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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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Fusion of infrared and visible images using nonsubsampled shearlet transform and block-based random image sampling

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Revista Tecnica de la Facultad de Ingenieria Universidad del Zulia 2016年第7期39卷 337-347页

作者： Chen, Lili Guo, Hongjun Laboratory of Intelligent Information Processing Suzhou University Suzhou Anhui234000 China Key Laboratory of Intelligent Computing and Signal Processing MOE Anhui University Hefei Anhui230039 China

This paper presents a novel image fusion method based on nonsubsampled shearlet transform (NSST) and block-based random image sampling for infrared and visible images. In the method, the NSST is firstly performed on each of the source images to obtain their low frequency and high frequency subbands coefficients. Then the low frequency coefficients are fused by combing the block-based random image sampling and the sliding widow technique, while the high frequency coefficients are fused using classical absolute value maximum choosing rule. The fused image is reconstructed though performing the inverse NSST. The experiments are carried out on five pairs of infrared and visible images using five traditional fusion methods to verify the effectiveness and efficiency of the proposed method and by comparing the fused results visually and objectively it is demonstrated that the proposed fusion method is competitive or even superior to the other wellknown methods.

关键词： Image fusion

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An image enhancement method based on improved fuzzy set

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Revista Tecnica de la Facultad de Ingenieria Universidad del Zulia 2016年第9期39卷 161-169页

At present, in related image processing field, the fuzzy set theory has also gained more successful applications to some extent. The image processing based on the fuzzy theory is an important research area. The information loss brought by 3D object projection in 2D image plane makes the image have the ambiguity exist in essence, thus there exists ambiguity when defining image characteristics such as the border, area and texture, therefore, because of the complexity of the image itself, uncertainty and inaccuracy or ambiguity may occur in the different stages of the processing. The algorithm in this paper improves the degree of membership function to make it suitable for the image fuzzy enhancement. The membership function curve is S-shaped, and at the inflection point, the function value on the left side drops rapidly while the function value on the right side rapidly rises. There is certain symmetry about the inflection point, and the function inflection point position can be decided by changing function parameters, and better enhancement effect can be gained by a small amount of iteration. By the experimental simulation, it is verified that the enhanced color image by adopting the method in this paper is bright in color on the visual effect with moderate increasing proportion of brightness and contrast, and best color maintaining performance and minimum chromaticity change, and also the image information entropy is improved when compared with the original image data.

关键词： Image processing

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Image enhancement method based on variable fuzzy sets

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Revista Tecnica de la Facultad de Ingenieria Universidad del Zulia 2016年第8期39卷 166-174页

作者： Chen, Lili Guo, Hongjun Pan, Zhenggao Laboratory of Intelligent Information Processing Suzhou University Suzhou Anhui234000 China Key Laboratory of Intelligent Computing and Signal Processing of MOE Anhui University Hefei Anhui230039 China

Image enhancement, as a means of digital image processing, often is fuzzy. Based on defects of excessive enhancement and insufficient detail enhancement existing in the traditional image enhancement method, this paper proposes a self-adaptive image enhancement method based on variable fuzzy sets, and such method can, according to the image's gray-scale properties, introduce the relative gray-scale level of the pixel as the fuzzy feature, and adopt the improved membership function to conduct the fuzzy enhancement, thus avoiding the loss of a great deal of gray-scale information after the enhancement. The paper also introduces the selection of optimal parameters, ensures the quality of the image enhanced and improves the feasibility and efficiency of this algorithm. This algorithm, on the basis of keeping the image's original brightness, enhances the image details at the same time. Experimental results show that such algorithm can obtain good visual effect and more obvious detail information.

关键词： Membership functions

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A whole-process WiFi security perception software system

A whole-process WiFi security perception software system

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International Conference on Circuits, System and Simulation (ICCSS)

作者： Heqing Huang Yanjun Hu Yan Ja Shiliang Ao Department of Computing Imperial College London London UK Key Laboratory of Intelligent Computing & Signal Processing Anhui University Hefei China Xidian University Xian China

ISBN: (纸本)9781538603932

A whole-process WiFi security perception software system is designed in this paper based on the analysis of client's wireless access process, it consists of three modules to protect user from security threats during the pre-connection, connection and after-connection. The system could detects WiFi environment and shows with 3D effect, marking the Rogue AP, which is found out by multi-factors analysis techniques. During the connection, it inspired by the idea of Fog computing, sending fake traffic to protect PSK from sniffing. After connection, the system detects Deauth attack in time, and traces the attacker. Finally, The software functionalities is realized, all the suspicious points are displayed on the User Interface (UI). The corresponding experimental testing shows that it could protect the surf in the WiFi environment effectively.

关键词： Protocols Wireless fidelity Encryption Software systems Phase shift keying

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New energy-efficient time synchronization algorithm design for wireless sensor networks

New energy-efficient time synchronization algorithm design f...

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

作者： Tengfei Xia Shuping He School College of Electrical Engineering and Automation Anhui University Hefei Key Laboratory of Intelligent Computing & Signal Processing Ministry of Education Anhui University Hefei

ISBN: (纸本)9781538629024

With the expansion of the scale of wireless sensor network (WSN), the network node number is increasing. Because of the huge network overhead and low precision, the reference broadcast time synchronization algorithm can not meet the actual demand. In this paper, a novel time synchronization algorithm for high precision energy efficient wireless sensor networks is proposed. Through a Markov random field-based maximum a posteriori estimation method of wireless sensor network in two nonadjacent nodes in receiving multiple reference broadcast messages, the algorithm estimated the clock drift under the condition of phase error estimation, tracked in real time by the Gardner loop, and then realized the time synchronization process. Finally, the MATLAB simulation showed the proposed algorithm not only has a further improvement in the time synchronization accuracy, but also effectively reduces the overall energy consumption level of the whole WSN.

关键词： Synchronization Wireless sensor networks Clocks Algorithm design and analysis Silicon Maximum a posteriori estimation

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On self-dual and LCD double circulant and double negacirculant codes over Fq+ uFq

arXiv

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arXiv 2018年

作者： Shi, Minjia Zhu, Hongwei Qian, Liqin Sok, Lin Sol, Patrick Key Laboratory of Intelligent Computing Signal Processing Ministry of Education Anhui University No.3 Feixi Road Hefei Anhui230039 China School of Mathematical Sciences Anhui University Hefei Anhui230601 China National Mobile Communications Research Laboratory Southeast University China Department of Mathematics Royal University of Phnom Penh Phnom Penh12156 Cambodia CNRS LAGA University of Paris 8 Saint-Denis93526 France

Double circulant codes of length 2n over the semilocal ring R = Fq + uFq, u2 = u, are studied when q is an odd prime power, and-1 is a square in Fq. Double negacirculant codes of length 2n are studied over R when n is even and q is an odd prime power. Exact enumeration of self-dual and LCD such codes for given length 2n is given. Employing a duality-preserving Gray map, self-dual and LCD codes of length 4n over Fq are constructed. Using random coding and the Artin conjecture, the relative distance of these codes is bounded below. The parameters of examples of the modest length are computed. Several such codes are optimal. Copyright © 2018, The Authors. All rights reserved.

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Design The Finite-Time H∞ Controller of A Class of Time-Delayed Uncertain Positive Systems

Design The Finite-Time H∞ Controller of A Class of Time-Del...

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第29届中国控制与决策会议

作者： C.C.Ren Q.L.Ai S.S.Wu S.P.He School of Electrical Engineering and Automation Anhui University Key Laboratory of Intelligent Computing & Signal Processing Ministry of EducationSchool of Electrical Engineering and AutomationAnhui University

This paper deals with the finite-time H,controller problem for a class of time-delay and with uncertain parameters continuous positive *** the systems with unknown disturbances,our aim is to design a suitable control law which makes the closed-loop system be finite-time bounded and satisfies the given H *** using the constructed Lyapunov function and linear matrix inequalities（LMIs） technique,sufficient conditions that the solution of the finite-time H∞controller existed are given and ***,a simulation example is presented to show the feasibility and validity of the present methods.

关键词： positive systems finite-time H_∞ controller linear matrix inequalities(LMIs) time-delays uncertain parameters

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Double circulant self-dual and LCD codes over Galois rings

arXiv

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arXiv 2018年

作者： Shi, Minjia Huang, Daitao Sok, Lin Solé, Patrick School of Mathematical Sciences Anhui University Hefei230601 China Key Laboratory of Intelligent Computing & Signal Processing Ministry of Education Anhui University No. 3 Feixi Road Hefei Anhui Province230039 China National Mobile Communications Research Laboratory Southeast University Nanjing210096 China Anhui University Hefei230601 China CNRS/LAGA University of Paris 8 2 rue de la Liberté Saint-Denis93 526 France

This paper investigates the existence, enumeration and asymptotic performance of self-dual and LCD double circulant codes over Galois rings of characteristic p2 and order p4 with p and odd prime. When p ≡ 3 (mod 4), we give an algorithm to construct a duality preserving bijective Gray map from such a Galois ring to Z2p2. Using random coding, we obtain families of asymptotically good self-dual and LCD codes over Zp2, for the metric induced by the standard Fp-valued Gray maps. Copyright © 2018, The Authors. All rights reserved.

关键词： Codes (symbols)

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How many weights can a linear code have?

arXiv

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arXiv 2018年

作者： Shi, Minjia Zhu, Hongwei Solé, Patrick Cohen, Gérard D. Key Laboratory of Intelligent Computing & Signal Processing Ministry of Education Anhui University No. 3 Feixi Road Hefei Anhui Province230039 China School of Mathematical Sciences Anhui University Hefei230601 China CNRS/LAGA University of Paris 8 2 rue de la Liberté Saint-Denis93 526 France TelecomParisTech 46 rue Barrault Paris75 013 France

We study the combinatorial function L(k, q), the maximum number of nonzero weights a linear code of dimension k over Fq can have. We determine it completely for q = 2, and for k = 2, and provide upper and lower bounds in the general case when both k and q are ≥ 3. A refinement L(n, k, q), as well as nonlinear analogues N(M, q) and N(n, M, q), are also introduced and studied. Copyright © 2018, The Authors. All rights reserved.

关键词： Codes (symbols)

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