Accurate Segmentation of Cerebrovasculature from TOF-MRA Images Using Appearance Descriptors

© 2013 IEEE. Analyzing cerebrovascular changes can significantly lead to not only detecting the presence of serious diseases e.g., hypertension and dementia, but also tracking their progress. Such analysis could be better performed using Time-of-Flight Magnetic Resonance Angiography (ToF-MRA) images, but this requires accurate segmentation of the cerebral vasculature from the surroundings. To achieve this goal, we propose a fully automated cerebral vasculature segmentation approach based on extracting both prior and current appearance features that have the ability to capture the appearance of macro and micro-vessels in ToF-MRA. The appearance prior is modeled with a novel translation and rotation invariant Markov-Gibbs Random Field (MGRF) of voxel intensities with pairwise interaction analytically identified from a set of training data sets. The appearance of the cerebral vasculature is also represented with a marginal probability distribution of voxel intensities by using a Linear Combination of Discrete Gaussians (LCDG) that its parameters are estimated by using a modified Expectation-Maximization (EM) algorithm. The extracted appearance features are separable and can be classified by any classifier, as demonstrated by our segmentation results. To validate the accuracy of our algorithm, we tested the proposed approach on in-vivo data using 270 data sets, which were qualitatively validated by a neuroradiology expert. The results were quantitatively validated using the three commonly used metrics for segmentation evaluation: the Dice coefficient, the modified Hausdorff distance, and the absolute volume difference. The proposed approach showed a higher accuracy compared to two of the existing segmentation approaches

Computer Vision Techniques for Transcatheter Intervention

Minimally invasive transcatheter technologies have demonstrated substantial promise for the diagnosis and treatment of cardiovascular diseases. For example, TAVI is an alternative to AVR for the treatment of severe aortic stenosis and TAFA is widely used for the treatment and cure of atrial fibrillation. In addition, catheter-based IVUS and OCT imaging of coronary arteries provides important information about the coronary lumen, wall and plaque characteristics. Qualitative and quantitative analysis of these cross-sectional image data will be beneficial for the evaluation and treatment of coronary artery diseases such as atherosclerosis. In all the phases (preoperative, intraoperative, and postoperative) during the transcatheter intervention procedure, computer vision techniques (e.g., image segmentation, motion tracking) have been largely applied in the field to accomplish tasks like annulus measurement, valve selection, catheter placement control, and vessel centerline extraction. This provides beneficial guidance for the clinicians in surgical planning, disease diagnosis, and treatment assessment. In this paper, we present a systematical review on these state-of-the-art methods.We aim to give a comprehensive overview for researchers in the area of computer vision on the subject of transcatheter intervention. Research in medical computing is multi-disciplinary due to its nature, and hence it is important to understand the application domain, clinical background, and imaging modality so that methods and quantitative measurements derived from analyzing the imaging data are appropriate and meaningful. We thus provide an overview on background information of transcatheter intervention procedures, as well as a review of the computer vision techniques and methodologies applied in this area

Generalizable automated pixel-level structural segmentation of medical and biological data

Over the years, the rapid expansion in imaging techniques and equipments has driven the demand for more automation in handling large medical and biological data sets. A wealth of approaches have been suggested as optimal solutions for their respective imaging types. These solutions span various image resolutions, modalities and contrast (staining) mechanisms. Few approaches generalise well across multiple image types, contrasts or resolution. This thesis proposes an automated pixel-level framework that addresses 2D, 2D+t and 3D structural segmentation in a more generalizable manner, yet has enough adaptability to address a number of specific image modalities, spanning retinal funduscopy, sequential fluorescein angiography and two-photon microscopy. The pixel-level segmentation scheme involves: i ) constructing a phase-invariant orientation field of the local spatial neighbourhood; ii ) combining local feature maps with intensity-based measures in a structural patch context; iii ) using a complex supervised learning process to interpret the combination of all the elements in the patch in order to reach a classification decision. This has the advantage of transferability from retinal blood vessels in 2D to neural structures in 3D. To process the temporal components in non-standard 2D+t retinal angiography sequences, we first introduce a co-registration procedure: at the pairwise level, we combine projective RANSAC with a quadratic homography transformation to map the coordinate systems between any two frames. At the joint level, we construct a hierarchical approach in order for each individual frame to be registered to the global reference intra- and inter- sequence(s). We then take a non-training approach that searches in both the spatial neighbourhood of each pixel and the filter output across varying scales to locate and link microvascular centrelines to (sub-) pixel accuracy. In essence, this \link while extract" piece-wise segmentation approach combines the local phase-invariant orientation field information with additional local phase estimates to obtain a soft classification of the centreline (sub-) pixel locations. Unlike retinal segmentation problems where vasculature is the main focus, 3D neural segmentation requires additional exibility, allowing a variety of structures of anatomical importance yet with different geometric properties to be differentiated both from the background and against other structures. Notably, cellular structures, such as Purkinje cells, neural dendrites and interneurons, all display certain elongation along their medial axes, yet each class has a characteristic shape captured by an orientation field that distinguishes it from other structures. To take this into consideration, we introduce a 5D orientation mapping to capture these orientation properties. This mapping is incorporated into the local feature map description prior to a learning machine. Extensive performance evaluations and validation of each of the techniques presented in this thesis is carried out. For retinal fundus images, we compute Receiver Operating Characteristic (ROC) curves on existing public databases (DRIVE & STARE) to assess and compare our algorithms with other benchmark methods. For 2D+t retinal angiography sequences, we compute the error metrics ("Centreline Error") of our scheme with other benchmark methods. For microscopic cortical data stacks, we present segmentation results on both surrogate data with known ground-truth and experimental rat cerebellar cortex two-photon microscopic tissue stacks.Open Acces

A novel automated approach of multi-modality retinal image registration and fusion

Biomedical image registration and fusion are usually scene dependent, and require intensive computational effort. A novel automated approach of feature-based control point detection and area-based registration and fusion of retinal images has been successfully designed and developed. The new algorithm, which is reliable and time-efficient, has an automatic adaptation from frame to frame with few tunable threshold parameters. The reference and the to-be-registered images are from two different modalities, i.e. angiogram grayscale images and fundus color images. The relative study of retinal images enhances the information on the fundus image by superimposing information contained in the angiogram image. Through the thesis research, two new contributions have been made to the biomedical image registration and fusion area. The first contribution is the automatic control point detection at the global direction change pixels using adaptive exploratory algorithm. Shape similarity criteria are employed to match the control points. The second contribution is the heuristic optimization algorithm that maximizes Mutual-Pixel-Count (MPC) objective function. The initially selected control points are adjusted during the optimization at the sub-pixel level. A global maxima equivalent result is achieved by calculating MPC local maxima with an efficient computation cost. The iteration stops either when MPC reaches the maximum value, or when the maximum allowable loop count is reached. To our knowledge, it is the first time that the MPC concept has been introduced into biomedical image fusion area as the measurement criteria for fusion accuracy. The fusion image is generated based on the current control point coordinates when the iteration stops. The comparative study of the presented automatic registration and fusion scheme against Centerline Control Point Detection Algorithm, Genetic Algorithm, RMSE objective function, and other existing data fusion approaches has shown the advantage of the new approach in terms of accuracy, efficiency, and novelty

Computer integrated system: medical imaging & visualization

The intent of this book’s conception is to present research work using a user centered design approach. Due to space constraints, the story of the journey, included in this book is relatively brief. However we believe that it manages to adequately represent the story of the journey, from its humble beginnings in 2008 to the point where it visualizes future trends amongst both researchers and practitioners across the Computer Science and Medical disciplines. This book aims not only to present a representative sampling of real-world collaboration between said disciplines but also to provide insights into the different aspects related to the use of real-world Computer Assisted Medical applications. Readers and potential clients should find the information particularly useful in analyzing the benefits of collaboration between these two fields, the products in and of their institutions. The work discussed here is a compilation of the work of several PhD students under my supervision, who have since graduated and produced several publications either in journals or proceedings of conferences. As their work has been published, this book will be more focused on the research methodology based on medical technology used in their research. The research work presented in this book partially encompasses the work under the MOA for collaborative Research and Development in the field of Computer Assisted Surgery and Diagnostics pertaining to Thoracic and Cardiovascular Diseases between UPM, UKM and IJN, spanning five years beginning from 15 Feb 2013

3D reconstruction of coronary arteries from angiographic sequences for interventional assistance

Introduction -- Review of literature -- Research hypothesis and objectives -- Methodology -- Results and discussion -- Conclusion and future perspectives

Intravascular Ultrasound

Intravascular ultrasound (IVUS) is a cardiovascular imaging technology using a specially designed catheter with a miniaturized ultrasound probe for the assessment of vascular anatomy with detailed visualization of arterial layers. Over the past two decades, this technology has developed into an indispensable tool for research and clinical practice in cardiovascular medicine, offering the opportunity to gather diagnostic information about the process of atherosclerosis in vivo, and to directly observe the effects of various interventions on the plaque and arterial wall. This book aims to give a comprehensive overview of this rapidly evolving technique from basic principles and instrumentation to research and clinical applications with future perspectives

Enhancing a Neurosurgical Imaging System with a PC-based Video Processing Solution

This work presents a PC-based prototype video processing application developed to be used with a specific neurosurgical imaging device, the OPMI® PenteroTM operating microscope, in the Department of Neurosurgery of Helsinki University Central Hospital at Töölö, Helsinki. The motivation for implementing the software was the lack of some clinically important features in the imaging system provided by the microscope. The imaging system is used as an online diagnostic aid during surgery. The microscope has two internal video cameras; one for regular white light imaging and one for near-infrared fluorescence imaging, used for indocyanine green videoangiography. The footage of the microscope’s current imaging mode is accessed via the composite auxiliary output of the device. The microscope also has an external high resolution white light video camera, accessed via a composite output of a separate video hub. The PC was chosen as the video processing platform for its unparalleled combination of prototyping and high-throughput video processing capabilities. A thorough analysis of the platform and efficient video processing methods was conducted in the thesis and the results were used in the design of the imaging station. The features found feasible during the project were incorporated into a video processing application running on a GNU/Linux distribution Ubuntu. The clinical usefulness of the implemented features was ensured beforehand by consulting the neurosurgeons using the original system. The most significant shortcomings of the original imaging system were mended in this work. The key features of the developed application include: live streaming, simultaneous streaming and recording, and playing back of upto two video streams. The playback mode provides full media player controls, with a frame-by-frame precision rewinding, in an intuitive and responsive interface. A single view and a side-by-side comparison mode are provided for the streams. The former gives more detail, while the latter can be used, for example, for before-after and anatomic-angiographic comparisons.fi=Opinnäytetyö kokotekstinä PDF-muodossa.|en=Thesis fulltext in PDF format.|sv=Lärdomsprov tillgängligt som fulltext i PDF-format

Automated retinal analysis

Diabetes is a chronic disease affecting over 2% of the population in the UK [1]. Long-term complications of diabetes can affect many different systems of the body including the retina of the eye. In the retina, diabetes can lead to a disease called diabetic retinopathy, one of the leading causes of blindness in the working population of industrialised countries. The risk of visual loss from diabetic retinopathy can be reduced if treatment is given at the onset of sight-threatening retinopathy. To detect early indicators of the disease, the UK National Screening Committee have recommended that diabetic patients should receive annual screening by digital colour fundal photography [2]. Manually grading retinal images is a subjective and costly process requiring highly skilled staff. This thesis describes an automated diagnostic system based oil image processing and neural network techniques, which analyses digital fundus images so that early signs of sight threatening retinopathy can be identified. Within retinal analysis this research has concentrated on the development of four algorithms: optic nerve head segmentation, lesion segmentation, image quality assessment and vessel width measurements. This research amalgamated these four algorithms with two existing techniques to form an integrated diagnostic system. The diagnostic system when used as a 'pre-filtering' tool successfully reduced the number of images requiring human grading by 74.3%: this was achieved by identifying and excluding images without sight threatening maculopathy from manual screening

Mri Assessment Of Maternal Uteroplacental Circulation In Pregnancy

Hypertensive pregnancy disorders (HPD) such as preeclampsia are highly associated with maternal vascular malperfusion of the placenta, an organ that exchanges nutrients and oxygen between the maternal circulation and the growing fetus. Adverse pregnancy outcomes are difficult to predict because there is insufficient understanding of how poor maternal arterial remodeling leads to disease. There is also a lack of reliable tools to evaluate these changes in early gestation. The hypothesis of this dissertation was that magnetic resonance imaging (MRI) could noninvasively evaluate uteroplacental function in vivo through a combination of arterial spin labeling (ASL), 4D flow, and time-of-flight (TOF) techniques which were already effective in the evalution of other cardiovascular diseases. These flow and perfusion imaging studies were conducted on human pregnant volunteers in their second and third trimesters at 1.5T. Many of them were also examined by conventional Doppler ultrasound (US) and followed through delivery. Flow-sensitive Alternating Inversion Recovery (FAIR) ASL MRI with background suppression was found to be feasible in detecting placental perfusion signal despite the presence of motion artifacts. An important consideration when studying placental ASL was the slow movement of maternal arterial blood in a large cavity called the intervillous space. This was a unique feature of placental anatomy which distinguished it from other organs containing capillaries. It became apparent that traditional models to estimate perfusion from MRI were no longer applicable. In this work, a statistical approach was first developed to filter out motion artifacts, followed by a coordinate transformation to better represent the lobular distribution of blood flow in the intervillous space of the placenta. The uterine arteries (UtAs) are the main maternal blood supply of the placenta and have also long been suspected to be involved in HPD, though US-based measurements have not yet been found to be highly predictive for widespread clinical use. In this work, 4D flow MRI enabled visualization of the tortuous UtAs while measuring volumetric flow rate. Its performance in predicting incidence of preeclampsia and small-for-gestational age births was comparable to Doppler US. When considering the innovative potential of 4D flow MRI to capture complex flow dynamics, this validation demonstrated the value of continuing technical development for improving HPD risk assessment. Furthermore, centerline extraction of the maternal pelvic arteries in TOF MRI, from the descending aorta to the UtAs and external iliac arteries, provided quantitative metrics to characterize the geometry including path length and curvature. Pulse wave velocity (PWV) was estimated using path length by TOF MRI and velocimetry by 2D phase contrast and 4D flow MRI with results showing sensitivity to differences between UtAs and external iliac arteries. These approaches provided physiological metrics to explore and characterize the remodeling process of the uteroplacental arteries. This dissertation demonstrates the feasibility of measuring structure and hemodynamics of the maternal vascular blood supply using non-contrast MRI that can lead to the more reliable biomarkers of adverse pregnancy outcomes needed to diagnose and treat HPD