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

Ultrafast Ultrasound Imaging

Among medical imaging modalities, such as computed tomography (CT) and magnetic resonance imaging (MRI), ultrasound imaging stands out due to its temporal resolution. Owing to the nature of medical ultrasound imaging, it has been used for not only observation of the morphology of living organs but also functional imaging, such as blood flow imaging and evaluation of the cardiac function. Ultrafast ultrasound imaging, which has recently become widely available, significantly increases the opportunities for medical functional imaging. Ultrafast ultrasound imaging typically enables imaging frame-rates of up to ten thousand frames per second (fps). Due to the extremely high temporal resolution, this enables visualization of rapid dynamic responses of biological tissues, which cannot be observed and analyzed by conventional ultrasound imaging. This Special Issue includes various studies of improvements to the performance of ultrafast ultrasoun

Measuring blood flow and pro-inflammatory changes in the rabbit aorta

Atherosclerosis is a chronic inflammatory disease that develops as a consequence of progressive entrapment of low density lipoprotein, fibrous proteins and inflammatory cells in the arterial intima. Once triggered, a myriad of inflammatory and atherogenic factors mediate disease progression. However, the role of pro-inflammatory activity in the initiation of atherogenesis and its relation to altered mechanical stresses acting on the arterial wall is unclear. Estimation of wall shear stress (WSS) and the inflammatory mediator NF-κB is consequently useful. In this thesis novel ultrasound tools for accurate measurement of spatiotemporally varying 2D and 3D blood flow, with and without the use of contrast agents, have been developed. This allowed for the first time accurate, broad-view quantification of WSS around branches of the rabbit abdominal aorta. A thorough review of the evidence for a relationship between flow, NF-κB and disease was performed which highlighted discrepancies in the current literature and was used to guide the study design. Subsequently, methods for the measurement and colocalization of the spatial distribution of NF-κB, arterial permeability and nuclear morphology in the aorta of New Zealand White rabbits were developed. It was demonstrated that endothelial pro-inflammatory changes are spatially correlated with patterns of WSS, nuclear morphology and arterial permeability in vivo in the rabbit descending and abdominal aorta. The data are consistent with a causal chain between WSS, macromolecule uptake, inflammation and disease, and with the hypothesis that lipids are deposited first, through flow-mediated naturally occurring transmigration that, in excessive amounts, leads to subsequent inflammation and disease.Open Acces

Developing Ultrasound-Based Computer-Aided Diagnostic Systems Through Statistical Pattern Recognition

Computer-aided diagnosis (CAD) is the use of a computer software to help physicians having a better interpretation of medical images. CAD systems can be viewed as pattern recognition algorithms that identify suspicious signs on a medical image and complement physicians' judgments, by reducing inter-/intra-observer variability and subjectivity. The proposed CAD systems in this thesis have been designed based on the statistical approach to pattern recognition as the most successfully used technique in practice. The main focus of this thesis has been on designing (new) feature extraction and classification algorithms for ultrasound-based CAD purposes. Ultrasound imaging has a broad range of usage in medical applications because it is a safe device which does not use harmful ionizing radiations, it provides clinicians with real-time images, it is portable and relatively cheap. The thesis was concerned with developing new ultrasound-based systems for the diagnosis of prostate cancer (PCa) and myocardial infarction (MI) where these issues have been addressed in two separate parts. In the first part, 1) a new CAD system was designed for prostate cancer biopsy by focusing on handling uncertainties in labels of the ground truth data, 2) the appropriateness of the independent component analysis (ICA) method for learning features from radiofrequency (RF) signals, backscattered from prostate tissues, was examined and, 3) a new ensemble scheme for learning ICA dictionaries from RF signals, backscattered from a tissue mimicking phantom, was proposed. In the second part, 1) principal component analysis (PCA) was used for the statistical modeling of the temporal deformation patterns of the left ventricle (LV) to detect abnormalities in its regional function, 2) a spatio-temporal representation of LV function based on PCA parameters was proposed to detect MI and, 3) a local-to-global statistical shape model based on PCA was presented to detect MI

Clutter Suppression in Ultrasound: Performance Evaluation of Low-Rank and Sparse Matrix Decomposition Methods

Vessel diseases are often accompanied by abnormalities related to vascular shape and size. Therefore, a clear visualization of vasculature is of high clinical significance. Ultrasound Color Flow Imaging (CFI) is one of the prominent techniques for flow visualization. However, clutter signals originating from slow-moving tissue is one of the main obstacles to obtain a clear view of the vascular network. Enhancement of the vasculature by suppressing the clutters is an essential step for many applications of ultrasound CFI. In this thesis, we focus on a state-of-art algorithm framework called Decomposition into Low-rank and Sparse Matrices (DLSM) framework for ultrasound clutter suppression. Currently, ultrasound clutter suppression is often performed by Singular Value Decomposition (SVD) of the data matrix, which is a branch of eigen-based filtering. This approach exhibits two well-known limitations. First, the performance of SVD is sensitive to the proper manual selection of the ranks corresponding to clutter and blood subspaces. Second, SVD is prone to failure in the presence of large random noise in the data set. A potential solution to these issues is the use of DLSM framework. SVD, as a means for singular values, is also one of the widely used algorithms for solving the minimization problem under the DLSM framework. Many other algorithms under DLSM avoid full SVD and use approximated SVD or SVD-free ideas which may have better performance with higher robustness and lower computing time due to the expensive computational cost of full SVD. In practice, these models separate blood from clutter based on the assumption that steady clutter represents a low-rank structure and the moving blood component is sparse. In this thesis, we exploit the feasibility of exploiting low-rank and sparse decomposition schemes, originally developed in the field of computer vision, in ultrasound clutter suppression. Since ultrasound images have different texture and statistical properties compared to images in computer vision, it is of high importance to evaluate how these methods translate to ultrasound CFI. We conduct this evaluation study by adapting 106 DLSM algorithms and validating them against simulation, phantom and in vivo rat data sets. The advantage of simulation and phantom experiments is that the ground truth vessel map is known, and the advantage of the in vivo data set is that it enables us to test algorithms in a realistic setting. Two conventional quality metrics, Signal-to-Noise Ratio (SNR) and Contrast-to-Noise Ratio (CNR), are used for performance evaluation. In addition, computation times required by different algorithms for generating the clutter suppressed images are reported. Our extensive analysis shows that the DLSM framework can be successfully applied to ultrasound clutter suppression

ARFI Ultrasound for the Detection and Characterization of Atherosclerosis in an FH Pig Model

Stroke is the third leading cause of death in the United States, with a large percentage of strokes caused by atherosclerotic rupture. Current methods of atherosclerotic detection include invasive techniques such as coronary angiography and intravascular ultrasound (IVUS), as well as noninvasive techniques such as magnetic resonance angiography and duplex ultrasound. These methods are known to be effective for detecting occlusive plaques associated with pronounced narrowing of the vessel lumen and/or blood flow obstruction. However, they are not effective for detecting nonstenotic plaques or for characterizing plaque composition. This lack of plaque compositional information prevents these imaging techniques from detecting plaque rupture risk. To accurately assess atherosclerotic plaques most vulnerable to rupture, novel detection and characterization techniques are needed. Acoustic radiation force impulse (ARFI) ultrasound, one of several elastographic techniques under development to meet this need, uses high intensity acoustic impulses to remotely displace tissue. By assessing ARFI-induced displacement and subsequent tissue recovery, the mechanical properties of tissue can be assessed and used to characterize atherosclerosis. In order to ensure the best possible plaque detection capability, the most appropriate beam sequences must be used. Following ex vivo and in vivo demonstration of ARFI capability for atherosclerotic plaque detection and characterization, a statistical reader study of ARFI beam sequences is performed in phantoms as well as ex vivo and in vivo in an FH pig model. Finally, a serial study of ARFI is performed to assess ARFI repeatability and potential for early plaque detection. This dissertation supports the hypothesis: in vivo, transcutaneous ARFI ultrasound will detect occlusive and nonocclusive plaques in peripheral arteries, assess plaque composition and structure and detect changes in atherosclerotic status over time