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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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Multiple attribute group decision making based on interval type-2 fuzzy cross-entropy and ranking value

Multiple attribute group decision making based on interval t...

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Youth Academic Annual Conference of Chinese Association of Automation (YAC)

作者： Liangli Du Ying Peng Junjun Mao Dengbao Yao School of Mathematical Science Anhui University Hefei PR China Key Lab of Intelligent Computing & Signal Processing of Ministry of Education Anhui University Hefei PR China Economics School Anhui University Hefei PR China

ISBN: (纸本)9781538629024

In this paper, we focus our attention on the issue of MAGDM under interval type-2 fuzzy environment where all the information provided by the decision makers is characterized by IT2FSs and the information about the attribute weights are partly known and completely unknown. Firstly, some basic concepts are introduced. Then, a new definition of the cross entropy which consider three aspects of fuzziness, hesitancy and interval information is given. Interval type-2 fuzzy entropy is proposed on the basis of the cross entropy. Furthermore, two ranking-entropy optimal models of each alternative are built. A new approach to multiple attribute group decision making with IT2FSs based on interval type-2 fuzzy cross-entropy and ranking value is shown. Finally, we give a practical example to verify the feasibility of our method and make some comparisons with other previous methods. The results verify the validity and effectiveness of our proposed method.

关键词： decision making entropy fuzzy set theory

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Downlink scheduling and coordinated transmission for CRE ues with ABS in ultra-dense networks

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International Journal of Simulation: Systems, Science and Technology 2016年第4期17卷 16.1-16.6页

作者： Wang, Yi Hu, Yanjun Key Laboratory of Intelligent Computing & Signal Processing Ministry of Education Anhui University Hefei China

Ultra-dense network (UDN) is a promising way to address the high throughput demand in future radio access networks. However, the downlink inter-cell interference to user equipments (UEs) in dense small cell environment is a key problem restricting the wide application. Although cell range expansion (CRE) and almost blank subframe (ABS) cancel the interference from macro cells, they cannot deal with the interference from small cells in a dense deployed network. To reduce the interference caused by high small cells density, we propose a downlink scheduling and coordinated transmission algorithm for CRE UEs. CRE UEs can be transferred to different protected subframes dynamically in time domain to avoid the main interference sources. And coordinated transmission between macro and pico eNB could help guarantee CRE UEs’ performance which are far from serving cells. Simulation results show that our proposed algorithm provides stable and substantial spectrum efficiency gains compared to traditional methods. © 2016, UK Simulation Society. All rights reserved.

关键词： Heterogeneous networks

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Multifractal analysis and topological properties of a new family of weighted Koch networks

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Physica A: Statistical Mechanics and its Applications 2017年 469卷 695-705页

作者： Da-Wen Huang Zu-Guo Yu Vo Anh Hunan Key Laboratory for Computation and Simulation in Science and Engineering Xiangtan University Xiangtan Hunan 411105 China Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education Xiangtan University Xiangtan Hunan 411105 China School of Mathematical Sciences Queensland University of Technology GPO Box 2434 Brisbane Q4001 Australia

Weighted complex networks, especially scale-free networks, which characterize real-life systems better than non-weighted networks, have attracted considerable interest in recent years. Studies on the multifractality of weighted complex networks are still to be undertaken. In this paper, inspired by the concepts of Koch networks and Koch island, we propose a new family of weighted Koch networks, and investigate their multifractal behavior and topological properties. We find some key topological properties of the new networks: their vertex cumulative strength has a power-law distribution; there is a power-law relationship between their topological degree and weight strength; the networks have a high weighted clustering coefficient of 0.41004 (which is independent of the scaling factor c ) in the limit of large generation t ; the second smallest eigenvalue μ 2 and the maximum eigenvalue μ n are approximated by quartic polynomials of the scaling factor c for the general Laplacian operator, while μ 2 is approximately a quartic polynomial of c and μ n = 1.5 for the normalized Laplacian operator. Then, we find that weighted koch networks are both fractal and multifractal, their fractal dimension is influenced by the scaling factor c . We also apply these analyses to six real-world networks, and find that the multifractality in three of them are strong.

关键词： Weighted Koch networks Modified sandbox algorithm Multifractal analysis Topological property

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Design the non-fragile H controller of a category of positive systems 31

Design the non-fragile H controller of a category of positiv...

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31st Youth Academic Annual Conference of Chinese Association of Automation, YAC 2016

作者： Ren, Chengcheng Wu, Shanshan He, Shuping School of Electrical Engineering and Automation Anhui University Hefei China Key Laboratory of Intelligent Computing and Signal Processing Ministry of Education School of Electrical Engineering and Automation Anhui University Hefei China

ISBN: (纸本)9781509044238

A non-fragile H controller design approach is studied in this paper for a class of system. The purpose is design a suitable non-fragile controller satisfied that the induced L∞ gain from disturbance signal to output signal is bounded and minimized. In order to ensure the existence of H∞ controller, the article given the sufficient conditions and proved that the condition is feasible. Simulation results are proposed to describe the validity of the designed approaches. © 2016 IEEE.

关键词： Controllers

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Construction of One-Gray Weight Codes and Two-Gray Weight Codes over Z4+uZ4

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Journal of Systems Science & Complexity 2016年第5期29卷 1472-1484页

作者： SHI Minjia WANG Dandan GAO Jian WU Bo Key Laboratory of Intelligent Computing & Signal Processing Ministry of Education Anhui University Hefei 230039 China National Mobile Communications Research Laboratory Southeast University Nanjing 210096China School of Mathematical Sciences Anhui University Hefei 230601 China. School of Science Shandong University of Technology Zibo 255091 China State Key Laboratory of Information Security Institute of Information Engineering Chinese Academy of Sciences Bcijing 100093 China

This paper firstly gives some necessary conditions on one-Gray weight linear codes. And then we use these results to construct several classes of one-Gray weight linear codes over Z_4 +uZ_4(u^2=u) with type 16^(k_1)8^(k_2)8^(k_3)4^(k_4)4^(k_5)4^(k_6)2^(k_7)2^(k_8) based on a distance-preserving Gray map from(Z4 + u Z4)n to Z2n4. Secondly, the authors use the similar approach to do works on two-Gray(projective) weight linear codes. Finally, some examples are given to illustrate the construction methods.

关键词： Generator matrix Gray map linear code one-Gray weight code two-Gray weight code

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A Routing Scheme Based on Spray-and-Wait and Connecting-Capability of Node

A Routing Scheme Based on Spray-and-Wait and Connecting-Capa...

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2016 IEEE International Conference on Progress in Informatics and computing

作者： Guizhu Wang Hui Zhang Dong Pan Jian Tao Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education Anhui University

DTNs overcome the problems associated with intermittent connectivity, long or variable delay, asymmetric data rates, and high error rates by using store-carry-forward message switching. In DTNs, a node is an entity with a bundle layer. A node may be a host, router, or gateway(or some combination)acting as a source, destination, or forwarder of bundles. In addition, the performance of node shows great differences. However,the previous DTN routings show blindly and randomly, which do not measure the performance of node when they forward messages. To deal with this issue, we present the concept of Node Connection Intensity(NCI) and Node Connection Stability(NCS), then propose a routing scheme based on Spray-and-Wait and Connecting-Capability of Node(SW-CCN), which evaluate relay node's forward capability synthetically according to the NCI and the NCS. The SW-CCN routing can allocate message replications dynamically and solve the problem of selecting the relay node blindly. Compared with the classical routing protocols, the simulation results show that the proposed algorithm can significantly enhance delivery rate and improve network performance.

关键词： DTNs Node Connection Intensity Node Connection Stability

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A Theoretical Analysis of Quantum-corrected Model in Metal Nanowire Dimer

A Theoretical Analysis of Quantum-corrected Model in Metal N...

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Progress in Electromagnetic Research Symposium

作者： Kaikun Niu Bo Wu Zhixiang Huang Key Laboratory of Intelligent Computing & Signal Processing Ministry of Education Anhui University

ISBN: (纸本)9781509060948

Using a quantum-corrected model, the optical cross section of a strongly coupled metallic nanowire dimer for variable separation widths of the junction between the nanowires is analysed by finite-different time-domain method. Numerical results show the classical electrodynamics fails to describe the coupling across sub-nanometer gaps, owing to non-local screening and the spill-out of electrons, where quantum effects become important. The quantum-corrected model approach models the junction between adjacent nanoparticles by means of a local dielectric response that includes electron tunnelling and tunnelling resistivity at the gap. The quantum-corrected model predicts optical properties in excellent agreement with fully quantum mechanical calculations for small interacting systems, opening a new venue for addressing quantum effects in realistic plasmonic systems.

关键词： Tunneling Electromagnetics Plasmons Electromagnetic scattering Nanoparticles Conductivity

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Compact 30:1 Bandwidth ratio balun for printed balanced antennas

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Progress In Electromagnetics Research C 2016年 64卷 125-132页

作者： Meng, Xueqing Wu, Bo Huang, Zhi-Xiang Wu, Xian-Liang The Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education Anhui University Hefei230039 China

A new compact 30 : 1 bandwidth ratio balun and its application to balanced antennas are presented in this paper. To realize the balun-type function, two different types of wideband transition structures are adopted for unbalanced and balanced outputs of the balun. Further, a Vivaldi antenna integrated with the proposed balun is designed and fabricated to validate the feasibility of the new approach. Results indicated that the proposed balun can operate from 0.2GHz to 6GHz (a bandwidth ratio of 30 : 1). And it exhibits a good balanced performance within 0.5 dB magnitude imbalance and less than 6 degree phase imbalance between the two balanced outputs. In addition, the antenna can operate from 0.9GHz to 6GHz with good unidirectional radiation patterns. © 2016, Electromagnetics Academy. All rights reserved.

关键词： Bandwidth

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Phase Retrieval based on Cosine Grating Modulation and Transport of Intensity Equation

Phase Retrieval based on Cosine Grating Modulation and Trans...

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International Symposium on Optoelectronic Technology and Application 2016(OTA 2016)——Conf.5 Optical Measurement Technology and Instrument

作者： Ya-ping CHEN Quan-bing ZHANG Hong CHENG Shan-feng HU Qian-qian LV Key Laboratory of Intelligent Computing & Signal Processing Ministry of EducationAnhui University

In order to calculate the lost phase from the intensity information effectively,a new method of phase retrieval which based on cosine grating modulation and transport of intensity equation is proposed

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