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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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A Whole Crow Search Algorithm for Solving Data Clustering

A Whole Crow Search Algorithm for Solving Data Clustering

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International Conference on Technologies and Applications of Artificial Intelligence (TAAI)

作者： Ze-Xue Wu Ko-Wei Huang Abba Suganda Girsang Department of Electrical Engineering National Kaohsiung University of Science and Technology Kaohsiung City Taiwan R.O.C Computer Science Department BINUS Graduate Program-Master of Computer Science Bina Nusantara University Jakarta Indonesia

Data clustering is a well-known data mining approach that usually used to minimizes the intra distance but maximizes inter distance of each data center. The cluster problem has been proved to be an NP-hard problem. In this paper, a hybrid algorithm based on Whole optimization algorithm (WOA) and Crow search algorithm (CSA) is proposed, namely HWCA. The HWCA algorithm has the advantages of the search strategy of the WOA and CSA. In addition to, there are two operators used to improve the quality of solution, namely hybrid individual operator and enhance diversity operator. The hybrid individual operator is used to exchanges individuals from the WOA and CSA systems by using the roulette wheel approach. In other hand, the HWCA performs enhance diversity operator to improve the quality of each system. More over, the HWCA is incorporated with center optimization strategy to enhance diversity of each system. In the performance evaluation, the proposed MPGO algorithm was comparison WOA and CSA algorithm with six well-known UCI benchmarks. The results show that the proposed algorithm has a higher measure of accuracy rate with comparison algorithms.

关键词： Clustering algorithms Optimization Whales Search problems Wheels Benchmark testing Random variables

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Generation of terahertz transients from Co2Fe0.4Mn0.6Si-Heusler-alloy/normal-metal nanobilayers excited by femtosecond optical pulses

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Physical Review Research 2021年第4期3卷 043025-043025页

作者： Sarah Heidtfeld Roman Adam Takahide Kubota Koki Takanashi Derang Cao Carolin Schmitz-Antoniak Daniel E. Bürgler Fangzhou Wang Christian Greb Genyu Chen Ivan Komissarov Hilde Hardtdegen Martin Mikulics Roman Sobolewski Shigemasa Suga Claus M. Schneider Research Centre Jülich Peter Grünberg Institute 52425 Jülich Germany Faculty of Physics University of Duisburg-Essen 47048 Duisburg Germany Institute for Materials Research Tohoku University Sendai 980-8577 Japan Center for Spintronics Research Network Tohoku University Sendai 980-8577 Japan Center for Science and Innovation in Spintronics (Core Research Cluster) Tohoku University Sendai 980-8577 Japan College of Physics National Demonstration Center for Experimental Applied Physics Education Qingdao University Qingdao 266071 China Materials Science Graduate Program University of Rochester Rochester New York 14627 USA Laboratory for Laser Energetics University of Rochester Rochester New York 14623 USA Department of Electrical and Computer Engineering University of Rochester Rochester New York 14627 USA Belarusian State University of Informatics and Radioelectronics Minsk 220013 Belarus Research Centre Jülich Ernst Ruska Centre for Microscopy and Spectroscopy with Electrons 52425 Jülich Germany Department of Physics and Astronomy University of Rochester Rochester New York 14627 USA The Institute of Scientific and Industrial Research Osaka University Ibaraki Osaka 567-0047 Japan Department of Physics University of California Davis Davis California 95616 USA

We generated pulses of electromagnetic radiation in the terahertz (THz) frequency range by optical excitation of Co2Fe0.4Mn0.6Si (CFMS)/normal-metal (NM) bilayer structures. The CFMS is a Heusler alloy showing a band gap in one spin channel and is therefore a half metal. We compared the THz emission efficiency in a systematic manner for four different CFMS/NM bilayers, where NM was either Pt, Ta, Cr, or Al. Our measurements show that the THz intensity is highest for a Pt capping. We also demonstrate the tunability of the THz amplitude by varying the magnetic field for all four bilayers. We attribute the THz generation to the inverse spin Hall effect. In order to investigate the role of the interface in THz generation, we measured the spin mixing conductance for each CFMS/NM bilayer using a ferromagnetic resonance method. We found that the spin-orbit coupling cannot completely describe the THz generation in the bilayers and that the spin transmission efficiency of the CFMS/NM interface and the spin diffusion length, as well as the oxidation of the NM layer, play crucial roles in the THz emission process.

关键词： Inverse spin Hall effect Magnetism Spin injection Spin pumping Spintronics Ferromagnetic resonance Terahertz time-domain spectroscopy

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Superiorization of preconditioned conjugate gradient algorithms for tomographic image reconstruction

arXiv

引用

arXiv 2018年

作者： Helou, Elias S. Herman, Gabor T. Lin, Chuan Zibetti, Marcelo V.W. Institute of Mathematical Science and Computation University of São Paulo SP Brazil Department of Computer Science Graduate Center City University of New York NY United States School of Electrical Engineering Southwest Jiaotong University Chengdu China Program in Electrical and Computer Engineering Federal University of Technology PR Brazil

Properties of Superiorized Preconditioned Conjugate Gradient (SupPCG) algorithms in image reconstruction from projections are examined. Least squares (LS) is usually chosen for measuring data-inconsistency in these inverse problems. Preconditioned Conjugate Gradient algorithms are fast methods for finding an LS solution. However, for ill-posed problems, such as image reconstruction, an LS solution may not provide good image quality. This can be taken care of by superiorization. A superiorized algorithm leads to images with the value of a secondary criterion (a merit function such as the total variation) improved as compared to images with similar data-inconsistency obtained by the algorithm without superiorization. Numerical experimentation shows that SupPCG can lead to high-quality reconstructions within a remarkably short time. A theoretical analysis is also provided.15A29, 65F22, 65F10, 94A08 Copyright © 2018, The Authors. All rights reserved.

关键词： Image reconstruction

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Chronic radiation-associated dysphagia in oropharyngeal cancer survivors: Towards age-adjusted dose constraints for deglutitive muscles

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CLINICAL AND TRANSLATIONAL RADIATION ONCOLOGY 2019年 18卷 16-22页

作者： Christopherson, Kaitlin M. Ghosh, Alokananda Sherif, Abdallah Mohamed, Radwan Kamal, Mona Fuller, David Department of Radiation Oncology The University of Texas MD Anderson Cancer Center Houston TX United States Department of Biostatistics and Data Science University of Texas School of Public Health Houston TX United States Department of Clinical Oncology University of Alexandria Alexandria Egypt Department of Emergency Medicine The University of Texas MD Anderson Cancer Center Houston TX United States Baylor College of Medicine Houston TX United States Athinoula A. Martinos Center for Biomedical Imaging Massachusetts General Hospital Charlestown MA United States Department of Radiation Oncology The University of Texas Medical Branch Galveston TX United States Department of Head and Neck Surgery The University of Texas MD Anderson Cancer Center Houston TX United States Department of Thoracic & Head and Neck Oncology The University of Texas MD Anderson Cancer Center Houston TX United States Medical Physics Program The University of Texas Graduate School of Biomedical Sciences Houston TX United States Department of Computer Science University of Illinois at Chicago Chicago IL United States Department of Electrical and Computer Engineering The University of Iowa Iowa City IA United States

Objectives: We sought to model chronic radiation-associated dysphagia (RAD) in patients given intensity-modulated radiation therapy (IMRT) for oropharyngeal squamous cell cancer (OPSCC) as a function of age and dose to non-target swallowing muscles. Methods: We reviewed 300 patients with T1-T4 N0-3 M0 OPSCC given definitive IMRT with concurrent chemotherapy. Chronic RAD was defined as aspiration or stricture on videoflouroscopy/endoscopy, gastrostomy tube, or aspiration pneumonia at >= 12 months after IMRT. Doses to autosegmented regions of interest (ROIs;inferior, middle and superior constrictors, anterior and posterior digastrics, mylo/geniohyoid complex, intrinsic tongue, and gengioglossus) were obtained from DICOM-RT plans and dose-volume histograms. The probability of chronic RAD as a function of mean ROI dose, stratified by age (<50, 50-59, 60-69, or >70 years), was estimated with logistic probability models and subsequent unsupervised nonlinear curves. Results: Chronic RAD was observed in 34 patients (11%). Age was a significant correlate of chronic RAD, both independently and with dose for all muscle groups examined. Distinct muscle-specific dose-response profiles were observed as a function of age (e.g., 5% of patients in their 50 s [but 20% of those 70 +] who received 60 Gy to the superior constrictor had chronic RAD). This effect was stable across all observed muscle ROIs, with a false discovery rate-corrected p < 0.05, for all dose/muscle/age models, suggesting that including age as a covariate improves modeling of chronic RAD. Conclusions: Age at treatment moderates the probability of chronic RAD after chemo-IMRT for OPSCC, with aging muscles showing lower dose thresholds. Uniform dose constraints may not predict toxicity in older patients. (C) 2019 The Authors. Published by Elsevier B.V. on behalf of European Society for Radiotherapy and Oncology.

关键词： Oropharynx IMRT Radiation Toxicity Presbyphagia

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All-electrical Determination of Crystal Orientation in Anisotropic Two-Dimensional Materials

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Physical Review Letters 2018年第8期120卷 086801-086801页

作者： Lintao Peng Spencer A. Wells Christopher R. Ryder Mark C. Hersam Matthew Grayson Applied Physics Graduate Program Northwestern University Evanston Illinois 60208 USA Department of Materials Science and Engineering Northwestern University Evanston Illinois 60208 USA Department of Electrical Engineering and Computer Science Northwestern University Evanston Illinois 60208 USA Department of Chemistry Northwestern University Evanston Illinois 60208 USA

The crystal orientation of an exfoliated black phosphorous flake is determined by purely electrical means. A sequence of three resistance measurements on an arbitrarily shaped flake with five contacts determines the three independent components of the anisotropic in-plane resistivity tensor, thereby revealing the crystal axes. The resistivity anisotropy ratio decreases linearly with increasing temperature T and carrier density reaching a maximum ratio of 3.0 at low temperatures and densities, while mobility indicates impurity scattering at low T and acoustic phonon scattering at high T.

关键词： Crystal orientation electrical conductivity Semiconductors Transport phenomena Multilayer thin films Phosphorene Transition metal dichalcogenides Resistivity measurements

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Comparison of time in processing frame as an error detection mechanism in network transmission 2

Comparison of time in processing frame as an error detection...

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2nd Nommensen International Conference on Technology and engineering, NICTE 2018

作者： Rahim, Robbi Manurung, Rosida Tiurma Napitupulu, Darmawan Ratnadewi, R. Nurdiyanto, Heri Rangka, Itsar Bolo Eterudin, Hamzah Susanto, Eko Hidayat, Arif Suseno, Nyoto School of Computer and Communication Engineering Universiti Malaysia Perlis Kubang Gajah Malaysia Graduate Program in Scientific Psychology Universitas Kristen Maranatha Bandung Indonesia Research Center for Quality System and Testing Technology Indonesian Institute of Sciences Jakarta Indonesia Electrical Engineering Universitas Kristen Maranatha Bandung Indonesia Department of Informatics STMIK Dharma Wacana Metro Lampung Indonesia Departement of Guidance and Counseling Universitas Indraprasta PGRI Jakarta Indonesia Departement of Electrical Universitas Lancang Kuning Pekanbaru Indonesia Universitas Muhammadiyah Metro Lampung Indonesia

Errors in data transmission cannot be known directly when the data transmission process is fulfilled, but error is often prevalent in data transmission. Faulty or missing frames or bits are standard errors and to control or check errors requires a unique method, in this case, the Stop-and-wait method, Go-Back-N and Selective Reject are methods that can be used to do so, comparison of time of error checking process with Stop-and-wait method, Go-Back-N and Selective Reject is very important to get the right method to check the ignorance, from testing performed that the method of Go-Back-N is much faster than the other methods. © Published under licence by IOP Publishing Ltd.

关键词： Errors

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Fast matrix inversion and determinant computation for polarimetric synthetic aperture radar

arXiv

引用

arXiv 2018年

作者： Coelho, D.F.G. Cintra, R.J. Frery, A.C. Dimitrov, V.S. Graduate Program of Electrical and Computer Engineering Department University of Calgary Canada Signal Processing Group Departamento de Es-tatística Universidade Federal de Pernambuco Department of Electrical and Computer Engineering University of Calgary CalgaryAB Canada Laboratório de Computação Científica e Análise Numérica Universidade Federal de Alagoas Brazil Department of Electrical and Computer Engineering University of Calgary CalgaryAB Canada

This paper introduces a fast algorithm for simultaneous inversion and determinant computation of small sized matrices in the context of fully Polarimetric Synthetic Aperture Radar (PolSAR) image processing and analysis. The proposed fast algorithm is based on the computation of the adjoint matrix and the symmetry of the input matrix. The algorithm is implemented in a general purpose graphical processing unit (GPGPU) and compared to the usual approach based on Cholesky factorization. The assessment with simulated observations and data from an actual PolSAR sensor show a speedup factor of about two when compared to the usual Cholesky factorization. Moreover, the expressions provided here can be implemented in any platform. Copyright © 2018, The Authors. All rights reserved.

关键词： Graphics processing unit

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Metasurfaces: Coherent Perfect Diffraction in Metagratings (Adv. Mater. 36/2020)

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Advanced Materials 2020年第36期32卷

作者： Ziying Zhang Ming Kang Xueqian Zhang Xi Feng Yuehong Xu Xieyu Chen Huifang Zhang Quan Xu Zhen Tian Weili Zhang Alex Krasnok Jiaguang Han Andrea Alù Center for Terahertz Waves College of Precision Instrument and Optoelectronics Engineering Key Laboratory of Optoelectronics Information and Technology Tianjin University Tianjin 300072 P. R. China Department of Electrical and Computer Engineering The University of Texas at Austin Austin TX 78712 USA School of Electrical and Computer Engineering Oklahoma State University Stillwater OK 74078 USA Photonics Initiative Advanced Science Research Center City University of New York New York NY 10031 USA Physics Program Graduate Center City University of New York New York NY 10016 USA

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Author Correction: Disrupting cellular memory to overcome drug resistance

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Nature communications 2024年第1期15卷 4264页

作者： Guillaume Harmange Raúl A Reyes Hueros Dylan L Schaff Benjamin Emert Michael Saint-Antoine Laura C Kim Zijian Niu Shivani Nellore Mitchell E Fane Gretchen M Alicea Ashani T Weeraratna M Celeste Simon Abhyudai Singh Sydney M Shaffer Cellular and Molecular Biology Graduate Group Perelman School of Medicine University of Pennsylvania Philadelphia PA USA. Department of Biochemistry and Molecular Biophysics Perelman School of Medicine University of Pennsylvania Philadelphia PA USA. Department of Bioengineering School of Engineering and Applied Sciences University of Pennsylvania Philadelphia PA USA. Division of Biology and Biological Engineering California Institute of Technology Pasadena CA 91125 USA. Department of Electrical and Computer Engineering University of Delaware Newark DE 19716 USA. Abramson Family Cancer Research Institute Perelman School of Medicine University of Pennsylvania Philadelphia PA USA. Department of Chemistry College of the Arts and Sciences University of Pennsylvania Philadelphia PA USA. Department of Physics College of the Arts and Sciences University of Pennsylvania Philadelphia PA USA. Department of Biology College of the Arts and Sciences University of Pennsylvania Philadelphia PA USA. The Wharton School University of Pennsylvania Philadelphia PA USA. Cancer Signaling and Microenvironment Research Program Fox Chase Cancer Center Philadelphia PA USA. Department of Biochemistry and Molecular Biology Johns Hopkins School of Public Health Baltimore MD USA. Sidney Kimmel Cancer Center Johns Hopkins School of Medicine Baltimore MD USA. Department of Cell and Developmental Biology Perelman School of Medicine University of Pennsylvania Philadelphia PA USA. Department of Bioengineering School of Engineering and Applied Sciences University of Pennsylvania Philadelphia PA USA. sydshaffer@***. Department of Pathology Perelman School of Medicine University of Pennsylvania Philadelphia PA USA. sydshaffer@***.

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