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Cancer nanomedicine meets immunotherapy: opportunities and challenges

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中国药理学报（英文版） 2020年第7期41卷 954-958页

作者： Qingxue Sun Xiangyang Bai Alexandros Marios Sofias Roy van der Meel Eduardo Ruiz-Hernandez Gert Storm Wim E.Hennink Bruno De Geest Fabian Kiessling Hai-jun Yu Twan Lammers Yang Shi Institute for Experimental Molecular Imaging Uniklinik RWTH Aachen and Helmholtz Institute for Biomedical Engineering Faculty of Medicine RWTH Aachen University AachenGermany Laboratory of Chemical Biology Department of Biomedical Engineering and Institute for Complex Molecular Systems Eindhoven University of Technology EindhovenThe Netherlands School of Pharmacy and Pharmaceutical Sciences Trinity College Dublin Dublin Ireland Department of Pharmaceutics Utrecht Institute for Pharmaceutical Sciences Utrecht University Utrecht The Netherlands Department of Targeted Therapeutics MIRA Institute for Biomedical Technology and Technical Medicine University of Twente Enschede The Netherlands Department of Pharmaceutics Ghent University Ghent Belgium Fraunhofer MEVlS Institute for Medical Image Computing AachenGermany State Key Laboratory of Drug Research & Center of Pharmaceutics Shanghai Institute of Materia Medica Chinese Academy of Sciences Shanghai 201203 China

Cancer nanomedicines have shown promise in combination immunotherapy,thus far mostly preclinically but also already in clinical *** nanomedicines with immunotherapy aims to reinforce the cancer-immunity cycle,via potentiating key steps in the immune reaction cascade,namely antigen release,antigen processing,antigen presentation,and immune cell-mediated *** nano-immunotherapy can be realized via three targeting strategies,i.e.,by targeting cancer cells,targeting the tumor immune microenvironment,and targeting the peripheral immune *** clinical potential of nano-immunotherapy has recently been demonstrated in a phase Ⅲ trial in which nano-albumin paclitaxel (Abraxane(R)) was combined with atezolizumab (Tecentriq(R)) for the treatment of patients suffering from advanced triple-negative breast *** the present paper,besides strategies and initial (pre)clinical success stories,we also discuss several key challenges in *** together,nanomedicines combined with immunotherapy are gaining significant attention,and it is anticipated that they will play an increasingly important role in clinical cancer therapy.

关键词： nanomedicine immunotherapy targeting combination therapy clinical translation

NIMG-22. AN AI-BASED COORDINATE SYSTEM ELUCIDATES RADIOGENOMIC HETEROGENEITY OF GLIOBLASTOMA VIA DEEP LEARNING AND MANIFOLD EMBEDDINGS

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Neuro-Oncology 2022年第SUPPLEMENT_7期24卷 vii166–vii166页

作者： Yu, Fanyang Kazerooni, Anahita Fathi Toorens, Erik Akbari, Hamed Sako, Chiharu Mamourian, Elizabeth Bagley, Stephen Binder, Zev A Lustig, Robert A Brem, Steven O’Rourke, Donald M Ganguly, Tapan Bakas, Spyridon Nasrallah, MacLean Chaudhari, Pratik Davatzikos, Christos Center for Biomedical Image Computing and Analytics and Department of Bioengineering University of Pennsylvania Philadelphia PA USA Center for Biomedical Image Computing and Analytics and Department of Radiology Perelman School of Medicine University of Pennsylvania Philadelphia PA USA University of Pennsylvania Philadelphia USA University of Pennsylvania Philadelphia PA USA Hospital of the University of Pennsylvania Philadelphia PA USA Hospital of the University of Pennsylvania Philadelphia USA University of Pennsylvania Phildelphia USA Center for Biomedical Image Computing and Analytics Department of Radiology and Department of Pathology and Laboratory Medicine Perelman School of Medicine University of Pennsylvania Philadelphia PA USA Department of Pathology and Laboratory Medicine Perelman School of Medicine University of Pennsylvania Philadelphia PA USA Department of Electrical and Systems Engineering University of Pennsylvania Philadelphia USA

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

Disorganization of language and working memory systems in frontal versus temporal lobe epilepsy

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Brain 2023年第3期146卷 935-953页

作者： Caciagli, Lorenzo Paquola, Casey He, Xiaosong Vollmar, Christian Centeno, Maria Wandschneider, Britta Braun, Urs Trimmel, Karin Vos, Sjoerd B. Sidhu, Meneka K. Thompson, Pamela J. Baxendale, Sallie Winston, Gavin P. Duncan, John S. Bassett, Dani S. Koepp, Matthias J. Bernhardt, Boris C. Department of Bioengineering University of Pennsylvania 240 Skirkanich Hall 210 South 33rd Street Philadelphia 19104 PA United States Department of Clinical and Experimental Epilepsy UCL Queen Square Institute of Neurology London WC1N 3BG United Kingdom MRI Unit Epilepsy Society Chalfont St Peter Buckinghamshire SL9 0RJ United Kingdom Multimodal Imaging and Connectome Analysis Laboratory McConnell Brain Imaging Centre Montreal Neurological Institute Montreal H3A 2B4 QC Canada Department of Neurology Ludwig-Maximilians-Universität Munich 81377 Germany Epilepsy Unit Hospital Clínic de Barcelona IDIBAPS Barcelona 08036 Spain Department of Psychiatry and Psychotherapy Central Institute of Mental Health Medical Faculty Mannheim University of Heidelberg Mannheim Germany Department of Neurology Medical University of Vienna Vienna Austria Centre for Medical Image Computing University College London London United Kingdom Neuroradiological Academic Unit UCL Queen Square Institute of Neurology University College London London United Kingdom Department of Medicine Division of Neurology Queen's University Kingston ON Canada Department of Physics and Astronomy University of Pennsylvania Philadelphia 19104 PA United States Department of Electrical and Systems Engineering University of Pennsylvania Philadelphia 19104 PA United States Department of Neurology University of Pennsylvania Philadelphia 19104 PA United States Department of Psychiatry University of Pennsylvania Philadelphia 19104 PA United States Santa Fe Institute Santa Fe 87501 NM United States

Cognitive impairment is a common comorbidity of epilepsy and adversely impacts people with both frontal lobe (FLE) and temporal lobe (TLE) epilepsy. While its neural substrates have been investigated extensively in TLE, functional imaging studies in FLE are scarce. In this study, we profiled the neural processes underlying cognitive impairment in FLE and directly compared FLE and TLE to establish commonalities and differences. We investigated 172 adult participants (56 with FLE, 64 with TLE and 52 controls) using neuropsychological tests and four functional MRI tasks probing expressive language (verbal fluency, verb generation) and working memory (verbal and visuo-spatial). Patient groups were comparable in disease duration and anti-seizure medication load. We devised a multiscale approach to map brain activation and deactivation during cognition and track reorganization in FLE and TLE. Voxel-based analyses were complemented with profiling of task effects across established motifs of functional brain organization: (i) canonical resting-state functional systems;and (ii) the principal functional connectivity gradient, which encodes a continuous transition of regional connectivity profiles, anchoring lower-level sensory and transmodal brain areas at the opposite ends of a spectrum. We show that cognitive impairment in FLE is associated with reduced activation across attentional and executive systems, as well as reduced deactivation of the default mode system, indicative of a large-scale disorganization of task-related recruitment. The imaging signatures of dysfunction in FLE are broadly similar to those in TLE, but some patterns are syndrome-specific: altered default-mode deactivation is more prominent in FLE, while impaired recruitment of posterior language areas during a task with semantic demands is more marked in TLE. Functional abnormalities in FLE and TLE appear overall modulated by disease load. On balance, our study elucidates neural processes underlying langua

关键词： cognition fMRI frontal lobe epilepsy multiscale functional mapping temporal lobe epilepsy

Automatic Detection of ECG Abnormalities by Using an Ensemble of Deep Residual Networks with Attention 1st

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Automatic Detection of ECG Abnormalities by Using an Ensembl...

1st International Workshop on Machine Learning and Medical Engineering for Cardiovasvular Healthcare, MLMECH 2019, and the 8th International Joint Workshops on computing and Visualization for Intravascular Imaging and Computer Assisted Stenting, CVII-STENT 2019, held in conjunction with 22nd International Conference on Medical image computing and Computer-Assisted Intervention, MICCAI 2019

作者： Liu, Yang He, Runnan Wang, Kuanquan Li, Qince Sun, Qiang Zhao, Na Zhang, Henggui Harbin150001 China School of Physics and Astronomy The University of Manchester ManchesterM13 9PL United Kingdom SPACEnter Space Science and Technology Institute Shenzhen518117 China International Laboratory for Smart Systems and Key Laboratory of Intelligent of Computing in Medical Image Ministry of Education Northeastern University Shenyang110004 China The Department of Pharmacology Beijing Electric Power Hospital Beijing100073 China

ISBN: (纸本)9783030333263

Heart disease is one of the most common diseases causing morbidity and mortality. Electrocardiogram (ECG) has been widely used for diagnosing heart diseases for its simplicity and non-invasive property. Automatic ECG analyzing technologies are expected to reduce human working load and increase diagnostic efficacy. However, there are still some challenges to be addressed for achieving this goal. In this study, we develop an algorithm to identify multiple abnormalities from 12-lead ECG recordings. In the algorithm pipeline, several preprocessing methods are firstly applied on the ECG data for denoising, augmentation and balancing recording numbers of variant classes. In consideration of efficiency and consistency of data length, the recordings are padded or truncated into a medium length, where the padding/truncating time windows are selected randomly to suppress overfitting. Then, the ECGs are used to train deep neural network (DNN) models with a novel structure that combines a deep residual network with an attention mechanism. Finally, an ensemble model is built based on these trained models to make predictions on the test data set. Our method is evaluated based on the test set of the First China ECG Intelligent Competition dataset by using the F1 metric that is regarded as the harmonic mean between the precision and recall. The resultant overall F1 score of the algorithm is 0.875, showing a promising performance and potential for practical use. © 2019, Springer Nature Switzerland AG.

关键词： Electrocardiograms

Hyperspectral image Classification with Spatial Consistence Using Fully Convolutional Spatial Propagation Network

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arXiv 2020年

作者： Jiang, Yenan Li, Ying Zou, Shanrong Zhang, Haokui Bai, Yunpeng School of Computer Science National Engineering Laboratory for Integrated Aero-Space-Ground-Ocean Big Data Application Technology Shaanxi Provincial Key Laboratory of Speech and Image Information Processing Northwestern Polytechnical University Xi’an710129 China School of Computer Science University of Adelaide AdelaideSA5005 Australia National Key Laboratory of Science and Technology on Space Microwave Xi’an710000 China School of Computing and Information Systems University of Melbourne MelbourneVIC3010 Australia

In recent years, deep convolutional neural networks (CNNs) have demonstrated impressive ability to represent hyperspectral images (HSIs) and achieved encouraging results in HSI classification. However, the existing CNN-based models operate at the patch-level, in which pixel is separately classified into classes using a patch of images around it. This patch-level classification will lead to a large number of repeated calculations, and it is hard to identify the appropriate patch size that is beneficial to classification accuracy. In addition, the conventional CNN models operate convolutions with local receptive fields, which cause the failure of contextual spatial information modeling. To overcome these aforementioned limitations, we propose a novel end-to-end, pixel-to-pixel fully convolutional spatial propagation network (FCSPN) for HSI classification. Our FCSPN consists of a 3D fully convolution network (3D-FCN) and a convolutional spatial propagation network (CSPN). Specifically, the 3D-FCN is firstly introduced for reliable preliminary classification, in which a novel dual separable residual (DSR) unit is proposed to effectively capture spectral and spatial information simultaneously with fewer parameters. Moreover, the channel-wise attention mechanism is adapted in the 3D-FCN to grasp the most informative channels from redundant channel information. Finally, the CSPN is introduced to capture the spatial correlations of HSI via learning a local linear spatial propagation, which allows maintaining the HSI spatial consistency and further refining the classification results. Experimental results on three HSI benchmark datasets demonstrate that the proposed FCSPN achieves state-of-the-art performance on HSI classification. Copyright © 2020, The Authors. All rights reserved.

关键词： Convolution

Metrics Reloaded: Recommendations for image analysis validation

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arXiv 2022年

作者： Maier-Hein, Lena Reinke, Annika Godau, Patrick Tizabi, Minu D. Buettner, Florian Christodoulou, Evangelia Glocker, Ben Isensee, Fabian Kleesiek, Jens Kozubek, Michal Reyes, Mauricio Riegler, Michael A. Wiesenfarth, Manuel Emre Kavur, A. Sudre, Carole H. Baumgartner, Michael Eisenmann, Matthias Heckmann-Nötzel, Doreen Rädsch, Tim Acion, Laura Antonelli, Michela Arbel, Tal Bakas, Spyridon Benis, Arriel Blaschko, Matthew B. Jorge Cardoso, M. Cheplygina, Veronika Cimini, Beth A. Collins, Gary S. Farahani, Keyvan Ferrer, Luciana Galdran, Adrian Ginneken, Bram Van Haase, Robert Hashimoto, Daniel A. Hoffman, Michael M. Huisman, Merel Jannin, Pierre Kahn, Charles E. Kainmueller, Dagmar Kainz, Bernhard Karargyris, Alexandros Karthikesalingam, Alan Kenngott, Hannes Kofler, Florian Kopp-Schneider, Annette 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 Rajpoot, Nasir Rieke, Nicola Saez-Rodriguez, Julio Sánchez, Clara I. Shetty, Shravya Smeden, Maarten Van Summers, Ronald M. Taha, Abdel A. Tiulpin, Aleksei Tsaftaris, Sotirios A. Calster, Ben Van Varoquaux, Gaël Jäger, Paul F. Heidelberg Division of Intelligent Medical Systems and HI Helmholtz Imaging Germany Faculty of Mathematics and Computer Science and Medical Faculty Heidelberg University Heidelberg Germany NCT Heidelberg a partnership between DKFZ University Medical Center Heidelberg Germany Faculty of Mathematics and Computer Science Heidelberg University Heidelberg Germany Heidelberg Division of Intelligent Medical Systems Germany partner site Frankfurt/Mainz a partnership between DKFZ and UCT Frankfurt-Marburg Germany Heidelberg Goethe University Frankfurt Germany Department of Medicine Goethe University Frankfurt Germany Department of Informatics Frankfurt Cancer Insititute Germany Department of Computing Imperial College London London United Kingdom Heidelberg Division of Medical Image Computing and HI Applied Computer Vision Lab Germany Institute for AI in Medicine University Medicine Essen Essen Germany Centre for Biomedical Image Analysis Faculty of Informatics Masaryk University Brno Czech Republic ARTORG Center for Biomedical Engineering Research University of Bern Bern Switzerland Department of Radiation Oncology University Hospital Bern University of Bern Bern Switzerland Simula Metropolitan Center for Digital Engineering Oslo Norway UiT The Arctic University of Norway Romsø Norway Heidelberg Division of Biostatistics Germany Heidelberg Division of Intelligent Medical Systems Division of Medical Image Computing HI Applied Computer Vision Lab 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 Heidelberg Division of Medical Image Computing Germany Instituto de Cálculo CONICET – Universidad de Buenos Aires Buenos Aires Argentina Centre for Medical Image Computing University College London London United Kingdom McGill University Montréal

Increasing evidence shows that flaws in machine learning (ML) algorithm validation are an underestimated global problem. Particularly in automatic biomedical image analysis, chosen performance metrics often do not reflect the domain interest, thus failing to adequately measure scientific progress and hindering translation of ML techniques into practice. To overcome this, we created Metrics Reloaded, a comprehensive framework guiding researchers in the problem-aware selection of metrics. It was developed by a large international consortium in a multi-stage Delphi process and is based on the novel concept of a problem fingerprint – a structured representation of the given problem that captures all aspects that are relevant for metric selection, from the domain interest to the properties of the target structure(s), data set and algorithm output. Based on the problem fingerprint, users are guided through the process of choosing and applying appropriate validation metrics while being made aware of potential pitfalls. Metrics Reloaded targets image analysis problems that can be interpreted as a classification task at image, object or pixel level, namely image-level classification, object detection, semantic segmentation, and instance segmentation tasks. To improve the user experience, we implemented the framework in the Metrics Reloaded online tool. Following the convergence of ML methodology across application domains, Metrics Reloaded fosters the convergence of validation methodology. Its applicability is demonstrated for various biomedical use cases. © 2022, CC BY.

关键词： Semantic Segmentation

Learning data-adaptive non-parametric kernels

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The Journal of Machine Learning Research

The Journal of Machine Learning Research 2020年第1期21卷 8590-8628页

作者： Fanghui Liu Xiaolin Huang Chen Gong Jie Yang Li Li Department of Electrical Engineering ESAT-STADIUS KU Leuven Belgium Institute of Image Processing and Pattern Recognition Institute of Medical Robotics Shanghai Jiao Tong University Shanghai China PCA Lab Key Laboratory of Intelligent Perception and Systems for High-Dimensional Information of Ministry of Education School of Computer Science and Engineering Nanjing University of Science and Technology China and Department of Computing Hong Kong Polytechnic University Hong Kong SAR China Department of Automation BNRist Tsinghua University China

In this paper, we propose a data-adaptive non-parametric kernel learning framework in margin based kernel methods. In model formulation, given an initial kernel matrix, a data-adaptive matrix with two constraints is imposed in an entry-wise scheme. Learning this data-adaptive matrix in a formulation-free strategy enlarges the margin between classes and thus improves the model flexibility. The introduced two constraints are imposed either exactly (on small data sets) or approximately (on large data sets) in our model, which provides a controllable trade-off between model flexibility and complexity with theoretical demonstration. In algorithm optimization, the objective function of our learning framework is proven to be gradient-Lipschitz continuous. Thereby, kernel and classifier/regressor learning can be efficiently optimized in a unified framework via Nesterov's acceleration. For the scalability issue, we study a decomposition-based approach to our model in the large sample case. The effectiveness of this approximation is illustrated by both empirical studies and theoretical guarantees. Experimental results on various classification and regression benchmark data sets demonstrate that our non-parametric kernel learning framework achieves good performance when compared with other representative kernel learning based algorithms.

关键词： support vector machines non-parametric kernel learning gradient-Lipschitz continuous

Common Limitations of image Processing Metrics: A Picture Story

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arXiv 2021年

作者： Reinke, Annika Tizabi, Minu D. Sudre, Carole H. Eisenmann, Matthias Rädsch, Tim Baumgartner, Michael Acion, Laura Antonelli, Michela Arbel, Tal Bakas, Spyridon Bankhead, Peter Benis, Arriel Blaschko, Matthew Buettner, Florian Cardoso, M. Jorge Chen, Jianxu Cheplygina, Veronika Christodoulou, Evangelia Cimini, Beth A. Collins, Gary S. Engelhardt, Sandy Farahani, Keyvan Ferrer, Luciana Galdran, Adrian van Ginneken, Bram Glocker, Ben Godau, Patrick Haase, Robert Hamprecht, Fred Hashimoto, Daniel A. Heckmann-Nötzel, Doreen Hirsch, Peter Hoffman, Michael M. Huisman, Merel Isensee, Fabian Jannin, Pierre Kahn, Charles E. Kainmueller, Dagmar Kainz, Bernhard Karargyris, Alexandros Karthikesalingam, Alan Kavur, A. Emre Kenngott, Hannes Kleesiek, Jens Kleppe, Andreas Koehler, Sven Kofler, Florian Kopp-Schneider, Annette Kooi, Thijs 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 Moher, David Moons, Karel G.M. Müller, Henning Nichyporuk, Brennan Nickel, Felix Noyan, M. Alican Petersen, Jens Polat, Gorkem Rafelski, Susanne M. Rajpoot, Nasir Reyes, Mauricio Rieke, Nicola Riegler, Michael A. Rivaz, Hassan Saez-Rodriguez, Julio Sánchez, Clara I. Schroeter, Julien Saha, Anindo Selver, M. Alper Sharan, Lalith Shetty, Shravya Smeden, Maarten V.A.N. Stieltjes, Bram Summers, Ronald M. Taha, Abdel A. Tiulpin, Aleksei Tsaftaris, Sotirios A. Calster, Ben V.A.N. Varoquaux, Gaël Wiesenfarth, Manuel Yaniv, Ziv R. Jäger, Paul Maier-Hein, Lena Division of Intelligent Medical Systems and HI Helmholtz Imaging Heidelberg Germany Faculty of Mathematics and Computer Science Heidelberg University Heidelberg Germany Division of Intelligent Medical Systems Heidelberg Germany NCT Heidelberg DKFZ University Medical Center Heidelberg 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 Division of Medical Image Computing Heidelberg Germany Instituto de Cálculo CONICET – Universidad de Buenos Aires Buenos Aires Argentina Centre for Medical Image Computing University College London London United Kingdom McGill University Montréal 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 Institute of Genetics and Cancer University of Edinburgh Edinburgh United Kingdom 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 Kasteelpark Arenberg 10 - box 2441 Leuven3001 Belgium Frankfurt/Mainz DKFZ UCT Frankfurt-Marburg Germany Heidelberg Germany Goethe University Frankfurt Department of Medicine Germany Goethe University Frankfurt Department of Informatics Germany Frankfurt Cancer Insititute Germany Leibniz-Institut für Analytische Wissenschaften – ISAS – e.V. Dortmund Germany Department of Computer Science IT University of Copenhagen Copenhagen Denmark Imaging Platform Broad Institute of MIT and Harvard CambridgeMA United States Centre for St

While the importance of automatic image analysis is continuously increasing, recent meta-research revealed major flaws with respect to algorithm validation. Performance metrics are particularly key for meaningful, objective, and transparent performance assessment and validation of the used automatic algorithms, but relatively little attention has been given to the practical pitfalls when using specific metrics for a given image analysis task. These are typically related to (1) the disregard of inherent metric properties, such as the behaviour in the presence of class imbalance or small target structures, (2) the disregard of inherent data set properties, such as the non-independence of the test cases, and (3) the disregard of the actual biomedical domain interest that the metrics should reflect. This living dynamically document has the purpose to illustrate important limitations of performance metrics commonly applied in the field of image analysis. In this context, it focuses on biomedical image analysis problems that can be phrased as image-level classification, semantic segmentation, instance segmentation, or object detection task. The current version is based on a Delphi process on metrics conducted by an international consortium of image analysis experts from more than 60 institutions worldwide. © 2021, CC BY.

关键词： Medical imaging