaterials Acoustic wave phenomena Beam control Beam optics Light propagation, transmission & absorption

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Tunneling spectroscopy of c-axis epitaxial cuprate junctions

arXiv

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arXiv 2020年

作者： Zhou, Panpan Chen, Liyang Sochnikov, Ilya Wu, Tsz Chun Foster, Matthew S. Bollinger, Anthony T. He, Xi Božović, Ivan Natelson, Douglas Department of Physics and Astronomy Rice University HoustonTX77005 United States Applied Physics Graduate Program Smalley-Curl Institute Rice University HoustonTX77005 United States Department of Physics University of Connecticut StorrsCT06269 United States Brookhaven National Laboratory UptonNY11973-5000 United States Department of Chemistry Yale University New HavenCT06520 United States Department of Electrical and Computer Engineering Rice University HoustonTX77005 United States Department of Materials Science and NanoEngineering Rice University HoustonTX77005 United States

Atomically precise epitaxial structures are unique systems for tunneling spectroscopy that minimize extrinsic effects of disorder. We present a systematic tunneling spectroscopy study, over a broad doping, temperature, and bias range, in epitaxial c-axis La2−xSrxCuO4/La2CuO4/La2−xSrxCuO4 heterostructures. The behavior of these superconductor/insulator/superconductor (SIS) devices is unusual. Down to 20 mK there is complete suppression of c-axis Josephson critical current with a barrier of only 2 nm of La2CuO4, and the zero-bias conductance remains at 20-30% of the normal-state conductance, implying a substantial population of in-gap states. Tunneling spectra show greatly suppressed coherence peaks. As the temperature is raised, the superconducting gap fills in rather than closing at Tc. For all doping levels, the spectra show an inelastic tunneling feature at ∼ 80 meV, suppressed as T exceeds Tc. These nominally simple epitaxial cuprate junctions deviate markedly from expectations based on the standard Bardeen-Cooper-Schrieffer (BCS) theory. Copyright © 2020, The Authors. All rights reserved.

关键词： Copper compounds

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Interplay of Purcell effect, stimulated emission, and leaky modes in photoluminescence spectra of microsphere cavities

arXiv

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arXiv 2019年

作者： Chien, Ching-Hang Wu, Shang-Hsuan Ngo, Trong Huynh-Buu Chang, Yia-Chung Research Center for Applied Sciences Academia Sinica Taipei115 Taiwan Nano Science and Technology Program TIGP Academia Sinica Taipei115 Taiwan Department of Engineering and System Science National Tsing Hua University Hsinchu300 Taiwan Department of Electrical and Computer Engineering University of Texas at Austin United States Department of Electrical and Computer Engineering University of Alberta EdmontonABT6G 2V4 Canada

A theoretical model for describing the emission spectra of microsphere cavities is presented, and its predictions of detailed lineshapes of emission spectra associated with whispering gallery modes (WGMs) of various orders in ZnO microspheres (MSs) are verified experimentally by photoluminescence (PL) spectroscopy. The interplay of Purcell effect, quality factor, and leaky modes in spontaneous and stimulated emission spectra related to WGMs of all orders is revealed. The key success of the theory is based on the expansion of the full Green function of the MS in terms of all possible resonance modes in complex frequency space, which allows incorporation of contributions from leaky modes, stimulated emission processes, and Purcell effect. We show that the spontaneous emission spectrum calculated according to Mie theory (without Purcell effect) is dominated by the contribution of leaky modes, while the spontaneous and stimulated emission enhanced by Purcell effect are responsible for the main WGM resonance peaks observed experimentally. It is found that the stimulated emission peaks are doubly enhanced by their respective mode quality factor Q: one factor from the Purcell effect and the other factor from the photon number derived from the rate equation. After combining all these effects the theory can provide a quantitative description of fine features of both TE and TM modes (including higher-order modes) observed in the PL spectra of ZnO MSs. Surprisingly, it is found that for ZnO MS with diameter larger than 5 µm, the PL emission spectrum is dominated by higher-order modes. The quantitative understanding of the interplay of these emission mechanisms should prove useful for optimizing the performance of light-emitting devices based on micro resonators. Copyright © 2019, The Authors. All rights reserved.

关键词： Microspheres

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Exciton Localization of High-Quality ZnO/Mg_xZn_1-xO Multiple Quantum Wells on Si (111) with a Y₂O₃ Buffer Layer (vol 1, pg 3829, 2018)

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ACS applied NANO MATERIALS 2018年第10期1卷 5958-5958页

作者： Liu, Wei-Rein Huang, Wei-Lun Wu, Yung-Chi Lai, Liang-Hsun Hsu, Chia-Hung Hsieh, Wen-Feng Chiang, Tsung-Hung Wan, H. W. Hong, M. Kao, J. National Synchrotron Radiation Research Center Hsinchu 30076 Taiwan Program for Science and Technology of Accelerator Light Source National Chiao Tung University Hsinchu 30010 Taiwan Department of Photonics College of Electrical and Computer Engineering National Chiao Tung University Hsinchu 30010 Taiwan Department of Photonics College of Electrical and Computer Engineering National Chiao Tung University Hsinchu 30010 Taiwan Department of Materials Science & Engineering National Tsing Hua University Hsinchu 30013 Taiwan Graduate Institute of Applied Physics and Department of Physics National Taiwan University Taipei 10617 Taiwan Department of Physics National Tsing Hua University Hsinchu 30013 Taiwan

We report the structural and optical properties of ten-period ZnO/MgxZn1–xO multiple quantum wells (MQWs) prepared on the most widely used semiconductor material, Si. The introduction of a nanometer thick high-k Y2O3transition layer between Si (111) substrate and a ZnO buffer layer significantly improves the structural perfection of the MQWs grown on top of it. The high structural quality of the ZnO/MgxZn1–xO MQWs is evidenced by the appearance of pronounced high order satellite peaks in X-ray crystal truncation rods; high resolution cross-sectional transmission electron microscopy images also confirmed the regularly arranged well and barrier layers. When the well width is less than ∼2.7 nm, the quantum-confined Stark effect in MQWs can be negligible. Not only the increasing exciton-binding energy but also reducing exciton–phonon coupling determined in temperature-dependent photoluminescence spectra indicate quantum-size effect. Our results demonstrate that ZnO/MgxZn1–xO MQWs integrated on Si have great potential in UV optoelectronic device applications.

关键词： Excitons Phonons Oxides Binding energy Layers

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