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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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Organ-On-A-Chip systems: Human-on-Leaf-Chip: A Biomimetic Vascular System Integrated with Chamber-Specific Organs (Small 22/2020)

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Small 2020年第22期16卷

作者： Mao Mao Ho Pan Bei Chun Hei Lam Pengyu Chen Shuqi Wang Ying Chen Jiankang He Xin Zhao Department of Biomedical Engineering The Hong Kong Polytechnic University Hung Hom Hong Kong China State Key Laboratory for Manufacturing Systems Engineering Xi'an Jiaotong University Xi'an 710049 China State Key Laboratory for Diagnosis and Treatment of Infectious Diseases National Clinical Research Center for Infectious Diseases National Medical Center for Infectious Diseases Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases The First Affiliated Hospital College of Medicine Zhejiang University Hangzhou Zhejiang 310003 China Institute for Translational Medicine Zhejiang University Hangzhou Zhejiang 310029 China Guangdong Provincial Key Laboratory of Functional Soft Condensed Matter School of Materials and Energy Guangdong University of Technology Guangzhou Guangdong 510000 China

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Fabrication of micro/nanostructures as SERS substrates with the feed-back controlled normal force 17

Fabrication of micro/nanostructures as SERS substrates with ...

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17th International Conference of the European Society for Precision engineering and Nanotechnology, EUSPEN 2017

作者： Zhang, Jingran Yan, Yongda Cai, Jianxiong Miao, Peng State Key Laboratory of Robotics and Systems Robotics Institute Harbin Institute of Technology Harbin150080 China Center for Precision Engineering Harbin Institute of Technology Harbin Heilongjiang150001 China School of Chemistry and Chemical Engineering Harbin Institute of Technology Harbin Heilongjiang150001 China

ISBN: (纸本)9780995775107

Different from the conventional scratching method, the normal force is feed-back controlled to mechanically machine the micro grooves in the present study. During the process, the normal force is controlled to a constant value which is similar to the mechanism of the commercial Atomic Force Microscope by which to measure the nanoscale sample topography through controlling the tip-sample interaction force. A simple and low cost micro machining device which can control the normal force is established. With the controlled normal force, the effects of the edge forward and face forward machining directions on the grooves' topography is studied. Moreover, the edge forward scratching direction is more suitable for the controlled normal force scratching process than the face forward scratching direction. Finally, the machined microsquares of aluminum alloy (2A12) surface is used as the Surface-enhanced Raman Scattering (SERS) substrate with the Rhodamine 6G (R6G) probe molecule as the detecting target in the present study. Experimental results show that using this simple low cost device, the perfect microstructures can be achieved by the controlled normal force machining method.

关键词： Microstructure

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Drug Delivery: Activated Platelets‐Targeting Micelles with Controlled Drug Release for Effective Treatment of Primary and Metastatic Triple Negative Breast Cancer (Adv. Funct. Mater. 13/2019)

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Advanced Functional Materials 2019年第13期29卷

作者： Yujie Zhang Xi Zhu Xinli Chen Qinjun Chen Wenxi Zhou Qin Guo Yifei Lu Chao Li Yu Zhang Donghui Liang Tao Sun Xunbin Wei Chen Jiang Key Laboratory of Smart Drug Delivery Ministry of Education State Key Laboratory of Medical Neurobiology Department of Pharmaceutics School of Pharmacy Fudan University 826 Zhangheng Road Shanghai 201203 China State Key Laboratory of Oncogenes and Related Genes Shanghai Cancer Institute Med‐X Research Institute and School of Biomedical Engineering Key Laboratory of Systems Biomedicine (Ministry of Education) Shanghai Jiao Tong University 1954 Huashan Road Shanghai 200030 China Beijing Advanced Innovation Center for Biomedical Engineering Beihang University Beijing 100083 China

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Multimode -symmetry thresholds and third-order exceptional points in coupled dielectric waveguides with loss and gain

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Journal of Optics 2021年第12期23卷

作者： Anton V Hlushchenko Denis V Novitsky Vitalii I Shcherbinin Vladimir R Tuz State Key Laboratory of Integrated Optoelectronics College of Electronic Science and Engineering International Center of Future Science Jilin University 2699 Qianjin Street Changchun 130012 People's Republic of China National Science Center 'Kharkiv Institute of Physics and Technology' of National Academy of Sciences of Ukraine 1 Akademicheskaya Street Kharkiv 61108 Ukraine B. I. Stepanov Institute of Physics National Academy of Sciences of Belarus 68 Nezavisimosti Avenue Minsk 220072 Belarus School of Radiophysics Biomedical Electronics and Computer Systems V. N. Karazin Kharkiv National University 4 Svobody Square Kharkiv 61022 Ukraine

A pair of coupled dielectric waveguides with balanced loss and gain is the basic system for observing the phenomena of parity-time () symmetry and exceptional points (EPs). We use the multimode analytical approach to study the peculiarities of interaction between the modes excited in such an archetypal structure. With this approach, the conditions for symmetry breaking are obtained in the special case of the hybrid HE and EH modes resulting in the ordinary second-order EPs (or -symmetry thresholds). The coupling of modes with the different azimuthal indices (the TM01 and HE21 modes in our study) generates the uncommon types of EPs. First, there are the so-called multimode -symmetry thresholds due to interaction of hybrid and transverse modes. Second, the third-order EPs appear as a result of three-modes degeneracy of real eigenvalues. It is noteworthy that an increase in the EPs order is achieved without both breaking the symmetry and introducing additional elements into the waveguide structure. The results obtained with the multimode analytical approach are in perfect agreement with the independent full-wave simulations.

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Rambutan-like hierarchically heterostructured CeO2-CuO hollow microspheres： Facile hydrothermal synthesis and applications

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Nano Research 2017年第2期10卷 381-396页

作者： Yongjun Ji Zheying Jin Jing Li Yu Zhang Hezhi Liu Laishun Shi Ziyi Zhong Fabing Su State Key Laboratory of Multiphase Complex Systems Institute of Process Engineering Chinese Academy of Sciences Beijing I O0190 China University of Chinese Academy of Sciences Beijing 100049 China School of Chemistry and Chemical Engineering Shandong University Jinan 250100 China Institute of Chemical Engineering and Sciences 1 Pesek Road Jurong Island Singapore 627833 Singapore School of Chemical & Biomedical Engineering Nanyang Technological University (NTU) 62 Nanyang Drive Singapore 637459 Singapore

Hierarchically heterostructured hollow spheres are of great interest for a wide range of applications owing to their unique structural features and properties. However, the fabrication of well-defined hollow spheres with highly specific morphology for mixed transition metal oxides on a large scale remains challenging. In this work, uniform rambutan-like heterostructured CeO2~CuO hollow microspheres with numerous copper-ceria interfacial sites and nanorods and nanoparticles as building blocks are prepared via a facile hydrothermal method followed by calcination. Importantly, this approach can be readily scaled up and is applicable to the synthesis of various CuO-based mixed metal oxide complex hollow spheres. The as-prepared CeO2-CuO hollow rambutans exhibit superior performance both as electrode materials for supercapacitors and as Cu-based catalysts for the Rochow reaction, mainly due to the small primary nanoparticle constituents, high surface area, and formation of numerous interior heterostructures.

关键词： heterostructure hollow sphere rambutan supercapacitors Rochow reaction

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Dynamic Human Gait VGRF Reference Profile Generation via Extreme Learning Machine

Dynamic Human Gait VGRF Reference Profile Generation via Ext...

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International Joint Conference on Neural Networks (IJCNN)

作者： Alexandra Vieira Bernardete Ribeiro Heloísa Sobral A. Paulo Coimbra Manuel Crisóstomo João P. Ferreira Tao Liu Dept. of Informatics Engineering CISUC Univ. of Coimbra Coimbra Portugal Dept. of Electrical and Computer Eng. Institute of Systems and Robotics Univ. of Coimbra Coimbra Portugal Dept. of Electrical Eng. Superior Institute of Eng. of Coimbra Institute of Systems and RoboticsUniv. of Coimbra Coimbra Portugal State Key Laboratory of Fluid Power and Mechatronic Systems School of Mechanical Engineering Zhejiang University Hangzhou China

Vertical Ground Reaction Forces (VGRF) reference profiles of human gait are important in medicine, for the recognition of gait disorders and in the assessment of rehabilitation treatments. A walking human is a dynamic varying system and in spite of the VGRF reference dependence on several patient's variables, doctors traditionally use the same static reference for all patients. The purpose of this study is to find out if an Extreme Learning Machine (ELM) is adequate to generate the dynamic VGRF reference profiles of healthy people depending on the subject's age, weight, height and stride duration. The ELM is compared with two other baseline Computational Intelligence (CI) methods, the Backpropagation Neural Network (BNN) and Multioutput Support Vector Regression (MSVR). Data from 28 healthy males walking at five different stride durations, collected using instrumented shoes, were used to train and test the CI models. The results showed that ELM is a well suited method to generate the dynamic VGRF reference profile for both dominant and non-dominant limbs, showing the lowest root mean square errors for the test set, 0.0201 and 0.0243 (fraction of body weight) for the dominant and non-dominant limbs respectively. This study reveals a promising methodology that can be implemented in real time gait analysis, allowing doctors to find a specific reference gait pattern for the gait analysis of an unhealthy person by specifying the age, weight, height and stride duration.

关键词： Training Biological neural networks Support vector machines Neurons Backpropagation Legged locomotion Adaptation models

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Visual Place Recognition in Long-term and Large-scale Environment based on CNN Feature

Visual Place Recognition in Long-term and Large-scale Enviro...

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2018 IEEE Intelligent Vehicles Symposium, IV 2018

作者： Zhu, Jianliang Ai, Yunfeng Tian, Bin Cao, Dongpu Scherer, Sebastian School of Artificial Intelligence University of Chinese Academy of Sciences Beijing100190 China State Key Laboratory of Management and Control for Complex Systems Institute of Automation Chinese Academy of Sciences Beijing100190 China Cloud Computing Center Chinese Academy of Sciences Dongguan523808 China Department of Mechanical and Mechatronics Engineering University of Waterloo WaterlooONN2L 3G1 Canada Robotics Institute Carnegie Mellon University PittsburghPA15213 United States

ISBN: (纸本)9781538644522

With the universal application of camera in intelligent vehicles, visual place recognition has become a major problem in intelligent vehicle localization. The traditional solution is to make visual description of place images using hand-crafted feature for matching places, but this description method is not very good for extreme variability, especially for seasonal transformation. In this paper, we propose a new method based on convolutional neural network (CNN), by putting images into the pre-trained network model to get automatically learned image descriptors, and through some operations of pooling, fusion and binarization to optimize them, then the similarity result of place recognition is presented with the Hamming distance of the place sequence. In the experimental part, we compare our method with some state-of-the-art algorithms, FABMAP, ABLE-M and SeqSLAM, to illustrate its advantages. The experimental results show that our method based on CNN achieves better performance than other methods on the representative public datasets. © 2018 IEEE.

关键词： Hamming distance

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Cryo-EM structure of human DNA-PK holoenzyme

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细胞研究（英文版） 2017年第11期27卷 1341-1350页

作者： Xiaotong Yin Mengjie Liu Yuan Tian Jiawei Wang Yanhui Xu Fudan University Shanghai Cancer Center Institute of Biomedical Sciences Shanghai Medical College of Fudan University Shanghai 200032 China Key Laboratory of Molecular Medicine Ministry of Education Department of Systems Biology for Medicine School of Basic Medical Sciences Shanghai Medical College of Fudan University Shanghai 200032 China State Key Laboratory of Genetic Engineering Collaborative Innovation Center of Genetics and Development School of Life SciencesFudan University Shanghai 200433 China State Key Laboratory of Membrane Biology School of Life Sciences Tsinghua University Beijing 100084 China Fudan University Shanghai Cancer Center Institute of Biomedical Sciences Shanghai Medical College of Fudan University Shanghai 200032 China Key Laboratory of Molecular Medicine Ministry of Education Department of Systems Biology for Medicine School of Basic Medical Sciences Shanghai Medical College of Fudan University Shanghai 200032 China State Key Laboratory of Genetic Engineering Collaborative Innovation Center of Genetics and Development School of Life SciencesFudan University Shanghai 200433 China CAS Center for Excellence in Molecular Cell Science Chinese Academy of Sciences Shanghai 200031 China

DNA-dependent protein kinase (DNA-PK) is a serine/threonine protein kinase complex composed of a catalytic subunit (DNA-PKcs) and KU70/80 heterodimer bound to ***-PK holoenzyme plays a critical role in non-homologous end joining (NHEJ),the major DNA repair ***,we determined cryo-electron microscopy structure of human DNA-PK holoenzyme at 6.6(A) *** the complex structure,DNA-PKcs,KU70,KU80 and DNA duplex form a 650-kDa heterotetramer with 1∶1∶1∶1 *** N-terminal a-solenoid (～2 800 residues)of DNA-PKcs adopts a double-ring fold and connects the catalytic core domain of DNA-PKcs and KU70/***-PKcs and KU70/80 together form a DNA-binding tunnel,which cradles ～30-bp DNA and prevents sliding inward of DNA-PKcs along with DNA duplex,suggesting a mechanism by which the broken DNA end is protected from unnecessary *** and biochemical analyses indicate that KU70/80 and DNA coordinately induce conformational changes of DNA-PKcs and allosterically stimulate its kinase *** propose a model for activation of DNA-PKcs in which allosteric signals are generated upon DNA-PK holoenzyme formation and transmitted to the kinase domain through N-terminal HEAT repeats and FAT domain of *** studies suggest a mechanism for recognition and protection of broken DNA ends and provide a structural basis for understanding the activation of DNA-PKcs and DNA-PK-mediated NHEJ pathway.

关键词： Cryo-EM structure DNA-PK DNA-PKcs activation NHEJ

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Robust positioning for measurement of freeform surfaces

Robust positioning for measurement of freeform surfaces

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ASPEN/ASPE 2017 Spring Topical Meeting on Manufacture and Metrology of Structured and Freeform Surfaces for Functional Applications

作者： Wang, Shixiang Cheung, Chi Fai Ren, Minjun Liu, Minyu Zhao, Chenyang Parnter State Key Laboratory of Ultra-precision Machining Technology Department of Industrial and Systems Engineering Hong Kong Polytechnic University Kowloon Hong Kong Robotics Institute School of Mechanical Engineering Shanghai Jiao Tong University Shanghai China

Form characterization of a manufactured freeform surface can be conducted by aligning the sampling points on a manufactured surface and comparing that with the design geometry through the localization. In this paper, a robust localization method named fiducial aided positioning method (FAPM) is developed to evaluate freeform surfaces with high efficiency and precision. The FAPM method makes use of fiducials to form a Fiducial-aided Computer Aided Design (FA-CAD) of the freeform surface which not only establishes an inherent surface feature but also links the different coordinate systems among design coordinate frame, machine tool and the measurement instrument. To verify the capability of the proposed method, a series of experiments have been undertaken. As compared with the traditional freeform measurement method such as least squared method, it is interesting to note that the robustness and accuracy of the measurement is significantly enhanced by the FAPM.

关键词： Machine tools

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