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arXiv 2022年

作者： Jelescu, Ileana O. Grussu, Francesco Ianus, Andrada Hansen, Brian Barrett, Rachel L.C. Aggarwal, Manisha Michielse, Stijn Nasrallah, Fatima Syeda, Warda Wang, Nian Veraart, Jelle Roebroeck, Alard Bagdasarian, Andrew F. Eichner, Cornelius Sepehrband, Farshid Zimmermann, Jan Soustelle, Lucas Bowman, Christien Tendler, Benjamin C. Hertanu, Andreea Jeurissen, Ben Verhoye, Marleen Frydman, Lucio de Looij, Yohan van Hike, David Dunn, Jeff F. Miller, Karla Landman, Bennett A. Shemesh, Noam Anderson, Adam McKinnon, Emilie Farquharson, Shawna Acqua, Flavio Dell Pierpaoli, Carlo Drobnjak, Ivana Leemans, Alexander Harkins, Kevin D. Descoteaux, Maxime Xu, Duan Huang, Hao Santin, Mathieu D. Grant, Samuel C. Obenaus, Andre Kim, Gene S. Wu, Dan Le Bihan, Denis Blackband, Stephen J. Ciobanu, Luisa Fieremans, Els Bai, Ruiliang Leergaard, Trygve B. Zhang, Jiangyang Dyrby, Tim B. Johnson, G. Allan Cohen-Adad, Julien Budde, Matthew D. Schilling, Kurt G. Department of Radiology Lausanne University Hospital University of Lausanne Lausanne Switzerland CIBM Center for Biomedical Imaging Ecole Polytechnique Fédérale de Lausanne Lausanne Switzerland Radiomics Group Vall d’Hebron Institute of Oncology Vall d’Hebron Barcelona Hospital Campus Barcelona Spain Queen Square MS Centre Queen Square Institute of Neurology Faculty of Brain Sciences University College London London United Kingdom Champalimaud Research Champalimaud Foundation Lisbon Portugal Center of Functionally Integrative Neuroscience Aarhus University Aarhus Denmark Department of Neuroimaging Institute of Psychiatry Psychology and Neuroscience King's College London London United Kingdom NatBrainLab Department of Forensics and Neurodevelopmental Sciences Institute of Psychiatry Psychology and Neuroscience King's College London London United Kingdom Russell H. Morgan Department of Radiology and Radiological Science Johns Hopkins University School of Medicine BaltimoreMD United States Maastricht University Medical Center Maastricht Netherlands The Queensland Brain Institute The University of Queensland Queensland Australia Melbourne Neuropsychiatry Centre The University of Melbourne ParkvilleVIC Australia Department of Radiology and Imaging Sciences Indiana University IN United States Stark Neurosciences Research Institute Indiana University School of Medicine IN United States Center for Biomedical Imaging NYU Grossman School of Medicine New YorkNY United States Faculty of psychology and Neuroscience Maastricht University Maastricht Netherlands Department of Chemical & Biomedical Engineering FAMU-FSU College of Engineering Florida State University TallahasseeFL United States Center for Interdisciplinary Magnetic Resonance National HIgh Magnetic Field Laboratory TallahasseeFL United States Department of Neuropsychology Max Planck Institute for Human Cognitive and Brain Sciences Leipzig Germany USC Stevens Neuroimaging and Informatics Instit

Small-animal diffusion MRI (dMRI) has been used for methodological development and validation, characterizing the biological basis of diffusion phenomena, and comparative anatomy. The steps from animal setup and monitoring, to acquisition, analysis, and interpretation are complex, with many decisions that may ultimately affect what questions can be answered using the resultant data. This work aims to present selected recommendations and guidelines from the diffusion community, on best practices for preclinical dMRI of in vivo animals. We describe the general considerations and foundational knowledge that must be considered when designing experiments. We briefly describe differences in animal species and disease models and discuss why some may be more or less appropriate for different studies. We then give guidelines for in vivo acquisition protocols, including decisions on hardware, animal preparation, and imaging sequences, followed by advice for data processing including pre-processing, model-fitting, and tractography. Finally, we provide an online resource which lists publicly available preclinical dMRI datasets and software packages, to promote responsible and reproducible research. In each section, we attempt to provide guides and recommendations, but also highlight areas for which no guidelines exist (and why), and where future work should focus. While we mainly cover the central nervous system (on which most preclinical dMRI studies are focused), we also provide, where possible and applicable, recommendations for other organs of interest. An overarching goal herein is to enhance the rigor and reproducibility of small animal dMRI acquisitions and analyses, and thereby advance biomedical knowledge. © 2022, CC BY-NC-ND.

关键词： Invertebrates

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Efficient T2 mapping with Blip-up/down EPI and gSlider-SMS (T2-BUDA-gSlider)

arXiv

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arXiv 2019年

作者： Cao, Xiaozhi Liao, Congyu Zhang, Zijing Iyer, Siddharth Srinivasan Chen, Zhifeng Lo, Wei-Ching Liu, Huafeng Wang, Kang He, Hongjian Setsompop, Kawin Zhong, Jianhui Bilgic, Berkin Center for Brain Imaging Science and Technology Department of Biomedical Engineering Zhejiang University Zhejiang Hangzhou China Athinoula A. Martinos Center for Biomedical Imaging Massachusetts General Hospital CharlestownMA United States Department of Radiology Harvard Medical School CharlestownMA United States State Key Laboratory of Modern Optical Instrumentation College of Optical Science and Engineering Zhejiang University Zhejiang Hangzhou China Department of Electrical Engineering and Computer Science Massachusetts Institute of Technology CambridgeMA United States School of Biomedical Engineering Guangdong Provincial Key Laboratory of Medical Image Processing Southern Medical University Guangzhou China Siemens Medical Solutions BostonMA United States Department of Neurology The First Affiliated Hospital School of Medicine Zhejiang University Hangzhou China Harvard-MIT Department of Health Sciences and Technology CambridgeMA United States Department of Imaging Sciences University of Rochester NY United States

Purpose: To rapidly obtain high isotropic-resolution T2 maps with whole-brain coverage and high geometric fidelity. Methods: A T2 blip-up/down echo planar imaging (EPI) acquisition with generalized Slice-dithered enhanced resolution (T2-BUDA-gSlider) is proposed. A radiofrequency (RF)-encoded multi-slab spin-echo EPI acquisition with multiple echo times (TEs) was developed to obtain high SNR efficiency with reduced repetition time (TR). This was combined with an interleaved 2-shot EPI acquisition using blip-up/down phase encoding. An estimated field map was incorporated into the joint multi-shot EPI reconstruction with a structured low rank constraint to achieve distortion-free and robust reconstruction for each slab without navigation. A Bloch simulated subspace model was integrated into gSlider reconstruction and utilized for T2 quantification. Results: In vivo results demonstrated that the T2 values estimated by the proposed method were consistent with gold standard spin-echo acquisition. Compared to the reference 3D fast spin echo (FSE) images, distortion caused by off-resonance and eddy current effects were effectively mitigated. Conclusion: BUDA-gSlider SE-EPI acquisition and gSlider-subspace joint reconstruction enabled distortion-free whole-brain T2 mapping in 2 min at ~1 mm3 isotropic resolution, which could bring significant benefits to related clinical and neuroscience applications. Copyright © 2019, The Authors. All rights reserved.

关键词： Spin polarization

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Deep learning enabled fast optical characterization of two-dimensional materials

arXiv

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arXiv 2019年

作者： Han, Bingnan Lin, Yuxuan Yang, Yafang Mao, Nannan Li, Wenyue Wang, Haozhe Fatemi, Valla Zhou, Lin Wang, Joel I-Jan Ma, Qiong Cao, Yuan Rodan-Legrain, Daniel Bie, Ya-Qing Navarro-Moratalla, Efrén Klein, Dahlia MacNeill, David Wu, Sanfeng Leong, Wei Sun Kitadai, Hikari Ling, Xi Jarillo-Herrero, Pablo Palacios, Tomás Yin, Jihao Kong, Jing Image Processing Center School of Astronautics Beihang University Beijing100191 China Department of Electrical Engineering and Computer Science Massachusetts Institute of Technology CambridgeMA02139 United States Department of Physics Massachusetts Institute of Technology CambridgeMA02139 United States Department of Chemistry Boston University BostonMA02215 United States Research Laboratory of Electronics Massachusetts Institute of Technology CambridgeMA02139 United States Instituto de Ciencia Molecular Universidad de Valencia c/Catedrático José Beltrán 2 Paterna46980 Spain Division of Materials Science and Engineering Boston University BostonMA02215 United States

Characterization of nanomaterial morphologies with advanced microscopy and/or spectroscopy tools plays an indispensable role in nanoscience and nanotechnology research 1 2, 3, 4, 5, as rich information about the chemical compositions, crystallography, other physical and chemical properties, as well as the growth mechanism can be extracted from morphology analysis. However, the interpretation of imaging data heavily relies on the "intuition" of experienced researchers. As a result, many of the deep graphical features are often unused because of difficulties in processing the data and finding the correlations. Such difficulties can be well addressed by deep learning 6 7, 8, 9. In this work, we use the optical characterization of two-dimensional (2D) materials as a case study, and demonstrate a neural network based algorithm for the material and thickness identification of exfoliated 2D materials with high prediction accuracy and real-time processing capability. Further analysis shows that the trained network can be used to predict physical properties of the materials. Finally, a transfer learning technique is applied to adapt the pretrained network to more optical characterization applications such as identifying layer numbers of chemically synthesized graphene domains. Copyright © 2019, The Authors. All rights reserved.

关键词： Data handling

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FWLBP: A scale invariant descriptor for texture classification

arXiv

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arXiv 2018年

作者： Roy, Swalpa Kumar Bhattacharya, Nilavra Chanda, Bhabatosh Chaudhuri, Bidyut B. Ghosh, Dipak Kumar Optical Character Recognition Laboratory Computer Vision and Pattern Recognition Unit Indian Statistical Institute Kolkata700108 India School of Information University of Texas AustinTX78712 United States Image Processing Laboratory Electronics and Communication Sciences Unit Indian Statistical Institute Kolkata700108 India Department of Electronics and Communication Engineering National Institute of Technology Rourkela Rourkela769008 India

In this paper we propose a novel texture descriptor called Fractal Weighted Local Binary Pattern (FWLBP). The fractal dimension (FD) measure is relatively invariant to scale-changes, and presents a good correlation with human viewpoint of surface roughness. We have utilized this property to construct a scale-invariant descriptor. Here, the input image is sampled using an augmented form of the local binary pattern (LBP) over three different radii, and then used an indexing operation to assign FD weights to the collected samples. The final histogram of the descriptor has its features calculated using LBP, and its weights computed from the FD image. The proposed descriptor is scale invariant, and is also robust in rotation or reflection, and partially tolerant to noise and illumination changes. In addition, the local fractal dimension is relatively insensitive to the bi-Lipschitz transformations, whereas its extension is adequate to precisely discriminate the fundamental of texture primitives. Experiment results carried out on standard texture databases show that the proposed descriptor achieved better classification rates compared to the state-of-the-art descriptors. Copyright © 2018, The Authors. All rights reserved.

关键词： Fractal dimension

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SEGMENTATION OF FLUORESCENCE MICROSCOPY imageS USING THREE DIMENSIONAL ACTIVE CONTOURS WITH INHOMOGENEITY CORRECTION

SEGMENTATION OF FLUORESCENCE MICROSCOPY IMAGES USING THREE D...

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International Symposium on Biomedical Imaging

作者： Soonam Lee Paul Salama Kenneth W. Dunn Edward J. Delp Video and Image Processing Laboratory School of Electrical and Computer Engineering Purdue University Department of Electrical and Computer Engineering Indiana University Division of Nephrology School of Medicine Indiana University

ISBN: (纸本)9781509011735

image segmentation is an important step in the quantitative analysis of fluorescence microscopy data. Since fluorescence microscopy volumes suffer from intensity inhomogeneity, low image contrast and limited depth resolution, poor edge details, and irregular structure shape, segmentation still remains a challenging problem. This paper describes a nuclei segmentation method for fluorescence microscopy based on the use of three dimensional (3D) active contours with inhomogeneity correction. The correction information utilizes 3D volume information while addressing intensity inhomogeneity across vertical and horizontal directions. Experimental results demonstrate that the proposed method achieves better performance than other reported methods.

关键词： image segmentation fluorescence microscopy multiphoton microscopy

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Stereo matching algorithm based on the combination of matching costs 7

Stereo matching algorithm based on the combination of matchi...

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7th IEEE Annual International Conference on CYBER Technology in Automation, Control, and Intelligent Systems, CYBER 2017

作者： Ende, Wang Yalong, Zhu Liangyu, Peng Yijun, Li Tianyao, Wu Shenyang Institute of Automation Chinese Academy of Sciences Shenyang110016 China Key Laboratory of Opto-Electronic Information Processing CAS Shenyang110016 China Key Lab of Image Understanding and Computer Vision Liaoning Province Shenyang110016 China College of Electrical Engineering Yanshan University Qinhuangdao066004 China School of Metallurgy Northeastern University Shenyang110819 China

ISBN: (纸本)9781538604892

Aiming at solving the problem of low accuracy of weak texture region and disparity discontinuous region and sensitivity to illumination caused by existing local stereo matching algorithm, a new stereo matching algorithm based on the combination of Sum of Absolute Difference algorithm and Absolute Difference of Gradient algorithm is presented here. Using the average of the pixels in the disparity range to apply adaptive weight to the SAD part. The new algorithm can adaptively adjust each part of the cost function in the proportion of the total cost function according to the different texture, illumination characteristics of image. Moreover, we use the semiglobal matching algorithm to calculate the cost of 8 directions, to carry out optimized processing on disparity image, finally a dense disparity map is obtained. The experimental results shows that the proposed method not only improve accuracy of stereo matching, but also has well results in weak texture region and disparity discontinuous region. © 2017 IEEE.

关键词： Textures

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Edgy salient local binary patterns in inter-plane relationship for image retrieval in Diabetic Retinopathy

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Procedia computer Science 2017年 115卷 440-447页

作者： Gajanan M. Galshetwar Laxman M. Waghmare Anil B. Gonde Subrahmanyam Murala Center of Excellence in Signal and Image Processing (COESIP) Department of ECE SGGSIET Nanded Maharashtra 431606 India Computer Vision and Pattern Recognition Laboratory Department of Electrical Engineering IIT Ropar Rupnagar 140001 India

In this paper, a novel approach for content based image retrieval (CBIR) in diabetic retinopathy (DR) is proposed. The concept of salient point selection and inter-plane relationship technique is used. Salient points are selected from edgy image and later using inter-planer relationship, Local Binary Patterns (LBPs) are calculated using the salient point as a center pixel. Our approach enhanced the results as we used color features in combination with LBP features. Experimentation is carried out on MESSIDOR database of 1200 retinal images, proposed approach has average precision of 57.82% as compared to the earlier approach whose average precision is 53.70%.

关键词： Content-Based image retrieval (CBIR) Diabetic Retinopathy (DR) Edgy Salient points Local Binary Patterns (LBPs)

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A Subpixel Target Detection Approach to Hyperspectral image Classification

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IEEE Transactions on Geoscience and Remote Sensing 2017年第9期55卷 5093-5114页

作者： Xue, Bai Yu, Chunyan Wang, Yulei Song, Meiping Li, Sen Wang, Lin Chen, Hsian-Min Chang, Chein-I Center for Hyperspectral Imaging in Remote Sensing Information and Technology College Dalian Maritime University Dalian China Remote Sensing Signal and Image Processing Laboratory Department of Computer Science and Electrical Engineering University of Maryland Baltimore County BaltimoreMD21250 United States Key Laboratory of Spectral Imaging Technology Chinese Academy of Sciences Xi'an China State Key Laboratory of Integrated Services Networks Xi'an China School of Physics and Optoelectronic Engineering Xidian University Xi'an China Department of Medical Research Taichung Veterans General Hospital Taichung Taiwan Department of Computer Science and Information Management Providence University Taichung02912 Taiwan

Hyperspectral image classification faces various levels of difficulty due to the use of different types of hyperspectral image data. Recently, spectral-spatial approaches have been developed by jointly taking care of spectral and spatial information. This paper presents a completely different approach from a subpixel target detection view point. It implements four stage processes, a preprocessing stage, which uses band selection (BS) and nonlinear band expansion, referred to as BS-then-nonlinear expansion (BSNE), a detection stage, which implements constrained energy minimization (CEM) to produce subpixel target maps, and an iterative stage, which develops an iterative CEM (ICEM) by applying Gaussian filters to capture spatial information, and then feeding the Gaussian-filtered CEM-detection maps back to BSNE band images to reprocess CEM in an iterative manner. Finally, in the last stage Otsu's method is applied to converting ICEM-detected real-valued maps to discrete values for classification. The entire process is called BSNE-ICEM. Experimental results demonstrate BSNE-ICEM, which has advantages over support vector machine-based approaches in many aspects, such as easy implementation, fewer parameters to be used, and better false classification and precision rates. © 1980-2012 IEEE.

关键词： Support vector machines

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VPx error resilient video coding using duplicated prediction information 7

VPx error resilient video coding using duplicated prediction...

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Visual Information processing and Communication VII 2016

作者： Gadgil, Neeraj Delp, Edward J. Video and Image Processing Laboratory School of Electrical and Computer Engineering Purdue University West LafayetteIN United States

Most real-Time video applications typically demand low endto- end latency and faithful reconstruction of the video sequence. Many popular video coding standards (e.g. VP8, VP9, H.264 and HEVC) aim at achieving high compression efficiencies by exploiting spatial and temporal redundancies. This makes the encoded bitstream vulnerable to errors. Thus, applications especially on mobile phones, tablet PCs and other portable devices that use WiFi or 3G/4G/LTE networks typically suffer from low quality of service typically characterized by frequent delays, jitter, frozen picture, partial/no picture and total loss of connection. Similar scenarios are also often observed while watching live streaming accompanied by service interruptions and a blank screen. Our approach is to investigate error resilient coding control for the VPx encoder to make the bitstream more error resilient for streaming applications under lossy channel conditions. In this paper, we describe an error resilient coding system that uses duplication of frame prediction information. Our "error resilience packet" consists of this prediction information of several frames, that can be used for error concealment in the case of packet loss ©2016 Society for Imaging Science and Technology.

关键词： Forecasting

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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

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

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