Bio: Pierre-Marc Jodoin is an academic researcher from Université de Sherbrooke. The author has contributed to research in topics: Segmentation & Image segmentation. The author has an hindex of 38, co-authored 130 publications receiving 8136 citations. Previous affiliations of Pierre-Marc Jodoin include Université de Montréal & IT University.
Papers published on a yearly basis
TL;DR: A fast and accurate fully automatic method for brain tumor segmentation which is competitive both in terms of accuracy and speed compared to the state of the art, and introduces a novel cascaded architecture that allows the system to more accurately model local label dependencies.
Abstract: In this paper, we present a fully automatic brain tumor segmentation method based on Deep Neural Networks (DNNs). The proposed networks are tailored to glioblastomas (both low and high grade) pictured in MR images. By their very nature, these tumors can appear anywhere in the brain and have almost any kind of shape, size, and contrast. These reasons motivate our exploration of a machine learning solution that exploits a flexible, high capacity DNN while being extremely efficient. Here, we give a description of different model choices that we've found to be necessary for obtaining competitive performance. We explore in particular different architectures based on Convolutional Neural Networks (CNN), i.e. DNNs specifically adapted to image data. We present a novel CNN architecture which differs from those traditionally used in computer vision. Our CNN exploits both local features as well as more global contextual features simultaneously. Also, different from most traditional uses of CNNs, our networks use a final layer that is a convolutional implementation of a fully connected layer which allows a 40 fold speed up. We also describe a 2-phase training procedure that allows us to tackle difficulties related to the imbalance of tumor labels. Finally, we explore a cascade architecture in which the output of a basic CNN is treated as an additional source of information for a subsequent CNN. Results reported on the 2013 BRATS test data-set reveal that our architecture improves over the currently published state-of-the-art while being over 30 times faster.
University of Lyon1, University of Burgundy2, Université de Sherbrooke3, The Chinese University of Hong Kong4, Pompeu Fabra University5, Stanford University6, Queen Mary University of London7, University of Crete8, Indian Institute of Technology Madras9, French Institute for Research in Computer Science and Automation10, German Cancer Research Center11, Mannheim University of Applied Sciences12, ETH Zurich13, Utrecht University14, Yonsei University15, University of Nice Sophia Antipolis16
TL;DR: How far state-of-the-art deep learning methods can go at assessing CMRI, i.e., segmenting the myocardium and the two ventricles as well as classifying pathologies is measured, to open the door to highly accurate and fully automatic analysis of cardiac CMRI.
Abstract: Delineation of the left ventricular cavity, myocardium, and right ventricle from cardiac magnetic resonance images (multi-slice 2-D cine MRI) is a common clinical task to establish diagnosis. The automation of the corresponding tasks has thus been the subject of intense research over the past decades. In this paper, we introduce the “Automatic Cardiac Diagnosis Challenge” dataset (ACDC), the largest publicly available and fully annotated dataset for the purpose of cardiac MRI (CMR) assessment. The dataset contains data from 150 multi-equipments CMRI recordings with reference measurements and classification from two medical experts. The overarching objective of this paper is to measure how far state-of-the-art deep learning methods can go at assessing CMRI, i.e., segmenting the myocardium and the two ventricles as well as classifying pathologies. In the wake of the 2017 MICCAI-ACDC challenge, we report results from deep learning methods provided by nine research groups for the segmentation task and four groups for the classification task. Results show that the best methods faithfully reproduce the expert analysis, leading to a mean value of 0.97 correlation score for the automatic extraction of clinical indices and an accuracy of 0.96 for automatic diagnosis. These results clearly open the door to highly accurate and fully automatic analysis of cardiac CMRI. We also identify scenarios for which deep learning methods are still failing. Both the dataset and detailed results are publicly available online, while the platform will remain open for new submissions.
••16 Jun 2012
TL;DR: A unique change detection benchmark dataset consisting of nearly 90,000 frames in 31 video sequences representing 6 categories selected to cover a wide range of challenges in 2 modalities (color and thermal IR).
Abstract: Change detection is one of the most commonly encountered low-level tasks in computer vision and video processing. A plethora of algorithms have been developed to date, yet no widely accepted, realistic, large-scale video dataset exists for benchmarking different methods. Presented here is a unique change detection benchmark dataset consisting of nearly 90,000 frames in 31 video sequences representing 6 categories selected to cover a wide range of challenges in 2 modalities (color and thermal IR). A distinguishing characteristic of this dataset is that each frame is meticulously annotated for ground-truth foreground, background, and shadow area boundaries — an effort that goes much beyond a simple binary label denoting the presence of change. This enables objective and precise quantitative comparison and ranking of change detection algorithms. This paper presents and discusses various aspects of the new dataset, quantitative performance metrics used, and comparative results for over a dozen previous and new change detection algorithms. The dataset, evaluation tools, and algorithm rankings are available to the public on a website1 and will be updated with feedback from academia and industry in the future.
••23 Jun 2014
TL;DR: The latest release of the changedetection.net dataset is presented, which includes 22 additional videos spanning 5 new categories that incorporate challenges encountered in many surveillance settings and highlights strengths and weaknesses of these methods and identifies remaining issues in change detection.
Abstract: Change detection is one of the most important lowlevel tasks in video analytics. In 2012, we introduced the changedetection.net (CDnet) benchmark, a video dataset devoted to the evalaution of change and motion detection approaches. Here, we present the latest release of the CDnet dataset, which includes 22 additional videos (70; 000 pixel-wise annotated frames) spanning 5 new categories that incorporate challenges encountered in many surveillance settings. We describe these categories in detail and provide an overview of the results of more than a dozen methods submitted to the IEEE Change DetectionWorkshop 2014. We highlight strengths and weaknesses of these methods and identify remaining issues in change detection.
••21 Jul 2017
TL;DR: A simplified convolutional neural network which combines local and global information through a multi-resolution 4×5 grid structure is proposed which implements a loss function inspired by the Mumford-Shah functional which penalizes errors on the boundary, enabling near real-time, high performance saliency detection.
Abstract: Saliency detection aims to highlight the most relevant objects in an image. Methods using conventional models struggle whenever salient objects are pictured on top of a cluttered background while deep neural nets suffer from excess complexity and slow evaluation speeds. In this paper, we propose a simplified convolutional neural network which combines local and global information through a multi-resolution 4×5 grid structure. Instead of enforcing spacial coherence with a CRF or superpixels as is usually the case, we implemented a loss function inspired by the Mumford-Shah functional which penalizes errors on the boundary. We trained our model on the MSRA-B dataset, and tested it on six different saliency benchmark datasets. Results show that our method is on par with the state-of-the-art while reducing computation time by a factor of 18 to 100 times, enabling near real-time, high performance saliency detection.
TL;DR: This paper reviews the major deep learning concepts pertinent to medical image analysis and summarizes over 300 contributions to the field, most of which appeared in the last year, to survey the use of deep learning for image classification, object detection, segmentation, registration, and other tasks.
Abstract: Deep learning algorithms, in particular convolutional networks, have rapidly become a methodology of choice for analyzing medical images. This paper reviews the major deep learning concepts pertinent to medical image analysis and summarizes over 300 contributions to the field, most of which appeared in the last year. We survey the use of deep learning for image classification, object detection, segmentation, registration, and other tasks. Concise overviews are provided of studies per application area: neuro, retinal, pulmonary, digital pathology, breast, cardiac, abdominal, musculoskeletal. We end with a summary of the current state-of-the-art, a critical discussion of open challenges and directions for future research.
••15 Jun 2016
TL;DR: In this article, a volumetric, fully convolutional neural network (FCN) was proposed to predict segmentation for the whole volume at one time, which can deal with situations where there is a strong imbalance between the number of foreground and background voxels.
Abstract: Convolutional Neural Networks (CNNs) have been recently employed to solve problems from both the computer vision and medical image analysis fields. Despite their popularity, most approaches are only able to process 2D images while most medical data used in clinical practice consists of 3D volumes. In this work we propose an approach to 3D image segmentation based on a volumetric, fully convolutional, neural network. Our CNN is trained end-to-end on MRI volumes depicting prostate, and learns to predict segmentation for the whole volume at once. We introduce a novel objective function, that we optimise during training, based on Dice coefficient. In this way we can deal with situations where there is a strong imbalance between the number of foreground and background voxels. To cope with the limited number of annotated volumes available for training, we augment the data applying random non-linear transformations and histogram matching. We show in our experimental evaluation that our approach achieves good performances on challenging test data while requiring only a fraction of the processing time needed by other previous methods.
TL;DR: In this article, a review of deep learning-based object detection frameworks is provided, focusing on typical generic object detection architectures along with some modifications and useful tricks to improve detection performance further.
Abstract: Due to object detection’s close relationship with video analysis and image understanding, it has attracted much research attention in recent years. Traditional object detection methods are built on handcrafted features and shallow trainable architectures. Their performance easily stagnates by constructing complex ensembles that combine multiple low-level image features with high-level context from object detectors and scene classifiers. With the rapid development in deep learning, more powerful tools, which are able to learn semantic, high-level, deeper features, are introduced to address the problems existing in traditional architectures. These models behave differently in network architecture, training strategy, and optimization function. In this paper, we provide a review of deep learning-based object detection frameworks. Our review begins with a brief introduction on the history of deep learning and its representative tool, namely, the convolutional neural network. Then, we focus on typical generic object detection architectures along with some modifications and useful tricks to improve detection performance further. As distinct specific detection tasks exhibit different characteristics, we also briefly survey several specific tasks, including salient object detection, face detection, and pedestrian detection. Experimental analyses are also provided to compare various methods and draw some meaningful conclusions. Finally, several promising directions and tasks are provided to serve as guidelines for future work in both object detection and relevant neural network-based learning systems.
TL;DR: An efficient and effective dense training scheme which joins the processing of adjacent image patches into one pass through the network while automatically adapting to the inherent class imbalance present in the data, and improves on the state-of-the‐art for all three applications.
Abstract: This work is supported by the EPSRC First Grant scheme (grant ref no. EP/N023668/1) and partially funded under the 7th Framework Programme by the European Commission (TBIcare: http: //www.tbicare.eu/ ; CENTER-TBI: https://www.center-tbi.eu/). This work was further supported by a Medical Research Council (UK) Program Grant (Acute brain injury: heterogeneity of mechanisms, therapeutic targets and outcome effects [G9439390 ID 65883]), the UK National Institute of Health Research Biomedical Research Centre at Cambridge and Technology Platform funding provided by the UK Department of Health. KK is supported by the Imperial College London PhD Scholarship Programme. VFJN is supported by a Health Foundation/Academy of Medical Sciences Clinician Scientist Fellowship. DKM is supported by an NIHR Senior Investigator Award. We gratefully acknowledge the support of NVIDIA Corporation with the donation of two Titan X GPUs for our research.
TL;DR: This review covers computer-assisted analysis of images in the field of medical imaging and introduces the fundamentals of deep learning methods and their successes in image registration, detection of anatomical and cellular structures, tissue segmentation, computer-aided disease diagnosis and prognosis, and so on.
Abstract: This review covers computer-assisted analysis of images in the field of medical imaging. Recent advances in machine learning, especially with regard to deep learning, are helping to identify, classify, and quantify patterns in medical images. At the core of these advances is the ability to exploit hierarchical feature representations learned solely from data, instead of features designed by hand according to domain-specific knowledge. Deep learning is rapidly becoming the state of the art, leading to enhanced performance in various medical applications. We introduce the fundamentals of deep learning methods and review their successes in image registration, detection of anatomical and cellular structures, tissue segmentation, computer-aided disease diagnosis and prognosis, and so on. We conclude by discussing research issues and suggesting future directions for further improvement.