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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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Parameter-transferred wasserstein generative adversarial network (PT-WGAN) for low-dose PET image denoising

arXiv

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arXiv 2019年

作者： Gong, Yu Shan, Hongming Teng, Yueyang Tu, Ning Li, Ming Liang, Guodong Wang, Ge Wang, Shanshan College of Medicine and Biological Information Engineering Northeastern University Shenyang110169 China Paul C. Lauterbur Research Center for Biomedical Imaging Shenzhen Institutes of Advanced Technology Chinese Academy of Sciences Shenzhen518055 China Key Laboratory of Intelligent Computing in Medical Images Ministry of Education Shenyang110169 China Department of Biomedical Engineering Rensselaer Polytechnic Institute TroyNY12180 United States PET-CT/MRI Center Molecular Imaging Center Wuhan University Renmin Hospital Wuhan430060 China Neusoft Medical Systems Co. Ltd Shenyang110167 China

Due to the widespread use of positron emission tomography (PET) in clinical practice, the potential risk of PET-associated radiation dose to patients needs to be minimized. However, with the reduction in the radiation dose, the resultant images may suffer from noise and artifacts that compromise diagnostic performance. In this paper, we propose a parameter-transferred Wasserstein generative adversarial network (PT-WGAN) for lowdose PET image denoising. The contributions of this paper are twofold: i) a PT-WGAN framework is designed to denoise lowdose PET images without compromising structural details, and ii) a task-specific initialization based on transfer learning is developed to train PT-WGAN using trainable parameters transferred from a pretrained model, which significantly improves the training efficiency of PT-WGAN. The experimental results on clinical data show that the proposed network can suppress image noise more effectively while preserving better image fidelity than recently published state-of-the-art methods. We make our code available at https://***/90n9-yu/PT-WGAN. Copyright © 2019, The Authors. All rights reserved.

关键词： Positron emission tomography

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Stability Analysis and Hopf Bifurcation Research for DNA Strand Displacement with Time Delay

Stability Analysis and Hopf Bifurcation Research for DNA Str...

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Symposia and Workshops on Ubiquitous, Autonomic and Trusted computing, UIC-ATC

作者： Yanhong Liu Hui Lv Changjun Zhou Zhixiang Yin Xianwen Fang Zhonglong Zheng Qiang Zhang Key Laboratory of Advanced Design and Intelligent Computing Ministry of Education Dalian University Dalian China School of Mathematics and Big Data Anhui University of Science and Technology Huaian China College of Mathematics Zhejiang Normal University Jinhua China Department of Computer Science and Technology Dalian University of Technology Dalian China

ISBN: (纸本)9781538693810;9781538693803

In this paper, a nonlinear system with time delay mode for DNA strand displacement based on toehold exchange firstly is proposed. The boundedness of all the state variables of the DNA strand displacement system is proved. After that, local stability analysis is performed around the positive equilibrium point to obtain a necessary and sufficient condition for local stability, which depend on the coefficients of the characteristic equation corresponding to linearization of the system. In addition, the existence of the Hopf bifurcation is analyzed, which shows that the time delay parameter will guarantee that the system is stable within a certain range. However, Hopf bifurcation and chaos occur when the time delay parameter increases continuously and even exceeds the critical value. At last, numerical simulations have verified the correctness and validity of the DNA strand displacement studies.

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An improved stochastic fractal search algorithm for 3D protein structure prediction

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Journal of molecular modeling 2018年第6期24卷 125页

作者： Changjun Zhou Chuan Sun Bin Wang Xiaojun Wang Key Laboratory of Advanced Design and Intelligent Computing (Dalian University) Ministry of Education Dalian 116622 China. zhou-chang231@***. Key Laboratory of Advanced Design and Intelligent Computing (Dalian University) Ministry of Education Dalian 116622 China.

Protein structure prediction (PSP) is a significant area for biological information research, disease treatment, and drug development and so on. In this paper, three-dimensional structures of proteins are predicted based on the known amino acid sequences, and the structure prediction problem is transformed into a typical NP problem by an AB off-lattice model. This work applies a novel improved Stochastic Fractal Search algorithm (ISFS) to solve the problem. The Stochastic Fractal Search algorithm (SFS) is an effective evolutionary algorithm that performs well in exploring the search space but falls into local minimums sometimes. In order to avoid the weakness, Lvy flight and internal feedback information are introduced in ISFS. In the experimental process, simulations are conducted by ISFS algorithm on Fibonacci sequences and real peptide sequences. Experimental results prove that the ISFS performs more efficiently and robust in terms of finding the global minimum and avoiding getting stuck in local minimums.

关键词： AB off-lattice model Internal feedback information Lvy flight Protein structure prediction Stochastic fractal search algorithm

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Extension of the non-parametric cluster-based time-frequency statistics to the full time windows and to single condition tests

arXiv

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arXiv 2018年

作者： Beste, Christian Kaping, Daniel Tzvetanov, Tzvetomir Cognitive Neurophysiology Department of Child and Adolescent Psychiatry Faculty of Medicine TU Dresden Germany National Institute of Mental Health Klecany Czech Republic CAS Key Laboratory of Brain Function and Disease School of Life Sciences University of Science and Technology of China Hefei Anhui230027 China Anhui Key Laboratory for Affective Computing and Advanced Intelligent Machines School of Computer and Information Hefei University of Technology Hefei Anhui230009 China

Oscillatory processes are central for the understanding of the neural bases of cognition and behaviour. To analyse these processes, time-frequency (TF) decomposition methods are applied and non-parametric cluster-based statistical procedure are used for comparing two or more conditions. While this combination is a powerful method, it has two drawbacks. One the unreliable estimation of signals outside the cone-of-influence and the second relates to the length of the time frequency window used for the analysis. Both impose constrains on the non-parametric statistical procedure for inferring an effect in the TF *** we extend the method to reliably infer oscillatory differences within the full TF mapand to test single *** show that it can be applied in small time windowsirrespective of the cone-of-influence and we further develop its application to single-condition case for testing the hypothesis of the presence or not of time-varying *** present tests of this new method on real EEG and behavioural data and show thatits sensitivity to single-condition testsis at least as good as classic Fourier *** inference in the full TF map is available and efficient in detecting differences between conditions as well as the presence of time-varying signal in single condition. Copyright © 2018, The Authors. All rights reserved.

关键词： Fourier analysis

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Sliding mode control of decaying-dimerizing system

Sliding mode control of decaying-dimerizing system

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Chinese Control Conference (CCC)

作者： Hui Lv Changjun Zhou Qiang Zhang Ministry of Education Key Laboratory of Advanced Design and Intelligent Computing (Dalian university) Dalian P.R.China

ISBN: (纸本)9781538629185

This paper is concerned with the sliding mode control of decaying-dimerizing system with three molecular species and four reaction channels. An integral sliding surface is designed, and the resulting dynamics is a nonlinear biochemical reaction system. By introducing some specified matrices, a sufficient condition is proposed in terms of strict linear matrix inequality (LMI), which guarantees the stability of the sliding mode dynamics. A sliding mode control law is also synthesized for reaching motion. Finally, simulation results illustrate the effectiveness of our methods.

关键词： Sliding mode control Stochastic processes Linear matrix inequalities Stability analysis Trajectory Biological system modeling

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A prediction model of edge gas flow development state based on BP neural network 5

A prediction model of edge gas flow development state based ...

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5th International Workshop on advanced Computational Intelligence and intelligent Informatics, IWACIII 2017

作者： Zhang, Jialiang An, Jianqi Wu, Min Cao, Weihua School of Automation China University of Geosciences Wuhan430074 China Hubei Key Laboratory of Advanced Control and Intelligent Automation for Complex Systems Wuhan430074 China Department of Computer Science School of Computing Tokyo Institute of Technology Yokohama226-8502 Japan

The development and distribution states of the blast furnace (BF) gas flow determine whether the reaction in the furnace can proceed normally and decide the utilization efficiency of the carbon in the furnace and the stable smooth operation of the furnace. The internal environment of BF is closed with high temperature and high pressure, which causes that the relationship between the development situation of edge gas flow of the BF and the BF operation is uncertain. In this paper, a prediction model of edge gas flow development state based on BP neural network (BPNN) is proposed, clarifying the relationship between the development state of edge gas flow and the edge burden parameters. Firstly, this paper gets the relative operation factors of effecting the development situation of edge gas flow through analyzing the process mechanism of the BF ironmaking, and proposes the development index of edge gas flow and the heat load of cooling stave to measure the development state of the edge gas flow. Secondly, the intrinsic correlation between the data is verified, and the data are analyzed by Spearman's rank correlation coefficient (SRCC) analysis. Finally, according to the analysis results, combined with the burden mechanism, the edge gas flow prediction model is established to realize the prediction of the development state of the edge gas flow. The calculation of the data collected in the metallurgy scene of the BF suggested that this prediction model of the edge gas flow development state of the BF could describe the relationship between BF operation parameters and the developing state of the edge gas flow.

关键词： Flow of gases

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Passivity of Reaction–Diffusion Genetic Regulatory Networks with Time-Varying Delays

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Neural Processing Letters 2017年第3期47卷 1115-1132页

作者： Zou, Chengye Wei, Xiaopeng Zhang, Qiang Zhou, Changjun Faculty of Electronic Information and Electrical Engineering Dalian University of Technology Dalian China Key Laboratory of Advanced and Intelligent Computing Dalian University Ministry of Education Dalian China

This article investigates the passivity of reaction–diffusion genetic regulatory networks (GRNs) with time-varying delays and uncertainty terms under Dirichlet, Neumann, and Robin boundary conditions. We provide delay-dependent stability criteria by constructing appropriate Lyapunov–Krasovskii functions and linear matrix inequalities, and offer conditions sufficient to ensure the passivity of GRNs. We conducted a comparative analysis of GRNs under these three conditions. Numerical examples of the proposed approaches are provided to illustrate its effectiveness, and represent the three-dimensional figures of the trajectories of the concentrations of mRNA and the proteins of GRNs under Dirichlet boundary conditions.

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Method of Age Estimation Based on ML-GMM Feature and Double Layers Estimation Model

Method of Age Estimation Based on ML-GMM Feature and Double ...

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作者： Min Hu Wendi Teng Yaona Zheng Keke Zhang AnHui Province Key Laboratory of Affective Computing and Advanced Intelligent Machine School of Computer and Information He Fei University of Technology

Feature extraction and estimation method are two key components of age estimation. This paper proposes a novel age estimation method based on Multi Levels Gaussian Mixture Model(MLGMM) and double layers estimation model. In the feature extraction phase, ML-GMM is used to construct different GMMs for different level features, which can well reflect the global and local age feature of facial images. In the estimation phase, double layers estimation model based on SVM-KNN is proposed. The first layer roughly divides age groups by using SVM. The second layer adopts KNN theory to find K images of consecutive age which have minimum sum of distance with the testing sample. The specific age is obtained by weighting these K age values. This paper performs a lot of experiments on mixed age database of FG-NET and MORPH-II databases. The mean absolute errors of age estimation are 3.22 years. Experimental results show that the proposed method is more effective than other methods of state-of-the-art for age estimation of facial images. It can extract more rich and complete age feature, improve the generalization ability of age estimation and reduce the mean absolute errors.

关键词： Multi Levels Gaussian Mixture Model SVM KNN Age Estimation

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A Fusion Decision Method Based on the Dynamic Fuzzy Density Assignment

A Fusion Decision Method Based on the Dynamic Fuzzy Density ...

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作者： Yanqiu Li Fuji Ren Min Hu Xiaohua Wang AnHui Province Key Laboratory of Affective Computing and Advanced Intelligent Machine School of Computer and Information He Fei University of Technology

Fuzzy density is an important part of fuzzy integral, which is used to describe the reliability of classifiers in the process of fusion. Most of the fuzzy density assignment methods are based on the training priori knowledge of the classifier and ignore the difference of the testing samples themselves. To better describe the real-time reliability of the classifier in the fusion process, the dispersion of the classifier is calculated according to the decision information which outputted by the classifier. Then the divisibility of the classifier is obtained through the information entropy of the dispersion. Finally, the divisibility and the priori knowledge are combined to get the fuzzy density which can be dynamically adjusted. Experiments on JAFFE and CK databases show that, compared with traditional fuzzy integral methods, the proposed method can effectively improve the decision performance of fuzzy integral and reduce the interference of unreliable output information to decision. And it is an effective multi-classifier fusion method.

关键词： Fuzzy Density Facial expression recognition (FER) Fuzzy integral Divisibility

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