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arXiv 2017年

作者： Mitianoudis, Nikolaos Image Processing and Multimedia Laboratory Department of Electrical and Computer Engineering Democritus University of Thrace Xanthi67100 Greece

—Directional or Circular statistics are pertaining to the analysis and interpretation of directions or rotations. In this work, a novel probability distribution is proposed to model multidimensional sparse directional data. The Generalised Directional Laplacian Distribution (DLD) is a hybrid between the Laplacian distribution and the von Mises-Fisher distribution. The distribution’s parameters are estimated using Maximum-Likelihood Estimation over a set of training data points. Mixtures of Directional Laplacian Distributions (MDLD) are also introduced in order to model multiple concentrations of sparse directional data. The author explores the application of the derived DLD mixture model to cluster sound sources that exist in an underdetermined instantaneous sound mixture. The proposed model can solve the general K × L (K Copyright © 2017, The Authors. All rights reserved.

关键词： Laplace transforms

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Stereo image de-fencing using smartphones

Stereo image de-fencing using smartphones

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IEEE International Conference on Acoustics, Speech and Signal Processing

作者： Sankaraganesh Jonna Sukla Satapathy Rajiv R. Sahay Computational Vision Laboratory Department of Computer Science and Engineering Indian Institute of Technology Kharagpur India Computational Vision Laboratory Department of Electrical Engineering Indian Institute of Technology Kharagpur India

ISBN: (纸本)9781509041183

Conventional approaches to image de-fencing have limited themselves to using only image data in adjacent frames of the captured video of an approximately static scene. In this work, we present a method to harness disparity using a stereo pair of fenced images in order to detect fence pixels. Tourists and amateur photographers commonly carry smartphones/phablets which can be used to capture a short video sequence of the fenced scene. We model the formation of the occluded frames in the captured video. Furthermore, we propose an optimization framework to estimate the de-fenced image using the total variation prior to regularize the ill-posed problem.

关键词： image de-fencing image inpainting stereo disparity map convolutional neural networks total variation Smartphone images imagery (Psychotherapy) image Stereo pairs Video sequences stereo imaging Frame image data Videotapes Photographers fencing FRAMES

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

arXiv

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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

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Automatic 3D cardiovascular MR segmentation with densely-connected volumetric convnets 1

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20th International Conference on Medical image Computing and computer-Assisted Intervention, MICCAI 2017

作者： Yu, Lequan Cheng, Jie-Zhi Dou, Qi Yang, Xin Chen, Hao Qin, Jing Heng, Pheng-Ann Department of Computer Science and Engineering The Chinese University of Hong Kong Shatin Hong Kong Department of Electrical Engineering Chang Gung University Taoyuan Taiwan Centre for Smart Health School of Nursing The Hong Kong Polytechnic University Kowloon Hong Kong Guangdong Provincial Key Laboratory of Computer Vision and Virtual Reality Technology Shenzhen Institutes of Advanced Technology Chinese Academy of Sciences Shenzhen China

ISBN: (数字)9783319661858

ISBN: (纸本)9783319661841

Automatic and accurate whole-heart and great vessel segmentation from 3D cardiac magnetic resonance (MR) images plays an important role in the computer-assisted diagnosis and treatment of cardiovascular disease. However, this task is very challenging due to ambiguous cardiac borders and large anatomical variations among different subjects. In this paper, we propose a novel densely-connected volumetric convolutional neural network, referred as DenseVoxNet, to automatically segment the cardiac and vascular structures from 3D cardiac MR images. The DenseVoxNet adopts the 3D fully convolutional architecture for effective volume-to-volume prediction. From the learning perspective, our DenseVoxNet has three compelling advantages. First, it preserves the maximum information flow between layers by a densely-connected mechanism and hence eases the network training. Second, it avoids learning redundant feature maps by encouraging feature reuse and hence requires fewer parameters to achieve high performance, which is essential for medical applications with limited training data. Third, we add auxiliary side paths to strengthen the gradient propagation and stabilize the learning process. We demonstrate the effectiveness of DenseVoxNet by comparing it with the state-of-the-art approaches from HVSMR 2016 challenge in conjunction with MICCAI, and our network achieves the best dice coefficient. We also show that our network can achieve better performance than other 3D ConvNets but with fewer parameters. © Springer International Publishing AG 2017.

关键词： Medical applications

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Linear unmixing for subsurface estimation on coastal shallow waters

Linear unmixing for subsurface estimation on coastal shallow...

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8th International Conference of Pattern Recognition Systems (ICPRS 2017)

作者： Emmanuel Carpena-Colón Luis O. Jiménez-Rodríguez Emmanuel Arzuaga-Cruz Laboratory for Applied Remote Sensing and Image Processing (LARSIP) Electrical and Computer Engineering Department University of Puerto Rico - Mayaguez Campus

ISBN: (纸本)9781785616525

This paper presents the development and enhancement of a subsurface (underwater) linear unmixing algorithm, called LIGU, specially conceived to determine individual contributions to the measured signal of given spectral reflectance of objects at the bottom of coastal shallow waters. This algorithm is part of a Hyperspectral Coastal image analysis Toolbox (HyCIAT), which is a repository of tools to be used to retrieve information from object embedded in a diffusive and murky medium. This paper discusses mathematical formulations behind the subsurface unmixing algorithm LIGU and presents enhancements made to the algorithm. Finally, quantitative and qualitative results will be presented using a hyperspectral data set from a controlled and well known environment. These results provide noticeable quantitative improvement when compared with the same algorithms without the enhancements.

关键词： Linear Unmixing Hyperspectral Data Subsurface Sensing Inverse Methods Estimation

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The Liver Tumor Segmentation Benchmark (LiTS)

arXiv

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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

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Single image super resolution - When model adaptation matters

arXiv

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arXiv 2017年

作者： Liang, Yudong Timofte, Radu Wang, Jinjun Gong, Yihong Zheng, Nanning Institute of Artificial Intelligence and Robotics Xi'an Jiaotong University China Computer Vision Laboratory Department of Information Technology and Electrical Engineering ETH Zürich Switzerland

In the recent years impressive advances were made for single image super-resolution. Deep learning is behind a big part of this success. Deep(er) architecture design and external priors modeling are the key ingredients. The internal contents of the low resolution input image is neglected with deep modeling despite the earlier works showing the power of using such internal priors. In this paper we propose a novel deep convolutional neural network carefully designed for robustness and efficiency at both learning and testing. Moreover, we propose a couple of model adaptation strategies to the internal contents of the low resolution input image and analyze their strong points and weaknesses. By trading runtime and using internal priors we achieve 0.1 up to 0.3dB PSNR improvements over best reported results on standard datasets. Our adaptation especially favors images with repetitive structures or under large resolutions. Moreover, it can be combined with other simple techniques, such as back-projection or enhanced prediction, for further improvements. Copyright © 2017, The Authors. All rights reserved.

关键词： Deep neural networks

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Prediction of rib motion during free-breathing from liver observations using 4D MRI 1

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4th International Workshop on Clinical image-Based Procedures, CLIP 2015 and Held in 18th International Conference on Medical image Computing and computer-Assisted Interventions, MICCAI MICCAI 2015

作者： Samei, Golnoosh Székely, Gábor Tanner, Christine Department of Electrical and Computer Engineering University of British Columbia VancouverBC Canada Computer Vision Laboratory ETH Zurich Zurich Switzerland

ISBN: (数字)9783319318080

ISBN: (纸本)9783319318073

Magnetic resonance guided high intensity focused ultrasound (MRgHIFU) is a new therapy for treating malignant liver tissues. However, the motion of the ribs in the beam path may compromise an effective and safe treatment. Due to poor visibility of bones in MR and US liver images, tracking them in real time is currently not feasible. We propose a method for modeling and registration of the respiratory motion of the ribs. Moreover, we show that it is possible to predict the ribs’ motion based on a few tracked points in the liver. Our registration had a mean error of 1.06mm for deep inhalations with an average motion of 2.71 mm. We developed subject-specific and population-based modeling methods, which recover 60% and 40% of the respiratory motion extracted through registration, respectively. To the best of our knowledge, this is the first time the ribs’ motion due to respiration has been directly studied during free breathing over a relatively long time (100 breathing cycles). © Springer International Publishing Switzerland 2016.

关键词： Magnetic resonance

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Nuclei segmentation of fluorescence microscopy images using convolutional neural networks

Nuclei segmentation of fluorescence microscopy images using ...

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IEEE International Symposium on Biomedical Imaging

作者： Chichen Fu David Joon Ho Shuo Han Paul Salama Kenneth W. Dunn Edward J. Delp Video and Image Processing Laboratory University West Lafayette Indiana Department of Electrical and Computer Engineering Indiana University-Purdue University Indianapolis Indiana Division of Nephrology University Indianapolis Indiana

ISBN: (纸本)9781509011735

Fluorescence microscopy has emerged as a powerful tool for studying cell biology because it enables the acquisition of 3D image volumes deeper into tissue and the imaging of complex subcellular structures. Quantitative analysis of these structures, which is needed to characterize the structure and constitution of tissue volumes, is facilitated by nuclei segmentation. However, manual segmentation is a laborious and intractable process due to the size and complexity of the data. In this paper, we describe a nuclei segmentation method using a deep convolutional neural network, data augmentation to generate training images of different shapes and contrasts, a refinement process combining segmentation results of horizontal, frontal, and sagittal planes in a volume, and a watershed technique to count the number of nuclei. Our results indicate that compared to 3D ground truth data, our method is able to successfully segment and count 3D nuclei.

关键词： image segmentation Three-dimensional displays Microscopy Convolutional codes Shape Two dimensional displays Neural networks

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Concerted alterations of functional connectivity and WM integrity in relationship to early amyloid deposition

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Alzheimer's & Dementia 2022年第S1期18卷

作者： Luigi Lorenzini Beatrice Orso David Vállez García Giuseppe Pontillo Silvia Ingala Sven Haller Kaj Blennow Giovanni B Frisoni Gael Chetelat Pierre Payoux Pablo Martinez-Lage Michael Ewers Adam Waldman Craig W. Ritchie Juan Domingo Gispert Pieter Jelle Visser Henri JMM Mutsaerts Betty M. Tijms Alle Meije Wink Frederik Barkhof Department of Radiology and Nuclear Medicine Amsterdam Neuroscience Vrije Universiteit Amsterdam Amsterdam UMC Amsterdam Netherlands Department of Radiology and Nuclear Medicine Amsterdam UMC Location VuMC Vijre Universiteit Amsterdam Amsterdam Netherlands Department of Neuroscience Rehabilitation Ophthalmology Genetics Maternal and Child Health (DINOGMI) University of Genoa Genova Italy Department of Radiology & Nuclear Medicine Amsterdam UMC location VUmc Amsterdam Netherlands Department of Advanced Biomedical Sciences University “Federico II” Naples Italy Department of Electrical Engineering and Information Technology University of Naples “Federico II” Naples Italy University of Geneva Faculty of Medicine Geneva Switzerland Uppsala University Uppsala Sweden Department of Psychiatry and Neurochemistry The Sahlgrenska Academy at the University of Gothenburg Mölndal Sweden Clinical Neurochemistry Laboratory Sahlgrenska University Hospital Mölndal Sweden IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli Brescia Italy Geneva Memory Center Department of Rehabilitation and Geriatrics Geneva University Hospitals Geneva Switzerland ToNIC Toulouse NeuroImaging Center Université de Toulouse Inserm UPS Toulouse France INSERM Imagerie cérébrale et handicaps neurologiques Toulouse France CITA-Alzheimer Foundation San Sebastian Spain German Center for Neurodegenerative Diseases (DZNE) Munich Germany Imperial College London London United Kingdom Centre for Clinical Brain Sciences The University of Edinburgh Edinburgh United Kingdom Centre for Dementia Prevention at the University of Edinburgh Edinburgh United Kingdom Centro de Investigación Biomédica en Red Bioingeniería Biomateriales y Nanomedicina Madrid Spain Barcelonaβeta Brain Research Center (BBRC) Pasqual Maragall Foundation Barcelona Spain IMIM (Hospital del Mar Medical Research Institute) Barcelona Spain Universitat Pompeu Fabra Barcelona Spain Alzheimer Centrum Limburg Maastricht Univ

Background Early amyloid deposition results in functional and structural brain alterations in predementia stages of Alzheimer's disease (AD). However, how early functional and structural brain changes are related to each other remains unclear. Investigating the simultaneous disruptions of functional-structural brain features within individuals in relation to amyloid deposition may increase our understanding of the neuropathological processes underlying AD. Method We included 648 non-demented participants from the European Prevention for Alzheimer’s Dementia (EPAD) cohort vIMI baseline data release. The cut-off for cerebrospinal fluid (CSF) amyloid-β positivity (A+) was defined at <1000pg/mL (Elecsys assay). Functional connectivity was estimated with functional eigenvector centrality (EC) from the resting state functional MRI. White matter (WM) integrity was estimated with fractional anisotropy (FA), computed on diffusion MRI. Both measures were computed at the voxel level within the gray and white matter, respectively. First, we used linear regression models to investigate differences between A+ and A- participants within each modality separately, adjusting for age, sex, and site. In the whole group, we performed sparse canonical correlation analysis (sCCA) on functional and structural measures, identifying shared components between the two modalities. Individual sCCA scores were compared between amyloid groups using a generalized linear model (GLM). To evaluate this association in A+ individuals, the same sCCA analysis was performed normalizing the structural and functional matrices using the mean and SD from A- participants. Results Sample characteristics are provided in Table 1 . Differences in voxelwise EC and FA between amyloid groups are shown in Figure 1 . In the whole group, sCCA analysis showed that EC in the default mode, executive and cerebellar networks covary with FA in parietal, temporal and cerebellar areas ( Figure 2 ). sCCA projections were differen

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