检索结果-内蒙古大学图书馆

arXiv 2021年

作者： Untracht, Gavrielle R. Matos, Rolando Dikaios, Nikolaos Bapir, Mariam Durrani, Abdullah K. Butsabong, Teemapron Campagnolo, Paola Sampson, David D. Heiss, Christian Sampson, Danuta M. Optical+Biomedical Engineering Laboratory School of Electrical Electronic and Computer Engineering The University of Western Australia 35 Stirling Highway PerthWA6009 Australia Surrey Biophotonics Advanced Technology Institute School of Physics School of Biosciences and Medicine University of Surrey Surrey GuildfordGU2 7XH United Kingdom Department of Biochemical Sciences Department of Clinical and Experimental Medicine School of Biosciences and Medicine University of Surrey Surrey GuildfordGU2 7XH United Kingdom Mathematics Research Center Academy of Athens Athens106 79 Greece Surrey and Sussex Healthcare NHS Trust East Surrey Hospital Surrey RedhillRH1 5RH United Kingdom Surrey Biophotonics Centre for Vision Speech and Signal Processing School of Biosciences and Medicine The University of Surrey GuildfordGU2 7XH United Kingdom

Optical coherence tomography angiography (OCTA) performs non-invasive visualization and characterization of microvasculature in research and clinical applications mainly in ophthalmology and dermatology. A wide variety of instruments, imaging protocols, processing methods and metrics have been used to describe the microvasculature, such that comparing different study outcomes is currently not feasible. With the goal of contributing to standardization of OCTA data analysis, we report a user-friendly, open-source toolbox, OCTAVA (OCTA Vascular Analyzer), to automate the pre-processing, segmentation, and quantitative analysis of en face OCTA maximum intensity projection images in a standardized workflow. We present each analysis step, including optimization of filtering and choice of segmentation algorithm, and definition of metrics. We perform quantitative analysis of OCTA images from different commercial and non-commercial instruments and samples and show OCTAVA can accurately and reproducibly determine metrics for characterization of microvasculature. Wide adoption could enable studies and aggregation of data on a scale sufficient to develop reliable microvascular biomarkers for early detection, and to guide treatment, of microvascular disease. © 2021, CC BY-NC-SA.

关键词： Optical tomography

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Radiomics analysis of baseline F-FDG PET/CT images for improved prognosis in nasopharyngeal carcinoma 15

Radiomics analysis of baseline F-FDG PET/CT images for impro...

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15th IEEE International Symposium on Biomedical Imaging, ISBI 2018

作者： Lv, Wenbing Yuan, Qingyu Wang, Quanshi Ma, Jianhua Feng, Qianjin Chen, Wufan Rahmim, Arman Lu, Lijun School of Biomedical Engineering and Guangdong Provincial Key Laboratory of Medical Image Processing Southern Medical University China Nanfang PET Center Nanfang Hospital Southern Medical University China Department of Radiology Johns Hopkins University United States Department of Electrical and Computer Engineering Johns Hopkins University United States

ISBN: (纸本)9781538636367

The purpose of this study is to investigate the prognostic performance of radiomics features on nasopharyngeal carcinoma (NPC) patients imaged with baseline 18F-FDG PET/CT. 128 NPC patients were retrospectively enrolled with 3348 radiomics features and 13 clinical features. Kaplan-Meier analysis was used to estimate progression-free survival (PFS), and log-rank test was used to screen the significant features. Cox proportional hazards regression modal with forward stepwise feature selection was adopted to identify independent predictors of PFS. 24 radiomics features and 8 clinical features were found to be significantly associated with PFS in univariate analysis. Radiomics features HGZE-GLSZM-HLL-32 (p=0.0061, HR: 0.66, 95%CI: 0.49-0.89), as well as clinical features N-stage, M-stage, antibody VCA-IgA and platelet count (PLT) retained the independent prognostic significance for PFS in multivariate analysis. Overall, radiomics features can provide complementary prognostic information for NPC patients imaged with baseline 18F-FDG PET/CT compared to clinical features. © 2018 IEEE.

关键词： Multivariant analysis

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Comparison of brain connectomes using geodesic distance on manifold: A twins study

arXiv

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arXiv 2019年

作者： Yamin, A. Dayan, M. Squarcina, L. Brambilla, P. Murino, V. Diwadkar, V. Sona, D. Pattern Analysis and Computer Vision Istituto Italiano di Tecnologia Genova Italy Department of Electrical Electronics and Telecommunication Engineering and Naval Architecture Università degli Studi di Genova Italy Scientific Institute IRCCS "E. Medea" Bosisio Parini Italy Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico Università di Milano Italy Department of Computer Science Università di Verona Italy Department of Psychiatry & Behavioral Neuroscience Wayne State University DetroitMI United States Neuroinformatics Laboratory Fondazione Bruno Kessler Trento Italy

fMRI is a unique non-invasive approach for understanding the functional organization of the human brain, and task-based fMRI promotes identification of functionally relevant brain regions associated with a given task. Here, we use fMRI (using the Poffenberger Paradigm) data collected in mono- and dizygotic twin pairs to propose a novel approach for assessing similarity in functional networks. In particular, we compared network similarity between pairs of twins in task-relevant and task-orthogonal networks. The proposed method measures the similarity between functional networks using a geodesic distance between graph Laplacians. With method we show that networks are more similar in monozygotic twins compared to dizygotic twins. Furthermore, the similarity in monozygotic twins is higher for task-relevant, than task-orthogonal networks. Copyright © 2019, The Authors. All rights reserved.

关键词： Brain

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An adaptive AI-based virtual reality sports system for adolescents with excess body weight: a randomized controlled trial

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Nature medicine 2025年 1-14页

作者： Jihong Wang Yiming Qin Qian Wu Dian Zeng Xiaojing Gao Qinyi Wang Zhen Li Yueqiong Ni Haoxuan Li Ping Zhang Jingyi Guo Weizhi Ma Mamatkasim Maitusun Xufeng Jin Minghong Chen Liping Zhu Qin Lu Qiandi Chen Yuna Wu Chengxiang Lin Rui Han Di Cheng Jiacheng Ni Xiaochun Wang Fangshu Yao Jie Zhuang Jun Xia Dan Liu Yuwei Lu Piao Kang Shujie Yu Anran Chen Ying Zhang Qian Li Wenli Ge Xiaoxue Long Zehua Jiang Zhouyu Guan Zihao Jin Pengfei Jin Tingyao Li Jia Shu Jiale Yang Jinyang Wang Nan Jiang Jing Qian Younhyun Jung Han Zhang Qing Yang Lifei Ma Xiaomeng Wu Xiaojun Huang Dongyang Si Jie Ren Hui Qiao Yuchen Guo Zhifeng Huang Wenxiao Wang Weihong Deng Lei Bi Danyue Zhao Yuehua Li Rynson W H Lau Yih-Chung Tham Xindong Ma Jing Ma Dinggang Shen Songhai Zhang Haibing Guan Weiwen Zou Minyi Guo Xinping Guan Xiaokang Yang Aimin Xu Jiarui Wu Gianni Panagiotou Michael Andrew Tse Jinman Kim Enhua Wu Daniel Thalmann Nadia Magnenat Thalmann Felipe Fregni Tien Yin Wong Weiping Jia Rong Zeng Chwee Teck Lim Bin Sheng Huating Li The Consortium for Digitalized and Intelligent Physical Education Assessment and Application School of Athletic Performance Shanghai University of Sport Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine Department of Computer Science and Engineering School of Electronic Information and Electrical Engineering Shanghai Jiao Tong University Shanghai China. School of Clinical Medicine Tsinghua University Beijing China. Department of Computer Science City University of Hong Kong Hong Kong Special Administrative Region China. MOE Key Laboratory of AI School of Electronic Information and Electrical Engineering Shanghai Jiao Tong University Shanghai China. Institute for Proactive Healthcare Antai College of Economics and Management Shanghai Jiao Tong University Shanghai China. Shanghai Diabetes Institute Shanghai Key Laboratory of Diabetes Mellitus Shanghai Clinical Center for Diabetes Shanghai China. Tsinghua Medicine Tsinghua University Beijing China. Shanghai Clinical Research and Trial Center ShanghaiTech University Shanghai China. Department of Microbiome Dynamics Leibniz Institute for Natural Product Research and Infection Biology - Leibniz-Hans Knöll Institute Jena Germany. Cluster of Excellence Balance of the Microverse Friedrich Schiller University Jena Germany. School of Exercise and Health Shanghai University of Sport Shanghai China. Department of Computer Science and Engineering The Ohio State University Columbus OH USA. Department of Biomedical Informatics The Ohio State University Columbus OH USA. Clinical Research Center Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine Shanghai China. Institute for AI Industry Research Tsinghua University Beijing China. Hotan District Secondary Vocational and Technical School Hotan China. Shanghai Baoshan High School Shanghai China. Shanghai Qiuzhen Middle School Shanghai China. School of Psychology Shanghai Universi

Adolescents with obesity face numerous health risks and encounter barriers that lead to physical inactivity. We developed a virtual reality sports system, named REVERIE (Real-World Exercise and VR-Based Exercise Research in Education), which used deep reinforcement learning to train transformer-based virtual coaching agents, offering immersive and effective sports guidance, with biomechanical performance comparable to real-world physical sports. We integrated REVERIE into a randomized controlled trial involving an 8-week intervention in adolescents with excess body weight (n = 227). Participants were randomized (1:1:1:1:1) to physical table tennis, physical soccer, REVERIE table tennis, REVERIE soccer or control. REVERIE sports intervention was effective in reducing primary outcome fat mass (mean -4.28 kg (95% confidence interval (CI) -6.35 to -2.22), relative to control), with no significant difference compared with physical sports (mean -5.06 kg (95% CI -7.13 to -2.98), relative to control). For secondary outcomes, decreases in liver enzymes and low-density lipoprotein cholesterol levels were found in physical and REVERIE sports groups compared to control. Physical and REVERIE sports showed improvements in physical fitness, psychological well-being and sports willingness after an 8-week intervention, which remained at the 6-month follow-up in the REVERIE sports group. REVERIE sports demonstrated superior cognitive enhancements compared to physical sports in exploratory analyses, as evidenced by olfactory tests (total score: mean 2.84 (95% CI 1.15 to 4.53)) and working memory paradigm (2-back accuracy: mean 10.88% (95% CI 1.19% to 20.56%)). Functional magnetic resonance imaging exhibited that REVERIE sports enhanced neural efficiency and neuroplasticity. Multi-omics analyses revealed distinct changes induced by REVERIE sports that were closely associated with cognitive improvement. Minimal injury rates were 7.69% for REVERIE and 13.48% for physical sports, with no

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Deep learning methods for lung cancer segmentation in whole-slide histopathology images - The ACDC@lungHP challenge 2019

arXiv

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arXiv 2020年

作者： Li, Zhang Zhang, Jiehua Tan, Tao Teng, Xichao Sun, Xiaoliang Li, Yang Liu, Lihong Xiao, Yang Lee, Byungjae Li, Yilong Zhang, Qianni Sun, Shujiao Zheng, Yushan Yan, Junyu Li, Ni Hong, Yiyu Ko, Junsu Jung, Hyun Liu, Yanling Chen, Yu-Cheng Wang, Ching-Wei Yurovskiy, Vladimir Maevskikh, Pavel Khanagha, Vahid Jiang, Yi Feng, Xiangjun Liu, Zhihong Li, Daiqiang Schüffler, Peter J. Yu, Qifeng Chen, Hui Tang, Yuling Litjens, Geert College of Aerospace Science and Engineering National University of Defense Technology Changsha410073 China Department of Mathematics and Computer Science Eindhoven University of Technology Netherlands and ScreenPoint Medical Eindhoven Nijmegen5600 MB Netherlands Pingan Technology Shenzhen China Lunit Inc. Seoul Korea Republic of School of Electrical Engineering and Computer Science Queen Mary University of London London United Kingdom Image Processing Center School of Astronautics Beihang University Beijing102206 China Beijing Advanced Innovation Center for Biomedical Engineering Beijing100191 China Beijing Advanced Innovation Center for Biomedical Engineering Beihang University Image Processing Center School of Astronautics Beihang University Beijing102206 China AstLab School of Automatationm Beihang University Beijing China Department of R&D Center Arontier Co. Ltd. Seoul Korea Republic of Frederick National Laboratory United States Center of Computer Vision and Medical Imaging Graduate Institute of Biomedical Engineering Graduate institute of Applied Science and Technology National Taiwan University of Science and Technology AI Explore Taipei Taiwan Research Department Sky-chain Global Yekaterinburg Russia Audio Solutions Team Motorola Solutions Inc. PlantationFL United States Second Xiangya Hospital Central South University Changsha China Hunan Biotechnology Ltd. Changsha China Hunan Cancer Hospital Central South University Changsha China Memorial Sloan Kettering Cancer Center United States First Hospital of Changsha City Changsha China Radboud University Medical Center Nijmegen Netherlands

Accurate segmentation of lung cancer in pathology slides is a critical step in improving patient care. We proposed the ACDC@LungHP (Automatic Cancer Detection and Classification in Whole-slide Lung Histopathology) challenge for evaluating different computer-aided diagnosis (CADs) methods on the automatic diagnosis of lung cancer. The ACDC@LungHP 2019 focused on segmentation (pixel-wise detection) of cancer tissue in whole slide imaging (WSI), using an annotated dataset of 150 training images and 50 test images from 200 patients. This paper reviews this challenge and summarizes the top 10 submitted methods for lung cancer segmentation. All methods were evaluated using the false positive rate, false negative rate, and DICE coefficient (DC). The DC ranged from 0.7354±0.1149 to 0.8372±0.0858. The DC of the best method was close to the inter-observer agreement (0.8398±0.0890). All methods were based on deep learning and categorized into two groups: multi-model method and single model method. In general, multi-model methods were significantly better (p Copyright © 2020, The Authors. All rights reserved.

关键词： Biological organs

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Cover Picture: Laser-scribed Graphene Electrodes as an Electrochemical Immunosensing Platform for Cancer Biomarker ‘eIF3d’ (Electroanalysis 4/2021)

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Electroanalysis 2021年第4期33卷

作者： Simge Balaban Tutku Beduk Ceren Durmus Eda Aydindogan Khaled Nabil Salama Suna Timur Department of Biochemistry Faculty of Science Ege University 35100 Bornova Izmir Turkey Sensors Lab Advanced Membranes and Porous Materials Center Computer Electrical and Mathematical Science and Engineering Division King Abdullah University of Science and Technology (KAUST) 23955-6900 Thuwal Saudi Arabia Central Research Testing and Analysis Laboratory Research and Application Center Ege University 35100 Bornova Izmir Turkey

The cover image is based on the Full Paper Laser‐scribed Graphene Electrodes as an Electrochemical Immunosensing Platform for Cancer Biomarker ‘eIF3d' by Simge Balaban et al., DOI: 10.1002/elan.202060482.

关键词： Laser-scribed graphene electrodes Cancer, Biosensors Affinity-based sensors Biomarkers, EIF3D

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Aggregation Signature for Small Object Tracking

arXiv

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arXiv 2019年

作者： Liu, Chunlei Ding, Wenrui Yang, Jinyu Murino, Vittorio Zhang, Baochang Han, Jungong Guo, Guodong School of Electrical and Information Engineering Beihang University Beijing China Unmanned System Research Institute Beihang University Beijing China School of Computer Science University of Birmingham British United Kingdom University of Verona Verona Italy Pattern Analysis and Computer Vision department Istituto Italiano di Tecnologia Genoa Italy School of Automation Science and Electrical Engineering Beihang University Beijing China Shenzhen Academy of Aerospace Technology Shenzhen China WMG Data Science Group University of Warwick CoventryCV4 7AL United Kingdom Institute of Deep Learning Baidu Research and National Engineering Laboratory for Deep Learning Technology and Application

—Small object tracking becomes an increasingly important task, which however has been largely unexplored in computer vision. The great challenges stem from the facts that: 1) small objects show extreme vague and variable appearances, and 2) they tend to be lost easier as compared to normal-sized ones due to the shaking of lens. In this paper, we propose a novel aggregation signature suitable for small object tracking, especially aiming for the challenge of sudden and large drift. We make three-fold contributions in this work. First, technically, we propose a new descriptor, named aggregation signature, based on saliency, able to represent highly distinctive features for small objects. Second, theoretically, we prove that the proposed signature matches the foreground object more accurately with a high probability. Third, experimentally, the aggregation signature achieves a high performance on multiple datasets, outperforming the state-of-the-art methods by large margins. Moreover, we contribute with two newly collected benchmark datasets, i.e., small90 and small112, for visually small object tracking. The datasets will be available in https://***/bczhangbczhang/. Copyright © 2019, The Authors. All rights reserved.

关键词： Large dataset

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QU-BraTS: MICCAI BraTS 2020 Challenge on Quantifying Uncertainty in Brain Tumor Segmentation - analysis of Ranking Scores and Benchmarking Results

arXiv

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arXiv 2021年

作者： Mehta, Raghav Filos, Angelos Baid, Ujjwal Sako, Chiharu McKinley, Richard Rebsamen, Michael Dätwyler, Katrin Meier, Raphael Radojewski, Piotr Murugesan, Gowtham Krishnan Nalawade, Sahil Ganesh, Chandan Wagner, Ben Yu, Fang F. Fei, Baowei Madhuranthakam, Ananth J. Maldjian, Joseph A. Daza, Laura Gómez, Catalina Arbeláez, Pablo Dai, Chengliang Wang, Shuo Reynaud, Hadrien Mo, Yuanhan Angelini, Elsa Guo, Yike Bai, Wenjia Banerjee, Subhashis Pei, Linmin Murat, A.K. Rosas-González, Sarahi Zemmoura, Ilyess Tauber, Clovis Vu, Minh H. Nyholm, Tufve Löfstedt, Tommy Ballestar, Laura Mora Vilaplana, Veronica McHugh, Hugh Talou, Gonzalo Maso Wang, Alan Patel, Jay Chang, Ken Hoebel, Katharina Gidwani, Mishka Arun, Nishanth Gupta, Sharut Aggarwal, Mehak Singh, Praveer Gerstner, Elizabeth R. Kalpathy-Cramer, Jayashree Boutry, Nicolas Huard, Alexis Vidyaratne, Lasitha Rahman, Md Monibor Iftekharuddin, Khan M. Chazalon, Joseph Puybareau, Elodie Tochon, Guillaume Ma, Jun Cabezas, Mariano Llado, Xavier Oliver, Arnau Valencia, Liliana Valverde, Sergi Amian, Mehdi Soltaninejad, Mohammadreza Myronenko, Andriy Hatamizadeh, Ali Feng, Xue Dou, Quan Tustison, Nicholas Meyer, Craig Shah, Nisarg A. Talbar, Sanjay Weber, Marc-André Mahajan, Abhishek Jakab, Andras Wiest, Roland Fathallah-Shaykh, Hassan M. Nazeri, Arash Milchenko, Mikhail Marcus, Daniel Kotrotsou, Aikaterini Colen, Rivka Freymann, John Kirby, Justin Davatzikos, Christos Menze, Bjoern Bakas, Spyridon Gal, Yarin Arbel, Tal McGill University MontrealQC Canada Group University of Oxford Oxford United Kingdom University of Pennsylvania PhiladelphiaPA United States Department of Radiology Perelman School of Medicine The University of Pennsylvania PhiladelphiaPA United States Department of Pathology and Laboratory Medicine Perelman School of Medicine University of Pennsylvania PhiladelphiaPA United States University Institute of Diagnostic and Interventional Neuroradiology University of Bern Inselspital Bern University Hospital Bern Switzerland Department of Radiology University of Texas Southwestern Medical Center DallasTX United States Department of Bioengineering University of Texas DallasTX United States Advanced Imaging Research Center University of Texas Southwestern Medical Center DallasTX United States Universidad de los Andes Bogotá Colombia Data Science Institute Imperial College London London United Kingdom NIHR Imperial BRC ITMAT Data Science Group Imperial College London London United Kingdom Department of Brain Sciences Imperial College London London United Kingdom Machine Intelligence Unit Indian Statistical Institute Kolkata India Department of CSE University of Calcutta Kolkata India Department of Information Technology Uppsala University Uppsala Sweden Department of Diagnostic Radiology The University of Pittsburgh Medical Center PittsburghPA United States UMR U1253 iBrain Université de Tours Inserm Tours France Department of Radiation Sciences Umeå University Umeå Sweden Department of Computing Science Umeå University Umeå Sweden Signal Theory and Communications Department Universitat Politècnica de Catalunya Barcelona Tech Barcelona Spain Faculty of Medical and Health Sciences University of Auckland Auckland New Zealand Radiology Department Auckland City Hospital Auckland New Zealand Auckland Bioengineering Institute University of Auckland New Zealand Athinoula A. Martinos Center for Biomedical Imaging Department of Radiology

Deep learning (DL) models have provided state-of-the-art performance in various medical imaging benchmarking challenges, including the Brain Tumor Segmentation (BraTS) challenges. However, the task of focal pathology multi-compartment segmentation (e.g., tumor and lesion sub-regions) is particularly challenging, and potential errors hinder translating DL models into clinical workflows. Quantifying the reliability of DL model predictions in the form of uncertainties could enable clinical review of the most uncertain regions, thereby building trust and paving the way toward clinical translation. Several uncertainty estimation methods have recently been introduced for DL medical image segmentation tasks. Developing scores to evaluate and compare the performance of uncertainty measures will assist the end-user in making more informed decisions. In this study, we explore and evaluate a score developed during the BraTS 2019 and BraTS 2020 task on uncertainty quantification (QU-BraTS) and designed to assess and rank uncertainty estimates for brain tumor multi-compartment segmentation. This score (1) rewards uncertainty estimates that produce high confidence in correct assertions and those that assign low confidence levels at incorrect assertions, and (2) penalizes uncertainty measures that lead to a higher percentage of under-confident correct assertions. We further benchmark the segmentation uncertainties generated by 14 independent participating teams of QU-BraTS 2020, all of which also participated in the main BraTS segmentation task. Overall, our findings confirm the importance and complementary value that uncertainty estimates provide to segmentation algorithms, highlighting the need for uncertainty quantification in medical image analyses. Finally, in favor of transparency and reproducibility, our evaluation code is made publicly available at https://***/RagMeh11/QU-BraTS. © 2021, CC BY.

关键词： Benchmarking

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Considerations and recommendations from the ISMRM Diffusion Study Group for preclinical diffusion MRI: Part 2 — Ex vivo imaging: added value and acquisition

arXiv

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arXiv 2022年

作者： Schilling, Kurt G. Grussu, Francesco Ianus, Andrada Hansen, Brian Howard, Amy F.D. 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. Allan Johnson, G. Cohen-Adad, Julien Budde, Matthew D. Jelescu, Ileana O. Radiology and Radiological Sciences Vanderbilt University Medical Center NashvilleTN United States Vanderbilt University Institute of Imaging Science Vanderbilt University NashvilleTN United States 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 Bioengineering Imperial College London London United Kingdom FMRIB Centre Wellcome Centre for Integrative Neuroimaging Nuffield Department of Clinical Neurosciences University of Oxford Oxford United Kingdom 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 Re

The value of preclinical diffusion MRI (dMRI) is substantial. While dMRI enables in vivo non-invasive characterization of tissue, ex vivo dMRI is increasingly being used to probe tissue microstructure and brain connectivity. Ex vivo dMRI has several experimental advantages including higher signal-to-noise ratio (SNR) and spatial resolution compared to in vivo studies, and enabling more advanced diffusion contrasts for improved microstructure and connectivity characterization. Another major advantage of ex vivo dMRI is the direct comparison with histological data, as a crucial methodological validation. However, there are a number of considerations that must be made when performing ex vivo experiments. The steps from tissue preparation, image acquisition and processing, and interpretation of results are complex, with many decisions that not only differ dramatically from in vivo imaging of small animals, but ultimately affect what questions can be answered using the data. This work represents "Part 2" of a 3-part series of recommendations and considerations for preclinical dMRI. We describe best practices for dMRI of ex vivo tissue, with a focus on the value that ex vivo imaging adds to the field of dMRI and considerations in ex vivo image acquisition. We first give general considerations and foundational knowledge that must be considered when designing experiments. We briefly describe differences in specimens and models and discuss why some may be more or less appropriate for different studies. We then give guidelines for ex vivo protocols, including tissue fixation, sample preparation, and MR scanning. In each section, we attempt to provide guidelines and recommendations, but also highlight areas for which no guidelines exist (and why), and where future work should lie. An overarching goal herein is to enhance the rigor and reproducibility of ex vivo dMRI acquisitions and analyses, and thereby advance biomedical knowledge. © 2022, CC BY.

关键词： image acquisition

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Considerations and Recommendations from the ISMRM Diffusion Study Group for preclinical diffusion MRI: Part 1 — In vivo small-animal imaging

arXiv

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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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