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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

Webvision challenge: Visual learning and understanding with web data

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arXiv 2017年

作者： Li, Wen Wang, Limin Li, Wei Agustsson, Eirikur Berent, Jesse Gupta, Abhinav Sukthankar, Rahul van Gool, Luc Computer Vision Laboratory ETH Zurich Switzerland Google Research Zurich Switzerland Robotics Institute Carnegie Mellon University Pittsburgh United States Google Research United States

We present the 2017 Webvision Challenge, a public image recognition challenge designed for deep learning based on web images without instance-level human annotation. Following the spirit of previous vision challenges, such as ILSVRC [1], Places2 [2] and PASCAL VOC [3], which have played critical roles in the development of computer vision by contributing to the community with large scale annotated data for model designing and standardized benchmarking, we contribute with this challenge a large scale web images dataset, and a public competition with a workshop co-located with CVPR 2017. The Webvision dataset contains more than 2.4 million web images crawled from the Internet by using queries generated from the 1, 000 semantic concepts of the benchmark ILSVRC 2012 dataset. Meta information is also included. A validation set and test set containing human annotated images are also provided to facilitate algorithmic development. The 2017 Webvision challenge consists of two tracks, the image classification task on Webvision test set, and the transfer learning task on PASCAL VOC 2012 dataset. In this paper, we describe the details of data collection and annotation, highlight the characteristics of the dataset, and introduce the evaluation metrics. Copyright © 2017, The Authors. All rights reserved.

关键词： Image classification

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

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arXiv 2021年

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

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

关键词： Benchmarking

Sparse-then-Dense Alignment based 3D Map Reconstruction Method for Endoscopic Capsule Robots

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arXiv 2017年

作者： Turan, Mehmet Pilavci, Yusuf Yigit Ganiyusufoglu, Ipek Araujo, Helder Konukoglu, Ender Sitti, Metin Max Planck Institute for Intelligent Systems Stuttgart Germany Computer Vision Laboratory ETH Zurich Switzerland Robotics Laboratory University of Coimbra Portugal Electrical and Electronics Engineering Middle East Technical University Turkey Computer Science Faculty of Engineering and Natural Sciences Sabanci University Turkey

In the gastrointestinal (GI) tract endoscopy field, ingestible wireless capsule endoscopy is emerging as a novel, minimally invasive diagnostic technology for inspection of the GI tract and diagnosis of a wide range of diseases and pathologies. Since the development of this technology, medical device companies and many research groups have made substantial progress in converting passive capsule endoscopes to robotic active capsule endoscopes which can be controlled by the doctor. However, robotic capsule endoscopy still has some challenges. In particular, the use of such devices to generate a precise and globally consistent three-dimensional (3D) map of the entire inner organ remains an unsolved problem. Such global 3D maps of inner organs would help doctors to detect the location and size of diseased areas more accurately, precisely, and intuitively, thus permitting more accurate and intuitive diagnoses. The proposed 3D reconstruction system is built in a modular fashion including preprocessing, frame stitching, and shading-based 3D reconstruction modules. We propose an efficient scheme to automatically select the key frames out of the huge quantity of raw endoscopic images. Together with a bundle fusion approach that aligns Copyright © 2017, The Authors. All rights reserved.

关键词： Endoscopy

Comprehensive parameter sweep for learning-based detector on traffic lights 12th

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Comprehensive parameter sweep for learning-based detector on...

12th International Symposium on Visual Computing, ISVC 2016

作者： Jensen, Morten B. Philipsen, Mark P. Moeslund, Thomas B. Trivedi, Mohan Visual Analysis of People Laboratory Aalborg University Aalborg Denmark Computer Vision and Robotics Research Laboratory UC San Diego La Jolla United States

ISBN: (纸本)9783319508313

Determining the optimal parameters for a given detection algorithm is not straightforward and what ends up as the final values is mostly based on experience and heuristics. In this paper we investigate the influence of three basic parameters in the widely used Aggregate Channel Features (ACF) object detector applied for traffic light detection. Additionally, we perform an exhaustive search for the optimal parameters for the night time data from the LISA Traffic Light Dataset. The optimized detector reaches an Area-Under-Curve of 66.63% on calculated precision-recall curve. © Springer International Publishing AG 2016.

关键词： Optimization

Augmented Cognition via Brainwave Entrainment in Virtual Reality: An Open, Integrated Brain Augmentation in a Neuroscience System Approach

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Augmented Human Research 2017年第1期2卷 1-14页

作者： Emanuele Argento George Papagiannakis Eva Baka Michail Maniadakis Panos Trahanias Michael Sfakianakis Ioannis Nestoros Computational Vision and Robotics Laboratory Institute of Computer Science Foundation for Research and Technology Heraklion Greece Department of Computer Science University of Crete Heraklion Greece Department of Medicine University of Greece Heraklion Greece Department of Business Administration University of Piraeus Piraeus Greece Synchronal Amphiaraia University of Crete Snip-off Company Athens Greece

Building on augmented cognition theory and technology, our novel contribution in this work enables accelerated, certain brain functions related to task performance as well as their enhancement. We integrated in an open-source framework, latest immersive virtual reality (VR) head-mounted displays, with the Emotiv EPOC EEG headset in an open neuro- and biofeedback system for cognitive state detection and augmentation. Our novel methodology allows to significantly accelerate content presentation in immersive VR, while lowering brain frequency at alpha level—without losing content retention by the user. In our pilot experiments, we tested our innovative VR platform by presenting to N = 25 subjects a complex 3D maze test and different learning procedures for them on how to exit it. The subjects exposed to our VR-induced entrainment learning technology performed significantly better than those exposed to other “classical” learning procedures. In particular, cognitive task performance augmentation was measured for: learning time, complex navigational skills and decision-making abilities, orientation ability.

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Deep EndoVO: A recurrent convolutional neural network (RCNN) based visual odometry approach for endoscopic capsule robots

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arXiv 2017年

作者： Turan, Mehmet Almalioglu, Yasin Araujo, Helder Konukoglu, Ender Sitti, Metin Physical Intelligence Department Max Planck Institute for Intelligent Systems Germany Computer Engineering Department Bogazici Univesity Turkey Institute for Systems and Robotics Universidade de Coimbra Portugal Computer Vision Laboratory Department of Information Technology and Electrical Engineering ETH Zurich Switzerland

Ingestible wireless capsule endoscopy is an emerging minimally invasive diagnostic technology for inspection of the GI tract and diagnosis of a wide range of diseases and pathologies. Medical device companies and many research groups have recently made substantial progresses in converting passive capsule endoscopes to active capsule robots, enabling more accurate, precise, and intuitive detection of the location and size of the diseased areas. Since a reliable real time pose estimation functionality is crucial for actively controlled endoscopic capsule robots, in this study, we propose a monocular visual odometry (VO) method for endoscopic capsule robot operations. Our method lies on the application of the deep Recurrent Convolutional Neural Networks (RCNNs) for the visual odometry task, where Convolutional Neural Networks (CNNs) and Recurrent Neural Networks (RNNs) are used for the feature extraction and inference of dynamics across the frames, respectively. Detailed analyses and evaluations made on a real pig stomach dataset proves that our system achieves high translational and rotational accuracies for different types of endoscopic capsule robot trajectories. Copyright © 2017, The Authors. All rights reserved.

关键词： vision

A fully dense and globally consistent 3D map reconstruction approach for GI tract to enhance therapeutic relevance of the endoscopic capsule robot

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arXiv 2017年

作者： Turan, Mehmet Pilavci, Yusuf Yigit Jamiruddin, Redhwan Araujo, Helder Konukoglu, Ender Sitti, Metin Physical Intelligence Department Max-Planck Institute Stuttgart Germany Computer Vision Laboratory Eth Zentrum Zurich Switzerland Biomedical Engineering Department Martin-Luther Univeristy Halle-Wittenberg Halle Germany Robotics Institute Coimbro University

In the gastrointestinal (GI) tract endoscopy field, ingestible wireless capsule endoscopy is emerging as a novel, minimally invasive diagnostic technology for inspection of the GI tract and diagnosis of a wide range of diseases and pathologies. Since the development of this technology, medical device companies and many research groups have made substantial progress in converting passive capsule endoscopes to robotic active capsule endoscopes with most of the functionality of current active flexible endoscopes. However, robotic capsule endoscopy still has some challenges. In particular, the use of such devices to generate a precise three-dimensional (3D) mapping of the entire inner organ remains an unsolved problem. Such global 3D maps of inner organs would help doctors to detect the location and size of diseased areas more accurately and intuitively, thus permitting more reliable diagnoses. To our knowledge, this paper presents the first complete pipeline for a complete 3D visual map reconstruction of the stomach. The proposed pipeline is modular and includes a preprocessing module, an image registration module, and a final shape-from-shading-based 3D reconstruction module;the 3D map is primarily generated by a combination of image stitching and shape-from-shading techniques, and is updated in a frame-by-frame iterative fashion via capsule motion inside the stomach. A comprehensive quantitative analysis of the proposed 3D reconstruction method is performed using an esophagus gastro duodenoscopy simulator, three different endoscopic cameras, and a 3D optical scanner. Copyright © 2017, The Authors. All rights reserved.

关键词： Endoscopy

Mobile beacon control algorithm that ensures observability in single range navigation

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IFAC-PapersOnLine 2016年第23期49卷 48-53页

作者： Mandi, Filip Mikovi, Nikola Palomeras, Narcís Carreras, Marc Vallicrosa, Guillem University of Zagreb Faculty of Electrical Engineering and Computing LABUST - Laboratory for Underwater Systems and Technologies Unska 3 Zagreb Croatia Computer Vision and Robotics Institute Universitat de Girona Parc Cientfic i Tecnolgic UdG Girona17003 Spain

Mobile beacon vehicles are used as navigational aid for autonomous underwater vehicles when performing navigation using single range measurements. They remove the constraints imposed on the underwater vehicle trajectory by executing trajectory that provides persistent range measurements. In this paper, control algorithm for beacon vehicle which ensures observability of the underwater vehicle's navigation filter is presented. It is characterized by small communication overhead, low computational complexity and it is deployable on both fully actuated and underactuated vehicles. The algorithm was tested in real-life environment and the acquired experimental results show that despite the presence of uncertainties and communication delays, the algorithm accomplishes its task. © 2016

关键词： Marine navigation Autonomous underwater vehicles Kalman filters Navigation Observability Autonomous Vehicles Communication delays Communication overheads Low computational complexity Marine systems Navigation filters Underactuated vehicles Underwater vehicles