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The 5th International Conference on Biomedical Engineering and Biotechnology (ICBEB 2016) Abstracts

BMC medical IMAGING 2016年第Sup1期16卷 65-65页

作者： [Anonymous] Department of MRI Shandong Medical Imaging Research Institute Affiliated to Shandong University Jinan Shandong 250021 People’s Republic of China Department of Interventional Radiology Shandong Provincial Hospital Affiliated to Shandong University Jinan Shandong 250021 People’s Republic of China College of Information Science and Technology Engr. Research Center of Digitized Textile & Fashion Tech. for Ministry of Education Donghua University Shanghai 201620 China Intelligent multimedia information processing Lab College of Software Northeastern University Shenyang Liaoning Province 110004 China Institute of Biomedical and Health Engineering Shenzhen Institutes of Advanced Technology Chinese Academy of Sciences Shenzhen 518055 China School of Computer Science and Technology Nanjing Normal University Nanjing China Department of Electrical Engineering The City College of New York CUNY New York USA Jiangsu Key Laboratory of 3D Printing Equipment and Manufacturing Nanjing China School of Electronic Science and Engineering Nanjing University Nanjing Jiangsu 210046 China College of Engineering Nanyang Technological University Singapore 639798 Singapore School of Electronic Information Shanghai Dianji University Shanghai China School of Natural Sciences and Mathematics Shepherd University Shepherdstown WV 25443 USA Davis College of Agriculture Natural Resources and Design West Virginia University Morgantown WV 26505 USA State Key Laboratory of Millimeter Waves Southeast University Nanjing 210096 China Center of Medical Physics and Technology Hefei Institutes of Physical Science Chinese Academy of Sciences Hefei China College of Agricultural and Life Sciences University of Florida Gainesville FL 32611 USA Courant Institute of Mathematical Sciences New York University New York NY 10012 USA Translational Imaging Division & MRI Unit Columbia University and New York State Psychiatric Institute New York NY 10032 USA Guangxi Key Laboratory of Manufacturing System & Adv

Shaoqing Wang1, Xiancun Yang2, Meixia Su1, Qiang Liu1 1Department of MRI, Shandong medical Imaging Research Institute Affiliated to Shandong University, Jinan, Shandong, 250021, People's Republic of China; 2Department of Interventional Radiology, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, Shandong, 250021, People's Republic of China Correspondence: Qiang Liu (2002md@***) Aims To evaluate the diagnostic value of three- dimensional rotational angiography (3D-RA) of intracranial micro-aneurysms (diameter ≤ 3 mm) and provide guidance on the value of endovascular treatment. Materials and methods 43 patients with intracranial micro-aneurysms were analyzed retrospectively, all patients had undergone angiography with both conventional 2D-DSA(Two-Dimensional Digital Subtraction Angiography) and rotational angiography with three-dimensional reconstruction; the frequency of detection of aneurysms, depiction of aneurysm neck, radiation dose, and the dosage of contrast agent were recorded respectively. Results 55 pieces of aneurysms were detected out from the 43 cases with intracranial micro-aneurysms by 3D-RA. But only 39 cases were detected out using 2D-DSA from the 55 samples, there were significant differences with regards to detection rate (P < 0.05). There were significant differences in radiation dose and dosage of contrast agent (P < 0.05) between the two methods of using 3D-RA can improve the detection rate of micro-aneurysms, which bestows obvious advantages on displaying the shape of aneurysms, the aneurysm neck at the best angle, and the relationship with the parent artery, at the same time, the amount of contrast agent and radiation dose are reduced in 3D-RA compared to 2D-DSA.

关键词： Convolutional Neural Network High Resolution Compute Tomography Intensity Inhomogeneity Kernel Support Vector Machine Clonal Selection Algorithm

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An Early Stage Researcher's Primer on Systems Medicine Terminology

Network and Systems Medicine

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Network and Systems Medicine 2021年第1期4卷 2-50页

作者： Zanin, Massimiliano Aitya, Nadim A.A. Basilio, José Baumbach, Jan Benis, Arriel Behera, Chandan K. Bucholc, Magda Castiglione, Filippo Chouvarda, Ioanna Comte, Blandine Dao, Tien-Tuan Ding, Xuemei Pujos-Guillot, Estelle Filipovic, Nenad Finn, David P. Glass, David H. Harel, Nissim Iesmantas, Tomas Ivanoska, Ilinka Joshi, Alok Boudjeltia, Karim Zouaoui Kaoui, Badr Kaur, Daman Maguire, Liam P. McClean, Paula L. McCombe, Niamh De Miranda, João Luís Moisescu, Mihnea Alexandru Pappalardo, Francesco Polster, Annikka Prasad, Girijesh Rozman, Damjana Sacala, Ioan Sanchez-Bornot, Jose M. Schmid, Johannes A. Sharp, Trevor Solé-Casals, Jordi Spiwok, Vojtěch Spyrou, George M. Stalidzans, Egils Stres, Blaa Sustersic, Tijana Symeonidis, Ioannis Tieri, Paolo Todd, Stephen Van Steen, Kristel Veneva, Milena Wang, Da-Hui Wang, Haiying Wang, Hui Watterson, Steven Wong-Lin, Kongfatt Yang, Su Zou, Xin Schmidt, Harald H.H.W. Centro de Tecnología Biomédica Universidad Politécnica de Madrid Madrid Spain Intelligent Systems Research Centre School of Computing Engineering and Intelligent Systems Ulster University Ulster United Kingdom Center for Physiology and Pharmacology Institute of Vascular Biology and Thrombosis Research Medical University of Vienna Vienna Austria TUM School of Life Sciences Weihenstephan Technical University of Munich Freising Germany Holon Israel CNR National Research Council IAC Institute for Applied Computing Rome Italy Lab of Computing Medical Informatics and Biomedical Imaging Technologies School of Medicine Aristotle University of Thessaloniki Thessaloniki Greece Université Clermont Auvergne INRAE UNH Plateforme d'Exploration du Métabolisme MetaboHUB Clermont Clermont-Ferrand France Université de Technologie de Compiègne Compiègne France Labex MS2T Control of Technological Systems-of-Systems CNRS and Université de Technologie de Compiègne Compiègne France Faculty of Engineering University of Kragujevac Kragujevac Serbia Kragujevac Serbia Steinbeis Advanced Risk Technologies Institute Doo Kragujevac Kragujevac Serbia Pharmacology and Therapeutics School of Medicine Galway Neuroscience Centre National University of Ireland Galway Ireland School of Computing Ulster University Ulster United Kingdom Holon Israel Department of Mathematics and Natural Sciences Kaunas University of Technology Kaunas Lithuania Faculty of Computer Science and Engineering Ss. Cyril and Methodius University Skopje Macedonia Medicine Faculty Université Libre de Bruxelles CHU de Charleroi Charleroi Belgium Northern Ireland Centre for Stratified Medicine Biomedical Sciences Research Institute Ulster University Ulster United Kingdom Escola Superior de Tecnologia e Gestão Instituto Politécnico de Portalegre Portalegre Portugal Instituto Superior Técnico Universidade de Lisboa Lisboa Portugal Faculty of Automatic Control and Computers University Politehnica of B

Background: Systems Medicine is a novel approach to medicine, that is, an interdisciplinary field that considers the human body as a system, composed of multiple parts and of complex relationships at multiple levels, and further integrated into an environment. Exploring Systems Medicine implies understanding and combining concepts coming from diametral different fields, including medicine, biology, statistics, modeling and simulation, and data science. Such heterogeneity leads to semantic issues, which may slow down implementation and fruitful interaction between these highly diverse fields. Methods: In this review, we collect and explain more than100 terms related to Systems Medicine. These include both modeling and data science terms and basic systems medicine terms, along with some synthetic definitions, examples of applications, and lists of relevant references. Results: This glossary aims at being a first aid kit for the Systems Medicine researcher facing an unfamiliar term, where he/she can get a first understanding of them, and, more importantly, examples and references for digging into the topic. © Massimiliano Zanin et al., 2021;Published by Mary Ann Liebert, Inc. 2021.

关键词： Semantics

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ADAM CHALLENGE: DETECTING AGE-RELATED MACULAR DEGENERATION FROM FUNDUS imageS

arXiv

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arXiv 2022年

作者： Fang, Huihui Li, Fei Fu, Huazhu Sun, Xu Cao, Xingxing Lin, Fengbin Son, Jaemin Kim, Sunho Quellec, Gwenole Matta, Sarah Shankaranarayana, Sharath M. Chen, Yi-Ting Wang, Chuen-Heng Shah, Nisarg A. Lee, Chia-Yen Hsu, Chih-Chung Xie, Hai Lei, Baiying Baid, Ujjwal Innani, Shubham Dang, Kang Shi, Wenxiu Kamble, Ravi Singhal, Nitin Wang, Ching-Wei Lo, Shih-Chang Orlando, José Ignacio Bogunović, Hrvoje Zhang, Xiulan Xu, Yanwu The ADAM Challenge State Key Laboratory of Ophthalmology Zhongshan Ophthalmic Center Sun Yat-Sen University Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science Guangzhou China Intelligent Healthcare Unit Baidu Inc. Beijing China The Institute of High Performance Computing Agency for Science Technology and Research Singapore CONICET Yatiris lab of Pladema Institute Tandil Argentina Department of Ophthalmology and Optometry Medical University of Vienna Vienna Austria VUNO Inc Seoul Korea Republic of Inserm UMR 1101 BrestF-29200 France Univ Bretagne Occidentale BrestF-29200 France Zasti India Pvt. Ltd. India Graphen.Inc Muen Biomedical and Optoelectronics Technologies Inc Taiwan Department of Electrical Engineering Indian Institute of Technology Rajasthan Jodhpur India Department of Electrical Engineering National United University Taiwan Institute of Data Science Department of Statistics National Cheng Kung University Taiwan Shenzhen University Shenzhen China SGGS Institute of Engineering and Technology Nanded India Suzhou Tisu Information Technology Co. Ltd China AIRA Matrix Mumbai India Graduate Institute of Biomedical Engineering National Taiwan University of Science and Technology Taiwan

Age-related macular degeneration (AMD) is the leading cause of visual impairment among elderly in the world. Early detection of AMD is of great importance, as the vision loss caused by this disease is irreversible and permanent. Color fundus photography is the most cost-effective imaging modality to screen for retinal disorders. Cutting edge deep learning based algorithms have been recently developed for automatically detecting AMD from fundus images. However, there are still lack of a comprehensive annotated dataset and standard evaluation benchmarks. To deal with this issue, we set up the Automatic Detection challenge on Age-related Macular degeneration (ADAM), which was held as a satellite event of the ISBI 2020 conference. The ADAM challenge consisted of four tasks which cover the main aspects of detecting and characterizing AMD from fundus images, including detection of AMD, detection and segmentation of optic disc, localization of fovea, and detection and segmentation of lesions. As part of the ADAM challenge, we have released a comprehensive dataset of 1200 fundus images with AMD diagnostic labels, pixel-wise segmentation masks for both optic disc and AMD-related lesions (drusen, exudates, hemorrhages and scars, among others), as well as the coordinates corresponding to the location of the macular fovea. A uniform evaluation framework has been built to make a fair comparison of different models using this dataset. During the ADAM challenge, 610 results were submitted for online evaluation, with 11 teams finally participating in the onsite challenge. This paper introduces the challenge, the dataset and the evaluation methods, as well as summarizes the participating methods and analyzes their results for each task. In particular, we observed that the ensembling strategy and the incorporation of clinical domain knowledge were the key to improve the performance of the deep learning models. © 2022, CC BY-NC-ND.

关键词： Cost effectiveness

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AGE Challenge: Angle Closure Glaucoma Evaluation in Anterior Segment Optical Coherence Tomography

arXiv

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arXiv 2020年

作者： Fu, Huazhu Li, Fei Sun, Xu Cao, Xingxing Liao, Jingan Orlando, José Ignacio Tao, Xing Li, Yuexiang Zhang, Shihao Tan, Mingkui Yuan, Chenglang Bian, Cheng Xie, Ruitao Li, Jiongcheng Li, Xiaomeng Wang, Jing Geng, Le Li, Panming Hao, Huaying Liu, Jiang Kong, Yan Ren, Yongyong Bogunović, Hrvoje Zhang, Xiulan Xu, Yanwu State Key Laboratory Zhongshan Ophthalmic Center Sun Yat-sen University Guangzhou510060 China Inception Institute of Artificial Intelligence Abu Dhabi United Arab Emirates Intelligent Healthcare Unit Baidu Beijing China School of Computer Science and Engineering South China University of Technology GuangzhouGuangdong China National Scientific and Technical Research Council CONICET Argentina Tandil Argentina School of Computer Science and Technology Hangzhou Dianzi University Hangzhou China Tencent Jarvis Lab Shenzhen China School of Software Engineering South China University of Technology Guangzhou China School of Biomedical Engineering Health Science Center Shenzhen University Shenzhen China School of Electronic and Information Engineering Shenzhen University Shenzhen China Department of Computer Science and Engineering Chinese University of Hong Kong Hong Kong School of Electronic and Information Engineering Soochow University Suzhou China Ningbo University Zhejiang China Ningbo Institute of Industrial Technology Chinese Academy of Sciences Zhejiang China Southern University of Science and Technology Shenzhen China Shanghai Jiaotong University Shanghai China Laboratory for Ophthalmic Image Analysis Department of Ophthalmology Medical University of Vienna Vienna Austria

Angle closure glaucoma (ACG) is a more aggressive disease than open-angle glaucoma, where the abnormal anatomical structures of the anterior chamber angle (ACA) may cause an elevated intraocular pressure and gradually leads to glaucomatous optic neuropathy and eventually to visual impairment and blindness. Anterior Segment Optical Coherence Tomography (AS-OCT) imaging provides a fast and contactless way to discriminate angle closure from open angle. Although many medical image analysis algorithms have been developed for glaucoma diagnosis, only a few studies have focused on AS-OCT imaging. In particular, there is no public AS-OCT dataset available for evaluating the existing methods in a uniform way, which limits the progress in the development of automated techniques for angle closure detection and assessment. To address this, we organized the Angle closure Glaucoma Evaluation challenge (AGE), held in conjunction with MICCAI 2019. The AGE challenge consisted of two tasks: scleral spur localization and angle closure classification. For this challenge, we released a large data of 4800 annotated AS-OCT images from 199 patients, and also proposed an evaluation framework to benchmark and compare different models. During the AGE challenge, over 200 teams registered online, and more than 1100 results were submitted for online evaluation. Finally, eight teams participated in the onsite challenge. In this paper, we summarize these eight onsite challenge methods and analyze their corresponding results in the two tasks. We further discuss limitations and future directions. In the AGE challenge, the top-performing approach had an average Euclidean Distance of 10 pixel (10µm) in scleral spur localization, while in the task of angle closure classification, all the algorithms achieved the satisfactory performances, especially, 100% accuracy rate for top-two performances. These artificial intelligence techniques were shown to have the potential to enable new developments in AS-OCT

关键词： Ophthalmology

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Common and Rare Fundus Diseases Identification Using Vision-Language Foundation Model with Knowledge of Over 400 Diseases

arXiv

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arXiv 2024年

作者： Wang, Meng Lin, Tian Lin, Aidi Yu, Kai Peng, Yuanyuan Wang, Lianyu Chen, Cheng Zou, Ke Liang, Huiyu Chen, Man Yao, Xue Zhang, Meiqin Huang, Binwei Zheng, Chaoxin Zhang, Peixin Chen, Wei Luo, Yilong Chen, Yifan Xia, Honghe Shi, Tingkun Zhang, Qi Guo, Jinming Chen, Xiaolin Wang, Jingcheng Chung Tham, Yih Liu, Dianbo Wong, Wendy Thakur, Sahil Fenner, Beau Fang, Danqi Liu, Siying Liu, Qingyun Huang, Yuqiang Zeng, Hongqiang Meng, Yanda Zhou, Yukun Jiang, Zehua Qiu, Minghui Zhang, Changqing Chen, Xinjian Wang, Sophia Y. Lee, Cecilia S. Sobrin, Lucia Cheung, Carol Y. Pang, Chi Pui Keane, Pearse A. Cheng, Ching-Yu Chen, Haoyu Fu, Huazhu Centre for Innovation & Precision Eye Health Yong Loo Lin School of Medicine National University of Singapore Singapore117549 Singapore Department of Ophthalmology Yong Loo Lin School of Medicine National University of Singapore Singapore117549 Singapore Joint Shantou International Eye Center Shantou University Chinese University of Hong Kong Guangdong Shantou515041 China Department of Radiology University of Pennsylvania PhiladelphiaPA19104 United States School of Biomedical Engineering Anhui Medical University Anhui Hefei230032 China College of Computer Science and Technology Nanjing University of Aeronautics and Astronautics Jiangsu Nanjing211100 China Center of Advanced Medical Computing and Analysis Massachusetts General Hospital Harvard Medical School BostonMA02114 United States National Key Laboratory of Fundamental Science on Synthetic Vision College of Computer Science Sichuan University Sichuan Chengdu610065 China Big Vision Medical Technology Ltd. Suzhou China Singapore Eye Research Institute Singapore National Eye Centre Singapore Duke-NUS Medical School Singapore Department of Ophthalmology and Visual Sciences The Chinese University of Hong Kong 999077 Hong Kong Shenzhen Longgang E.N.T Hospital Guangdong Shenzhen518172 China Dongguan Songshan Lake Central Hospital Guangdong Dongguan523326 China Department of Computer Science University of Exeter ExeterEX4 4RN United Kingdom Centre for Medical Image Computing University College London London United Kingdom NIHR Biomedical Research Centre Moorfields Eye Hospital NHS Foundation Trust London United Kingdom Institute of Ophthalmology University College London London United Kingdom Tsinghua Medicine of Tsinghua University Beijing100084 China School of Clinical Medicine Beijing Tsinghua Changgung Hospital Beijing102218 China Foshan Aier Eye Hospital Guangdong Foshan528000 China College of Intelligence and Computing Tianjin University Tianjin300350 China School of Electr

Previous foundation models for retinal images were pre-trained with limited disease categories and knowledge base. Here we introduce RetiZero, a vision-language foundation model that leverages knowledge from over 400 fundus diseases. For RetiZero's pre-training, we compiled 341,896 fundus images paired with text descriptions, sourced from public datasets, ophthalmic literature, and online resources, encompassing a diverse range of diseases across multiple ethnicities and countries. RetiZero exhibits superior performance in several downstream tasks, including zero-shot disease recognition, image-to-image retrieval, and internal- and cross-domain disease identification. In zero-shot scenarios, RetiZero achieves Top5 accuracy scores of 0.8430 for 15 fundus diseases and 0.7561 for 52 fundus diseases. For image retrieval, it achieves Top5 scores of 0.9500 and 0.8860 for the same disease sets, respectively. Clinical evaluations show that RetiZero's Top3 zero-shot performance surpasses the average of 19 ophthalmologists from Singapore, China, and the United States. Furthermore, RetiZero significantly enhances clinicians' accuracy in diagnosing fundus disease. These findings underscore the value of integrating the RetiZero foundation model into clinical settings, where a variety of fundus diseases are encountered. © 2024, CC0.

关键词： Ophthalmology

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Why is the Winner the Best?

Why is the Winner the Best?

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Conference on Computer Vision and Pattern Recognition (CVPR)

作者： M. Eisenmann A. Reinke V. Weru M. D. Tizabi F. Isensee T. J. Adler S. Ali V. Andrearczyk M. Aubreville U. Baid S. Bakas N. Balu S. Bano J. Bernal S. Bodenstedt A. Casella V. Cheplygina M. Daum M. De Bruijne A. Depeursinge R. Dorent J. Egger D. G. Ellis S. Engelhardt M. Ganz N. Ghatwary G. Girard P. Godau A. Gupta L. Hansen K. Harada M. Heinrich N. Heller A. Hering A. Huaulmé P. Jannin A. E. Kavur O. Kodym M. Kozubek J. Li H. Li J. Ma C. Martín-Isla B. Menze A. Noble V. Oreiller N. Padoy S. Pati K. Payette T. Rädsch J. Rafael-Patiño V. Singh Bawa S. Speidel C. H. Sudre K. Van Wijnen M. Wagner D. Wei A. Yamlahi M. H. Yap C. Yuan M. Zenk A. Zia D. Zimmerer D. Aydogan B. Bhattarai L. Bloch R. Brüngel J. Cho C. Choi Q. Dou I. Ezhov C. M. Friedrich C. Fuller R. R. Gaire A. Galdran Á. García Faura M. Grammatikopoulou S. Hong M. Jahanifar I. Jang A. Kadkhodamohammadi I. Kang F. Kofler S. Kondo H. Kuijf M. Li M. Luu T. Martinčič P. Morais M. A. Naser B. Oliveira D. Owen S. Pang J. Park S. Park S. Płotka E. Puybareau N. Rajpoot K. Ryu N. Saeed A. Shephard P. Shi D. Štepec R. Subedi G. Tochon H. R. Torres H. Urien J. L. Vilaça K. A. Wahid H. Wang J. Wang L. Wang X. Wang B. Wiestler M. Wodzinski F. Xia J. Xie Z. Xiong S. Yang Y. Yang Z. Zhao K. Maier-Hein P. F. Jäger A. Kopp-Schneider L. Maier-Hein Division of Intelligent Medical Systems German Cancer Research Center (DKFZ) Heidelberg Germany Helmholtz Imaging German Cancer Research Center (DKFZ) Heidelberg Germany Faculty of Mathematics and Computer Science Heidelberg University Heidelberg Germany Division of Biostatistics German Cancer Research Center (DKFZ) Heidelberg Germany Division of Medical Image Computing German Cancer Research Center (DKFZ) Heidelberg Germany Faculty of Engineering and Physical Sciences School of Computing University of Leeds Leeds UK Institute of Informatics School of Management HES-SO Valais-Wallis University of Applied Sciences and Arts Western Switzerland Sierre Switzerland Department of Nuclear Medicine and Molecular Imaging Lausanne University Hospital Lausanne Switzerland Technische Hochschule Ingolstadt Ingolstadt Germany Center for Artificial Intelligence and Data Science for Integrated Diagnostics (AI2D) and Center for Biomedical Image Computing and Analytics (CBICA) University of Pennsylvania Philadelphia PA USA Department of Pathology and Laboratory Medicine Perelman School of Medicine University of Pennsylvania Philadelphia PA USA Department of Radiology Perelman School of Medicine University of Pennsylvania Philadelphia PA USA Department of Radiology University of Washington Seattle WA USA Department of Computer Science Wellcome/EPSRC Centre for Interventional and Surgical Sciences (WEISS) University College London London UK Universitat Autònoma de Barcelona & Computer Vision Center Barcelona Spain Division of Translational Surgical Oncology National Center for Tumor Diseases (NCT/UCC) Dresden Dresden Germany Department of Advanced Robotics Istituto Italiano di Tecnologia Italy Department of Electronics Information and Bioengineering Politecnico di Milano Milan Italy IT University of Copenhagen Copenhagen Denmark Department of General Visceral and Transplantation Surgery Heidelberg University Hospital Heidelberg Germany Department of Radiology and Nuc

International benchmarking competitions have become fundamental for the comparative performance assessment of image analysis methods. However, little attention has been given to investigating what can be learnt from these competitions. Do they really generate scientific progress? What are common and successful participation strategies? What makes a solution superior to a competing method? To address this gap in the literature, we performed a multicenter study with all 80 competitions that were conducted in the scope of IEEE ISBI 2021 and MICCAI 2021. Statistical analyses performed based on comprehensive descriptions of the submitted algorithms linked to their rank as well as the underlying participation strategies revealed common characteristics of winning solutions. These typically include the use of multi-task learning (63%) and/or multi-stage pipelines (61%), and a focus on augmentation (100%), image preprocessing (97%), data curation (79%), and post-processing (66%). The “typical” lead of a winning team is a computer scientist with a doctoral degree, five years of experience in biomedical image analysis, and four years of experience in deep learning. Two core general development strategies stood out for highly-ranked teams: the reflection of the metrics in the method design and the focus on analyzing and handling failure cases. According to the organizers, 43% of the winning algorithms exceeded the state of the art but only 11% completely solved the respective domain problem. The insights of our study could help researchers (1) improve algorithm development strategies when approaching new problems, and (2) focus on open research questions revealed by this work.

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Biomedical image analysis competitions: The state of current participation practice

arXiv

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arXiv 2022年

作者： Eisenmann, Matthias Reinke, Annika Weru, Vivienn Tizabi, Minu Dietlinde Isensee, Fabian Adler, Tim J. Godau, Patrick Cheplygina, Veronika Kozubek, Michal Maier-Hein, Klaus Jäger, Paul F. Kopp-Schneider, Annette Maier-Hein, Lena Ali, Sharib Gupta, Anubha Kybic, Jan Noble, Alison de Solórzano, Carlos Ortiz Pachade, Samiksha Petitjean, Caroline Sage, Daniel Wei, Donglai Wilden, Elizabeth Alapatt, Deepak Andrearczyk, Vincent Baid, Ujjwal Bakas, Spyridon Balu, Niranjan Bano, Sophia Bawa, Vivek Singh Bernal, Jorge Bodenstedt, Sebastian Casella, Alessandro Choi, Jinwook Commowick, Olivier Daum, Marie Depeursinge, Adrien Dorent, Reuben Egger, Jan Eichhorn, Hannah Engelhardt, Sandy Ganz, Melanie Girard, Gabriel Hansen, Lasse Heinrich, Mattias Heller, Nicholas Hering, Alessa Huaulmé, Arnaud Kim, Hyunjeong Li, Hongwei Bran Landman, Bennett Li, Jianning Ma, Jun Martel, Anne Martín-Isla, Carlos Menze, Bjoern Nwoye, Chinedu Innocent Oreiller, Valentin Padoy, Nicolas Pati, Sarthak Payette, Kelly Sudre, Carole van Wijnen, Kimberlin Vardazaryan, Armine Vercauteren, Tom Wagner, Martin Wang, Chuanbo Yap, Moi Hoon Yu, Zeyun Yuan, Chun Zenk, Maximilian Zia, Aneeq Zimmerer, David Bao, Rina Choi, Chanyeol Cohen, Andrew Dzyubachyk, Oleh Galdran, Adrian Gan, Tianyuan Guo, Tianqi Gupta, Pradyumna Haithami, Mahmood Ho, Edward Jang, Ikbeom Li, Zhili Luo, Zhengbo Lux, Filip Makrogiannis, Sokratis Müller, Dominik Oh, Young-Tack Pang, Subeen Pape, Constantin Polat, Gorkem Reed, Charlotte Rosalie Ryu, Kanghyun Scherr, Tim Thambawita, Vajira Wang, Haoyu Wang, Xinliang Xu, Kele Yeh, Hung Yeo, Doyeob Yuan, Yixuan Zeng, Yan Zhao, Xin Abbing, Julian Adam, Jannes Adluru, Nagesh Agethen, Niklas Ahmed, Salman Al Khalil, Yasmina Alenyà, Mireia Alhoniemi, Esa An, Chengyang Arega, Tewodros Weldebirhan Avisdris, Netanell Aydogan, Dogu Baran Bai, Yingbin Calisto, Maria Baldeon Basaran, Berke Doga Beetz, Marcel Bian, Hao Blansit, Kevin Bloch, Louise Bohnsack, Robert Bosticardo, Sara Breen, Jack Brudfors, Mikael Brüngel, Raphael Cabezas, Mariano Cacciola, Alb Heidelberg Division of Intelligent Medical Systems Germany Heidelberg HI Helmholtz Imaging Germany Faculty of Mathematics and Computer Science Heidelberg University Heidelberg Germany Heidelberg Division of Biostatistics Germany Heidelberg Division of Medical Image Computing Germany Heidelberg HI Applied Vision Lab Germany IT University of Copenhagen Copenhagen Denmark Centre for Biomedical Image Analysis Masaryk University Brno Czech Republic Heidelberg Interactive Machine Learning Group Germany Faculty of Mathematics and Computer Science and Medical Faculty Heidelberg University Heidelberg Germany NCT Heidelberg DKFZ University Hospital Heidelberg Germany School of Computing University of Leeds Leeds United Kingdom SBILab Department of ECE IIIT-Delhi India Faculty of Electrical Engineering Czech Technical University Prague Czech Republic Institute of Biomedical Engineering University of Oxford United Kingdom Center for Applied Medical Research Pamplona Spain Shri Guru Gobind Singhji Institute of Engineering and Technology Maharashtra Nanded India Université de Rouen Normandie France Lausanne Switzerland School of Engineering and Applied Science Harvard University United States ICube University of Strasbourg CNRS France Institute of Informatics School of Management HES-SO Valais-Wallis University of Applied Sciences and Arts Western Switzerland Techno-Pôle 3 Sierre3960 Switzerland Department of Nuclear Medicine and Molecular Imaging Lausanne University Hospital Rue du Bugnon 46 LausanneCH-1011 Switzerland University of Pennsylvania PhiladelphiaPA United States Department of Radiology University of Washington United States Wellcome EPSRC Centre for Interventional and Surgical Sciences University College London London United Kingdom Visual Artificial Intelligence Lab Oxford Brookes University Oxford United Kingdom Universitat Autònoma de Barcelona & Computer Vision Center Spain Dresden Fetscherstraße 74 PF 64 Dresden01307 Germany

The number of international benchmarking competitions is steadily increasing in various fields of machine learning (ML) research and practice. So far, however, little is known about the common practice as well as bottlenecks faced by the community in tackling the research questions posed. To shed light on the status quo of algorithm development in the specific field of biomedical imaging analysis, we designed an international survey that was issued to all participants of challenges conducted in conjunction with the IEEE ISBI 2021 and MICCAI 2021 conferences (80 competitions in total). The survey covered participants' expertise and working environments, their chosen strategies, as well as algorithm characteristics. A median of 72% challenge participants took part in the survey. According to our results, knowledge exchange was the primary incentive (70%) for participation, while the reception of prize money played only a minor role (16%). While a median of 80 working hours was spent on method development, a large portion of participants stated that they did not have enough time for method development (32%). 25% perceived the infrastructure to be a bottleneck. Overall, 94% of all solutions were deep learning-based. Of these, 84% were based on standard architectures. 43% of the respondents reported that the data samples (e.g., images) were too large to be processed at once. This was most commonly addressed by patch-based training (69%), downsampling (37%), and solving 3D analysis tasks as a series of 2D tasks. K-fold cross-validation on the training set was performed by only 37% of the participants and only 50% of the participants performed ensembling based on multiple identical models (61%) or heterogeneous models (39%). 48% of the respondents applied postprocessing steps. © 2022, CC BY.

关键词： Benchmarking

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Harmonized-Multinational qEEG norms (HarMNqEEG)

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NEUROimage 2022年 256卷 119190-119190页

作者： Li, Min Wang, Ying Lopez-Naranjo, Carlos Hu, Shiang Reyes, Ronaldo Cesar Garcia Paz-Linares, Deirel Areces-Gonzalez, Ariosky Hamid, Aini Ismafairus Abd Evans, Alan C. Savostyanov, Alexander N. Calzada-Reyes, Ana Villringer, Arno Tobon-Quintero, Carlos A. Garcia-Agustin, Daysi Yao, Dezhong Dong, Li Aubert-Vazquez, Eduardo Reza, Faruque Razzaq, Fuleah Abdul Omar, Hazim Abdullah, Jafri Malin Galler, Janina R. Ochoa-Gomez, John F. Prichep, Leslie S. Galan-Garcia, Lidice Morales-Chacon, Lilia Valdes-Sosa, Mitchell J. Trondle, Marius Zulkifly, Mohd Faizal Mohd Rahman, Muhammad Riddha Bin Abdul Milakhina, Natalya S. Langer, Nicolas Rudych, Pavel Koenig, Thomas Virues-Alba, Trinidad A. Lei, Xu Bringas-Vega, Maria L. Bosch-Bayard, Jorge F. Valdes-Sosa, Pedro Antonio [a]The Clinical Hospital of Chengdu Brain Science Institute MOE Key Lab for Neuroinformation School of Life Science and Technology University of Electronic Science and Technology of China Chengdu China [b]Cuban Center for Neurocience La Habana Cuba [c]McGill Centre for Integrative Neuroscience Ludmer Centre for Neuroinformatics and Mental Health Montreal Neurological Institute Canada [d]Department of Neurosciences School of Medical Sciences Universiti Sains Malaysia Universiti Sains Malaysia Health Campus Kota Bharu Kelantan 16150 Malaysia [e]Brain and Behaviour Cluster School of Medical Sciences Universiti Sains Malaysia Health Campus Kota Bharu Kelantan 16150 Malaysia [f]Hospital Universiti Sains Malaysia Universiti Sains Malaysia Health Campus Kota Bharu Kelantan 16150 Malaysia [g]Humanitarian Institute Novosibirsk State University Novosibirsk 630090 Russia [h]Laboratory of Psychophysiology of Individual Differences Federal State Budgetary Scientific Institution Scientific Research Institute of Neurosciences and Medicine Novosibirsk 630117 Russia [i]Laboratory of Psychological Genetics at the Institute of Cytology and Genetics Siberian Branch of the Russian Academy of Sciences Novosibirsk 630090 Russia [j]University of Pinar del Río “Hermanos Saiz Montes de Oca” Pinar del Río Cuba [k]Department of Neurology Max Planck Institute for Human Cognitive and Brain Sciences Leipzig Germany [l]Department of Cognitive Neurology University Hospital Leipzig Leipzig Germany [m]Center for Stroke Research Charité-Universitätsmedizin Berlin Berlin Germany [n]Grupo Neuropsicología y Conducta - GRUNECO Faculty of Medicine Universidad de Antioquia Colombia [o]Research Department Institución Prestadora de Servicios de Salud IPS Universitaria Colombia [p]The Cuban center aging longevity and health Havana Cuba [q]Research Unit of NeuroInformation Chinese Academy of Medical Sciences Chengdu 2019RU035 China [r]School of Electrical Engineering Zhengzhou University Zhengzhou 4500

This paper extends frequency domain quantitative electroencephalography (qEEG) methods pursuing higher sensitivity to detect Brain Developmental Disorders. Prior qEEG work lacked integration of cross-spectral information omitting important functional connectivity descriptors. Lack of geographical diversity precluded accounting for site-specific variance, increasing qEEG nuisance variance. We ameliorate these weaknesses. (i) Create lifespan Riemannian multinational qEEG norms for cross-spectral tensors. These norms result from the HarMNqEEG project fostered by the Global Brain Consortium. We calculate the norms with data from 9 countries, 12 devices, and 14 studies, including 1564 subjects. Instead of raw data, only anonymized metadata and EEG cross spectral tensors were shared. After visual and automatic quality control, developmental equations for the mean and standard deviation of qEEG traditional and Riemannian DPs were calculated using additive mixed-effects models. We demonstrate qEEG "batch effects " and provide methods to calculate harmonized z-scores. (ii) We also show that harmonized Riemannian norms produce z-scores with increased diagnostic accuracy predicting brain dysfunction produced by malnutrition in the first year of life and detecting COVID induced brain dysfunction. (iii) We offer open code and data to calculate different individual z-scores from the HarMNqEEG dataset. These results contribute to developing bias-free, low-cost neuroimaging technologies applicable in various health settings.

关键词： Quantitative EEG EEG cross-spectrum Riemannian geometry Batch effects Z-score Harmonization Malnutrition Covid induced brain dysfunction Developmental Brain Chart

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CMRxRecon2024: A Multi-Modality, Multi-View K-Space Dataset Boosting Universal Machine Learning for Accelerated Cardiac MRI

arXiv

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arXiv 2024年

作者： Wang, Zi Wang, Fanwen Qin, Chen Lyu, Jun Ouyang, Cheng Wang, Shuo Li, Yan Yu, Mengyao Zhang, Haoyu Guo, Kunyuan Shi, Zhang Li, Qirong Xu, Ziqiang Zhang, Yajing Li, Hao Hua, Sha Chen, Binghua Sun, Longyu Sun, Mengting Li, Qin Chu, Ying-Hua Bai, Wenjia Qin, Jing Zhuang, Xiahai Prieto, Claudia Young, Alistair Markl, Michael Wang, He Wu, Lianming Yang, Guang Qu, Xiaobo Wang, Chengyan Department of Electronic Science Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance National Institute for Data Science in Health and Medicine Xiamen University Xiamen China Department of Bioengineering and Imperial-X Imperial College London London United Kingdom Cardiovascular Research Centre Royal Brompton Hospital London United Kingdom Department of Electrical and Electronic Engineering & Imperial-X Imperial College London London United Kingdom Psychiatry Neuroimaging Laboratory Brigham and Women’s Hospital Harvard Medical School Boston United States Department of Computing Department of Brain Sciences Imperial College London London United Kingdom Digital Medical Research Center School of Basic Medical Sciences Fudan University Shanghai China Department of Radiology Ruijin Hospital Shanghai Jiao Tong University School of Medicine Shanghai China Human Phenome Institute Fudan University Shanghai China Department of Radiology Zhongshan Hospital Fudan University Shanghai China School of Health Science and Engineering University of Shanghai for Science and Technology Shanghai China GE Healthcare Beijing China Institute of Science and Technology for Brain-Inspired Intelligence Fudan University Shanghai China Department of Cardiovascular Medicine Ruijin Hospital Lu Wan Branch Shanghai Jiao Tong University School of Medicine Shanghai China Department of Radiology Ren Ji Hospital School of Medicine Shanghai Jiao Tong University Shanghai China Siemens Healthineers Ltd. Shanghai China School of Nursing The Hong Kong Polytechnic University Hong Kong School of Data Science Fudan University Shanghai China School of Engineering Pontificia Universidad Católica de Chile Santiago Chile School of Biomedical Engineering and Imaging Sciences King’s College London London United Kingdom Millenium Institute for Intelligent Healthcare Engineering Santiago Chile Department of Radiology Feinberg School of Medicine Northwestern University Chicago Unit

The released CMRxRecon2024 dataset is currently the largest and most protocol-diverse publicly available k-space dataset including multi-modality and multi-view cardiac MRI data from 330 healthy volunteers, and each o... 详细信息

关键词： Adversarial machine learning

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Author Correction: Why rankings of biomedical image analysis competitions should be interpreted with care

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Nature communications 2019年第1期10卷 588页

作者： Lena Maier-Hein Matthias Eisenmann Annika Reinke Sinan Onogur Marko Stankovic Patrick Scholz Tal Arbel Hrvoje Bogunovic Andrew P Bradley Aaron Carass Carolin Feldmann Alejandro F Frangi Peter M Full Bram van Ginneken Allan Hanbury Katrin Honauer Michal Kozubek Bennett A Landman Keno März Oskar Maier Klaus Maier-Hein Bjoern H Menze Henning Müller Peter F Neher Wiro Niessen Nasir Rajpoot Gregory C Sharp Korsuk Sirinukunwattana Stefanie Speidel Christian Stock Danail Stoyanov Abdel Aziz Taha Fons van der Sommen Ching-Wei Wang Marc-André Weber Guoyan Zheng Pierre Jannin Annette Kopp-Schneider Division of Computer Assisted Medical Interventions (CAMI) German Cancer Research Center (DKFZ) 69120 Heidelberg Germany. l.maier-hein@dkfz.de. Division of Computer Assisted Medical Interventions (CAMI) German Cancer Research Center (DKFZ) 69120 Heidelberg Germany. Centre for Intelligent Machines McGill University Montreal QC H3A0G4 Canada. Christian Doppler Laboratory for Ophthalmic Image Analysis Department of Ophthalmology Medical University Vienna 1090 Vienna Austria. Science and Engineering Faculty Queensland University of Technology Brisbane QLD 4001 Australia. Department of Electrical and Computer Engineering Department of Computer Science Johns Hopkins University Baltimore MD 21218 USA. CISTIB - Center for Computational Imaging & Simulation Technologies in Biomedicine The University of Leeds Leeds Yorkshire LS2 9JT UK. Department of Radiology and Nuclear Medicine Medical Image Analysis Radboud University Center 6525 GA Nijmegen The Netherlands. Institute of Information Systems Engineering TU Wien 1040 Vienna Austria. Complexity Science Hub Vienna 1080 Vienna Austria. Heidelberg Collaboratory for Image Processing (HCI Heidelberg University 69120 Heidelberg Germany. Centre for Biomedical Image Analysis Masaryk University 60200 Brno Czech Republic. Electrical Engineering Vanderbilt University Nashville TN 37235-1679 USA. Institute of Medical Informatics Universität zu Lübeck 23562 Lübeck Germany. Division of Medical Image Computing (MIC) German Cancer Research Center (DKFZ) 69120 Heidelberg Germany. Institute for Advanced Studies Department of Informatics Technical University of Munich 80333 Munich Germany. Information System Institute HES-SO Sierre 3960 Switzerland. Departments of Radiology Nuclear Medicine and Medical Informatics Erasmus MC 3015 GD Rotterdam The Netherlands. Department of Computer Science University of Warwick Coventry CV4 7AL UK. Department of Radiation Oncology Massachusetts General Hospital Boston MA

In the original version of this Article the values in the rightmost column of Table 1 were inadvertently shifted relative to the other columns. This has now been corrected in the PDF and HTML versions of the Article.

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