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23rd International Conference on Medical Image computing and Computer-Assisted Intervention, MICCAI 2020

作者： Zhang, Hao Xia, Likun Song, Ran Yang, Jianlong Hao, Huaying Liu, Jiang Zhao, Yitian College of Information Engineering Capital Normal University Beijing China Cixi Institute of Biomedical Engineering Ningbo Institute of Industrial Technology Chinese Academy of Sciences Ningbo China School of Control Science and Engineering Shandong University Jinan China Department of Computer Science and Engineering Southern University of Science and Technology Shenzhen China International Science and Technology Cooperation Base of Electronic System Reliability and Mathematical Interdisciplinary Capital Normal University Beijing China Laboratory of Neural Computing and Intelligent Perception Capital Normal University Beijing China Beijing Advanced Innovation Center for Imaging Theory and Technology Capital Normal University Beijing China

ISBN: (纸本)9783030597245

Automated extraction of cerebrovascular is of great importance in understanding the mechanism, diagnosis, and treatment of many cerebrovascular pathologies. However, segmentation of cerebrovascular networks from magnetic resonance angiography (MRA) imagery continues to be challenging because of relatively poor contrast and inhomogeneous backgrounds, and the anatomical variations, complex geometry and topology of the networks themselves. In this paper, we present a novel cerebrovascular segmentation framework that consists of image enhancement and segmentation phases. We aim to remove redundant features, while retaining edge information in shallow features when combining these with deep features. We first employ a Retinex model, which is able to model noise explicitly to aid removal of imaging noise, as well as reducing redundancy within an image and emphasizing the vessel regions, thereby simplifying the subsequent segmentation problem. Subsequently, a reverse edge attention module is employed to discover edge information by paying particular attention to the regions that are not salient in high-level semantic features. The experimental results show that the proposed framework enables the reverse edge attention network to deliver a reliable cerebrovascular segmentation. © 2020, Springer Nature Switzerland AG.

关键词： Image enhancement

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Compact convolutional neural networks for classification of asynchronous steady-state visual evoked potentials

arXiv

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arXiv 2018年

作者： Waytowich, Nicholas R. Lawhern, Vernon J. Garcia, Javier O. Cummings, Jennifer Faller, Josef Sajda, Paul Vettel, Jean M. U.S. Army Research Laboratory Maryland United States Laboratory for Intelligent Imaging and Neural Computing Columbia University New York United States Department of Bioengineering University of Pennsylvania Pennsylvania United States Department of Physiological Brain Sciences University of California Santa BarbaraCA United States

Objective. Steady-State Visual Evoked Potentials (SSVEPs) are neural oscillations from the parietal and occipital regions of the brain that are evoked from flickering visual stimuli. SSVEPs are robust signals measurable in the electroencephalogram (EEG) and are commonly used in brain-computer interfaces (BCIs). However, methods for high-accuracy decoding of SSVEPs usually require hand-crafted approaches that leverage domain-specific knowledge of the stimulus signals, such as specific temporal frequencies in the visual stimuli and their relative spatial arrangement. When this knowledge is unavailable, such as when SSVEP signals are acquired asynchronously, such approaches tend to fail. Approach. In this paper, we show how a compact convolutional neural network (Compact-CNN), which only requires raw EEG signals for automatic feature extraction, can be used to decode signals from a 12-class SSVEP dataset without the need for user-specific calibration. Main results. The Compact-CNN demonstrates across subject mean accuracy of approximately 80 %, out-performing current state-of-the-art, handcrafted approaches using canonical correlation analysis (CCA) and Combined-CCA. Furthermore, the Compact-CNN approach can reveal the underlying feature representation, revealing that the deep learner extracts additional phase- and amplitude-related features associated with the structure of the dataset. Significance. We discuss how our Compact-CNN shows promise for BCI applications that allow users to freely gaze/attend to any stimulus at any time (e.g., asynchronous BCI) as well as provides a method for analyzing SSVEP signals in a way that might augment our understanding about the basic processing in the visual cortex. Copyright © 2018, The Authors. All rights reserved.

关键词： Electroencephalography

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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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Author Correction: 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 2024年第10期21卷 1959页

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An extendable simulation framework for benchmarking EEG-based brain connectivity estimation methodologies

An extendable simulation framework for benchmarking EEG-base...

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Annual International Conference of the IEEE Engineering in Medicine and Biology Society

作者： Stefan Haufe Laboratory for Intelligent Imaging and Neural Computing Columbia University New York NY 10027 USA

ISBN: (纸本)9781424492695

Due to its high temporal resolution, electroencephalography (EEG) is a promising research tool for studying functional and effective brain interaction. Yet, it is rather uncommon for researchers to validate their connectivity estimation methodologies prior to applying them to real data, even though problems have been pointed out regarding the validity of some of the predominant approaches. We here provide an extendable simulation framework that enables researchers to test their analysis pipelines on customizable realistically simulated EEG data. We define three simple criteria to measure source localization, connectivity detection and directionality estimation performance. All data and code needed to generate pseudo-EEG data and to benchmark a method's estimation performance are provided.

关键词： EEG studying functional effective brain interaction

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Multivariate Machine Learning Methods for Fusing Multimodal Functional Neuroimaging Data

Multivariate Machine Learning Methods for Fusing Multimodal ...

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作者： Dahne, Sven Bieszmann, Felix Samek, Wojciech Haufe, Stefan Goltz, Dominique Gundlach, Christopher Villringer, Arno Fazli, Siamac Muller, Klaus-Robert Machine Learning Group Department of Computer Science Berlin Institute of Technology Berlin10623 Germany Amazon Berlin10178 Germany Machine Learning Group Department of Video Coding and Analytics Fraunhofer Heinrich Hertz Institute Berlin10587 Germany Laboratory for Intelligent Imaging and Neural Computing Columbia University New YorkNY10027 United States Institute of Psychology University of Leipzig Leipzig04109 Germany Department for Neurology Max Planck Institute for Human Cognitive and Brain Sciences Leipzig04103 Germany Mind-Brain Institute Charite Universitätsmedizin Berlin Humboldt-University Berlin10117 Germany Clinic for Cognitive Neurology University of Leipzig Leipzig04109 Germany Department of Brain and Cognitive Engineering Korea University Seoul136-713 Korea Republic of

Multimodal data are ubiquitous in engineering, communications, robotics, computer vision, or more generally speaking in industry and the sciences. All disciplines have developed their respective sets of analytic tools to fuse the information that is available in all measured modalities. In this paper, we provide a review of classical as well as recent machine learning methods (specifically factor models) for fusing information from functional neuroimaging techniques such as: LFP, EEG, MEG, fNIRS, and fMRI. Early and late fusion scenarios are distinguished, and appropriate factor models for the respective scenarios are presented along with example applications from selected multimodal neuroimaging studies. Further emphasis is given to the interpretability of the resulting model parameters, in particular by highlighting how factor models relate to physical models needed for source localization. The methods we discuss allow for the extraction of information from neural data, which ultimately contributes to 1) better neuroscientific understanding;2) enhance diagnostic performance;and 3) discover neural signals of interest that correlate maximally with a given cognitive paradigm. While we clearly study the multimodal functional neuroimaging challenge, the discussed machine learning techniques have a wide applicability, i.e., in general data fusion, and may thus be informative to the general interested reader. © 2015 IEEE.

关键词： Neurophysiology

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In vivo snapshot hyperspectral image analysis of age-related macular degeneration

In vivo snapshot hyperspectral image analysis of age-related...

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Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC)

作者： N. Lee J. Wielaard A. A. Fawzi P. Sajda A. F. Laine G. Martin M. S. Humayun R. T. Smith Biomedical Imaging Laboratory HBIL Department fo Biomedical Engineering Columbia University New York NY USA Laboratory of Intelligent Imaging and Neural Computing LIINC and the Department of Ophthalmology and Biomedical Engineering Columbia University New York NY USA Doheny Eye Institute University of Southern California Los Angeles CA USA Reichert Ophthalmic Instruments Inc. Depew NY USA Department of Biomedical Engineering and Cell and Neurobiology and the Doheny Eye Institute University of Southern California Los Angeles CA USA Department of Ophthalmology Columbia University New York NY USA

Drusen, the hallmark lesions of age related macular degeneration (AMD), are biochemically heterogeneous and the identification of their biochemical distribution is key to the understanding of AMD. Yet the challenges are to develop imaging technology and analytics, which respect the physical generation of the hyperspectral signal in the presence of noise, artifacts, and multiple mixed sources while maximally exploiting the full data dimensionality to uncover clinically relevant spectral signatures. This paper reports on the statistical analysis of hyperspectral signatures of drusen and anatomical regions of interest using snapshot hyperspectral imaging and non-negative matrix factorization (NMF). We propose physical meaningful priors as initialization schemes to NMF for finding low-rank decompositions that capture the underlying physiology of drusen and the macular pigment. Preliminary results show that snapshot hyperspectral imaging in combination with NMF is able to detect biochemically meaningful components of drusen and the macular pigment. To our knowledge, this is the first reported demonstration in vivo of the separate absorbance peaks for lutein and zeaxanthin in macular pigment.

关键词： Hyperspectral imaging Pigments Retina Biomedical imaging Sparse matrices In vivo

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Contributions of trabecular rods of various orientations in determining the elastic properties of human vertebral trabecular bone

Contributions of trabecular rods of various orientations in ...

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2007 ASME Summer Bioengineering Conference, SBC 2007

作者： Liu, Xiaowei S. Zhang, X. Henry Sajda, Paul Saha, Punam K. Wehrli, Felix W. Guo, X. Edward Bone Bioengineering Laboratory Department of Biomedical Engineering Columbia University NY United States Laboratory for Intelligent Imaging and Neural Computing Department of Biomedical Engineering Columbia University NY United States Department of Electrical and Computer Engineering and Radiology University of Iowa Iowa City IA United States Laboratory for Structural NMR Imaing Department of Radiology University of Pennsylvania Philadelphia PA United States

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