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arXiv 2025年

作者： Sun, Yingying Jun, A. Liu, Zhiwei Sun, Rui Qian, Liujia Payne, Samuel H. Bittremieux, Wout Ralser, Markus Li, Chen Chen, Yi Dong, Zhen Perez-Riverol, Yasset Khan, Asif Sander, Chris Aebersold, Ruedi Vizcaíno, Juan Antonio Krieger, Jonathan R. Yao, Jianhua Wen, Han Zhang, Linfeng Zhu, Yunping Xuan, Yue Sun, Benjamin Boyang Qiao, Liang Hermjakob, Henning Tang, Haixu Gao, Huanhuan Deng, Yamin Zhong, Qing Chang, Cheng Bandeira, Nuno Li, Ming Weinan, E. Sun, Siqi Yang, Yuedong Omenn, Gilbert S. Zhang, Yue Xu, Ping Fu, Yan Liu, Xiaowen Overall, Christopher M. Wang, Yu Deutsch, Eric W. Chen, Luonan Cox, Jürgen Demichev, Vadim He, Fuchu Huang, Jiaxing Jin, Huilin Liu, Chao Li, Nan Luan, Zhongzhi Song, Jiangning Yu, Kaicheng Wan, Wanggen Wang, Tai Zhang, Kang Zhang, Le Bell, Peter A. Mann, Matthias Zhang, Bing Guo, Tiannan Affiliated Hangzhou First People’s Hospital State Key Laboratory of Medical Proteomics School of Medicine Westlake University Zhejiang Province Hangzhou China Westlake Center for Intelligent Proteomics Westlake Laboratory of Life Sciences and Biomedicine Zhejiang Province Hangzhou China Biology Department Brigham Young University ProvoUT84602 United States Department of Computer Science University of Antwerp Antwerp2020 Belgium Department of Biochemistry CharitéUniversitätsmedizin Berlin Berlin Germany Biomedicine Discovery Institute Department of Biochemistry and Molecular Biology Monash University MelbourneVICVIC 3800 Australia Wellcome Genome Campus Hinxton CambridgeCB10 1SD United Kingdom Harvard Medical School Ludwig Center at Harvard United States Harvard Medical School Broad Institute Ludwig Center at Harvard Dana-Farber Cancer Institute United States Department of Biology Institute of Molecular Systems Biology ETH Zürich Zürich Switzerland Bruker Ltd. MiltonONL9T 6P4 Canada AI for Life Sciences Lab Tencent Shenzhen518057 China State Key Laboratory of Medical Proteomics AI for Science Institute Beijing100080 China Beijing Institute of Lifeomics Beijing102206 China Thermo Fisher Scientific GmbH Hanna-Kunath Str. 11 Bremen28199 Germany Informatics and Predictive Sciences Research Bristol Myers Squibb United States Department of Chemistry Fudan University Songhu Road 2005 Shanghai200438 China Department of Computer Science Luddy School of Informatics Computing and Engineering Indiana University IN47408 United States ProCan® Children’s Medical Research Institute Faculty of Medicine and Health The University of Sydney WestmeadNSW Australia La Jolla CA United States Central China Institute of Artificial Intelligence University of Waterloo Canada AI for Science Institute Center for Machine Learning Research School of Mathematical Sciences Peking University China Research Institute of Intelligent Complex Systems Fudan U

Artificial intelligence (AI) is transforming scientific research, including proteomics. Advances in mass spectrometry (MS)-based proteomics data quality, diversity, and scale, combined with groundbreaking AI techniques, are unlocking new challenges and opportunities in biological discovery. Here, we highlight key areas where AI is driving innovation, from data analysis to new biological insights. These include developing an AI-friendly ecosystem for proteomics data generation, sharing, and analysis;improving peptide and protein identification and quantification;characterizing protein-protein interactions and protein complexes;advancing spatial and perturbation proteomics;integrating multi-omics data;and ultimately enabling AI-empowered virtual cells. © 2025, CC BY.

关键词： Biotic

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Controlled Cyclic Remote State Preparation of Arbitrary Qubit States

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Computers, Materials & Continua 2018年第5期55卷 321-329页

作者： Mingming Wang Chen Yang Reza Mousoli Shanxi Key Laboratory of Clothing Intelligence School of Computer ScienceXi’an Polytechnic UniversityXi’an 710048China State and Local Joint Engineering Research Center for Advanced Networking&Intelligent Information Services School of Computer ScienceXi’an Polytechnic UniversityXi’an 710048China School of Law Criminal Justice and ComputingCanterbury Christ Church UniversityCanterburyKentUK

Quantum secure communications could securely transmit quantum information by using quantum ***,novel applications such as bidirectional and asymmetric quantum protocols have been *** this paper,we propose a new method for generating entanglement which is highly useful for multiparty quantum communications such as teleportation and Remote State Preparation(RSP).As one of its applications,we propose a new type of quantum secure communications,*** RSP *** from a four-party controlled cyclic RSP protocol of one-qubit states,we show that this cyclic protocol can be generalized to a multiparty controlled cyclic RSP protocol for preparation of arbitrary qubit *** point out that previous bidirectional and asymmetric protocols can be regarded as a simpler form of our cyclic RSP protocols.

关键词： Quantum secure communications remote state preparation cyclic communications asymmetric communications bidirectional communications quantum control.

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Common and Rare Fundus Diseases Identification Using Vision-Language Foundation Model with Knowledge of Over 400 Diseases

arXiv

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arXiv 2024年

作者： Wang, Meng Lin, Tian Lin, Aidi Yu, Kai Peng, Yuanyuan Wang, Lianyu Chen, Cheng Zou, Ke Liang, Huiyu Chen, Man Yao, Xue Zhang, Meiqin Huang, Binwei Zheng, Chaoxin Zhang, Peixin Chen, Wei Luo, Yilong Chen, Yifan Xia, Honghe Shi, Tingkun Zhang, Qi Guo, Jinming Chen, Xiaolin Wang, Jingcheng Chung Tham, Yih Liu, Dianbo Wong, Wendy Thakur, Sahil Fenner, Beau Fang, Danqi Liu, Siying Liu, Qingyun Huang, Yuqiang Zeng, Hongqiang Meng, Yanda Zhou, Yukun Jiang, Zehua Qiu, Minghui Zhang, Changqing Chen, Xinjian Wang, Sophia Y. Lee, Cecilia S. Sobrin, Lucia Cheung, Carol Y. Pang, Chi Pui Keane, Pearse A. Cheng, Ching-Yu Chen, Haoyu Fu, Huazhu Centre for Innovation & Precision Eye Health Yong Loo Lin School of Medicine National University of Singapore Singapore117549 Singapore Department of Ophthalmology Yong Loo Lin School of Medicine National University of Singapore Singapore117549 Singapore Joint Shantou International Eye Center Shantou University Chinese University of Hong Kong Guangdong Shantou515041 China Department of Radiology University of Pennsylvania PhiladelphiaPA19104 United States School of Biomedical Engineering Anhui Medical University Anhui Hefei230032 China College of Computer Science and Technology Nanjing University of Aeronautics and Astronautics Jiangsu Nanjing211100 China Center of Advanced Medical Computing and Analysis Massachusetts General Hospital Harvard Medical School BostonMA02114 United States National Key Laboratory of Fundamental Science on Synthetic Vision College of Computer Science Sichuan University Sichuan Chengdu610065 China Big Vision Medical Technology Ltd. Suzhou China Singapore Eye Research Institute Singapore National Eye Centre Singapore Duke-NUS Medical School Singapore Department of Ophthalmology and Visual Sciences The Chinese University of Hong Kong 999077 Hong Kong Shenzhen Longgang E.N.T Hospital Guangdong Shenzhen518172 China Dongguan Songshan Lake Central Hospital Guangdong Dongguan523326 China Department of Computer Science University of Exeter ExeterEX4 4RN United Kingdom Centre for Medical Image Computing University College London London United Kingdom NIHR Biomedical Research Centre Moorfields Eye Hospital NHS Foundation Trust London United Kingdom Institute of Ophthalmology University College London London United Kingdom Tsinghua Medicine of Tsinghua University Beijing100084 China School of Clinical Medicine Beijing Tsinghua Changgung Hospital Beijing102218 China Foshan Aier Eye Hospital Guangdong Foshan528000 China College of Intelligence and Computing Tianjin University Tianjin300350 China School of Electr

Previous foundation models for retinal images were pre-trained with limited disease categories and knowledge base. Here we introduce RetiZero, a vision-language foundation model that leverages knowledge from over 400 fundus diseases. For RetiZero's pre-training, we compiled 341,896 fundus images paired with text descriptions, sourced from public datasets, ophthalmic literature, and online resources, encompassing a diverse range of diseases across multiple ethnicities and countries. RetiZero exhibits superior performance in several downstream tasks, including zero-shot disease recognition, image-to-image retrieval, and internal- and cross-domain disease identification. In zero-shot scenarios, RetiZero achieves Top5 accuracy scores of 0.8430 for 15 fundus diseases and 0.7561 for 52 fundus diseases. For image retrieval, it achieves Top5 scores of 0.9500 and 0.8860 for the same disease sets, respectively. Clinical evaluations show that RetiZero's Top3 zero-shot performance surpasses the average of 19 ophthalmologists from Singapore, China, and the United States. Furthermore, RetiZero significantly enhances clinicians' accuracy in diagnosing fundus disease. These findings underscore the value of integrating the RetiZero foundation model into clinical settings, where a variety of fundus diseases are encountered. © 2024, CC0.

关键词： Ophthalmology

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MODMA dataset: a Multi-modal Open Dataset for Mental-disorder Analysis

arXiv

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arXiv 2020年

作者： Cai, Hanshu Gao, Yiwen Sun, Shuting Li, Na Tian, Fuze Xiao, Han Li, Jianxiu Yang, Zhengwu Li, Xiaowei Zhao, Qinglin Liu, Zhenyu Yao, Zhijun Yang, Minqiang Peng, Hong Zhu, Jing Zhang, Xiaowei Gao, Guoping Zheng, Fang Li, Rui Guo, Zhihua Ma, Rong Yang, Jing Zhang, Lan Hu, Xiping Li, Yumin Hu, Bin Gansu Provincial Key Laboratory of Wearable Computing School of Information Science and Engineering Lanzhou University China CAS Center for Excellence in Brain Science and Intelligence Technology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences China Joint Research Center for Cognitive Neurosensor Technology of Lanzhou University Institute of Semiconductors Chinese Academy of Sciences China Open Source Software and Real-Time System Lanzhou University Ministry of Education China Shenzhen Institutes of Advanced Technology Chinese Academy of Sciences China Lanzhou University Second Hospital China

According to the World Health Organization, the number of mental disorder patients, especially depression patients, has grown rapidly and become a leading contributor to the global burden of disease. However, the present common practice of depression diagnosis is based on interviews and clinical scales carried out by doctors, which is not only labor-consuming but also time-consuming. One important reason is due to the lack of physiological indicators for mental disorders. With the rising of tools such as data mining and artificial intelligence, using physiological data to explore new possible physiological indicators of mental disorder and creating new applications for mental disorder diagnosis has become a new research hot topic. However, good quality physiological data for mental disorder patients are hard to acquire. We present a multi-modal open dataset for mental-disorder analysis. The dataset includes EEG and audio data from clinically depressed patients and matching normal controls. All our patients were carefully diagnosed and selected by professional psychiatrists in hospitals. The EEG dataset includes not only data collected using traditional 128-electrodes mounted elastic cap, but also a novel wearable 3-electrode EEG collector for pervasive applications. The 128-electrodes EEG signals of 53 subjects were recorded as both in resting state and under stimulation;the 3-electrode EEG signals of 55 subjects were recorded in resting state;the audio data of 52 subjects were recorded during interviewing, reading, and picture description. We encourage other researchers in the field to use it for testing their methods of mental-disorder analysis. Copyright © 2020, The Authors. All rights reserved.

关键词： Diagnosis

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Inequality-Type Zhang Equivalency Originating from Neural Dynamics for Time-Varying Problems Solving

Inequality-Type Zhang Equivalency Originating from Neural Dy...

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IEEE International Conference on Mechatronics and Automation

作者： Yunong Zhang Liangjie Ming Min Yang Binbin Qiu Zhonghua Li School of Data and Computer Science Sun Yat-sen University Guangzhou P. R. China Research Institute of Sun Yat-sen University in Shenzhen Shenzhen P. R. China Key Laboratory of Machine Intelligence and Advanced Computing Ministry of Education Guangzhou P. R. China School of Electronics and Information Technology Sun Yat-sen University Guangzhou P. R. China School of Intelligent Systems Engineering Sun Yat-sen University Guangzhou P. R. China

ISBN: (数字)9781728164168

ISBN: (纸本)9781728164175

In this paper, a concept of Zhang equivalency (ZE) is presented, and its type of inequality to inequality (simply termed, inequality type) is further discussed. By applying Zhang neural dynamics method, we thus propose the order-1, order2, and order-3 ZE general formulas of such an inequality type, respectively. Then, the inequalities in four different situations are investigated, i.e., the robot situation, matrix situation (including matrix-vector situation), state-control situation, and state situation. We propose the corresponding order-1, order-2, and order-3 ZE formulas to prepare for solving corresponding time-varying inequality-related problems.

关键词： Mechatronics Automation Conferences Linear matrix inequalities Problem-solving Robots

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An Early Stage Researcher's Primer on Systems Medicine Terminology

Network and Systems Medicine

引用

Network and Systems Medicine 2021年第1期4卷 2-50页

作者： Zanin, Massimiliano Aitya, Nadim A.A. Basilio, José Baumbach, Jan Benis, Arriel Behera, Chandan K. Bucholc, Magda Castiglione, Filippo Chouvarda, Ioanna Comte, Blandine Dao, Tien-Tuan Ding, Xuemei Pujos-Guillot, Estelle Filipovic, Nenad Finn, David P. Glass, David H. Harel, Nissim Iesmantas, Tomas Ivanoska, Ilinka Joshi, Alok Boudjeltia, Karim Zouaoui Kaoui, Badr Kaur, Daman Maguire, Liam P. McClean, Paula L. McCombe, Niamh De Miranda, João Luís Moisescu, Mihnea Alexandru Pappalardo, Francesco Polster, Annikka Prasad, Girijesh Rozman, Damjana Sacala, Ioan Sanchez-Bornot, Jose M. Schmid, Johannes A. Sharp, Trevor Solé-Casals, Jordi Spiwok, Vojtěch Spyrou, George M. Stalidzans, Egils Stres, Blaa Sustersic, Tijana Symeonidis, Ioannis Tieri, Paolo Todd, Stephen Van Steen, Kristel Veneva, Milena Wang, Da-Hui Wang, Haiying Wang, Hui Watterson, Steven Wong-Lin, Kongfatt Yang, Su Zou, Xin Schmidt, Harald H.H.W. Centro de Tecnología Biomédica Universidad Politécnica de Madrid Madrid Spain Intelligent Systems Research Centre School of Computing Engineering and Intelligent Systems Ulster University Ulster United Kingdom Center for Physiology and Pharmacology Institute of Vascular Biology and Thrombosis Research Medical University of Vienna Vienna Austria TUM School of Life Sciences Weihenstephan Technical University of Munich Freising Germany Holon Israel CNR National Research Council IAC Institute for Applied Computing Rome Italy Lab of Computing Medical Informatics and Biomedical Imaging Technologies School of Medicine Aristotle University of Thessaloniki Thessaloniki Greece Université Clermont Auvergne INRAE UNH Plateforme d'Exploration du Métabolisme MetaboHUB Clermont Clermont-Ferrand France Université de Technologie de Compiègne Compiègne France Labex MS2T Control of Technological Systems-of-Systems CNRS and Université de Technologie de Compiègne Compiègne France Faculty of Engineering University of Kragujevac Kragujevac Serbia Kragujevac Serbia Steinbeis Advanced Risk Technologies Institute Doo Kragujevac Kragujevac Serbia Pharmacology and Therapeutics School of Medicine Galway Neuroscience Centre National University of Ireland Galway Ireland School of Computing Ulster University Ulster United Kingdom Holon Israel Department of Mathematics and Natural Sciences Kaunas University of Technology Kaunas Lithuania Faculty of Computer Science and Engineering Ss. Cyril and Methodius University Skopje Macedonia Medicine Faculty Université Libre de Bruxelles CHU de Charleroi Charleroi Belgium Northern Ireland Centre for Stratified Medicine Biomedical Sciences Research Institute Ulster University Ulster United Kingdom Escola Superior de Tecnologia e Gestão Instituto Politécnico de Portalegre Portalegre Portugal Instituto Superior Técnico Universidade de Lisboa Lisboa Portugal Faculty of Automatic Control and Computers University Politehnica of B

Background: Systems Medicine is a novel approach to medicine, that is, an interdisciplinary field that considers the human body as a system, composed of multiple parts and of complex relationships at multiple levels, and further integrated into an environment. Exploring Systems Medicine implies understanding and combining concepts coming from diametral different fields, including medicine, biology, statistics, modeling and simulation, and data science. Such heterogeneity leads to semantic issues, which may slow down implementation and fruitful interaction between these highly diverse fields. Methods: In this review, we collect and explain more than100 terms related to Systems Medicine. These include both modeling and data science terms and basic systems medicine terms, along with some synthetic definitions, examples of applications, and lists of relevant references. Results: This glossary aims at being a first aid kit for the Systems Medicine researcher facing an unfamiliar term, where he/she can get a first understanding of them, and, more importantly, examples and references for digging into the topic. © Massimiliano Zanin et al., 2021;Published by Mary Ann Liebert, Inc. 2021.

关键词： Semantics

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Active interactions between animals and technology: biohybrid approaches for animal behaviour research

引用

Animal Behaviour 2025年 224卷

作者： Papadopoulou, M. Ball, M. Bartashevich, P. Burns, A.L.J. Chiara, V. Clark, M.A. Costelloe, B.R. Fele, M. French, F. Hauert, S. Heinrich, M.K. Herbert-Read, J.E. Hoitt, J. Ioannou, C.C. Landgraf, T. Matchette, S.R. Polverino, G. Sankey, D.W.E. Scott, D.M. Sridhar, V.H. Strömbom, D. Trianni, V. Vo-Doan, T.T. King, A.J. Department of Biosciences Faculty of Science and Engineering Swansea University Swansea United Kingdom Department of Biology Lafayette College Easton PA United States Institute for Theoretical Biology Department of Biology Humboldt-Universität zu Berlin Berlin Germany Cluster of Excellence ‘Science of Intelligence’ Berlin Germany Department Fish Biology Fisheries and Aquaculture Leibniz Institute of Freshwater Ecology and Inland Fisheries Berlin Germany Faculty of Life Sciences Albrecht Daniel Thaer-Institute of Agricultural and Horticultural Sciences Humboldt-Universität zu Berlin Berlin Germany Museum and Institute of Zoology Polish Academy of Science Warszawa Poland School of Biological Sciences University of Bristol Bristol United Kingdom School of Natural Sciences Macquarie University Sydney Australia Centre for the Advanced Study of Collective Behaviour University of Konstanz Konstanz Germany Department of Biology University of Konstanz Konstanz Germany Department of Collective Behavior Max Planck Institute of Animal Behavior Konstanz Germany School of Computing and Digital Media London Metropolitan University London United Kingdom Bristol Robotics Laboratory University of Bristol Bristol United Kingdom IRIDIA Université Libre de Bruxelles Brussels Belgium Department of Zoology University of Cambridge Cambridge United Kingdom Department of Mathematics and Computer Science Freie Universität Berlin Berlin Germany Department of Ecological and Biological Sciences University of Tuscia Viterbo Italy School of Natural and Environmental Science Newcastle University Newcastle upon Tyne United Kingdom Centre for Ecology and Conservation Faculty of Environment Science and Economy University of Exeter Penryn Campus Cornwall United Kingdom School of Animal Rural and Environmental Sciences Nottingham Trent University Nottingham United Kingdom Department for the Ecology of Animal Societies Max Planck Institute of Animal Behavior Konstanz Germany Ins

Biohybrid approaches (where living and engineered components are combined) provide new opportunities for advancing animal behaviour research and its applications. This review article and accompanying special issue explores how different types of novel technologies can be used in the field of animal behaviour from three perspectives: (1) comprehension, (2) application and (3) integration. Under the perspective of ‘comprehension,’ we present examples of how technologies like virtual animals or robots can be used in experimental settings to interact with living animals in a standardized manner. Such interactions can advance our understanding of fundamental topics such as mate choice, social learning and collective behaviour. Under ‘application,’ we investigate the potential for technologies to monitor, react and interact with animals in a variety of scenarios. For example, we discuss how drones can be used to keep large herbivores away from valuable crops and robotic predators to deter invasive species. Under ‘integration,’ we discuss possibilities for the coexistence of engineered and biological systems, augmenting the capacity or resilience of either or both components. Integration can be physical, for example, livestock can have sensors sit in their inner body for temperature monitoring, or within the environment, where sensors or robots monitor and interact with animals, such as a short-term earthquake forecasting method. Based upon these three themes, we discuss and classify existing biohybrid animal behaviour research, including the four articles included in our special issue. We also consider the ethics of this emerging field, highlight the advantages and potential issues associated with using technologies to create biohybrid systems and emphasize how such technologies can support the advancement of animal behaviour research. © 2025 The Author(s)

关键词： behavioural control behavioural monitoring biomimetic robotics ethorobotics interspecies interaction sensory integration

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Ultra-scalable spectral clustering and ensemble clustering

arXiv

引用

arXiv 2019年

作者： Huang, Dong Wang, Chang-Dong Wu, Jian-Sheng Lai, Jian-Huang Kwoh, Chee-Keong College of Mathematics and Informatics South China Agricultural University Guangzhou China School of Computer Science and Engineering Nanyang Technological University Singapore Singapore School of Data and Computer Science Sun Yat-sen University Guangzhou China Guangdong Key Laboratory of Information Security Technology Guangzhou China Key Laboratory of Machine Intelligence and Advanced Computing Ministry of Education China School of Information Engineering Nanchang University Nanchang China School of Computer Science and Engineering Nanyang Technological University Singapore Singapore

This paper focuses on scalability and robustness of spectral clustering for extremely large-scale datasets with limited resources. Two novel algorithms are proposed, namely, ultra-scalable spectral clustering (U-SPEC) and ultra-scalable ensemble clustering (U-SENC). In U-SPEC, a hybrid representative selection strategy and a fast approximation method for K-nearest representatives are proposed for the construction of a sparse affinity sub-matrix. By interpreting the sparse sub-matrix as a bipartite graph, the transfer cut is then utilized to efficiently partition the graph and obtain the clustering result. In U-SENC, multiple U-SPEC clusterers are further integrated into an ensemble clustering framework to enhance the robustness of U-SPEC while maintaining high efficiency. Based on the ensemble generation via multiple U-SEPC's, a new bipartite graph is constructed between objects and base clusters and then efficiently partitioned to achieve the consensus clustering result. It is noteworthy that both U-SPEC and U-SENC have nearly linear time and space complexity, and are capable of robustly and efficiently partitioning ten-million-level nonlinearly-separable datasets on a PC with 64GB memory. Experiments on various large-scale datasets have demonstrated the scalability and robustness of our algorithms. The MATLAB code and experimental data are available at https://***/publication/330760669. Copyright © 2019, The Authors. All rights reserved.

关键词： Clustering algorithms

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Big data analytics for manufacturing internet of things: Opportunities, challenges and enabling technologies

arXiv

引用

arXiv 2019年

作者： Dai, Hong-Ning Wang, Hao Xu, Guangquan Wan, Jiafu Imran, Muhammad Faculty of Information Technology Macau University of Science and Technology China Faculty of Engineering and Natural Sciences Norwegian University of Science & Technology Gjøvik Norway Tianjin Key Laboratory of Advanced Networking College of Intelligence and Computing Tianjin University Tianjin China School of Mechanical & Automotive Engineering South China University of Technology Guangzhou China College of Computer and Information Sciences King Saud University Saudi Arabia

The recent advances in information and communication technology (ICT) have promoted the evolution of conventional computer-aided manufacturing industry to smart data-driven manufacturing. Data analytics in massive manufacturing data can extract huge business values while can also result in research challenges due to the heterogeneous data types, enormous volume and real-time velocity of manufacturing data. This paper provides an overview on big data analytics in manufacturing Internet of Things (MIoT). This paper first starts with a discussion on necessities and challenges of big data analytics in manufacturing data of MIoT. Then, the enabling technologies of big data analytics of manufacturing data are surveyed and discussed. Moreover, this paper also outlines the future directions in this promising area. Copyright © 2019, The Authors. All rights reserved.

关键词： Internet of things

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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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