Visual Quality Enhancement in Optoacoustic Tomography using Active Contour Segmentation Priors

Segmentation of biomedical images is essential for studying and characterizing anatomical structures, detection and evaluation of pathological tissues. Segmentation has been further shown to enhance the reconstruction performance in many tomographic imaging modalities by accounting for heterogeneities of the excitation field and tissue properties in the imaged region. This is particularly relevant in optoacoustic tomography, where discontinuities in the optical and acoustic tissue properties, if not properly accounted for, may result in deterioration of the imaging performance. Efficient segmentation of optoacoustic images is often hampered by the relatively low intrinsic contrast of large anatomical structures, which is further impaired by the limited angular coverage of some commonly employed tomographic imaging configurations. Herein, we analyze the performance of active contour models for boundary segmentation in cross-sectional optoacoustic tomography. The segmented mask is employed to construct a two compartment model for the acoustic and optical parameters of the imaged tissues, which is subsequently used to improve accuracy of the image reconstruction routines. The performance of the suggested segmentation and modeling approach are showcased in tissue-mimicking phantoms and small animal imaging experiments.Comment: Accepted for publication in IEEE Transactions on Medical Imagin

Imaging Informatics and the Human Brain Project: the Role of Structure, Review

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From 4D medical images (CT, MRI, and Ultrasound) to 4D structured mesh models of the left ventricular endocardium for patient-specific simulations

With cardiovascular disease (CVD) remaining the primary cause of death worldwide, early detection of CVDs becomes essential. The intracardiac flow is an important component of ventricular function, motion kinetics, wash-out of ventricular chambers, and ventricular energetics. Coupling between Computational Fluid Dynamics (CFD) simulations and medical images can play a fundamental role in terms of patient-specific diagnostic tools. From a technical perspective, CFD simulations with moving boundaries could easily lead to negative volumes errors and the sudden failure of the simulation. The generation of high-quality 4D meshes (3D in space + time) with 1-to-l vertex becomes essential to perform a CFD simulation with moving boundaries. In this context, we developed a semiautomatic morphing tool able to create 4D high-quality structured meshes starting from a segmented 4D dataset. To prove the versatility and efficiency, the method was tested on three different 4D datasets (Ultrasound, MRI, and CT) by evaluating the quality and accuracy of the resulting 4D meshes. Furthermore, an estimation of some physiological quantities is accomplished for the 4D CT reconstruction. Future research will aim at extending the region of interest, further automation of the meshing algorithm, and generating structured hexahedral mesh models both for the blood and myocardial volume

Sketching-out virtual humans: A smart interface for human modelling and animation

In this paper, we present a fast and intuitive interface for sketching out 3D virtual humans and animation. The user draws stick figure key frames first and chooses one for “fleshing-out” with freehand body contours. The system automatically constructs a plausible 3D skin surface from the rendered figure, and maps it onto the posed stick figures to produce the 3D character animation. A “creative model-based method” is developed, which performs a human perception process to generate 3D human bodies of various body sizes, shapes and fat distributions. In this approach, an anatomical 3D generic model has been created with three distinct layers: skeleton, fat tissue, and skin. It can be transformed sequentially through rigid morphing, fatness morphing, and surface fitting to match the original 2D sketch. An auto-beautification function is also offered to regularise the 3D asymmetrical bodies from users’ imperfect figure sketches. Our current system delivers character animation in various forms, including articulated figure animation, 3D mesh model animation, 2D contour figure animation, and even 2D NPR animation with personalised drawing styles. The system has been formally tested by various users on Tablet PC. After minimal training, even a beginner can create vivid virtual humans and animate them within minutes

3D shape reconstruction of the femur from planar X-ray images using statistical shape and appearance models

Major trauma is a condition that can result in severe bone damage. Customised orthopaedic reconstruction allows for limb salvage surgery and helps to restore joint alignment. For the best possible outcome three dimensional (3D) medical imaging is necessary, but its availability and access, especially in developing countries, can be challenging. In this study, 3D bone shapes of the femur reconstructed from planar radiographs representing bone defects were evaluated for use in orthopaedic surgery. Statistical shape and appearance models generated from 40 cadaveric X-ray computed tomography (CT) images were used to reconstruct 3D bone shapes. The reconstruction simulated bone defects of between 0% and 50% of the whole bone, and the prediction accuracy using anterior–posterior (AP) and anterior–posterior/medial–lateral (AP/ML) X-rays were compared. As error metrics for the comparison, measures evaluating the distance between contour lines of the projections as well as a measure comparing similarities in image intensities were used. The results were evaluated using the root-mean-square distance for surface error as well as differences in commonly used anatomical measures, including bow, femoral neck, diaphyseal–condylar and version angles between reconstructed surfaces from the shape model and the intact shape reconstructed from the CT image. The reconstructions had average surface errors between 1.59 and 3.59 mm with reconstructions using the contour error metric from the AP/ML directions being the most accurate. Predictions of bow and femoral neck angles were well below the clinical threshold accuracy of 3°, diaphyseal–condylar angles were around the threshold of 3° and only version angle predictions of between 5.3° and 9.3° were above the clinical threshold, but below the range reported in clinical practice using computer navigation (i.e., 17° internal to 15° external rotation). This study shows that the reconstructions from partly available planar images using statistical shape and appearance models had an accuracy which would support their potential use in orthopaedic reconstruction

Volumetric segmentation of multiple basal ganglia structures

We present a new active contour-based, statistical method for simultaneous volumetric segmentation of multiple subcortical structures in the brain. Neighboring anatomical structures in the human brain exhibit co-dependencies which can aid in segmentation, if properly analyzed and modeled. Motivated by this observation, we formulate the segmentation problem as a maximum a posteriori estimation problem, in which we incorporate statistical prior models on the shapes and inter-shape (relative) poses of the structures of interest. This provides a principled mechanism to bring high level information about the shapes and the relationships of anatomical structures into the segmentation problem. For learning the prior densities based on training data, we use a nonparametric multivariate kernel density estimation framework. We combine these priors with data in a variational framework, and develop an active contour-based iterative segmentation algorithm. We test our method on the problem of volumetric segmentation of basal ganglia structures in magnetic resonance (MR) images. We compare our technique with existing methods and demonstrate the improvements it provides in terms of segmentation accuracy

Creation of 3D Multi-Body Orthodontic Models by Using Independent Imaging Sensors

In the field of dental health care, plaster models combined with 2D radiographs are widely used in clinical practice for orthodontic diagnoses. However, complex malocclusions can be better analyzed by exploiting 3D digital dental models, which allow virtual simulations and treatment planning processes. In this paper, dental data captured by independent imaging sensors are fused to create multi-body orthodontic models composed of teeth, oral soft tissues and alveolar bone structures. The methodology is based on integrating Cone-Beam Computed Tomography (CBCT) and surface structured light scanning. The optical scanner is used to reconstruct tooth crowns and soft tissues (visible surfaces) through the digitalization of both patients’ mouth impressions and plaster casts. These data are also used to guide the segmentation of internal dental tissues by processing CBCT data sets. The 3D individual dental tissues obtained by the optical scanner and the CBCT sensor are fused within multi-body orthodontic models without human supervisions to identify target anatomical structures. The final multi-body models represent valuable virtual platforms to clinical diagnostic and treatment planning

Reconstruction of Patient-Specific Bone Models from X-Ray Radiography

The availability of a patient‐specific bone model has become an increasingly invaluable addition to orthopedic case evaluation and planning [1]. Utilized within a wide range of specialized visualization and analysis tools, such models provide unprecedented wealth of bone shape information previously unattainable using traditional radiographic imaging [2]. In this work, a novel bone reconstruction method from two or more x‐ray images is described. This method is superior to previous attempts in terms of accuracy and repeatability. The new technique accurately models the radiological scene in a way that eliminates the need for expensive multi‐planar radiographic imaging systems. It is also flexible enough to allow for both short and long film imaging using standard radiological protocols, which makes the technology easily utilized in standard clinical setups

Gait recognition based on shape and motion analysis of silhouette contours

This paper presents a three-phase gait recognition method that analyses the spatio-temporal shape and dynamic motion (STS-DM) characteristics of a human subject’s silhouettes to identify the subject in the presence of most of the challenging factors that affect existing gait recognition systems. In phase 1, phase-weighted magnitude spectra of the Fourier descriptor of the silhouette contours at ten phases of a gait period are used to analyse the spatio-temporal changes of the subject’s shape. A component-based Fourier descriptor based on anatomical studies of human body is used to achieve robustness against shape variations caused by all common types of small carrying conditions with folded hands, at the subject’s back and in upright position. In phase 2, a full-body shape and motion analysis is performed by fitting ellipses to contour segments of ten phases of a gait period and using a histogram matching with Bhattacharyya distance of parameters of the ellipses as dissimilarity scores. In phase 3, dynamic time warping is used to analyse the angular rotation pattern of the subject’s leading knee with a consideration of arm-swing over a gait period to achieve identification that is invariant to walking speed, limited clothing variations, hair style changes and shadows under feet. The match scores generated in the three phases are fused using weight-based score-level fusion for robust identification in the presence of missing and distorted frames, and occlusion in the scene. Experimental analyses on various publicly available data sets show that STS-DM outperforms several state-of-the-art gait recognition methods