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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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Author Correction: Advances and prospects for the Human BioMolecular Atlas Program (HuBMAP)

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Nature cell biology 2024年第5期26卷 839页

作者： Sanjay Jain Liming Pei Jeffrey M Spraggins Michael Angelo James P Carson Nils Gehlenborg Fiona Ginty Joana P Gonçalves James S Hagood John W Hickey Neil L Kelleher Louise C Laurent Shin Lin Yiing Lin Huiping Liu Alexandra Naba Ernesto S Nakayasu Wei-Jun Qian Andrea Radtke Paul Robson Brent R Stockwell Raf Van de Plas Ioannis S Vlachos Mowei Zhou Katy Börner Michael P Snyder Department of Medicine Washington University School of Medicine St Louis MO USA. sanjayjain@wustl.edu. Department of Pediatrics Washington University School of Medicine St Louis MO USA. sanjayjain@wustl.edu. Department of Pathology and Immunology Washington University School of Medicine St. Louis MO USA. sanjayjain@wustl.edu. Center for Mitochondrial and Epigenomic Medicine Department of Pathology and Laboratory Medicine Children's Hospital of Philadelphia and Perelman School of Medicine University of Pennsylvania Philadelphia PA USA. lpei@pennmedicine.upenn.edu. Department of Cell and Developmental Biology and the Mass Spectrometry Research Center Vanderbilt University School of Medicine Nashville TN USA. jeff.spraggins@vanderbilt.edu. Department of Pathology Stanford School of Medicine Stanford CA USA. Texas Advanced Computing Center University of Texas at Austin Austin TX USA. Department of Biomedical Informatics Harvard Medical School Boston MA USA. GE Research Center Niskayuna NY USA. Department of Intelligent Systems Delft University of Technology Delft Netherlands. Department of Pediatrics (Pulmonology) and Program for Rare and Interstitial Lung Disease University of North Carolina at Chapel Hill Chapel Hill NC USA. Department of Microbiology and Immunology Stanford University Stanford CA USA. Departments of Medicine Chemistry and Molecular Biosciences Northwestern University Evanston IL USA. Department of Obstetrics Gynecology and Reproductive Sciences University of California San Diego La Jolla CA USA. Division of Cardiology University of Washington School of Medicine Seattle WA USA. Department of Surgery Washington University School of Medicine St Louis MO USA. Departments of Pharmacology Medicine (Hematology and Oncology) Lurie Cancer Center Northwestern University Feinberg School of Medicine Chicago IL USA. Department of Physiology and Biophysics University of Illinois at Chicago Chicago IL USA. Biological Sciences Division

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Preface

International Journal of Simulation and Process Modelling 2018年第2期13卷 89-90页

作者： Chen, Yinong School of Computing Informatics and Decision Systems Engineering Arizona State University TempeAZ85287-8809 United States

ECGNET: Learning Where to Attend for Detection of Atrial Fibrillation with Deep Visual Attention

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arXiv 2018年

作者： Mousavi, Sajad Afghah, Fatemeh Razi, Abolfazl Acharya, U. Rajendra School of Informatics Computing and Cyber Systems Northern Arizona University Flagstaff United States Department of Electronics and Computer Engineering Ngee Ann Polytechnic Singapore Department of Biomedical Engineering School of Science and Technology Singapore University of Social Sciences Singapore Department of Biomedical Engineering Faculty of Engineering University of Malaya Malaysia

The complexity of the patterns associated with Atrial Fibrillation (AF) and the high level of noise affecting these patterns have significantly limited the current signal processing and shallow machine learning approaches to get accurate AF detection results. Deep neural networks have shown to be very powerful to learn the non-linear patterns in the data. While a deep learning approach attempts to learn complex pattern related to the presence of AF in the ECG, they can benefit from knowing which parts of the signal is more important to focus during learning. In this paper, we introduce a two-channel deep neural network to more accurately detect AF presented in the ECG signal. The first channel takes in a preprocessed ECG signal and automatically learns where to attend for detection of AF. The second channel simultaneously takes in the preprocessed ECG signal to consider all features of entire signals. The model shows via visualization that what parts of the given ECG signal are important to attend while trying to detect atrial fibrillation. In addition, this combination significantly improves the performance of the atrial fibrillation detection (achieved a sensitivity of 99.53%, specificity of 99.26% and accuracy of 99.40% on the MIT-BIH atrial fibrillation database with 5-s ECG segments.) 1. Copyright © 2018, The Authors. All rights reserved.

关键词： Diseases

Weakly-supervised learning-based feature localization for confocal laser endomicroscopy glioma images

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arXiv 2018年

作者： Izadyyazdanabadi, Mohammadhassan Belykh, Evgenii Cavallo, Claudio Zhao, Xiaochun Gandhi, Sirin Moreira, Leandro Borba Eschbacher, Jennifer Nakaji, Peter Preul, Mark C. Yang, Yezhou School of Computing Informatics and Decision System Engineering Arizona State University TempeAZ85281 United States Department of Neurosurgery Barrow Neurological Institute PhoenixAZ85013 United States Department of Neurosurgery Irkutsk State Medical University Irkutsk664003 Russia

Confocal Laser Endomicroscopy (CLE) is novel handheld fluorescence imaging technology that has shown promise for rapid intraoperative diagnosis of brain tumor tissue. Currently CLE is capable of image display only and lacks an automatic system to aid the surgeon in diagnostically analyzing the images. The goal of this project was to develop a computer-aided diagnostic approach for CLE imaging of human glioma with feature localization function. Despite the tremendous progress in object detection and image segmentation methods in recent years, most of such methods require large annotated datasets for training. However, manual annotation of thousands of histopathology images by physicians is costly and time consuming. To overcome this problem, we constructed a Weakly-Supervised Learning (WSL)-based model for feature localization that trains on image-level annotations, and then localizes incidences of a class-of-interest in the test image. We developed a novel convolutional neural network for diagnostic features localization from CLE images by employing a novel multiscale activation map that is laterally inhibited and collaterally integrated. To validate our method, we compared the model output to the manual annotation performed by four neurosurgeons on test images. The model achieved 88% mean accuracy and 86% mean intersection over union on intermediate features and 87% mean accuracy and 88% mean intersection over union on restrictive fine features, while outperforming other state of the art methods tested. This system can improve accuracy and efficiency in characterization of CLE images of glioma tissue during surgery, and may augment intraoperative decision-making regarding the tumor margin and improve brain tumor resection. Copyright © 2018, The Authors. All rights reserved.

关键词： Convolution

Challenges in cybersecurity: Lessons from biological defense systems

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arXiv 2021年

作者： Schrom, Edward Kinzig, Ann Forrest, Stephanie Graham, Andrea L. Levin, Simon A. Bergstrom, Carl T. Castillo-Chavez, Carlos Collins, James P. De Boer, Rob J. Doupé, Adam Ensafi, Roya Feldman, Stuart Grenfell, Bryan T. Halderman, J. Alex Huijben, Silvie Maley, Carlo Moses, Melanie Perelson, Alan S. Perrings, Charles Plotkin, Joshua Rexford, Jennifer Tiwari, Mohit Department of Ecology and Evolutionary Biology Princeton University 106A Guyot Hall PrincetonNJ08544 United States School of Life Sciences Arizona State University TempeAZ85287 United States Julie Ann Wrigley Global Institute of Sustainability Arizona State University TempeAZ85287 United States Biodesign Center for Biocomputation Security and Society Arizona State University TempeAZ85287 United States School of Computing Informatics and Decision Sciences Engineering Arizona State University TempeAZ85287 United States Santa Fe Institute Santa FeNM87501 United States Department of Biology University of Washington SeattleWA98195 United States Arizona State University TempeAZ85287 United States Theoretical Biology and Bioinformatics Utrecht University Utrecht3584 CH Netherlands Center for Cybersecurity and Digital Forensics Global Security Initiative Arizona State University TempeAZ85287 United States Department of Electrical Engineering and Computer Science Computer Science and Engineering Division University of Michigan Ann ArborMI48109 United States Schmidt Futures New YorkNY10011 United States Princeton School of Public and International Affairs Princeton University PrincetonNJ08544 United States Center for Computer Security and Society University of Michigan Ann ArborMI48109 United States Center for Evolution and Medicine School of Life Sciences Arizona State University TempeAZ85287 United States Arizona Cancer Evolution Center Arizona State University TempeAZ85287 United States Department of Computer Science University of New Mexico AlbuquerqueNM87131 United States University of New Mexico Department of Computer Science AlbuquerqueNM87131 United States Department of Biology University of New Mexico AlbuquerqueNM87131 United States Theoretical Biology and Biophysics Group Los Alamos National Laboratory Los AlamosNM87545 United States Department of Biology University of Pennsylvania PhiladelphiaPA19104 Unite

We explore the commonalities between methods for assuring the security of computer systems (cybersecurity) and the mechanisms that have evolved through natural selection to protect vertebrates against pathogens, and how insights derived from studying the evolution of natural defenses can inform the design of more effective cybersecurity systems. More generally, security challenges are crucial for the maintenance of a wide range of complex adaptive systems, including financial systems, and again lessons learned from the study of the evolution of natural defenses can provide guidance for the protection of such *** Codes A.0. Copyright © 2021, The Authors. All rights reserved.

关键词： Cybersecurity

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GLOBAL CLIMATE

Bulletin of the American Meteorological Society 2024年第8期105卷 S12-S155页

作者： Dunn, R.J.H. Blannin, J. Gobron, N. Miller, J.B. Willett, K.M. Met Office Hadley Centre Exeter United Kingdom European Commission Joint Research Centre Ispra Italy NOAA Global Monitoring Laboratory Boulder Colorado European Centre for Medium-Range Weather Forecasts Reading United Kingdom University of Maryland College Park Maryland European Centre for Medium-Range Weather Forecasts Bonn Germany Department of Meteorology and National Centre for Earth Observation University of Reading Reading United Kingdom Hampton University Hampton Virginia National Research Institute for Agriculture Food and Environment (INRAE) CARRTEL Université Savoie Mont Blanc Thonon les Bains France Graduate School of Agriculture Osaka Metropolitan University Sakai Japan NOAA/NESDIS National Centers for Environmental Information Asheville North Carolina Science Faculty Universidad Nacional de Colombia Bogotá Colombia University of Bremen Bremen Germany Centro de Investigaciones sobre Desertificación – Spanish National Research Council (CSIC-UV-GVA) Valencia Spain Hydro-Climate Extremes Lab (H-CEL) Ghent University Ghent Belgium Laboratoire des Sciences du Climat et de l’Environnement (LSCE) LSCE/IPSL CEA-CNRS-UVSQ Gif-sur-Yvette France Instituto de Geografía Pontificia Universidad Católica de Valparaíso Valparaíso Chile Physical Science and Engineering Division King Abdullah University of Science and Technology Thuwal Saudi Arabia University of Reading Reading United Kingdom Institute Pierre Simon Laplace (IPSL) Guyancourt France School of Engineering Newcastle University Newcastle-upon-Tyne United Kingdom Université Paris Cité Institut de physique du globe de Paris CNRS IGN F-75005 Paris France Univ Gustave Eiffel ENSG IGN F-77455 Marne-la-Vallée France Laboratoire EDYTEM CNRS/Université Savoie Mont-Blanc Le Bourget-du-Lac France Global Modeling and Assimilation Office NASA Goddard Space Flight Center Greenbelt Maryland Universität Hamburg Hamburg Germany Climate Dynamics Lab University of St Andrews St Andrews United Kingdom Ea

Controlling the uncertain response of real multiplex networks to random damage

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arXiv 2018年

作者： Coghi, Francesco Radicchi, Filippo Bianconi, Ginestra School of Mathematical Sciences Queen Mary University of London LondonE1 4NS United Kingdom Center for Complex Networks and Systems Research School of Informatics Computing and Engineering Indiana University BloomingtonIN47408 United States

We reveal large fluctuations in the response of real multiplex networks to random damage of nodes. These results indicate that the average response to random damage, traditionally considered in mean-field approaches to percolation, is a poor metric of system robustness. We show instead that a large-deviation approach to percolation provides a more accurate characterization of system robustness. We identify an effective percolation threshold at which we observe a clear abrupt transition separating two distinct regimes in which the most likely response to damage is either a functional or a dismantled multiplex network. We leverage our findings to propose a new metric, named safeguard centrality, able to single out the nodes that control the response of the entire multiplex network to random damage. We show that safeguarding the function of top-scoring nodes is sufficient to prevent system collapse. Copyright © 2018, The Authors. All rights reserved.

关键词： Solvents

Examining scientific writing styles from the perspective of linguistic complexity

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arXiv 2018年

作者： Lu, Chao Bu, Yi Wang, Jie Ding, Ying Torvik, Vetle Schnaars, Matthew Zhang, Chengzhi School of Economics and Management Nanjing University of Science and Technology Nanjing Jiangsu China School of Informatics Computing and Engineering Indiana University BloomingtonIN United States Center for Complex Networks and Systems Research School of Informatics Computing and Engineering Indiana University BloomingtonIN United States School of Information Management Nanjing University Nanjing Jiangsu China School of Information Management Wuhan University Wuhan Hubei China School of Information Sciences University of Illinois UrbanaIL United States Jiangsu Key Laboratory of Data Engineering and Knowledge Service Nanjing University Nanjing Jiangsu China

Publishing articles in high-impact English journals is difficult for scholars around the world, especially for non-native English-speaking scholars (NNESs), most of whom struggle with proficiency in English. In order to uncover the differences in English scientific writing between native English-speaking scholars (NESs) and NNESs, we collected a large-scale data set containing more than 150,000 full-text articles published in PLoS between 2006 and 2015. We divided these articles into three groups according to the ethnic backgrounds of the first and corresponding authors, obtained by Ethnea, and examined the scientific writing styles in English from a two-fold perspective of linguistic complexity: (1) syntactic complexity, including measurements of sentence length and sentence complexity;and (2) lexical complexity, including measurements of lexical diversity, lexical density, and lexical sophistication. The observations suggest marginal differences between groups in syntactical and lexical complexity. Copyright © 2018, The Authors. All rights reserved.

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