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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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DEA Model with Hesitant Fuzzy Polyhedral Set in Benchmarking 1

DEA Model with Hesitant Fuzzy Polyhedral Set in Benchmarking

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1st International Conference of SNIKOM 2018, ICoSNIKOM 2018

作者： Abdullah, Dahlan Hartono, H. Erliana, Cut Ita Irwansyah, Defi Siregar, Nurintan Asyiah Sari, Ayu Esteka Hasibuan, Abdurrozzaq Abdussakir Kurniasih, Nuning Mas'Ut Rangkuti, Irma Yanti Nurmawati Buston, Erni Abdurrahman, Apridar Handayani, Tita Septi Hadikurniawati, Wiwien Winarno, Edy Department of Informatics Universitas Malikussaleh Aceh Indonesia Department of Computer Science STMIK IBBI Medan Indonesia Department of Industrial Engineering Universitas Malikussaleh Aceh Indonesia Department of Management STIE Labuhanbatu Sumatera Utara Indonesia Department of Management STIE Sakti Alam Kerinci Jambi Indonesia Faculty of Engineering Universitas Islam Sumatera Utara Medan Indonesia Department of Mathematics Education State Islamic University of Malang Malang Indonesia Faculty of Communication Sciences Library and Information Science Program Universitas Padjadjaran Bandung Indonesia Faculty of Economic Universitas Islam Sumatera Utara Medan Indonesia Faculty of Medical Universitas Islam Sumatera Utara Medan Indonesia Faculty of Industry Technique University of 45 Surabaya Indonesia Departement of Nursing Politeknik Kesehatan Kementerian Bengkulu Indonesia Department of Management Universitas Malikussaleh Aceh Indonesia Departemen of Nursing Universitas Dehasen Bengkulu Indonesia Faculty of Information Technology Universitas Stikubank Semarang Indonesia

Data Envelopment Analysis (DEA) method is a linear programming approach that has been widely used as a framework for evaluating efficiency and measurement. DEA decision making is often faced with situations where the existing DMU has input and output that contains fuzzy and hesitant elements so that it is difficult to make efficiency measurements. This study will design a DEA model in the state of inputs and outputs that contain hesitant elements by using polyhedral uncertainty sets. The results of this study are expected to produce a benchmarking model with DEA that can overcome the hesitant element and have the advantage of using a polyhedral uncertainty set that can measure the linearity of the nominal problem. © Published under licence by IOP Publishing Ltd.

关键词： Data envelopment analysis

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Design of Hexapod Robot Movement Based on Arduino Mega 2560

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Journal of Physics: Conference Series 2019年第1期1165卷

作者： K U Ariawan G S Santyadiputra I W Sutaya Electronics Engineering Study Program Technical and Vocational Faculty Universitas Pendidikan Ganesha Informatics Engineering Education Departement Technical and Vocational Faculty Universitas Pendidikan Ganesha

This study aims to design the movement of the hexapod robot so that it can move straight forward, turn 90 degrees forward, and move forward 180 degrees by applying the tripod gait method to produce a maximum movement pattern. The robot control system uses Arduino Mega 2560 to control the motion of 18 servo motors through the I2C interface servo motor driver - PCA9685. In straight forward motion testing, an average velocity of 6 cm/s was obtained, 90 degree forward motion testing obtained an average speed of 18 degrees/s, while the 180 degree rotational forward motion test also obtained an average speed of 18 degrees/s.

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ENIGMA-Meditation: Worldwide Consortium for Neuroscientific Investigations of Meditation Practices

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Biological Psychiatry: Cognitive Neuroscience and Neuroimaging 2025年第4期10卷 425-436页

作者： Ganesan, Saampras Barrios, Fernando A. Batta, Ishaan Bauer, Clemens C.C. Braver, Todd S. Brewer, Judson A. Brown, Kirk Warren Cahn, Rael Cain, Joshua A. Calhoun, Vince D. Cao, Lei Chetelat, Gaël Ching, Christopher R.K. Creswell, J. David Dagnino, Paulina Clara Davanger, Svend Davidson, Richard J. Deco, Gustavo Dutcher, Janine M. Escrichs, Anira Eyler, Lisa T. Fani, Negar Farb, Norman A.S. Fialoke, Suruchi Fresco, David M. Garg, Rahul Garland, Eric L. Goldin, Philippe Hafeman, Danella M. Jahanshad, Neda Kang, Yoona Khalsa, Sahib S. Kirlic, Namik Lazar, Sara W. Lutz, Antoine McDermott, Timothy J. Pagnoni, Giuseppe Piguet, Camille Prakash, Ruchika S. Rahrig, Hadley Reggente, Nicco Saccaro, Luigi F. Sacchet, Matthew D. Siegle, Greg J. Tang, Yi-Yuan Thomopoulos, Sophia I. Thompson, Paul M. Torske, Alyssa Treves, Isaac N. Tripathi, Vaibhav Tsuchiyagaito, Aki Turner, Matthew D. Vago, David R. Valk, Sofie Zeidan, Fadel Zalesky, Andrew Turner, Jessica A. King, Anthony P. Department of Biomedical Engineering The University of Melbourne Carlton VIC Australia Contemplative Studies Centre Melbourne School of Psychological Sciences The University of Melbourne Melbourne VIC Australia Systems Lab of Neuroscience Neuropsychiatry and Neuroengineering The University of Melbourne Parkville VIC Australia Universidad Nacional Autónoma de México Instituto de Neurobiolgía México Querétaro Mexico Center for Translational Research in Neuroimaging and Data Science: Georgia State University Georgia Institute of Technology and Emory University Atlanta GA United States Department of Psychology Northeastern University Boston Massachusetts Brain and Cognitive Science McGovern Institute for Brain Research Massachusetts Institute of Technology Cambridge Massachusetts Department of Psychological and Brain Sciences Washington University St. Louis Missouri Department of Behavioral and Social Sciences Brown University School of Public Health Providence Rhode Island Department of Psychology Carnegie Mellon University Pittsburgh PA United States University of Southern California Department of Psychiatry & Behavioral Sciences Los Angeles California University of Southern California Center for Mindfulness Science Los Angeles California Institute for Advanced Consciousness Studies Santa Monica California Department of Psychiatry and Behavioral Health The Ohio State University College of Medicine Columbus OH United States Normandie University Université de Caen Normandie INSERM U1237 Neuropresage Team Cyceron Caen France Imaging Genetics Center Mark and Mary Stevens Neuroimaging and Informatics Institute Keck School of Medicine of the University of Southern California Los Angeles California Desert-Pacific Mental Illness Research Education and Clinical Center VA San Diego Healthcare System San Diego California Computational Neuroscience Group Center for Brain and Cognition Department of Information and Communication Technologies Universitat Pompeu Fa

Meditation is a family of ancient and contemporary contemplative mind-body practices that can modulate psychological processes, awareness, and mental states. Over the last 40 years, clinical science has manualized meditation practices and designed various meditation interventions that have shown therapeutic efficacy for disorders including depression, pain, addiction, and anxiety. Over the past decade, neuroimaging has been used to examine the neuroscientific basis of meditation practices, effects, states, and outcomes for clinical and nonclinical populations. However, the generalizability and replicability of current neuroscientific models of meditation have not yet been established, because they are largely based on small datasets entrenched with heterogeneity along several domains of meditation (e.g., practice types, meditation experience, clinical disorder targeted), experimental design, and neuroimaging methods (e.g., preprocessing, analysis, task-based, resting-state, structural magnetic resonance imaging). These limitations have precluded a nuanced and rigorous neuroscientific phenotyping of meditation practices and their potential benefits. Here, we present ENIGMA (Enhancing Neuro Imaging Genetics through Meta Analysis)–Meditation, the first worldwide collaborative consortium for neuroscientific investigations of meditation practices. ENIGMA-Meditation will enable systematic meta- and mega-analyses of globally distributed neuroimaging datasets of meditation using shared, standardized neuroimaging methods and tools to improve statistical power and generalizability. Through this powerful collaborative framework, existing neuroscientific accounts of meditation practices can be extended to generate novel and rigorous neuroscientific insights that account for multidomain heterogeneity. ENIGMA-Meditation will inform neuroscientific mechanisms that underlie therapeutic action of meditation practices on psychological and cognitive attributes, thereby advancing the f

关键词： Consortium ENIGMA Magnetic resonance imaging (MRI) Meditation Mindfulness Neuroimaging

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Testing Real-Time Applications on Windows 10 IOT Using the Nyquist Theory

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Journal of Physics: Conference Series 2019年第1期1255卷

作者： Zulfahmi Syahputa M. Zarlis Beny B. Nasution Informatics Engineering Study Program Magister Faculty of Computer Science and Information Technology Universitas Sumatera Utara Medan-Indonesia

Raspberry Pi is a mini-computer that is provided to carry out activities quickly and precisely, but Raspberry Pi was created to not be able to do the real-time system with the support of Windows 10 IoT operating system, so the real-time system can be done on Raspberry Pi. The real-time applied in the application needs to be tested with the Nyquist theory. The purpose of this study was to get real-time system measurements available on Windows 10 IoT. This test is done using the Nyquist theory by calculating the results of measurements on mp3 streaming performed on Windows 10 IoT.

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Web based testing application security system using semantic comparison method 2

Web based testing application security system using semantic...

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

作者： Iskandar, Akbar Fahlepi Tuasamu, Muhammad Resa Syamsu, Suryadi Mansyur, M. Listyorini, Tri Sallu, Sulfikar Supriyono, S. Saddhono, Kundharu Napitupulu, Darmawan Rahim, Robbi Informatics Engineering STMIK AKBA Makassar Indonesia Graduate Program Universitas Negeri Makassar Makassar Indonesia Informatics Engineering Universitas Maria Kudus Central Java Indonesia Computer Information Systems Universitas Sembilan Belas November Kolaka Indonesia Department of Geography Education Universitas Prof Dr Hazairin SH Bengkulu Indonesia Indonesian Language Education Departement Faculty of Teacher Training and Education Universitas Sebelas Maret Surakarta Indonesia Research Center for Quality System and Testing Technology Indonesian Institute of Sciences Indonesia Sekolah Tinggi Ilmu Manajemen Sukma Medan Indonesia

computer and web security system is an attempt to avoid attacks from crackers because a form and method of crime on internet network can not be predicted. Therefore, we just keep trying to use various methods in securing the system that is running. It is the same in web testing that can be accessed online by people who are not responsible from along distance to change and remove the test results or even damage the web testing system. So, the purpose of this paper is to design and implement web security testing system by using semantic comparison method to avoid structured query language injection (SQLI) attack and to do security on web testing application using Message Digest 5 encryption (MD5). Research data were obtained by using direct observation and documentation and literature review. After the design and application of the system, it can be obtained that by using semantic comparison method in web testing can prevent the occurrence of SQL injection attacks and can secure account from web testing users by using MD5. © Published under licence by IOP Publishing Ltd.

关键词： Semantics

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Adjusted Framework of M-Learning in Blended Learning System for Mathematics study Field of Junior High School Level VII

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IOP Conference Series: Materials Science and engineering 2018年第1期336卷

作者： Lipur Sugiyanta Moch. Sukardjo Study Program of Education for Informatics and Computer Engineering/Faculty of Engineering State University of Jakarta

The 2013 curriculum requires teachers to be more productive, creative, and innovative in encouraging students to be more independent by strengthening attitudes, skills and knowledge. Teachers are given the options to create lesson plan according to the environment and conditions of their students. At the junior level, Core Competence (KI) and Basic Competence (KD) have been completely designed. In addition, there had already guidebooks, both for teacher manuals (Master's Books) and for learners (Student Books). The lesson plan and guidebooks which already exist are intended only for learning in the classroom/in-school. Many alternative classrooms and alternatives learning models opened up using educational technology. The advance of educational technology opened opportunity for combination of class interaction using mobile learning applications. Mobile learning has rapidly evolved in education for the last ten years and many initiatives have been conducted worldwide. However, few of these efforts have produced any lasting outcomes. It is evident that mobile education applications are complex and hence, will not become sustainable. Long-term sustainability remains a risk. Long-term sustainability usually was resulted from continuous adaptation to changing conditions [4]. Frameworks are therefore required to avoid sustainability pitfalls. The implementation should start from simple environment then gradually become complex through adaptation steps. Therefore, our paper developed the framework of mobile learning (m-learning) adaptation for grade 7th (junior high school). The environment setup was blended mobile learning (not full mobile learning) and emphasize on Algebra. The research is done by R&D method (research and development). Results of the framework includes requirements and adaptation steps. The adjusted m-learning framework is designed to be a guidance for teachers to adopt m-learning to support blended learning environments. During mock-up prototype, the ad

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Retracted: Implementation Method CUSUM to Determine the Accident Prone Areas in Web Based

Retracted: Implementation Method CUSUM to Determine the Acci...

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2018 Workshop on Multidisciplinary and Its Applications: Applied Mathematics, computer Science, Information Systems, and Information Technology, WMA-Mathcomtech 2018

作者： Dinata, Rozzi Kesuma Abdullah, Dahlan Hartono, H. Erliana, Cut Ita Riasti, Berliana Kusuma Iskandar, Akbar Sari, Ifit Novita Nurmawati, N. Nanuru, Ricardo Freedom Putri, Lusi Dwi Manurung, Rosida Tiurma Sriadhi, S. Saleh, A.A. Astari, T. Khaddafi, Muammar Department of Informatics Universitas Malikussaleh Aceh Indonesia Department of Computer Science STMIK IBBI Medan Indonesia Department of Industrial Engineering Universitas Malikussaleh Aceh Indonesia Department of Informatics Universitas Sebelas Maret Surakarta Indonesia Department of Informatics STMIK AKBA Makassar Indonesia Departement Of: Social Science Education Program Post Graduate Program Universitas Kanjuruhan Malang Malang Indonesia Faculty of Industry Technique University of 45 Surabaya Indonesia Universitas Kristen Indonesia Maluku Ambon Indonesia Department of Civil Engineering Universitas Lancang Kuning Pekanbaru Indonesia Graduate Program in Scientific Psychology Universitas Kristen Maranatha Indonesia Department of Electrical Engineering Universitas Negeri Medan Indonesia Statistics Financial and Social Sciences Research Group Indonesia Department of Elementary School Teacher Education STKIP Citra Bangsa Aceh Utara Indonesia Department of Accounting Universitas Malikussaleh Aceh Indonesia

At the Unit Laka Lantas Polres Lhokseumawe determining accident-prone areas on roads in Lhokseumawe still using manual systems. Determination of accident-prone areas are less effective because the police Unit Laka Lantas Polres Lhokseumawe just using the data of the last year and had to repeatedly calculate manually accident-prone areas based on the number of human casualties. In this study the system implementation CUSUM method (Cummulative Summary) to determine the accident-prone areas designed using the web-based programming language PHP. In this system there are three processes to determine areas prone to accidents, the accident rate calculations based on the weighted severity, blacksite calculations using the Z-Score method for determining areas prone to accident blackspots and calculations using the CUSUM method to determine the critical points of an accident. The data used are secondary data obtained from the Police Unit Laka Lantas Polres Lhokseumawe years 2009-2013. © Published under licence by IOP Publishing Ltd.

关键词： Accidents

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Bisindo information system as potential daily sign language learning

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AIP Conference Proceedings 2019年第1期2114卷

作者： Umi Fadlilah Decky Wismoyohadi Abd Kadir Mahamad Bana Handaga 1Electronic Study Program Faculty of Engineering Universitas Muhammadiyah Surakarta Sukoharjo Central Java Indonesia 2Informatics Study Program Faculty of Engineering Universitas Muhammadiyah Surakarta Sukoharjo Central Java Indonesia 3Computer Engineering Faculty of Electrical and Electronic Universiti Tun Hussein Onn Malaysia Parit Raja Johor Malaysia

Bisindo or Bahasa Isyarat Indonesia is one of sign language methods in Indonesia, besides SIBI or Sistem Isyarat Bahasa Indonesia. Generally, Bisindo is used by deaf people in their daily communication. Deaf people tend to have barriers to communicate with others. Yet, in the educational realm, some of them still have high spirit to continue their education until university. So, they must improve their abilities or competences in communicating with others and try to get information from around the world, for example using sophisticated technology with sign language. Information system of sign language learning is important to help deaf and heard people who want to understand the deaf conversation meaning. Bisindo information system is in website form that is built by PHP, MySQL, and sublime text 3. Based on the black box method, the Bisindo information system can run well. The results of the trial to the user describe that the maximum percentage for each level of testing is above 50% except for testing of conformity with the needs of deaf only at maximum of 42%. The Bisindo information system still has weakness, but it already gives benefits especially for deaf people in Indonesia.

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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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