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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 model for the construction of an inter-domain ontology: Corporate Sustainability Index and the G4 Guidelines of the Global Reporting Initiative

A model for the construction of an inter-domain ontology: Co...

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Brazilian Seminar on Ontologies, ONTOBRAS 2015

作者： Reis, Tâmara Batista Da Silva, Paulo Caetano Master Program in Systems and Computing Salvador University Brazil

Ontologies are tools for knowledge representation that can help solve the diversity of representation of concepts that have similar meaning. Therefore, this paper proposes a method for building an ontology for the representation of a common knowledge base among the Corporate Sustainability Index, adopted in Brazil, with the G4 Guidelines of the Global Reporting Initiative, an international standard.

关键词： Ontology

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A Risk management model for service-oriented architecture: An application in the implementation of SOA services 8

A Risk management model for service-oriented architecture: A...

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8th IADIS International Conference on Information systems, IS 2015

作者： Da Silva, Paulo Caetano Monteiro, Erasmo Leite Master's Program in Systems and Computing Salvador University UNIFACS Salvador Brazil

ISBN: (纸本)9789898533333

The risk may be approached through two perspectives: a threat that, should it happen, will cause a negative effect on at least one project objective;and an opportunity, when it causes a positive effect on the project. Managing risks aims to increase the likelihood and impact of positive events and decrease the likelihood and impact of adverse events. In this article, an IT risk management model for service-oriented architecture is presented, formed from the use of the NIST 800-30, FAIR and OCTAVE Allegro. With this model is expected to ensure that any failure in the implementation of service-oriented architecture does not endanger the strategic objectives of the corporation. It is important to consider a related risk to operations-failures and security vulnerabilities or even design and development-may have an impact on the success of the corporation in a campaign or specific initiative or in your image. To demonstrate its use, an application is shown, so the main ideas and contributions of a model of IT risk management will applied in the implementation of service-oriented architecture.

关键词： Risk management

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Influence Value: Quantifying Topic Influence on Social Media

Influence Value: Quantifying Topic Influence on Social Media

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IEEE International Conference on Multimedia Big Data (BigMM)

作者： Fernando H. Calderon Yi-Shin Chen Taiwan International Graduate Program Social Networks and Human-Centered Computing Academia Sinica Taipei Taiwan Institute of Information Systems and Applications National Tsing Hua University Hsinchu Taiwan Institute of Information Systems and Applications National Tsing Hua University Hsinchu Taiwan

ISBN: (纸本)9781509021802

Social Media specifically Micro-blogging sites have become very rich data repositories. However the generated data is dynamic by nature, tied to temporal conditions and the subjectivity of its users. Everyday life experiences, discussions or events have a direct impact on the behaviors reflected in social networks. It is therefore of great importance to asses the impact these interactions are having over a social group. An alternative to answer this is determining how influential a topic is according to the behavior presented on a social network over time. It is then necessary to find and develop methods that can contribute towards this task. Having identified a topic in social media we can first classify it as time specific or long term, then posts relevant to the topic are collected and each one is assigned an emotion label. We then propose an Influence Value score which will be given to each topic based on its lifespan, emotion transition and reach. This lays ground to quantify how influential a topic is over a social group, specifically from events detected on twitter.

关键词： Media Social groups Twitter Wheels Measurement Big data

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Modelling and solving university course timetabling problems through XHSTT 11

Modelling and solving university course timetabling problems...

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11th International Conference on the Practice and Theory of Automated Timetabling, PATAT 2016

作者： Fonseca, George H.G. Santos, Haroldo G. Carrano, Eduardo G. Stidsen, Thomas J.R. Department of Computing and Information Systems Federal University of Ouro Preto St. Diogo de Vasconcelos 328 Ouro Preto MG35400-000 Brazil Department of Computing Federal University of Ouro Preto St. Diogo de Vasconcelos 328 Ouro Preto MG35400-000 Brazil Graduate Program in Electrical Engineering Federal University of Minas Gerais Av. Antônio Carlos 6627 Belo Horizonte MG31270-901 Brazil Department of Management Engineering Technical University of Denmark Produktionstorvet Kgs. LyngbyDK-2800 Denmark

ISBN: (纸本)9780992998417

The XHSTT was proposed as a standard format to express a wide range of School Timetabling problems. Although the format is powerful to represent different timetabling features, its application to University Course Timetabling (UCT) problems was not formally studied. The goal of this work is to present encodings from Curriculum-Based Course Timetabling (CB-CTT) and Post-Enrolment Course Timetabling (PE-CTT) to XHSTT and to evaluate how a state-of-art XHSTT solver performs on these problems. Computational experiments performed suggested that this approach is suitable for dealing with UCT: XHSTT solver would be ranked as fourth in CB-CTT track of the Second International Timetabling Competition (ITC2007) and it achieved feasible solutions for most PE-CTT instances within one hour. Although the results do not outperform the best known approaches for these problems, XHSTT solvers were designed to handle a wide range of features and constraints beyond the ones present in these models, making it able to fit the specific requirements of several universities. © PATAT *** rights reserved.

关键词： Curricula

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Understanding perceived privacy: A privacy boundary management model 19

Understanding perceived privacy: A privacy boundary manageme...

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19th Pacific Asia Conference on Information systems, PACIS 2015

作者： Chang, Younghoon Wong, Siew Fan Lee, Hwansoo Department of Computing and Information Systems Sunway University Petaling Jaya Malaysia IT Law Program Dankook University Yongin-si Korea Republic of

Consumer data is asset to organizations. Analysis of consumers' transactional data helps organizations to understand customer behaviors and preferences. Before organizations could capitalize on these data, they ought to have effective plans to address consumers' privacy concerns because violation of consumer privacy brings long-term reputational damage to organizations. This paper proposes and tests a Privacy Boundary Management Model that explains how consumers formulate and manage their privacy boundary. Survey data was collected from 98 users of online banking websites who have used the system for a minimum of six months. The PLS results showed that the model accounts for high variance in perceived privacy. Three elements of the FIPs (notice, access, and enforcement) have significant impact on perceived effectiveness of privacy policy. Perceived effectiveness in turns significantly influences privacy control and privacy risks. Privacy control affects perceived privacy and trust while privacy risk influences privacy concern and perceived privacy. Privacy concern has a negative relationship with perceived privacy and trust has a positive relationship with perceived privacy. The findings have novel implications for organizations and policy makers.

关键词： Consumer behavior

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Discounted Markov Decision Processes via Time Aggregation

Discounted Markov Decision Processes via Time Aggregation

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European Control Conference

作者： Edilson F. Arruda Marcelo D. Fragoso Industrial Engineering Program Alberto Luiz Coimbra Institute - Graduate School and Research in Engineering Federal University of Rio de Janeiro Rio de Janeiro RJ Brazil Center for Systems and Control National Laboratory for Scientific Computing Petropolis RJ Brazil

ISBN: (纸本)9781509025923

This paper applies two-phase time aggregation to solve discounted Markov decision processes (MDP). This procedure, recently proposed for average cost MDPs, is extended here discounted MDPs with a view at easing the computational burden associated to finding a quality solution within a reasonable time frame. Numerical examples are presented to illustrate the results.

关键词： Discounted Markov Decision Processes Time Aggregation

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Optimization of Grounding Grid's Multidesign Geometry

Optimization of Grounding Grid's Multidesign Geometry

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IEEE International Conference on Environment and Electrical Engineering

作者： Carlos L.B. Silva Diogo N. Oliveira Thyago G. Pires José W.L. Nerys Paulo H.S. Barbosa Wesley P. Calixto Aylton J. Alves. Graduate Program in Electronic and Automation Systems Engineering University of Brasilia Brasilia Brazil School of Electric and Computing Engineering Federal University of Goias Goiania Brazil Experimental Technologic Research and Study Group Federal Institute of Education Science and Technology Goiania.Brazil

ISBN: (纸本)9781509023219

This paper deals with the optimization of grounding grids geometry. The goal is to reduce the amount of material to deploy a grounding grid, while keeping the system security. The touch voltages, step voltages, GPR and ground resistance are parameters of grounding grids and are related to safety aspect. Also discussed is a genetic algorithm used for optimizing ground grids, which can assume any form in a limited space of the project. The simulation is based in images method. The results are presented and discussed.

关键词： Grounding grid systems image method optimization

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Input optics systems of the KAGRA detector during O3GK (vol 2023, 023F01, 2023)

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PROGRESS OF THEORETICAL AND EXPERIMENTAL PHYSICS 2023年第5期2023卷

作者： Akutsu, T. Ando, M. Arai, K. Arai, Y. Araki, S. Araya, A. Aritomi, N. Asada, H. Aso, Y. Bae, S. Bae, Y. Baiotti, L. Bajpai, R. Barton, M. A. Cannon, K. Cao, Z. Capocasa, E. Chan, M. Chen, C. Chen, K. Chen, Y. Chiang, C-I Chu, H. Chu, Y-K Eguchi, S. Enomoto, Y. Flaminio, R. Fujii, Y. Fujikawa, Y. Fukunaga, M. Fukushima, M. Furuhata, T. Gao, D. Ge, G-G Ha, S. Hagiwara, A. Haino, S. Han, W-B Hasegawa, K. Hattori, K. Hayakawa, H. Hayama, K. Himemoto, Y. Hiranuma, Y. Hirata, N. Hirose, E. Hong, Z. Hsieh, B-H Huang, G-Z Huang, H-Y Huang, P. Huang, Y-C Huang, Y-J Hui, D. C. Y. Ide, S. Ikenoue, B. Imam, S. Inayoshi, K. Inoue, Y. Ioka, K. Ito, K. Itoh, Y. Izumi, K. Jeon, C. Jin, H-B Jung, K. Jung, P. Kaihotsu, K. Kajita, T. Kakizaki, M. Kamiizumi, M. Kanbara, S. Kanda, N. Kang, G. Kataoka, Y. Kawaguchi, K. Kawai, N. Kawasaki, T. Kim, C. Kim, J. Kim, J. C. Kim, Ws Kim, Y-M Kimura, N. Kita, N. Kitazawa, H. Kojima, Y. Kokeyama, K. Komori, K. Kong, A. K. H. Kotake, K. Kozakai, C. Kozu, R. Kumar, R. Kume, J. Kuo, C. Kuo, H-S Kuromiya, Y. Kuroyanagi, S. Kusayanagi, K. Kwak, K. Lee, H. K. Lee, H. W. Lee, R. Leonardi, M. Li, K. L. Lin, L. C-C Lin, C-Y Lin, F-K Lin, F-L Lin, H. L. Liu, G. C. Luo, L-W Majorana, E. Marchio, M. Michimura, Y. Mio, N. Miyakawa, O. Miyamoto, A. Miyazaki, Y. Miyo, K. Miyoki, S. Mori, Y. Morisaki, S. Moriwaki, Y. Nagano, K. Nagano, S. Nakamura, K. Nakano, H. Nakano, M. Nakashima, R. Nakayama, Y. Narikawa, T. Naticchioni, L. Negishi, R. Quynh, L. Nguyen Ni, W-T Nishizawa, A. Nozaki, S. Obuchi, Y. Ogaki, W. Oh, J. J. Oh, S. H. Ohashi, M. Ohishi, N. Ohkawa, M. Ohta, H. Okutani, Y. Okutomi, K. Oohara, K. Ooi, C. Oshino, S. Otabe, S. Pan, K-C Pang, H. Parisi, A. Park, J. Arellano, F. E. Pena Pinto, I. Sago, N. Saito, S. Saito, Y. Sakai, K. Sakai, Y. Sakuno, Y. Sato, S. Sato, T. Sawada, T. Sekiguchi, T. Sekiguchi, Y. Shao, L. Shibagaki, S. Shimizu, R. Shimoda, T. Shimode, K. Shinkai, H. Shishido, T. Shoda, A. Somiya, K. Son, E. J. Sotani, H. Sugimoto, R. Suresh, J. Suzuki, T. Suzuki, T. Tagoshi, H. Takahashi, H Gravitational Wave Science Project National Astronomical Observatory of Japan 2-21-1 Osawa Mitaka City Tokyo 181-8588 Japan Advanced Technology Center National Astronomical Observatory of Japan 2-21-1 Osawa Mitaka City Tokyo 181-8588 Japan Department of Physics The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan Research Center for the Early Universe The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan Institute for Cosmic Ray Research KAGRA Observatory The University of Tokyo 5-1-5 Kashiwa-no-Ha Kashiwa City Chiba 277-8582 Japan Accelerator Laboratory High Energy Accelerator Research Organization (KEK) 1-1 Oho Tsukuba City Ibaraki 305-0801 Japan Earthquake Research Institute The University of Tokyo 1-1-1 Yayoi Bunkyo-ku Tokyo 113-0032 Japan Department of Mathematics and Physics Graduate School of Science and Technology Hirosaki University 3 Bunkyo-cho Hirosaki Aomori 036-8561 Japan Kamioka Branch National Astronomical Observatory of Japan 238 Higashi-Mozumi Kamioka-cho Hida City Gifu 506-1205 Japan The Graduate University for Advanced Studies (SOKENDAI) 2-21-1 Osawa Mitaka City Tokyo 181-8588 Japan Korea Institute of Science and Technology Information 245 Daehak-ro Yuseong-gu Daejeon 34141 Republic of Korea National Institute for Mathematical Sciences 70 Yuseong-daero 1689 Beon-gil Yuseong-gu Daejeon 34047 Republic of Korea International College Osaka University 1-1 Machikaneyama-cho Toyonaka City Osaka 560-0043 Japan School of High Energy Accelerator Science The Graduate University for Advanced Studies (SOKENDAI) 1-1 Oho Tsukuba City Ibaraki 305-0801 Japan Department of Astronomy Beijing Normal University Xinjiekouwai Street 19 Haidian District Beijing 100875 China Department of Applied Physics Fukuoka University 8-19-1 Nanakuma Jonan Fukuoka City Fukuoka 814-0180 Japan Department of Physics Tamkang University No. 151 Yingzhuan Road Danshui Dist. New Taipei City 25137 Taiwan Department of Physics

KAGRA, the underground and cryogenic gravitational-wave detector, was operated for its solo observation from February 25 to March 10, 2020, and its first joint observation with the GEO 600 detector from April 7 to April 21, 2020 (O3GK). This study presents an overview of the input optics systems of the KAGRA detector, which consist of various optical systems, such as a laser source, its intensity and frequency stabilization systems, modulators, a Faraday isolator, mode-matching telescopes, and a high-power beam dump. These optics were successfully delivered to the KAGRA interferometer and operated stably during the observations. The laser frequency noise was observed to limit the detector sensitivity above a few kilohertz, whereas the laser intensity did not significantly limit the detector sensitivity.

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Mapping the Human Body at Cellular Resolution -- The NIH Common Fund Human BioMolecular Atlas program

arXiv

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arXiv 2019年

作者： Snyder, Michael P. Lin, Shin Posgai, Amanda Atkinson, Mark Regev, Aviv Rood, Jennifer Rozenblatt-Rosen, Orit Gaffney, Leslie Hupalowska, Anna Satija, Rahul Gehlenborg, Nils Shendure, Jay Laskin, Julia Harbury, Pehr Nystrom, Nicholas A. Bar-Joseph, Ziv Zhang, Kun Börner, Katy Lin, Yiing Conroy, Richard Procaccini, Dena Roy, Ananda L. Pillai, Ajay Brown, Marishka Galis, Zorina S. Cai, Long Shendure, Jay Trapnell, Cole Lin, Shin Jackson, Dana Snyder, Michael P. Nolan, Garry Greenleaf, William James Lin, Yiing Plevritis, Sylvia Ahadi, Sara Lee, Hayan Nevins, Stephanie Esplin, Ed Horning, Aaron Bahmani, Amir Zhang, Kun Sun, Xin Jain, Sanjay Hagood, James Kharchenko, Peter Atkinson, Mark Bodenmiller, Bernd Brusko, Todd Clare-Salzler, Michael Nick, Harry Otto, Kevin Posgai, Amanda Wasserfall, Clive Maffioletti, Sergio Caprioli, Richard M. Spraggins, Jeffrey M. Gutierrez, Danielle Patterson, Nathan Heath Neumann, Elizabeth K. Harris, Raymond deCaestecker, Mark de Plas, Raf Van Lau, Ken Cai, Long Yuan, Guo-Cheng Zhu, Qian Dries, Ruben Yin, Peng Saka, Sinem K. Kishi, Jocelyn Y. Wang, Yu Goldaracena, Isabel Laskin, Julia Ye, DongHye Burnum-Johnson, Kristin E. Piehowski, Paul D. Ansong, Charles Zhu, Ying Harbury, Pehr Desai, Tushar Mulye, Jay Chou, Peter Nagendran, Monica Bar-Joseph, Ziv Teichmann, Sarah A. Paten, Benedict Murphy, Robert F. Ma, Jian Kiselev, Vladimir Yu Kingsford, Carl Ricarte, Allyson Ruffalo, Matthew Gehlenborg, Nils Kharchenko, Peter Vella, Margaret McCallum, Chuck Börner, Katy Cross, Leonard E. Friedman, Samuel H. Heiland, Randy Herr, Bruce Macklin, Paul Quardokus, Ellen M. Record, Lisel Sluka, James P. Weber, Griffin M. Nystrom, Nicholas A. Silverstein, Jonathan C. Blood, Philip D. Ropelewski, Alexander J. Shirey, William E. Mabee, Paula Lenhardt, W. Christopher Robasky, Kimberly Michailidis, Stavros Satija, Rahul Marioni, John Regev, Aviv Butler, Andrew Stuart, Tim Fisher, Eyal Ghazanfar, Shila Rood, Jennifer Gaffney, Leslie Ersalan, Gokcen Biancalani, Tommaso Conroy, Richard Procaccini, Dena Roy, Anan School of Medicine Stanford University 300 Pasteur Drive United States Department of Genetics Stanford School of Medicine StanfordCA94305 United States Department of Medicine University of Washington SeattleWA98195 United States Department of Pathology University of Florida Diabetes Institute GainesvilleFL32610 United States Klarman Cell Observatory Broad Institute of MIT and Harvard CambridgeMA02142 United States Howard Hughes Medical Institute Koch Institute of Integrative Cancer Research Department of Biology Massachusetts Institute of Technology CambridgeMA02140 United States New York Genome Center New York CityNY10013 United States New York University New YorkNY10012 United States Department of Biomedical Informatics Harvard Medical School BostonMA02115 United States Department of Genome Sciences University of Washington SeattleWA98105 United States Department of Chemistry Purdue University West LafayetteIN47907 United States Department of Biochemistry Stanford University School of Medicine StanfordCA94305 United States Pittsburgh Supercomputing Center Carnegie Mellon University PittsburghPA15213 United States Department of Computational Biology School of Computer Science Carnegie Mellon University PittsburghPA15213 United States Department of Bioengineering University of California San Diego La JollaCA92093 United States Department of Intelligent Systems Engineering School of Informatics Computing and Engineering Indiana University BloomingtonIN47408 United States Department of Surgery Washington University School of Medicine St LouisMO63110 United States Division of Program Coordination Planning and Strategic Initiatives National Institutes of Health BethesdaMD20892 United States National Human Genome Research Institute National Institutes of Health BethesdaMD20892 United States National Heart Lung and Blood Institute National Institutes of Health BethesdaMD20892 United States Caltech-UW TMC Departmen

Transformative technologies are enabling the construction of three dimensional (3D) maps of tissues with unprecedented spatial and molecular resolution. Over the next seven years, the NIH Common Fund Human Biomolecular Atlas program (HuBMAP) intends to develop a widely accessible framework for comprehensively mapping the human body at single-cell resolution by supporting technology development, data acquisition, and detailed spatial mapping. HuBMAP will integrate its efforts with other funding agencies, programs, consortia, and the biomedical research community at large towards the shared vision of a comprehensive, accessible 3D molecular and cellular atlas of the human body, in health and various disease settings. Copyright © 2019, The Authors. All rights reserved.

关键词： Mapping

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