Segmentación de Lesiones Hepáticas Adquiridas por Resonancia Magnética.

La detección y caracterización de lesiones hepáticas resulta fundamental en la práctica clínica, desde las etapas de diagnosis hasta la evolución de la respuesta terapéutica. La resonancia magnética hepática es una práctica habitual en la localización y cuantificación de las lesiones. Se presenta la segmentación automática de lesiones hepáticas en imágenes potenciadas en T1. La segmentación propuesta se basa en un procesado de difusión anisotrópica 3D adaptativo y carente de parámetros de control. A la imagen realzada se le aplica una combinación de técnicas de detección de bordes 3D, análisis del histograma, post procesado morfológico y evolución de un contorno activo 3D. Éste último fusiona información de apariencia y forma de la lesión

Robust semi-automated path extraction for visualising stenosis of the coronary arteries

Computed tomography angiography (CTA) is useful for diagnosing and planning treatment of heart disease. However, contrast agent in surrounding structures (such as the aorta and left ventricle) makes 3-D visualisation of the coronary arteries difficult. This paper presents a composite method employing segmentation and volume rendering to overcome this issue. A key contribution is a novel Fast Marching minimal path cost function for vessel centreline extraction. The resultant centreline is used to compute a measure of vessel lumen, which indicates the degree of stenosis (narrowing of a vessel). Two volume visualisation techniques are presented which utilise the segmented arteries and lumen measure. The system is evaluated and demonstrated using synthetic and clinically obtained datasets

Intelligent Segmentation of Medical Images using Fuzzy Bitplane Thresholding

The performance of assessment in medical image segmentation is highly correlated with the extraction of anatomic structures from them, and the major task is how to separate the regions of interests from the background and soft tissues successfully. This paper proposes a fuzzy logic based bitplane method to automatically segment the background of images and to locate the region of interest of medical images. This segmentation algorithm consists of three steps, namely identification, rule firing, and inference. In the first step, we begin by identifying the bitplanes that represent the lungs clearly. For this purpose, the intensity value of a pixel is separated into bitplanes. In the second step, the triple signum function assigns an optimum threshold based on the grayscale values for the anatomical structure present in the medical images. Fuzzy rules are formed based on the available bitplanes to form the membership table and are stored in a knowledge base. Finally, rules are fired to assign final segmentation values through the inference process. The proposed new metrics are used to measure the accuracy of the segmentation method. From the analysis, it is observed that the proposed metrics are more suitable for the estimation of segmentation accuracy. The results obtained from this work show that the proposed method performs segmentation effectively for the different classes of medical images

A novel MRA-based framework for the detection of changes in cerebrovascular blood pressure.

Background: High blood pressure (HBP) affects 75 million adults and is the primary or contributing cause of mortality in 410,000 adults each year in the United States. Chronic HBP leads to cerebrovascular changes and is a significant contributor for strokes, dementia, and cognitive impairment. Non-invasive measurement of changes in cerebral vasculature and blood pressure (BP) may enable physicians to optimally treat HBP patients. This manuscript describes a method to non-invasively quantify changes in cerebral vasculature and BP using Magnetic Resonance Angiography (MRA) imaging. Methods: MRA images and BP measurements were obtained from patients (n=15, M=8, F=7, Age= 49.2 ± 7.3 years) over a span of 700 days. A novel segmentation algorithm was developed to identify brain vasculature from surrounding tissue. The data was processed to calculate the vascular probability distribution function (PDF); a measure of the vascular diameters in the brain. The initial (day 0) PDF and final (day 700) PDF were used to correlate the changes in cerebral vasculature and BP. Correlation was determined by a mixed effects linear model analysis. Results: The segmentation algorithm had a 99.9% specificity and 99.7% sensitivity in identifying and delineating cerebral vasculature. The PDFs had a statistically significant correlation to BP changes below the circle of Willis (p-value = 0.0007), but not significant (p-value = 0.53) above the circle of Willis, due to smaller blood vessels. Conclusion: Changes in cerebral vasculature and pressure can be non-invasively obtained through MRA image analysis, which may be a useful tool for clinicians to optimize medical management of HBP

3-D fracture tracing for X-ray computed tomography data

X-ray computed tomography (CT) is a nondestructive imaging method that shows differences in X-ray attenuation, which is a proxy for density. Sensitivity to density differences makes CT a good choice for imaging open natural fractures because of the significant density contrast between air and rock. The image data, however, are prone to artifacts and blurring, which makes taking accurate measurements challenging. As a first step to addressing this problem, a tool was created to quantify the spatial resolution of CT data with a point-spread function (PSF). The PSF tool permits accurate measurement of fine-scale features in CT data – critical for measuring fractures, which are often thinner in one dimension than the PSF size, in turn influencing measurement of aperture. The difference between the measurements given by the PSF method and a simple threshold value pick is shown to demonstrate a non-trivial improvement in accuracy. In addition, a 3-D fracture network tracing algorithm was developed, for which the PSF is a necessary input, to characterize accurately the network’s attributes, such as fracture orientations, apertures, and roughnesses. To date, only single, isolated, relatively flat fractures have been characterized thoroughly in 3-D for CT data, and most numerical modeling has been conducted on 2D subsets. Additionally, research involving fracture networks is currently limited to simplified numerical models and simulations. This new work extends CT fracture characterization to the majority of fractured materials with 3-D networks, thus providing a source of real data for studying the difference between fracture networks and single fractures. A sample of Packsaddle schist, with a large number of thin fractures and complex, anastomosing bifurcations, was selected as a testing ground for the network tracing algorithms being developed. Preliminary analysis verifies the method’s efficacy.Geological Science

Computational Anatomy for Multi-Organ Analysis in Medical Imaging: A Review

The medical image analysis field has traditionally been focused on the development of organ-, and disease-specific methods. Recently, the interest in the development of more 20 comprehensive computational anatomical models has grown, leading to the creation of multi-organ models. Multi-organ approaches, unlike traditional organ-specific strategies, incorporate inter-organ relations into the model, thus leading to a more accurate representation of the complex human anatomy. Inter-organ relations are not only spatial, but also functional and physiological. Over the years, the strategies 25 proposed to efficiently model multi-organ structures have evolved from the simple global modeling, to more sophisticated approaches such as sequential, hierarchical, or machine learning-based models. In this paper, we present a review of the state of the art on multi-organ analysis and associated computation anatomy methodology. The manuscript follows a methodology-based classification of the different techniques 30 available for the analysis of multi-organs and multi-anatomical structures, from techniques using point distribution models to the most recent deep learning-based approaches. With more than 300 papers included in this review, we reflect on the trends and challenges of the field of computational anatomy, the particularities of each anatomical region, and the potential of multi-organ analysis to increase the impact of 35 medical imaging applications on the future of healthcare.Comment: Paper under revie

RAPID 3D TRACING OF THE MOUSE BRAIN NEUROVASCULATURE WITH LOCAL MAXIMUM INTENSITY PROJECTION AND MOVING WINDOWS

Neurovascular models have played an important role in understanding neuronal function or medical conditions. In the past few decades, only small volumes of neurovascular data have been available. However, huge data sets are becoming available with high throughput instruments like the Knife-Edge Scanning Microscope (KESM). Therefore, fast and robust tracing methods become necessary for tracing such large data sets. However, most tracing methods are not effective in handling complex structures such as branches. Some methods can solve this issue, but they are not computationally efficient (i.e., slow). Motivated by the issue of speed and robustness, I introduce an effective and efficient fiber tracing algorithm for 2D and 3D data. In 2D tracing, I have implemented a Moving Window (MW) method which leads to a mathematical simplification and noise robustness in determining the trace direction. Moreover, it provides enhanced handling of branch points. During tracing, a Cubic Tangential Trace Spline (CTTS) is used as an accurate and fast nonlinear interpolation approach. For 3D tracing, I have designed a method based on local maximum intensity projection (MIP). MIP can utilize any existing 2D tracing algorithms for use in 3D tracing. It can also significantly reduce the search space. However, most neurovascular data are too complex to directly use MIP on a large scale. Therefore, we use MIP within a limited cube to get unambiguous projections, and repeat the MIP-based approach over the entire data set. For processing large amounts of data, we have to automate the tracing algorithms. Since the automated algorithms may not be 100 percent correct, validation is needed. I validated my approach by comparing the traced results to human labeled ground truth showing that the result of my approach is very similar to the ground truth. However, this validation is limited to small-scale real-world data due to the limitation of the manual labeling. Therefore, for large-scale data, I validated my approach using a model-based generator. The result suggests that my approach can also be used for large-scale real-world data. The main contributions of this research are as follows. My 2D tracing algorithm is fast enough to analyze, with linear processing time based on fiber length, large volumes of biological data and is good at handling branches. The new local MIP approach for 3D tracing provides significant performance improvement and it allows the reuse of any existing 2D tracing methods. The model-based generator enables tracing algorithms to be validated for large-scale real-world data. My approach is widely applicable for rapid and accurate tracing of large amounts of biomedical data

Interactive Segmentation of 3D Medical Images with Implicit Surfaces

To cope with a variety of clinical applications, research in medical image processing has led to a large spectrum of segmentation techniques that extract anatomical structures from volumetric data acquired with 3D imaging modalities. Despite continuing advances in mathematical models for automatic segmentation, many medical practitioners still rely on 2D manual delineation, due to the lack of intuitive semi-automatic tools in 3D. In this thesis, we propose a methodology and associated numerical schemes enabling the development of 3D image segmentation tools that are reliable, fast and interactive. These properties are key factors for clinical acceptance. Our approach derives from the framework of variational methods: segmentation is obtained by solving an optimization problem that translates the expected properties of target objects in mathematical terms. Such variational methods involve three essential components that constitute our main research axes: an objective criterion, a shape representation and an optional set of constraints. As objective criterion, we propose a unified formulation that extends existing homogeneity measures in order to model the spatial variations of statistical properties that are frequently encountered in medical images, without compromising efficiency. Within this formulation, we explore several shape representations based on implicit surfaces with the objective to cover a broad range of typical anatomical structures. Firstly, to model tubular shapes in vascular imaging, we introduce convolution surfaces in the variational context of image segmentation. Secondly, compact shapes such as lesions are described with a new representation that generalizes Radial Basis Functions with non-Euclidean distances, which enables the design of basis functions that naturally align with salient image features. Finally, we estimate geometric non-rigid deformations of prior templates to recover structures that have a predictable shape such as whole organs. Interactivity is ensured by restricting admissible solutions with additional constraints. Translating user input into constraints on the sign of the implicit representation at prescribed points in the image leads us to consider inequality-constrained optimization

1 Segmentation of Thin Structures in Volumetric Medical Images

Abstract — We present a new segmentation method for extracting thin structures embedded in 3D medical images based on modern variational principles. We demonstrate the importance of the edge alignment and homogeneity terms in the segmentation of blood vessels and vascular trees. For that goal the Chan-Vese minimal variance method is combined with the boundary alignment, and the geodesic active surface models. An efficient numerical scheme is proposed. In order to simultaneously detect a number of different objects in the image, a hierarchal approach is applied. Index Terms — image segmentation, active contours, deformable models, energy minimization, level sets, variational principle I