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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

Millimeter-wave radar image analysis for the traffic sensing

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Journal of Physics: Conference Series 2020年第5期1507卷

作者： H M Wu F Qi J K Wang Y Wang School of communication science and engineering Northeastern University Liaoning Province Shenyang 110819 China Shenyang Institute of Automation Chinese Academy of Sciences China Institutes for Robotics and Intelligent Manufacturing Chinese Academy of Sciences China Key Laboratory of Opto-Electronic Information Processing Chinese Academy of Sciences China Key Lab of Image Understanding and Computer Vision Liaoning Province Shenyang 110016 China

Millimeter-wave(MMW) radar sensing is one of the most promising technologies to provide safe navigation for autonomous vehicles due to its expected high-resolution imaging capability However, driverless cars have higher request for different environment and light conditions. Therefore, millimetre-wave imaging is of paramount importance for complex load scenario. In this paper, we have built models of pavement pits and bulges and analysed their with differences ways of antennas. A comparison of the imaging performance of experimental systems operating at a MMW radar and a Lidar is presented with the analysis of features for initial image interpretation Experimental images of the complex road surface are made by a 94GHz frequency-modulated continuous-wave (FMCW) radar technique with 3mm wavelength.

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Robot Localisation and 3D Position Estimation Using a Free-Moving Camera and Cascaded Convolutional Neural Networks

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Robot Localisation and 3D Position Estimation Using a Free-M...

IEEE/ASME (AIM) International Conference on Advanced Intelligent Mechatronics

作者： Justinas Miseikis Patrick Knobelreiter Inka Brijacak Saeed Yahyanejad Kyrre Glette Ole Jakob Elle Jim Torresen Department of Informatics Universitv of Oslo Oslo Norway Institute of computer Graphics and Vision Graz University of Technology Graz Austria Joanneum Research - Robotics Klagenfurt am Worthersee Austria The Intervention Centre Oslo University Hospital Oslo Norway

Many works in collaborative robotics and human-robot interaction focuses on identifying and predicting human behaviour while considering the information about the robot itself as given. This can be the case when sensors and the robot are calibrated in relation to each other and often the reconfiguration of the system is not possible, or extra manual work is required. We present a deep learning based approach to remove the constraint of having the need for the robot and the vision sensor to be fixed and calibrated in relation to each other. The system learns the visual cues of the robot body and is able to localise it, as well as estimate the position of robot joints in 3D space by just using a 2D color image. The method uses a cascaded convolutional neural network, and we present the structure of the network, describe our own collected dataset, explain the network training and achieved results. A fully trained system shows promising results in providing an accurate mask of where the robot is located and a good estimate of its joints positions in 3D. The accuracy is not good enough for visual servoing applications yet, however, it can be sufficient for general safety and some collaborative tasks not requiring very high precision. The main benefit of our method is the possibility of the vision sensor to move freely. This allows it to be mounted on moving objects, for example, a body of the person or a mobile robot working in the same environment as the robots are operating in.

关键词： Robot kinematics Robot sensing systems Collision avoidance vision sensors Cameras Three-dimensional displays

Robot Localisation and 3D Position Estimation Using a Free-Moving Camera and Cascaded Convolutional Neural Networks

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arXiv 2018年

作者： Mišeikis, Justinas Knöbelreiter, Patrick Brijacak, Inka Yahyanejad, Saeed Glette, Kyrre Elle, Ole Jakob Torresen, Jim Department of Informatics University of Oslo Oslo Norway Institute of Computer Graphics and Vision Graz University of Technology Graz Austria Joanneum Research - Robotics Klagenfurt am Wörthersee Austria Intervention Centre Oslo University Hospital Oslo Norway

— Many works in collaborative robotics and human-robot interaction focuses on identifying and predicting human behaviour while considering the information about the robot itself as given. This can be the case when sensors and the robot are calibrated in relation to each other and often the reconfiguration of the system is not possible, or extra manual work is required. We present a deep learning based approach to remove the constraint of having the need for the robot and the vision sensor to be fixed and calibrated in relation to each other. The system learns the visual cues of the robot body and is able to localise it, as well as estimate the position of robot joints in 3D space by just using a 2D color image. The method uses a cascaded convolutional neural network, and we present the structure of the network, describe our own collected dataset, explain the network training and achieved results. A fully trained system shows promising results in providing an accurate mask of where the robot is located and a good estimate of its joints positions in 3D. The accuracy is not good enough for visual servoing applications yet, however, it can be sufficient for general safety and some collaborative tasks not requiring very high precision. The main benefit of our method is the possibility of the vision sensor to move freely. This allows it to be mounted on moving objects, for example, a body of the person or a mobile robot working in the same environment as the robots are operating in. Copyright © 2018, The Authors. All rights reserved.

关键词： Convolution

A Novel LOS Rate Estimation Method Based on Images for Strap-down Inertial Guidance

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Journal of Physics: Conference Series 2020年第1期1570卷

作者： Zheng Xu Haibo Luo Bin Hui Zheng Chang Shenyang Institute of Automation Chinese Academy of Sciences Shenyang 110016 China Tel.: +86-024-2397-0757 Institutes for Robotics and Intelligent Manufacturing Chinese Academy of Sciences Shenyang 110016 China University of Chinese Academy of Sciences Beijing 100049 China Key Laboratory of Opto-Electronic Information Processing Chinese Academy of Science Shenyang 110016 China The Key Lab of Image Understanding and Computer Vision Shenyang 110016 China

With the development of technology, precision guided weapon is becoming more and more important in modern war. In order to launch our recent guidance system on medium and small guided weapons, we propose a method to obtain the LOS rate by combining information from both camera and gyroscope. To be specific, we firstly calculate the body LOS angle through transforming the image pixel coordinate system into the image physical coordinate system according to camera internal parameters; then subtract the missile motion information contained in the measurement signal of the seeker and finally the LOS rate is deduced. Comparing with traditional gimballed seekers, our strap-down seekers with camera have significantly reduced costs and influences caused by external environments on platform.

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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

One-shot domain adaptation in multiple sclerosis lesion segmentation using convolutional neural networks

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arXiv 2018年

作者： Valverde, Sergi Salem, Mostafa Cabezas, Mariano Pareto, Deborah Vilanova, Joan C. Ramió-Torrentà, Lluís Rovira, Àlex Salvi, Joaquim Oliver, Arnau Lladó, Xavier Research institute of Computer Vision and Robotics University of Girona Spain Computer Science Department Faculty of Computers and Information Assiut University Egypt Magnetic Resonance Unit Dept of Radiology Vall d’Hebron University Hospital Spain Girona Magnetic Resonance Center Spain Multiple Sclerosis and Neuroimmunology Unit Dr. Josep Trueta University Hospital Spain

In recent years, several convolutional neural network (CNN) methods have been proposed for the automated white matter lesion segmentation of multiple sclerosis (MS) patient images, due to their superior performance compared with those of other state-of-the-art methods. However, the accuracies of CNN methods tend to decrease significantly when evaluated on different image domains compared with those used for training, which demonstrates the lack of adaptability of CNNs to unseen imaging data. In this study, we analyzed the effect of intensity domain adaptation on our recently proposed CNN-based MS lesion segmentation method. Given a source model trained on two public MS datasets, we investigated the transferability of the CNN model when applied to other MRI scanners and protocols, evaluating the minimum number of annotated images needed from the new domain and the minimum number of layers needed to re-train to obtain comparable accuracy. Our analysis comprised MS patient data from both a clinical center and the public ISBI2015 challenge database, which permitted us to compare the domain adaptation capability of our model to that of other state-of-the-art methods. In both datasets, our results showed the effectiveness of the proposed model in adapting previously acquired knowledge to new image domains, even when a reduced number of training samples was available in the target dataset. For the ISBI2015 challenge, our one-shot domain adaptation model trained using only a single image showed a performance similar to that of other CNN methods that were fully trained using the entire available training set, yielding a comparable human expert rater performance. We believe that our experiments will encourage the MS community to incorporate its use in different clinical settings with reduced amounts of annotated data. This approach could be meaningful not only in terms of the accuracy in delineating MS lesions but also in the related reductions in time and economic costs deri

关键词： Magnetic resonance imaging

Real-time Fish Detection in Trawl Nets

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Real-time Fish Detection in Trawl Nets

Oceans (Conference)

作者： R. Prados R. Garcia N. Gracias L. Neumann Havard Vagstol Computer Vision and Robotics Institute University of Girona Girona Spain ICREA Pg. Lluís Companys 23 Barcelona Spain Scantrol Deep Vision AS Bergen Norway

This work presents advances towards the development of the Deep vision system, consisting of a stereo camera setup attached to a trawl, which will make it possible to identify and measure the fish passing through without bringing them aboard the boat. This identification and measuring task requires a preprocessing in which the specimens should be segmented from the image background. Several lighting artifacts such as non-uniform illumination, shadows and reflections are some of the challenges to be addressed during the segmentation procedure. This paper describes the segmentation pipeline used to segment the fish from the background in an efficient and robust way.

关键词： Fish segmentation Trawl camera system HSV

Automated sub-cortical brain structure segmentation combining spatial and deep convolutional features

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arXiv 2017年

作者： Kushibar, Kaisar Valverde, Sergi González-Villà, Sandra Bernal, Jose Cabezas, Mariano Oliver, Arnau Lladó, Xavier Institute of Computer Vision and Robotics University of Girona Ed. P-IV Campus Montilivi University of Girona Girona17003 Spain

Sub-cortical brain structure segmentation in Magnetic Resonance Images (MRI) has attracted the interest of the research community for a long time because morphological changes in these structures are related to different neurodegenerative disorders. However, manual segmentation of these structures can be tedious and prone to variability, highlighting the need for robust automated segmentation methods. In this paper, we present a novel convolutional neural network based approach for accurate segmentation of the sub-cortical brain structures that combines both convolutional and prior spatial features for improving the segmentation accuracy. In order to increase the accuracy of the automated segmentation, we propose to train the network using a restricted sample selection to force the network to learn the most difficult parts of the structures. We evaluate the accuracy of the proposed method on the public MICCAI 2012 challenge and IBSR 18 datasets, comparing it with different available state-of-the-art methods and other recently proposed deep learning approaches. On the MICCAI 2012 dataset, our method shows an excellent performance comparable to the best challenge participant strategy, while performing significantly better than state-of-the-art techniques such as FreeSurfer and FIRST. On the IBSR 18 dataset, our method also exhibits a significant increase in the performance with respect to not only FreeSurfer and FIRST, but also comparable or better results than other recent deep learning approaches. Moreover, our experiments show that both the addition of the spatial priors and the restricted sampling strategy have a significant effect on the accuracy of the proposed method. In order to encourage the reproducibility and the use of the proposed method, a public version of our approach is available to download for the neuroimaging community. Copyright © 2017, The Authors. All rights reserved.

关键词： Convolution