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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

Low-dose CT denoising with convolutional neural network 14

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Low-dose CT denoising with convolutional neural network

14th IEEE International Symposium on Biomedical Imaging, ISBI 2017

作者： Chen, Hu Zhang, Yi Zhang, Weihua Liao, Peixi Li, Ke Zhou, Jiliu Wang, Ge College of Computer Science Sichuan University Chengdu610065 China National Key Laboratory of Fundamental Science on Synthetic Vision Sichuan University Chengdu610065 China Department of Scientific Research and Education Sixth People's Hospital of Chengdu Chengdu610065 China Department of Biomedical Engineering Rensselaer Polytechnic Institute TroyNY12180 United States

ISBN: (纸本)9781509011711

To reduce the potential radiation risk, low-dose CT has attracted much attention. However, simply lowering the radiation dose will lead to significant deterioration of the image quality. In this paper, we propose a noise reduction method for low-dose CT via deep neural network without accessing original projection data. A deep convolutional neural network is trained to transform low-dose CT images towards normal-dose CT images, patch by patch. Visual and quantitative evaluation demonstrates a competing performance of the proposed method. © 2017 IEEE.

关键词： Convolution

The 2017 DAVIS challenge on video object segmentation

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arXiv 2017年

作者： Pont-Tuset, Jordi Perazzi, Federico Caelles, Sergi Arbeláez, Pablo Sorkine-Hornung, Alexander Gool, Luc Van Computer Vision Laboratory Eth Zürich Switzerland Switzerland Disney Research Zürich Switzerland Department of Biomedical Engineering Universidad de Los Andes

We present the 2017 DAVIS Challenge on Video Object Segmentation, a public dataset, benchmark, and competition specifically designed for the task of video object segmentation. Following the footsteps of other successful initiatives, such as ILSVRC [1] and PASCAL VOC [2], which established the avenue of research in the fields of scene classification and semantic segmentation, the DAVIS Challenge comprises a dataset, an evaluation methodology, and a public competition with a dedicated workshop co-located with CVPR 2017. The DAVIS Challenge follows up on the recent publication of DAVIS (Densely-Annotated VIdeo Segmentation [3]), which has fostered the development of several novel state-of-the-art video object segmentation techniques. In this paper we describe the scope of the benchmark, highlight the main characteristics of the dataset, define the evaluation metrics of the competition, and present a detailed analysis of the results of the participants to the challenge. Copyright © 2017, The Authors. All rights reserved.

关键词： Semantics

Evaluation of algorithms for multi-modality whole heart segmentation: An open-access grand challenge

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arXiv 2019年

作者： Zhuang, Xiahai Li, Lei Payer, Christian Štern, Darko Urschler, Martin Heinrich, Mattias P. Oster, Julien Wang, Chunliang Smedby, Örjan Bian, Cheng Yang, Xin Heng, Pheng-Ann Mortazi, Aliasghar Bagci, Ulas Yang, Guanyu Sun, Chenchen Galisot, Gaetan Ramel, Jean-Yves Brouard, Thierry Tong, Qianqian Si, Weixin Liao, Xiangyun Zeng, Guodong Shi, Zenglin Zheng, Guoyan Wang, Chengjia MacGillivray, Tom Newby, David Rhode, Kawal Ourselin, Sebastien Mohiaddin, Raad Keegan, Jennifer Firmin, David Yang, Guang School of Data Science Fudan University Shanghai200433 China Fudan-Xinzailing Joint Research Center for Big Data Fudan University Shanghai200433 China School of Biomedical Engineering Shanghai Jiao Tong University Shanghai200240 China Institute of Computer Graphics and Vision Graz University of Technology Graz8010 Austria Ludwig Boltzmann Institute for Clinical Forensic Imaging Graz8010 Austria Institute of Medical Informatics University of Lubeck Lubeck23562 Germany Inserm Université de Lorraine U1254 IADI Nancy France School for Technology and Health KTH Royal Institute of Technology StockholmSE-10044 Sweden School of Biomed. Eng. Health Science Centre Shenzhen University Shenzhen518060 China Dept. of Comp. Sci. and Eng. Chinese University of Hong Kong Hong Kong China University of Central Florida Orlando32816 United States School of Computer Science and Engineering Southeast University Nanjing210096 China Université de Tours 64 avenue Jean Portalis Tours37200 France School of Computer Science Wuhan University Wuhan430072 China Guangdong Provincial Key Laboratory of Computer Vision and Virtual Reality Technology SIAT Shenzhen China Shenzhen Institutes of Advanced Technology Chinese Academy of Sciences Shenzhen518055 China Institute for Surgical Technology & Biomechanics University of Bern Bern3014 Switzerland BHF Centre for Cardiovascular Science University of Edinburgh Edinburgh United Kingdom Edinburgh Imaging Facility QMRI University of Edinburgh Edinburgh United Kingdom Department of Imaging Sciences & Biomedical Engineering Kings College London London United Kingdom Cardiovascular Research Centre Royal Brompton Hospital LondonSW3 6NP United Kingdom National Heart and Lung Institute Imperial College London London LondonSW7 2AZ United Kingdom

Knowledge of whole heart anatomy is a prerequisite for many clinical applications. Whole heart segmentation (WHS), which delineates substructures of the heart, can be very valuable for modeling and analysis of the anatomy and functions of the heart. However, automating this segmentation can be arduous due to the large variation of the heart shape, and different image qualities of the clinical data. To achieve this goal, a set of training data is generally needed for constructing priors or for training. In addition, it is difficult to perform comparisons between different methods, largely due to differences in the datasets and evaluation metrics used. This manuscript presents the methodologies and evaluation results for the WHS algorithms selected from the submissions to the Multi-Modality Whole Heart Segmentation (MM-WHS) challenge, in conjunction with MICCAI 2017. The challenge provides 120 three-dimensional cardiac images covering the whole heart, including 60 CT and 60 MRI volumes, all acquired in clinical environments with manual delineation. Ten algorithms for CT data and eleven algorithms for MRI data, submitted from twelve groups, have been evaluated. The results show that many of the deep learning (DL) based methods achieved high accuracy, even though the number of training datasets were limited. A number of them also reported poor results in the blinded evaluation, probably due to overfitting in their training. The conventional algorithms, mainly based on multi-atlas segmentation, demonstrated robust and stable performance, even though the accuracy is not as good as the best DL method in CT segmentation. The challenge, including provision of the annotated training data and the blinded evaluation for submitted algorithms on the test data, continues as an ongoing benchmarking resource via its homepage (***/zhuangxiahai/0/mmwhs/). Copyright © 2019, The Authors. All rights reserved.

关键词： Heart

The Liver Tumor Segmentation Benchmark (LiTS)

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arXiv 2019年

作者： Bilic, Patrick Christ, Patrick Li, Hongwei Bran Vorontsov, Eugene Ben-Cohen, Avi Kaissis, Georgios Szeskin, Adi Jacobs, Colin Mamani, Gabriel Efrain Humpire Chartrand, Gabriel Lohöfer, Fabian Holch, Julian Walter Sommer, Wieland Hofmann, Felix Hostettler, Alexandre Lev-Cohain, Naama Drozdzal, Michal Amitai, Michal Marianne Vivanti, Refael Sosna, Jacob Ezhov, Ivan Sekuboyina, Anjany Navarro, Fernando Kofler, Florian Paetzold, Johannes C. Shit, Suprosanna Hu, Xiaobin Lipková, Jana Rempfler, Markus Piraud, Marie Kirschke, Jan Wiestler, Benedikt Zhang, Zhiheng Hülsemeyer, Christian Beetz, Marcel Ettlinger, Florian Antonelli, Michela Bae, Woong Bellver, Míriam Bi, Lei Chen, Hao Chlebus, Grzegorz Dam, Erik B. Dou, Qi Fu, Chi-Wing Georgescu, Bogdan Giró-I-Nieto, Xavier Gruen, Felix Han, Xu Heng, Pheng-Ann Hesser, Jürgen Moltz, Jan Hendrik Igel, Christian Isensee, Fabian Jäger, Paul Jia, Fucang Kaluva, Krishna Chaitanya Khened, Mahendra Kim, Ildoo Kim, Jae-Hun Kim, Sungwoong Kohl, Simon Konopczynski, Tomasz Kori, Avinash Krishnamurthi, Ganapathy Li, Fan Li, Hongchao Li, Junbo Li, Xiaomeng Lowengrub, John Ma, Jun Maier-Hein, Klaus Maninis, Kevis-Kokitsi Meine, Hans Merhof, Dorit Pai, Akshay Perslev, Mathias Petersen, Jens Pont-Tuset, Jordi Qi, Jin Qi, Xiaojuan Rippel, Oliver Roth, Karsten Sarasua, Ignacio Schenk, Andrea Shen, Zengming Torres, Jordi Wachinger, Christian Wang, Chunliang Weninger, Leon Wu, Jianrong Xu, Daguang Yang, Xiaoping Yu, Simon Chun-Ho Yuan, Yading Yue, Miao Zhang, Liping Cardoso, Jorge Bakas, Spyridon Braren, Rickmer Heinemann, Volker Pal, Christopher Tang, An Kadoury, Samuel Soler, Luc van Ginneken, Bram Greenspan, Hayit Joskowicz, Leo Menze, Bjoern Department of Informatics Technical University of Munich Germany Department of Quantitative Biomedicine University of Zurich Switzerland Ecole Polytechnique de Montréal Canada Department of Medical Imaging Radboud University Medical Center Nijmegen Netherlands Department of Biomedical Engineering Tel-Aviv University Israel Germany Pattern Analysis and Learning Group Department of Radiation Oncology Heidelberg University Hospital Heidelberg Germany Philips Research China Philips China Innovation Campus Shanghai China School of Biomedical Engineering & Imaging Sciences King0s College London London United Kingdom Institute for AI in Medicine Technical University of Munich Germany Department of Computer Science Guangdong University of Foreign Studies China Institute for diagnostic and interventional radiology Klinikum rechts der Isar Technical University of Munich Germany Institute for Diagnostic and Interventional Neuroradiology Klinikum Rechts der Isar Technical University of Munich Germany Department of Hepatobiliary Surgery The Affiliated Drum Tower Hospital Nanjing University Medical School China Department of Computing Imperial College London London United Kingdom Institute for Tissue Engineering and Regenerative Medicine Helmholtz Zentrum München Neuherberg Germany Brigham and Women's Hospital Harvard Medical School United States School of Computer Science and Engineering The Hebrew University of Jerusalem Israel University of Pennsylvania PA United States Pte. Ltd. Singapore Medical Imaging and Reconstruction Lab Department of Engineering Design Indian Institute of Technology Madras India Sensetime Shanghai China Department of Radiology Perelman School of Medicine University of Pennsylvania United States Department of Pathology and Laboratory Medicine Perelman School of Medicine University of Pennsylvania PA United States Co. Ltd China MontréalQC Canada Department of Radiology Radiation Oncology and Nuclear Medicine University of Montréal

In this work, we report the set-up and results of the Liver Tumor Segmentation Benchmark (LiTS), which was organized in conjunction with the IEEE International Symposium on Biomedical Imaging (ISBI) 2017 and the International Conferences on Medical Image Computing and computer-Assisted Intervention (MICCAI) 2017 and 2018. The image dataset is diverse and contains primary and secondary tumors with varied sizes and appearances with various lesion-to-background levels (hyper-/hypo-dense), created in collaboration with seven hospitals and research institutions. Seventy-five submitted liver and liver tumor segmentation algorithms were trained on a set of 131 computed tomography (CT) volumes and were tested on 70 unseen test images acquired from different patients. We found that not a single algorithm performed best for both liver and liver tumors in the three events. The best liver segmentation algorithm achieved a Dice score of 0.963, whereas, for tumor segmentation, the best algorithms achieved Dices scores of 0.674 (ISBI 2017), 0.702 (MICCAI 2017), and 0.739 (MICCAI 2018). Retrospectively, we performed additional analysis on liver tumor detection and revealed that not all top-performing segmentation algorithms worked well for tumor detection. The best liver tumor detection method achieved a lesion-wise recall of 0.458 (ISBI 2017), 0.515 (MICCAI 2017), and 0.554 (MICCAI 2018), indicating the need for further research. LiTS remains an active benchmark and resource for research, e.g., contributing the liver-related segmentation tasks in http://***/. In addition, both data and online evaluation are accessible via ***. © 2019, CC BY-NC-ND.

关键词： Deep learning

Author Correction: The power of genetic diversity in genome-wide association studies of lipids

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Nature 2023年第7965期618卷 E19-E20页

作者： Sarah E Graham Shoa L Clarke Kuan-Han H Wu Stavroula Kanoni Greg J M Zajac Shweta Ramdas Ida Surakka Ioanna Ntalla Sailaja Vedantam Thomas W Winkler Adam E Locke Eirini Marouli Mi Yeong Hwang Sohee Han Akira Narita Ananyo Choudhury Amy R Bentley Kenneth Ekoru Anurag Verma Bhavi Trivedi Hilary C Martin Karen A Hunt Qin Hui Derek Klarin Xiang Zhu Gudmar Thorleifsson Anna Helgadottir Daniel F Gudbjartsson Hilma Holm Isleifur Olafsson Masato Akiyama Saori Sakaue Chikashi Terao Masahiro Kanai Wei Zhou Ben M Brumpton Humaira Rasheed Sanni E Ruotsalainen Aki S Havulinna Yogasudha Veturi QiPing Feng Elisabeth A Rosenthal Todd Lingren Jennifer Allen Pacheco Sarah A Pendergrass Jeffrey Haessler Franco Giulianini Yuki Bradford Jason E Miller Archie Campbell Kuang Lin Iona Y Millwood George Hindy Asif Rasheed Jessica D Faul Wei Zhao David R Weir Constance Turman Hongyan Huang Mariaelisa Graff Anubha Mahajan Michael R Brown Weihua Zhang Ketian Yu Ellen M Schmidt Anita Pandit Stefan Gustafsson Xianyong Yin Jian'an Luan Jing-Hua Zhao Fumihiko Matsuda Hye-Mi Jang Kyungheon Yoon Carolina Medina-Gomez Achilleas Pitsillides Jouke Jan Hottenga Gonneke Willemsen Andrew R Wood Yingji Ji Zishan Gao Simon Haworth Ruth E Mitchell Jin Fang Chai Mette Aadahl Jie Yao Ani Manichaikul Helen R Warren Julia Ramirez Jette Bork-Jensen Line L Kårhus Anuj Goel Maria Sabater-Lleal Raymond Noordam Carlo Sidore Edoardo Fiorillo Aaron F McDaid Pedro Marques-Vidal Matthias Wielscher Stella Trompet Naveed Sattar Line T Møllehave Betina H Thuesen Matthias Munz Lingyao Zeng Jianfeng Huang Bin Yang Alaitz Poveda Azra Kurbasic Claudia Lamina Lukas Forer Markus Scholz Tessel E Galesloot Jonathan P Bradfield E Warwick Daw Joseph M Zmuda Jonathan S Mitchell Christian Fuchsberger Henry Christensen Jennifer A Brody Mary F Feitosa Mary K Wojczynski Michael Preuss Massimo Mangino Paraskevi Christofidou Niek Verweij Jan W Benjamins Jorgen Engmann Rachel L Kember Roderick C Slieker Ken Sin Lo Nuno R Zilhao Phuong Le Marcus E Kleber Graciela E Delgado Shaofeng Huo Dai Department of Internal Medicine Division of Cardiology University of Michigan Ann Arbor MI USA. VA Palo Alto Health Care System Palo Alto CA USA. Department of Medicine Division of Cardiovascular Medicine Stanford University School of Medicine Stanford CA USA. Department of Computational Medicine and Bioinformatics University of Michigan Ann Arbor MI USA. William Harvey Research Institute Barts and the London School of Medicine and Dentistry Queen Mary University of London London UK. Department of Biostatistics and Center for Statistics Genetics University of Michigan Ann Arbor MI USA. Department of Genetics Perelman School of Medicine University of Pennsylvania Philadelphia PA USA. Clinical Pharmacology William Harvey Research Institute Barts and The London School of Medicine and Dentistry Queen Mary University of London London UK. Endocrinology Boston Children's Hospital Boston MA USA. Medical and Population Genetics Broad Institute Cambridge MA USA. Department of Genetic Epidemiology University of Regensburg Regensburg Germany. McDonnell Genome Institute and Department of Medicine Washington University St Louis MO USA. Department of Precision Medicine Division of Genome Science National Institute of Health Cheongju-si South Korea. Tohoku Medical Megabank Organization Tohoku University Sendai Japan. Sydney Brenner Institute for Molecular Bioscience Faculty of Health Sciences University of the Witwatersrand Johannesburg South Africa. Center for Research on Genomics and Global Health National Human Genome Research Institute National Institutes of Health Bethesda MD USA. Blizard Institute Barts and the London School of Medicine and Dentistry Queen Mary University of London London UK. Wellcome Sanger Institute Hinxton UK. Department of Epidemiology Emory University Rollins School of Public Health Atlanta GA USA. Atlanta VA Health Care System Decatur GA USA. Malcolm Randall VA Medical Center Gainesville FL USA. Division of Vascular Sur

Is the winner really the best? A critical analysis of common research practice in biomedical image analysis competitions

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arXiv 2018年

作者： Maier-Hein, Lena Eisenmann, Matthias Reinke, Annika Onogur, Sinan Stankovic, Marko Scholz, Patrick Arbel, Tal Bogunovic, Hrvoje Bradley, Andrew P. Carass, Aaron Carolin Feldmann Frangi, Alejandro F. Ful, Peter M. van Ginneken, Bram Hanbury, Allan Honauer, Katrin Kozubek, Michal Landman, Bennett A. Marz, Keno Maier, Oskar Maier-Hein, Klaus Menze, Bjoern H. Müller, Henning Neher, Peter F. Niessen, Wiro Rajpoot, Nasir Sharp, Gregory C. Sirinukunwattana, Korsuk Speidel, Stefanie Stock, Christian Stoyanov, Danail Taha, Abdel Aziz van der Sommen, Fons Wang, Ching-Wei Weber, Marc-André Zheng, Guoyan Jannin, Pierre Kopp-Schneider, Annette Heidelberg Germany Centre for Intelligent Machines McGill University MontrealQC Canada Christian Doppler Laboratory for Ophthalmic Image Analysis Department of Ophthalmology Medical University Vienna Vienna Austria Science and Engineering Faculty Queensland University of Technology BrisbaneQLD Australia Department of Electrical and Computer Engineering Department of Computer Science Johns Hopkins University Baltimore United States CISTIB Centre for Computational Imaging and Simulation Technologies in Biomedicine University of Sheffield Sheffield United Kingdom Department of Radiology and Nuclear Medicine Medical Image Analysis Radboud University Center Nijmegen Netherlands Institute of Information Systems Engineering TU Wien Vienna Austria Heidelberg University Heidelberg Germany Centre for Biomedical Image Analysis Masaryk University Brno Czech Republic Electrical Engineering Vanderbilt University NashvilleTN United States Institute of Medical Informatics Universität zu Lübeck Lübeck Germany Heidelberg Germany Institute for Advanced Studies Department of Informatics Technical University of Munich Munich Germany Information System Institute HES-SO Sierre Switzerland Departments of Radiology Nuclear Medicine and Medical Informatics Erasmus MC Rotterdam Netherlands Department of Computer Science University of Warwick Coventry United Kingdom Department of Radiation Oncology Massachusetts General Hospital BostonMA United States Institute of Biomedical Engineering University of Oxford Oxford United Kingdom National Center for Tumor Diseases Dresden Dresden Germany Heidelberg Germany Department of Computer Science University College London London United Kingdom Data Science Studio Research Studios Austria FG Vienna Austria Department of Electrical Engineering Eindhoven University of Technology Eindhoven Netherlands AIExplore NTUST Center of Computer Vision and Medical Imaging Graduate Institute of Biomedical Engineering National Ta

International challenges have become the standard for validation of biomedical image analysis methods. Given their scientific impact, it is surprising that a critical analysis of common practices related to the organization of challenges has not yet been performed. In this paper, we present a comprehensive analysis of biomedical image analysis challenges conducted up to now. We demonstrate the importance of challenges and show that the lack of quality control has critical consequences. First, reproducibility and interpretation of the results is often hampered as only a fraction of relevant information is typically provided. Second, the rank of an algorithm is generally not robust to a number of variables such as the test data used for validation, the ranking scheme applied and the observers that make the reference annotations. To overcome these problems, we recommend best practice guidelines and define open research questions to be addressed in the future. Copyright © 2018, The Authors. All rights reserved.

关键词： Quality control

Optoacoustic tomographic imaging of myelinated structures in rodent brains

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Optoacoustic tomographic imaging of myelinated structures in...

Optics and the Brain, BRAIN 2017

作者： Lockwood, Joshua Ringuette, Dene Zhou, Xun Yucel, Yeni Levi, Ofer The Institute of Biomaterials and Biomedical Engineering University of Toronto 164 College Street TorontoONM5S 3G9 Canada Department of Ophthalmology and Vision Sciences Laboratory Medicine and Pathobiology University of Toronto Keenan Research Centre for Biomedical Science 209 Victoria St TorontoONM5B 1T8 Canada The Edward S. Rogers Sr. Department of Electrical and Computer Engineering University of Toronto 164 College Street TorontoONM5S 3G9 Canada

Myelinated structures in rodent brains were identified using multispectral optoacoustic tomography;exploiting the 930 nm lipid absorbance maximum. Results support optoacoustic imaging as an inventigative tool for rode... 详细信息

ISBN: (纸本)9781943580255

关键词： Photoacoustic effect

A virtual reality platform for dynamic human-scene interaction 16

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A virtual reality platform for dynamic human-scene interacti...

2016 SIGGRAPH ASIA Virtual Reality Meets Physical Reality: Modelling and Simulating Virtual Humans and Environments, SA 2016

作者： Lin, Jenny Guo, Xingwen Shao, Jingyu Jiang, Chenfanfu Zhu, Yixin Zhu, Song-Chun UCLA Center for Vision Cognition Learning and Autonomy United States University of Hong Kong Electrical and Electronic Engineering Department Hong Kong UCLA Computer Graphics and Vision Laboratory United States

ISBN: (纸本)9781450345484

Both synthetic static and simulated dynamic 3D scene data is highly useful in the fields of computer vision and robot task planning. Yet their virtual nature makes it difficult for real agents to interact with such data in an intuitive way. Thus currently available datasets are either static or greatly simplified in terms of interactions and dynamics. In this paper, we propose a system in which Virtual Reality and human/finger pose tracking is integrated to allow agents to interact with virtual environments in real time. Segmented object and scene data is used to construct a scene within Unreal Engine 4, a physics-based game engine. We then use the Oculus Rift headset with a Kinect sensor, Leap Motion controller and a dance pad to navigate and manipulate objects inside synthetic scenes in real time. We demonstrate how our system can be used to construct a multi-jointed agent representation as well as fine-grained finger pose. In the end, we propose how our system can be used for robot task planning and image semantic segmentation. © 2016 Copyright held by the owner/author(s). SA '16, December 05-08 2016.

关键词： Virtual reality