A Survey on Deep Learning in Medical Image Analysis

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 and provide concise overviews of studies per application area. Open challenges and directions for future research are discussed.Comment: Revised survey includes expanded discussion section and reworked introductory section on common deep architectures. Added missed papers from before Feb 1st 201

Object-based 2D-to-3D video conversion for effective stereoscopic content generation in 3D-TV applications

Three-dimensional television (3D-TV) has gained increasing popularity in the broadcasting domain, as it enables enhanced viewing experiences in comparison to conventional two-dimensional (2D) TV. However, its application has been constrained due to the lack of essential contents, i.e., stereoscopic videos. To alleviate such content shortage, an economical and practical solution is to reuse the huge media resources that are available in monoscopic 2D and convert them to stereoscopic 3D. Although stereoscopic video can be generated from monoscopic sequences using depth measurements extracted from cues like focus blur, motion and size, the quality of the resulting video may be poor as such measurements are usually arbitrarily defined and appear inconsistent with the real scenes. To help solve this problem, a novel method for object-based stereoscopic video generation is proposed which features i) optical-flow based occlusion reasoning in determining depth ordinal, ii) object segmentation using improved region-growing from masks of determined depth layers, and iii) a hybrid depth estimation scheme using content-based matching (inside a small library of true stereo image pairs) and depth-ordinal based regularization. Comprehensive experiments have validated the effectiveness of our proposed 2D-to-3D conversion method in generating stereoscopic videos of consistent depth measurements for 3D-TV applications

Attention Gated Networks: Learning to Leverage Salient Regions in Medical Images

We propose a novel attention gate (AG) model for medical image analysis that automatically learns to focus on target structures of varying shapes and sizes. Models trained with AGs implicitly learn to suppress irrelevant regions in an input image while highlighting salient features useful for a specific task. This enables us to eliminate the necessity of using explicit external tissue/organ localisation modules when using convolutional neural networks (CNNs). AGs can be easily integrated into standard CNN models such as VGG or U-Net architectures with minimal computational overhead while increasing the model sensitivity and prediction accuracy. The proposed AG models are evaluated on a variety of tasks, including medical image classification and segmentation. For classification, we demonstrate the use case of AGs in scan plane detection for fetal ultrasound screening. We show that the proposed attention mechanism can provide efficient object localisation while improving the overall prediction performance by reducing false positives. For segmentation, the proposed architecture is evaluated on two large 3D CT abdominal datasets with manual annotations for multiple organs. Experimental results show that AG models consistently improve the prediction performance of the base architectures across different datasets and training sizes while preserving computational efficiency. Moreover, AGs guide the model activations to be focused around salient regions, which provides better insights into how model predictions are made. The source code for the proposed AG models is publicly available.Comment: Accepted for Medical Image Analysis (Special Issue on Medical Imaging with Deep Learning). arXiv admin note: substantial text overlap with arXiv:1804.03999, arXiv:1804.0533

Computerized Analysis of Magnetic Resonance Images to Study Cerebral Anatomy in Developing Neonates

The study of cerebral anatomy in developing neonates is of great importance for the understanding of brain development during the early period of life. This dissertation therefore focuses on three challenges in the modelling of cerebral anatomy in neonates during brain development. The methods that have been developed all use Magnetic Resonance Images (MRI) as source data. To facilitate study of vascular development in the neonatal period, a set of image analysis algorithms are developed to automatically extract and model cerebral vessel trees. The whole process consists of cerebral vessel tracking from automatically placed seed points, vessel tree generation, and vasculature registration and matching. These algorithms have been tested on clinical Time-of- Flight (TOF) MR angiographic datasets. To facilitate study of the neonatal cortex a complete cerebral cortex segmentation and reconstruction pipeline has been developed. Segmentation of the neonatal cortex is not effectively done by existing algorithms designed for the adult brain because the contrast between grey and white matter is reversed. This causes pixels containing tissue mixtures to be incorrectly labelled by conventional methods. The neonatal cortical segmentation method that has been developed is based on a novel expectation-maximization (EM) method with explicit correction for mislabelled partial volume voxels. Based on the resulting cortical segmentation, an implicit surface evolution technique is adopted for the reconstruction of the cortex in neonates. The performance of the method is investigated by performing a detailed landmark study. To facilitate study of cortical development, a cortical surface registration algorithm for aligning the cortical surface is developed. The method first inflates extracted cortical surfaces and then performs a non-rigid surface registration using free-form deformations (FFDs) to remove residual alignment. Validation experiments using data labelled by an expert observer demonstrate that the method can capture local changes and follow the growth of specific sulcus

Tetrahedral Image-to-Mesh Conversion Software for Anatomic Modeling of Arteriovenous Malformations

We describe a new implementation of an adaptive multi-tissue tetrahedral mesh generator targeting anatomic modeling of Arteriovenous Malformation (AVM) for surgical simulations. Our method, initially constructs an adaptive Body-Centered Cubic (BCC) mesh of high quality elements. Then, it deforms the mesh surfaces to their corresponding physical image boundaries, hence, improving the mesh fidelity and smoothness. Our deformation scheme, which builds upon the ITK toolkit, is based on the concept of energy minimization, and relies on a multi-material point-based registration. It uses non-connectivity patterns to implicitly control the number of the extracted feature points needed for the registration, and thus, adjusts the trade-off between the achieved mesh fidelity and the deformation speed. While many medical imaging applications require robust mesh generation, there are few codes available to the public. We compare our implementation with two similar open-source image-to-mesh conversion codes: (1) Cleaver from US, and (2) CGAL from EU. Our evaluation is based on five isotropic/anisotropic segmented images, and relies on metrics like geometric & topologic fidelity, mesh quality, gradation and smoothness. The implementation we describe is open- source and it will be available within: (i) the 3D Slicer package for visualization and image analysis from Harvard Medical School, and (ii) an interactive simulator for neurosurgical procedures involving vasculature using SOFA, a framework for real-time medical simulation developed by INRIA