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Identifying the best machine learning algorithms for brain tumor segmentation, progression assessment, and overall survival prediction in the BRATS challenge

arXiv

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arXiv 2018年

作者： Bakas, Spyridon Reyes, Mauricio Jakab, Andras Bauer, Stefan Rempfler, Markus Crimi, Alessandro Shinohara, Russell Takeshi Berger, Christoph Ha, Sung Min Rozycki, Martin Prastawa, Marcel Alberts, Esther Lipkova, Jana Freymann, John Kirby, Justin Bilello, Michel Fathallah-Shaykh, Hassan M. Wiest, Roland Kirschke, Jan Wiestler, Benedikt Colen, Rivka Kotrotsou, Aikaterini Lamontagne, Pamela Marcus, Daniel Milchenko, Mikhail Nazeri, Arash Weber, Marc-Andr Mahajan, Abhishek Baid, Ujjwal Gerstner, Elizabeth Kwon, Dongjin Acharya, Gagan Agarwal, Manu Alam, Mahbubul Albiol, Alberto Albiol, Antonio Albiol, Francisco J. Alex, Varghese Allinson, Nigel Amorim, Pedro H.A. Amrutkar, Abhijit Anand, Ganesh Andermatt, Simon Arbel, Tal Arbelaez, Pablo Avery, Aaron Azmat, Muneeza Pranjal, B. Bai, Wenjia Banerjee, Subhashis Barth, Bill Batchelder, Thomas Batmanghelich, Kayhan Battistella, Enzo Beers, Andrew Belyaev, Mikhail Bendszus, Martin Benson, Eze Bernal, Jose Bharath, Halandur Nagaraja Biros, George Bisdas, Sotirios Brown, James Cabezas, Mariano Cao, Shilei Cardoso, Jorge M. Carver, Eric N. Casamitjana, Adri Castillo, Laura Silvana Cat, Marcel Cattin, Philippe Cérigues, Albert Chagas, Vinicius S. Chandra, Siddhartha Chang, Yi-Ju Chang, Shiyu Chang, Ken Chazalon, Joseph Chen, Shengcong Chen, Wei Chen, Jefferson W. Chen, Zhaolin Cheng, Kun Choudhury, Ahana Roy Chylla, Roger Clrigues, Albert Colleman, Steven Colmeiro, Ramiro German Rodriguez Combalia, Marc Costa, Anthony Cui, Xiaomeng Dai, Zhenzhen Dai, Lutao Daza, Laura Alexandra Deutsch, Eric Ding, Changxing Dong, Chao Dong, Shidu Dudzik, Wojciech Eaton-Rosen, Zach Egan, Gary Escudero, Guilherme Estienne, Tho Everson, Richard Fabrizio, Jonathan Fan, Yong Fang, Longwei Feng, Xue Ferrante, Enzo Fidon, Lucas Fischer, Martin French, Andrew P. Fridman, Naomi Fu, Huan Fuentes, David Gao, Yaozong Gates, Evan Gering, David Gholami, Amir Gierke, Willi Glocker, Ben Gong, Mingming Gonzlez-Vill, Sandra Grosges, T. Guan, Yuanfang Guo, Sheng Gupta, Sudeep Han, Woo-Sup Han, Il Song Harmuth, Ko Center for Biomedical Image Computing and Analytics University of Pennsylvania PhiladelphiaPA United States Department of Radiology Perelman School of Medicine University of Pennsylvania PhiladelphiaPA United States Department of Pathology and Laboratory Medicine Perelman School of Medicine University of Pennsylvania PhiladelphiaPA United States Institute for Surgical Technology and Biomechanics University of Bern Bern Switzerland Center for MR-Research University Children's Hospital Zurich Zurich Switzerland Support Centre for Advanced Neuroimaging Inselspital Institute for Diagnostic and Interventional Neuroradiology Bern University Hospital Bern Switzerland University Hospital of Zurich Zurich Switzerland Center for Clinical Epidemiology and Biostatistics University of Pennsylvania Philadelphia United States Image-Based Biomedical Modeling Group Technical University of Munich Munich Germany Icahn School of Medicine Mount Sinai Health System New YorkNY United States Leidos Biomedical Research Inc. Frederick National Laboratory for Cancer Research FrederickMD21701 United States Cancer Imaging Program National Cancer Institute National Institutes of Health BethesdaMD20814 United States Department of Neurology University of Alabama at Birmingham BirminghamAL United States Department of Diagnostic Radiology University of Texas MD Anderson Cancer Center HoustonTX United States Department of Psychology Washington University St. LouisMO United States Neuroimaging Informatics and Analysis Center Washington University St. LouisMO United States Department of Radiology Washington University St. LouisMO United States Institute of Diagnostic and Interventional Radiology Pediatric Radiology and Neuroradiology University Medical Center Rostock Ernst-Heydemann-Str. 6 Rostock18057 Germany Tata Memorial Centre Homi Bhabha National Institute Mumbai India Shri Guru Gobind Singhji Institute of Engineering and Technology Nanded India NVIDIA Santa Clara

Gliomas are the most common primary brain malignancies, with different degrees of aggressiveness, variable prognosis and various heterogeneous histologic sub-regions, i.e., peritumoral edematous/invaded tissue, necrotic core, active and non-enhancing core. This intrinsic heterogeneity is also portrayed in their radio-phenotype, as their sub-regions are depicted by varying intensity profiles disseminated across multi-parametric magnetic resonance imaging (mpMRI) scans, reflecting varying biological properties. Their heterogeneous shape, extent, and location are some of the factors that make these tumors difficult to resect, and in some cases inoperable. The amount of resected tumor is a factor also considered in longitudinal scans, when evaluating the apparent tumor for potential diagnosis of progression. Furthermore, there is mounting evidence that accurate segmentation of the various tumor sub-regions can offer the basis for quantitative image analysis towards prediction of patient overall survival. This study assesses the state-of-the-art machine learning (ML) methods used for brain tumor image analysis in mpMRI scans, during the last seven instances of the International Brain Tumor Segmentation (BraTS) challenge, i.e., 2012-2018. Specifically, we focus on i) evaluating segmentations of the various glioma sub-regions in pre-operative mpMRI scans, ii) assessing potential tumor progression by virtue of longitudinal growth of tumor sub-regions, beyond use of the RECIST/RANO criteria, and iii) predicting the overall survival from pre-operative mpMRI scans of patients that underwent gross total resection. Finally, we investigate the challenge of identifying the best ML algorithms for each of these tasks, considering that apart from being diverse on each instance of the challenge, the multi-institutional mpMRI BraTS dataset has also been a continuously evolving/growing dataset. Copyright © 2018, The Authors. All rights reserved.

关键词： Tumors

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Combining Efficient Hand-Crafted Features with Learned Filters for Fast and Accurate Corneal Nerve Fibre Centreline Detection

Combining Efficient Hand-Crafted Features with Learned Filte...

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Annual International Conference of the IEEE Engineering in Medicine and Biology Society

作者： Roberto Annunziata Ahmad Kheirkhah Pedram Hamrah Emanuele Trucco the Computer Vision and Image Processing group School of Computing University of Dundee Dundee UK. the Massachusetts Eye and Ear Infirmary Harvard Medical School Boston USA.

ISBN: (纸本)9781424492695

We propose a new approach to corneal nerve fibre centreline detection for in vivo confocal microscopy images. Relying on a combination of efficient hand-crafted features and learned filters, our method offers an excellent compromise between accuracy and running time. Unlike previous solutions using sparse coding to learn small filter banks, we employ K-means to efficiently learn the high amount of filters needed to cope with the multiple challenges involved, e.g., low contrast and resolution, non-uniform illumination, tortuosity and confounding non-target structures. The use of K-means for dictionary learning allows us to learn banks of 100 filters in less than 30 seconds compared to several days needed when using sparse coding. Experimental results using a dataset including 100 images show that our approach outperforms significantly state-of-the-art methods in terms of precision-recall curves.

关键词： multiple challenges precision-recall curves vivo confocal microscopy

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DeWAFF: A novel image abstraction approach to improve the performance of a cell tracking system

DeWAFF: A novel image abstraction approach to improve the pe...

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International Work Conference on Bio-inspired Intelligence (IWOBI)

作者： S. Calderón A. Sáenz R. Mora F. Siles I. Orozco M.E. Buemi Department of Electrical Engineering School of Engineering Cancer-Lab Universidad de Costa Rica San José Costa Rica Image Processing and Computer Vision Group Universidad de Buenos Aires Buenos Aires Argentina

This paper presents a new image abstraction approach, aiming to improve typical image related pattern recognition tasks such as segmentation, tracking, and classification. The proposed image abstraction framework performs image denoising and homogeneous region simplification, along with border and region enhancement. The proposed framework consists in a novel generalized approach of common weighted averaging denoising algorithms mixed with Unsharp Masking (USM) border enhancement techniques, to avoid typical USM artifacts as ringing. Results of the different configurations within the image abstraction framework for a cell tracking application are presented.

关键词： image edge detection Noise reduction Histograms AWGN Pattern recognition image segmentation

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Automatic normal-abnormal video frame classification for colonoscopy

Automatic normal-abnormal video frame classification for col...

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IEEE International Symposium on Biomedical Imaging

作者： Siyamalan Manivannan Ruixuan Wang Emanuele Trucco Adrian Hood CVIP Computer Vision and Image Processing group School of Computing University of Dundee UK Leeds Institute of Molecular Medicine University of Leeds UK

ISBN: (纸本)9781467364560

Two novel schemes are proposed to represent intermediate-scale features for normal-abnormal classification of colonoscopy images. The first scheme works on the full-resolution image, the second on a multi-scale pyramid space. Both schemes support any feature descriptor; here we use multi-resolution local binary patterns which outperformed other features reported in the literature in our comparative experiments. We also compared experimentally two types of features not previously used in colonoscopy image classification, bag of features and sparse coding, each with and without spatial pyramid matching (SPM). We find that SPM improves performance, therefore supporting the importance of intermediate-scale features as in the proposed schemes for classification. Within normal-abnormal frame classification, we show that our representational schemes outperforms other features reported in the literature in leave-N-out tests with a database of 2100 colonoscopy images.

关键词： image color analysis Feature extraction Colonoscopy Histograms Accuracy Hemorrhaging Lesions

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Single Cluster PHD SLAM: Application to Autonomous Underwater Vehicles using Stereo vision

Single Cluster PHD SLAM: Application to Autonomous Underwate...

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Oceans 2013 - Norway

作者： Sharad Nagappa Narcis Palomeras Chee Sing Lee Nuno Gracias Daniel E. Clark Joaquim Salvi Computer Vision and Robotics Group University of Girona Joint Research Institute in Signal and Image Processing Heriot-Watt University

ISBN: (纸本)9781479900022

This paper considers the application of feature-based simultaneous localisation and mapping (SLAM) using a random finite sets (RFS) framework for an autonomous underwater vehicle. SLAM allows for reduction in localisation error by tracking features which provide a fixed external reference. The SLAM problem is addressed here using a single-cluster probability hypothesis density (PHD) filter. The filter uses a particle approximation for the vehicle position with a conditional Gaussian mixture PHD for the feature map. Map features are selected as unique point features generated from a stereo camera on-board the vehicle. We demonstrate the improvement in localisation applying the algorithm to a dataset obtained in an indoor test tank.

关键词： Autonomous underwater vehicles Stereoviews supersonic low altitude missile underwater vehicles Automatic vehicle location Stereo cameras simultaneous localization and mapping

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A Passive Stereo System for 3D Human Face Reconstruction and Recognition at a Distance

A Passive Stereo System for 3D Human Face Reconstruction and...

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IEEE computer Society Conference on computer vision and Pattern Recognition Workshops

作者： Mostafa Abdelrahman Asem Ali Shireen Elhabian Ham Rara Aly A. Farag Computer Vision and Image Processing Laboratory (CVIP) University of Louisville Louisville KY 40292

ISBN: (纸本)9781467316118

In this paper, we propose a front-end framework for 3D human face reconstruction and recognition at a distance. A stereo acquisition system is built and deployed to capture stereo pairs of subjects at different distances. Three main issues are addressed to achieve accurate face reconstruc- tion, which leads to good recognition;Different illumina- tion conditions between the stereo pair due to larger base- line and further distances, where a fast similarity measure based on normalized cross correlation is shown to tackle such problem. Due to the non-convexity nature of a human face, concave regions introduce occluded regions where cu- bic Splines are used to estimate the disparity. Disparity discontinuities are introduced due to the sparse nature of stereo reconstruction, where surface fitting is performed at prominent facial points. We present our database of 99 sub- jects at different ranges where reconstruction and recogni- tion results are presented.

关键词： Passive Stereo System 3D Human Reconstruction Stereo pairs Recognition (Psychology) Cross correlation Face Face Acoustic equipment Reconstructive Surgical Procedures surface fitting acquisition system similar measure Reconstructions DISTANCE

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A highly efficient GPU implementation for variational optic flow based on the Euler-Lagrange framework

A highly efficient GPU implementation for variational optic ...

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11th European Conference on computer vision, ECCV 2010

作者： Gwosdek, Pascal Zimmer, Henning Grewenig, Sven Bruhn, Andrés Weickert, Joachim Mathematical Image Analysis Group Faculty of Mathematics and Computer Science Saarland University Saarbrücken 66041 Germany Vision and Image Processing Group Cluster of Excellence Multimodal Computing and Interaction Saarland University Saarbrücken 66123 Germany

ISBN: (纸本)9783642357398

The Euler-Lagrange (EL) framework is the most widely-used strategy for solving variational optic flow methods. We present the first approach that solves the EL equations of state-of-the-art methods on sequences with pixels in near-realtime on GPUs. This performance is achieved by combining two ideas: (i) We extend the recently proposed Fast Explicit Diffusion (FED) scheme to optic flow, and additionally embed it into a coarse-to-fine strategy. (ii) We parallelise our complete algorithm on a GPU, where a careful optimisation of global memory operations and an efficient use of on-chip memory guarantee a good performance. Applying our approach to the variational 'Complementary Optic Flow' method (Zimmer et al. (2009)), we obtain highly accurate flow fields in less than a second. This currently constitutes the fastest method in the top 10 of the widely used Middlebury benchmark. © 2012 Springer-Verlag.

关键词： Graphics processing unit

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Rapid shallow coastal coral reef mapping using the teardrop system

Rapid shallow coastal coral reef mapping using the teardrop ...

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OCEANS 2012 MTS/IEEE Hampton Roads Conference: Harnessing the Power of the Ocean

作者： Corpuz, Francis James Naval Jr., Prospero Capili, Eusebio Jauod, Jaylord Judilla, Roel John Soriano, Maricor Vision and Image Processing Group National Institute of Physics University of the Philippines Diliman Quezon City Philippines Computer Vision and Machine Intelligence Group Department of Computer Science University of the Philippines Diliman Quezon City Philippines Mapua Robotics Center Institutional Laboratory Mgmt Office Mapua Institute of Technology Intramuros Manila Philippines

ISBN: (纸本)9781467308298

We present a rapid shallow coastal reef mapping system using a previously developed inexpensive diver less video capture system coupled with a fast-image mosaicking technique, using an affordable GPS logging device. The system replaces the traditional manta tow system of assessing and monitoring large areas of coastal coral reefs and at the same time provides historical visual record for future references. The system utilizes Teardrop, a hollow, teardrop-shaped that houses a commercial underwater point-and-shoot camera. The camera is set to video mode and captures video of the reef while the Teardrop is being towed by a wooden fishing boat. The resulting video is parsed into frames and mosaicked by using fast image labeling. The approximate location of the mosaicked images is recorded by using an inexpensive GPS logger. The coordinates are embedded on the mosaicked images and overlaid on mapping software such as Google Earth for visual record and spatial information integration. The same points are used to compute for the total distance covered by the capturing process. The whole process from coral reef video capture to mosaicking the images and finally embedding the mosaics in mapping software can be done in as short as 1 day, providing coastal managers and local government units with a tool to rapidly visualize and monitor shallow coral reefs. © 2012 IEEE.

关键词： Mapping

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New Approach for Classification of Autistic vs. Typically Developing Brain Using White Matter Volumes

New Approach for Classification of Autistic vs. Typically De...

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Canadian Conference on computer and Robot vision, CRV

作者： Mostafa Abdelrahman Asem Ali Ahmed Farag Manuel F. Casanova Aly Farag Computer Vision & Image Processing Laboratory (CVIP) Univ. of Louisville Louisville KY Department of Psychiatry and Behavioral Sciences Univ. of Louisville Louisville KY

Autism is a complex developmental disability, characterized by deficits in social interaction, communication skills, range of interests, and occasionally the presence of stereotyped behaviors. Several studies show that changes in brain weight and volume over aging follow a unique trajectory in those affected by the condition~\cite{MICCAIMost00}. In this work, we develop a robust technique for evaluating the volume of white matter (WM), and use it as the main classification criteria. We perform MRI-based analysis on the brains of 14 autistic and 28 control subjects, male and female between aged 7 to 38 years. The proposed framework consists of several stages. First, the entire T1-weighted MRI scans are filtered out from noise using anisotropic diffusion filter. Then, the white matter (WM) is segmented from the skull. The segmentation framework is the search for maximum-a-posterior configurations in a Markov Gibbs Random Field (MGRF) model. A 3D mesh is then generated from the segmented WM. Finally, the volume of the 3D mesh is computed using a new algorithm. The experiments show accurate classification results of the proposed framework.

关键词： Autism image segmentation Solid modeling Magnetic resonance imaging Object segmentation Labeling Visualization

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SLAM with single cluster PHD filters

SLAM with single cluster PHD filters

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IEEE International Conference on Robotics and Automation (ICRA)

作者： Chee Sing Lee Daniel E. Clark Joaquim Salvi Computer Vision and Robotics Group (VICOROB) University of Girona Girona Spain Signal and Image Processing Heriot-Watt University Edinburgh UK

Recent work by Mullane, Vo, and Adams has re-examined the probabilistic foundations of feature-based Simultaneous Localization and Mapping (SLAM), casting the problem in terms of filtering with random finite sets. Algorithms were developed based on Probability Hypothesis Density (PHD) filtering techniques that provided superior performance to leading feature-based SLAM algorithms in challenging measurement scenarios with high false alarm rates, high missed detection rates, and high levels of measurement noise. We investigate this approach further by considering a hierarchical point process, or single-cluster multi-object, model, where we consider the state to consist of a map of landmarks conditioned on a vehicle state. Using Finite Set Statistics, we are able to find tractable formulae to approximate the joint vehicle-landmark state based on a single Poisson multi-object assumption on the predicted density. We describe the single-cluster PHD filter and the practical implementation developed based on a particle-system representation of the vehicle state and a Gaussian mixture approximation of the map for each particle. Synthetic simulation results are presented to compare the novel algorithm against the previous PHD filter SLAM algorithm. Results presented indicate a superior performance in vehicle and map landmark localization, and comparable performance in landmark cardinality estimation.

关键词： Simultaneous localization and mapping Filtering algorithms Prediction algorithms Weight measurement Clustering algorithms Marine animals

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