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MONAI: An open-source framework for deep learning in healthcare

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arXiv 2022年

作者： Cardoso, M. Jorge Li, Wenqi Brown, Richard Ma, Nic Kerfoot, Eric Wang, Yiheng Murrey, Benjamin Myronenko, Andriy Zhao, Can Yang, Dong Nath, Vishwesh He, Yufan Xu, Ziyue Hatamizadeh, Ali Zhu, Wentao Liu, Yun Zheng, Mingxin Tang, Yucheng Yang, Isaac Zephyr, Michael Hashemian, Behrooz Alle, Sachidanand Darestani, Mohammad Zalbagi Budd, Charlie Modat, Marc Vercauteren, Tom Wang, Guotai Li, Yiwen Hu, Yipeng Fu, Yunguan Gorman, Benjamin Johnson, Hans Genereaux, Brad Erdal, Barbaros S. Gupta, Vikash Diaz-Pinto, Andres Dourson, Andre Maier-Hein, Lena Jaeger, Paul F. Baumgartner, Michael Kalpathy-Cramer, Jayashree Flores, Mona Kirby, Justin Cooper, Lee A.D. Roth, Holger R. Xu, Daguang Bericat, David Floca, Ralf Zhou, S. Kevin Shuaib, Haris Farahani, Keyvan Maier-Hein, Klaus H. Aylward, Stephen Dogra, Prerna Ourselin, Sebastien Feng, Andrew School of Biomedical Engineering & Imaging Sciences King’s College London London United Kingdom NVIDIA Corporation Santa Clara and Bethesda United States School of Electrical and Computer Engineering Rice University Houston United States Department of Engineering Science University of Oxford Oxford United Kingdom Department of Medical Physics and Biomedical Engineering University College London London United Kingdom Department of BioAI InstaDeep Ltd London United Kingdom Department of Electrical & Computer Engineering University of Iowa Iowa City United States Mayo Clinic Jacksonville United States Mars Incorporated United States Div. Intelligent Medical Systems German Cancer Research Center Heidelberg Germany Division of Medical Image Computing German Cancer Research Center Heidelberg Germany Pattern Analysis and Learning Group Department of Radiation Oncology Heidelberg University Hospital Heidelberg Germany School of Biomedical Engineering Suzhou Institute for Advanced Research University of Science and Technology of China Suzhou China Department of Medical Physics Guy’s & St Thomas’ NHS Foundation Trust London United Kingdom National Cancer Institute Bethesda United States Kitware Inc. Clifton Park United States Department of Ophthalmology University of Colorado Aurora United States Frederick National Laboratory for Cancer Research Frederick United States Department of Pathology Northwestern University Chicago United States

Artificial Intelligence (AI) is having a tremendous impact across most areas of science. Applications of AI in healthcare have the potential to improve our ability to detect, diagnose, prognose, and intervene on human disease. For AI models to be used clinically, they need to be made safe, reproducible and robust, and the underlying software framework must be aware of the particularities (e.g. geometry, physiology, physics) of medical data being processed. This work introduces MONAI, a freely available, community-supported, and consortium-led PyTorch-based framework for deep learning in healthcare. MONAI extends PyTorch to support medical data, with a particular focus on imaging, and provide purpose-specific AI model architectures, transformations and utilities that streamline the development and deployment of medical AI models. MONAI follows best practices for software-development, providing an easy-to-use, robust, well-documented, and well-tested software framework. MONAI preserves the simple, additive, and compositional approach of its underlying PyTorch libraries. MONAI is being used by and receiving contributions from research, clinical and industrial teams from around the world, who are pursuing applications spanning nearly every aspect of healthcare. © 2022, CC BY.

关键词： Clinical research

Understanding metric-related pitfalls in image analysis validation

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arXiv 2023年

作者： Reinke, Annika Tizabi, Minu D. Baumgartner, Michael Eisenmann, Matthias Heckmann-Nötzel, Doreen Kavur, A. Emre Rädsch, Tim Sudre, Carole H. Acion, Laura Antonelli, Michela Arbel, Tal Bakas, Spyridon Benis, Arriel Blaschko, Matthew B. Buettner, Florian Cardoso, M. Jorge Cheplygina, Veronika Chen, Jianxu Christodoulou, Evangelia Cimini, Beth A. Collins, Gary S. Farahani, Keyvan Ferrer, Luciana Galdran, Adrian van Ginneken, Bram Glocker, Ben Godau, Patrick Haase, Robert Hashimoto, Daniel A. Hoffman, Michael M. Huisman, Merel Isensee, Fabian Jannin, Pierre Kahn, Charles E. Kainmueller, Dagmar Kainz, Bernhard Karargyris, Alexandros Karthikesalingam, Alan Kenngott, Hannes Kleesiek, Jens Kofler, Florian Kooi, Thijs Kopp-Schneider, Annette Kozubek, Michal Kreshuk, Anna Kurc, Tahsin Landman, Bennett A. Litjens, Geert Madani, Amin Maier-Hein, Klaus Martel, Anne L. Mattson, Peter Meijering, Erik Menze, Bjoern Moons, Karel G.M. Müller, Henning Nichyporuk, Brennan Nickel, Felix Petersen, Jens Rafelski, Susanne M. Rajpoot, Nasir Reyes, Mauricio Riegler, Michael A. Rieke, Nicola Saez-Rodriguez, Julio Sánchez, Clara I. Shetty, Shravya Summers, Ronald M. Taha, Abdel A. Tiulpin, Aleksei Tsaftaris, Sotirios A. van Calster, Ben Varoquaux, Gaël Yaniv, Ziv R. Jäger, Paul F. Maier-Hein, Lena Faculty of Mathematics and Computer Science Heidelberg University Heidelberg Germany Heidelberg Division of Intelligent Medical Systems Germany NCT Heidelberg A Partnership Between DKFZ University Medical Center Heidelberg Germany Heidelberg Division of Medical Image Computing Germany Heidelberg Division of Intelligent Medical Systems Germany MRC Unit for Lifelong Health and Ageing UCL Centre for Medical Image Computing Department of Computer Science University College London London United Kingdom School of Biomedical Engineering and Imaging Science King’s College London London United Kingdom Instituto de Cálculo CONICET – Universidad de Buenos Aires Buenos Aires Argentina Centre for Medical Image Computing University College London London United Kingdom McGill University Montreal Canada Division of Computational Pathology Dept of Pathology & Laboratory Medicine Indiana University School of Medicine IU Health Information and Translational Sciences Building Indianapolis United States University of Pennsylvania Richards Medical Research Laboratories FL7 PhiladelphiaPA United States Department of Digital Medical Technologies Holon Institute of Technology Holon Israel European Federation for Medical Informatics Le Mont-sur-Lausanne Switzerland Center for Processing Speech and Images Department of Electrical Engineering KU Leuven Leuven Belgium partner site Frankfurt/Mainz a partnership between DKFZ and UCT Frankfurt Marburg Germany Heidelberg Germany Goethe University Frankfurt Department of Medicine Germany Goethe University Frankfurt Department of Informatics Germany and Frankfurt Cancer Insititute Germany Department of Computer Science IT University of Copenhagen Copenhagen Denmark Leibniz-Institut für Analytische Wissenschaften – ISAS – e.V. Dortmund Germany Imaging Platform Broad Institute of MIT and Harvard CambridgeMA United States Centre for Statistics in Medicine University of Oxford Oxford United Kingdom Center for Biomedical In

Validation metrics are key for tracking scientific progress and bridging the current chasm between artificial intelligence (AI) research and its translation into practice. However, increasing evidence shows that particularly in image analysis, metrics are often chosen inadequately. While taking into account the individual strengths, weaknesses, and limitations of validation metrics is a critical prerequisite to making educated choices, the relevant knowledge is currently scattered and poorly accessible to individual researchers. Based on a multi-stage Delphi process conducted by a multidisciplinary expert consortium as well as extensive community feedback, the present work provides the first reliable and comprehensive common point of access to information on pitfalls related to validation metrics in image analysis. While focused on biomedical image analysis, the addressed pitfalls generalize across application domains and are categorized according to a newly created, domain-agnostic taxonomy. The work serves to enhance global comprehension of a key topic in image analysis validation. © 2023, CC BY.

关键词： computer vision

DAIS: Automatic Channel Pruning via Differentiable Annealing Indicator Search

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arXiv 2020年

作者： Guan, Yushuo Liu, Ning Zhao, Pengyu Che, Zhengping Bian, Kaigui Wang, Yanzhi Tang, Jian The School of Computer Science Peking University Beijing100871 China Midea Group Beijing100102 China The School of Computer Science National Engineering Laboratory for Big Data Analysis and Applications Peking University Beijing100871 China The Department of Electrical & Computer Engineering Northeastern University BostonMA02115 United States

The convolutional neural network has achieved great success in fulfilling computer vision tasks despite large computation overhead against efficient deployment. Channel pruning is usually applied to reduce the model redundancy while preserving the network structure, such that the pruned network can be easily deployed in practice. However, existing channel pruning methods require hand-crafted rules, which can result in a degraded model performance with respect to the tremendous potential pruning space given large neural networks. In this paper, we introduce Differentiable Annealing Indicator Search (DAIS) that leverages the strength of neural architecture search in the channel pruning and automatically searches for the effective pruned model with given constraints on computation overhead. Specifically, DAIS relaxes the binarized channel indicators to be continuous and then jointly learns both indicators and model parameters via bi-level optimization. To bridge the non-negligible discrepancy between the continuous model and the target binarized model, DAIS proposes an annealing-based procedure to steer the indicator convergence towards binarized states. Moreover, DAIS designs various regularizations based on a priori structural knowledge to control the pruning sparsity and to improve model performance. Experimental results show that DAIS outperforms state-of-the-art pruning methods on CIFAR-10, CIFAR-100, and imageNet. Copyright © 2020, The Authors. All rights reserved.

关键词： Annealing

The ZTF Source Classification Project: III. A Catalog of Variable Sources

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arXiv 2023年

作者： Healy, Brian F. Coughlin, Michael W. Mahabal, Ashish A. Laz, Theophile Jegou du Drake, Andrew Graham, Matthew J. Hillenbrand, Lynne A. van Roestel, Jan Szkody, Paula Zielske, LeighAnna Guiga, Mohammed Hassan, Muhammad Yusuf Hughes, Jill L. Nir, Guy Parikh, Saagar Park, Sungmin Purohit, Palak Rebbapragada, Umaa Reed, Draco Warshofsky, Daniel Wold, Avery Bloom, Joshua S. Masci, Frank J. Riddle, Reed Smith, Roger School of Physics and Astronomy University of Minnesota MinneapolisMN55455 United States Division of Physics Mathematics and Astronomy California Institute of Technology PasadenaCA91125 United States Center for Data Driven Discovery California Institute of Technology PasadenaCA91125 United States Department of Astronomy California Institute of Technology PasadenaCA91125 United States Anton Pannekoek Institute for Astronomy University of Amsterdam Amsterdam1090 GE Netherlands Department of Astronomy University of Washington SeattleWA98195 United States Department of Physics Pacific Lutheran University TacomaWA98447 United States Department of Computer Science and Engineering University of Minnesota MinneapolisMN55455 United States Department of Electrical Engineering Indian Institute of Technology Gandhinagar Gujarat 382055 India Department of Astronomy University of California BerkeleyCA94720 United States Lawrence Berkeley National Laboratory 1 Cyclotron Road MS 50B-4206 BerkeleyCA94720 United States Department of Electrical and Computer Engineering Carnegie Mellon University PittsburghPA15213 United States Computer Vision Imaging and Graphics Lab Indian Institute of Technology Gujarat Gandhinagar382055 India School of Statistics University of Minnesota MinneapolisMN55455 United States Division of Engineering and Applied Science California Institute of Technology PasadenaCA91125 United States Jet Propulsion Laboratory California Institute of Technology PasadenaCA91125 United States IPAC California Institute of Technology 1200 E. California Blvd. PasadenaCA91125 United States Caltech Optical Observatories California Institute of Technology PasadenaCA91125 United States

The classification of variable objects provides insight into a wide variety of astrophysics ranging from stellar interiors to galactic nuclei. The Zwicky Transient Facility (ZTF) provides time-series observations that record the variability of more than a billion sources. The scale of these data necessitates automated approaches to make a thorough analysis. Building on previous work, this paper reports the results of the ZTF Source Classification Project (SCoPe), which trains neural network and XGBoost machine-learning (ML) algorithms to perform dichotomous classification of variable ZTF sources using a manually constructed training set containing 170,632 light curves. We find that several classifiers achieve high precision and recall scores, suggesting the reliability of their predictions for 209,991,147 light curves across 77 ZTF fields. We also identify the most important features for XGB classification and compare the performance of the two ML algorithms, finding a pattern of higher precision among XGB classifiers. The resulting classification catalog is available to the public, and the software developed for SCoPe is open-source and adaptable to future time-domain surveys. Copyright © 2023, The Authors. All rights reserved.

关键词： Classification (of information)

Why is the winner the best?

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arXiv 2023年

作者： Eisenmann, M. Reinke, A. Weru, V. Tizabi, M.D. Isensee, F. Adler, T.J. Ali, S. Andrearczyk, V. Aubreville, M. Baid, U. Bakas, S. Balu, N. Bano, S. Bernal, J. Bodenstedt, S. Casella, A. Cheplygina, V. Daum, M. de Bruijne, M. Depeursinge, A. Dorent, R. Egger, J. Ellis, D.G. Engelhardt, S. Ganz, M. Ghatwary, N. Girard, G. Godau, P. Gupta, A. Hansen, L. Harada, K. Heinrich, M. Heller, N. Hering, A. Huaulmé, A. Jannin, P. Kavur, A.E. Kodym, O. Kozubek, M. Li, J. Li, H. Ma, J. Martín-Isla, C. Menze, B. Noble, A. Oreiller, V. Padoy, N. Pati, S. Payette, K. Rädsch, T. Rafael-Patiño, J. Bawa, V. Singh Speidel, S. Sudre, C.H. van Wijnen, K. Wagner, M. Wei, D. Yamlahi, A. Yap, M.H. Yuan, C. Zenk, M. Zia, A. Zimmerer, D. Aydogan, D. Bhattarai, B. Bloch, L. Brüngel, R. Cho, J. Choi, C. Dou, Q. Ezhov, I. Friedrich, C.M. Fuller, C. Gaire, R.R. Galdran, A. Faura, Á. García Grammatikopoulou, M. Hong, S. Jahanifar, M. Jang, I. Kadkhodamohammadi, A. Kang, I. Kofler, F. Kondo, S. Kuijf, H. Li, M. Luu, M. Martinčič, T. Morais, P. Naser, M.A. Oliveira, B. Owen, D. Pang, S. Park, J. Park, S. Plotka, S. Puybareau, E. Rajpoot, N. Ryu, K. Saeed, N. Shephard, A. Shi, P. Štepec, D. Subedi, R. Tochon, G. Torres, H.R. Urien, H. Vilaça, J.L. Wahid, K.A. Wang, H. Wang, J. Wang, L. Wang, X. Wiestler, B. Wodzinski, M. Xia, F. Xie, J. Xiong, Z. Yang, S. Yang, Y. Zhao, Z. Maier-Hein, K. Jäger, P.F. Kopp-Schneider, A. Maier-Hein, L. Heidelberg Germany Heidelberg Germany Faculty of Mathematics and Computer Science Heidelberg University Heidelberg Germany Heidelberg Germany Heidelberg Germany School of Computing Faculty of Engineering and Physical Sciences University of Leeds Leeds United Kingdom 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 University of Pennsylvania PhiladelphiaPA United States Department of Pathology and Laboratory Medicine Perelman School of Medicine University of Pennsylvania PhiladelphiaPA United States Department of Radiology Perelman School of Medicine University of Pennsylvania PhiladelphiaPA United States Department of Radiology University of Washington SeattleWA United States Department of Computer Science University College London London United Kingdom Universitat Autònoma de Barcelona & Computer Vision Center Barcelona Spain Dresden Dresden Germany Department of Advanced Robotics Istituto Italiano di Tecnologia Italy IT University of Copenhagen Copenhagen Denmark Department of General Visceral and Transplantation Surgery Heidelberg University Hospital Heidelberg Germany Biomedical Imaging Group Rotterdam Department of Radiology and Nuclear Medicine Erasmus MC Rotterdam Netherlands Department of Computer Science University of Copenhagen Copenhagen Denmark Sierre Switzerland Harvard Medical School Brigham and Women’s Hospital BostonMA United States School of Biomedical Engineering and Imaging Sciences King’s College London London United Kingdom Essen Germany University of Nebraska Medical Center OmahaNE United States Department of Internal Medicine III Heidelberg University Hospital Heidelberg Germany Neurobiology Research Unit Copenhagen University Hospital Rigshospitalet C

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 postprocessing (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. © 2023, CC BY.

关键词： Benchmarking

REFUGE2 CHALLENGE: A TREASURE TROVE FOR MULTI-DIMENSION analysis AND EVALUATION IN GLAUCOMA SCREENING

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arXiv 2022年

作者： Fang, Huihui Li, Fei Wu, Junde Fu, Huazhu Sun, Xu Son, Jaemin Yu, Shuang Zhang, Menglu Yuan, Chenglang Bian, Cheng Lei, Baiying Zhao, Benjian Xu, Xinxing Li, Shaohua Fumero, Francisco Sigut, José Almubarak, Haidar Bazi, Yakoub Guo, Yuanhao Zhou, Yating Baid, Ujjwal Innani, Shubham Guo, Tianjiao Yang, Jie Orlando, José Ignacio Bogunović, Hrvoje Zhang, Xiulan Xu, Yanwu The REFUGE2 Challenge Australia 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 Yatiris Group PLADEMA Institute CONICET UNICEN Tandil Argentina Christian Doppler Lab for Artificial Intelligence in Retina Department of Ophthalmology and Optometry Medical University of Vienna Vienna Austria VUNO Inc Seoul Korea Republic of Tencent HealthCare Tencent Shenzhen China Computer Vision Institute College of Computer Science and Software Engineering of Shenzhen University Shenzhen China School of Biomedical Engineering Health Science Center Shenzhen University China Xiaohe Healthcare ByteDance Guangdong Guangzhou510000 China School of Biomedical Engineering Shenzhen University China College of Computer Science & Software Engineering Shenzhen University China Department of Computer Science and Systems Engineering Universidad de La Laguna Spain Saudi Electronic University Saudi Arabia King Saud University Saudi Arabia Institute of Automation Chinese Academy of Sciences Beijing China University of Chinese Academy of Sciences Beijing China SGGS Institute of Engineering and Technology India Institute of Medical Robotics Shanghai Jiao Tong University China Institute of Image Processing and Pattern Recognition Shanghai Jiao Tong University China

With the rapid development of artificial intelligence (AI) in medical image processing, deep learning in color fundus photography (CFP) analysis is also evolving. Although there are some open-source, labeled datasets of CFPs in the ophthalmology community, large-scale datasets for screening only have labels of disease categories, and datasets with annotations of fundus structures are usually small in size. In addition, labeling standards are not uniform across datasets, and there is no clear information on the acquisition device. Here we release a multi-annotation, multi-quality, and multi-device color fundus image dataset for glaucoma analysis on an original challenge-Retinal Fundus Glaucoma Challenge 2nd Edition (REFUGE2). The REFUGE2 dataset contains 2000 color fundus images with annotations of glaucoma classification, optic disc/cup segmentation, as well as fovea localization. Meanwhile, the REFUGE2 challenge sets three sub-tasks of automatic glaucoma diagnosis and fundus structure analysis and provides an online evaluation framework. Based on the characteristics of multi-device and multi-quality data, some methods with strong generalizations are provided in the challenge to make the predictions more robust. This shows that REFUGE2 brings attention to the characteristics of real-world multi-domain data, bridging the gap between scientific research and clinical application. © 2022, CC BY-NC-ND.

关键词： Color

IRIS: Interactive real-time feedback image segmentation with deep learning

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IRIS: Interactive real-time feedback image segmentation with...

Medical Imaging 2020: Biomedical Applications in Molecular, Structural, and Functional Imaging

作者： Pepe, Antonio Schussnig, Richard Li, Jianning Gsaxner, Christina Chen, Xiaojun Fries, Thomas-Peter Egger, Jan Stanford University School of Medicine Department of Radiology 300 Pasteur Dr StanfordCA United States Graz University of Technology Institute of Computer Graphics and Vision Inffeldgasse 16c/II GrazA-8010 Austria Computer Algorithms for Medicine Laboratory GrazA-8010 Austria Graz University of Technology Institute of Structural Analysis Lessingstraße 25/II GrazA-8010 Austria Medical University of Graz Department of Oral and Maxillofacial Surgery Auenbruggerplatz 5/1 GrazA-8036 Austria Shanghai Jiao Tong University School of Mechanical Engineering 800 Dong Chuan Road Shanghai200240 China

ISBN: (纸本)9781510634015

Volumetric examinations of the aorta are nowadays of crucial importance for the management of critical pathologies such as aortic dissection, aortic aneurism, and other pathologies, which affect the morphology of the artery. These examinations usually begin with the acquisition of a Computed Tomography Angiography (CTA) scan from the patient, which is later on postprocessed to reconstruct the 3D geometry of the aorta. The first postprocessing step is referred to as segmentation. Different algorithms have been suggested for the segmentation of the aorta;including interactive methods, as well as fully automatic methods. Interactive methods need to be fine-tuned on each single CTA scan and result in longer duration of the process, whereas fully automatic methods require the possession of a large amount of labeled training data. In this work, we introduce a hybrid approach by combining a deep learning method with a consolidated interaction technique. In particular, we trained a 2D and a 3D U-Net on a limited number of patches extracted from 25 labeled CTA scans. Afterwards, we use an interactive approach, which consists in defining a region of interest (ROI) by just placing a seed point. This seed point is later used as the center of a 2D or 3D patch to be fed to the 2D or 3D U-Net, respectively. Due to the low content variation of these patches, this method allows to correctly segment the ROIs without the need for parameter tuning for each dataset and with a smaller training dataset, requiring the same minimal interaction as state-of-the-art interactive methods. Later on, the new segmented CTA scans can be further used to train a convolutional network for a fully automatic approach. © 2020 SPIE

关键词： Angiography

Why is the Winner the Best?

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Why is the Winner the Best?

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.

关键词：

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arXiv 2023年

作者： Bilgic, Berkin Costagli, Mauro Chan, Kwok-Shing Duyn, Jeff Langkammer, Christian Lee, Jongho Li, Xu Liu, Chunlei Marques, José P. Milovic, Carlos Robinson, Simon Schweser, Ferdinand Shmueli, Karin Spincemaille, Pascal Straub, Sina van Zijl, Peter Wang, Yi Martinos Center for Biomedical Imaging Massachusetts General Hospital Harvard Medical School CharlestownMA United States University of Genoa Genoa Italy Laboratory of Medical Physics and Magnetic Resonance IRCCS Stella Maris Pisa Italy Donders Institute for Brain Cognition and Behaviour Radboud University Nijmegen Netherlands Advanced MRI Section NINDS National Institutes of Health BethesdaMD United States Department of Neurology Medical University of Graz Graz Austria Department of Electrical and Computer Engineering Seoul National University Seoul Korea Republic of Russell H. Morgan Department of Radiology and Radiological Science Johns Hopkins University School of Medicine BaltimoreMD United States F.M. Kirby Research Center for Functional Brain Imaging Kennedy Krieger Institute BaltimoreMD United States Department of Electrical Engineering and Computer Sciences University of California BerkeleyCA United States Helen Wills Neuroscience Institute University of California BerkeleyCA United States Pontificia Universidad Catolica de Valparaiso Valparaiso Chile High Field MR Centre Department of Biomedical Imaging and Image-Guided Therapy Medical University of Vienna Austria Buffalo Neuroimaging Analysis Center Department of Neurology Jacobs School of Medicine and Biomedical Sciences the University at Buffalo BuffaloNY United States Center for Biomedical Imaging Clinical and Translational Science Institute the University at Buffalo BuffaloNY United States Department of Medical Physics and Biomedical Engineering University College London London United Kingdom MRI Research Institute Department of Radiology Weill Cornell Medicine New YorkNY United States Department of Radiology Mayo Clinic JacksonvilleFL United States MRI Research Institute Departments of Radiology and Biomedical Engineering Cornell University New YorkNY United States

This article provides recommendations for implementing quantitative susceptibility mapping (QSM) for clinical brain research. It is a consensus of the ISMRM Electro-Magnetic Tissue Properties Study Group. While QSM technical development continues to advance rapidly, the current QSM methods have been demonstrated to be repeatable and reproducible for generating quantitative tissue magnetic susceptibility maps in the brain. However, the many QSM approaches available give rise to the need in the neuroimaging community for guidelines on implementation. This article describes relevant considerations and provides specific implementation recommendations for all steps in QSM data acquisition, processing, analysis, and presentation in scientific publications. We recommend that data be acquired using a monopolar 3D multi-echo GRE sequence, that phase images be saved and exported in DICOM format and unwrapped using an exact unwrapping approach. Multi-echo images should be combined before background removal, and a brain mask created using a brain extraction tool with the incorporation of phase-quality-based masking. Background fields should be removed within the brain mask using a technique based on SHARP or PDF, and the optimization approach to dipole inversion should be employed with a sparsity-based regularization. Susceptibility values should be measured relative to a specified reference, including the common reference region of whole brain as a region of interest in the analysis, and QSM results should be reported with – as a minimum – the acquisition and processing specifications listed in the last section of the article. These recommendations should facilitate clinical QSM research and lead to increased harmonization in data acquisition, analysis, and reporting. © 2023, CC BY.

关键词： Magnetic resonance imaging