Upper airways segmentation using principal curvatures

Esta tesis propone una nueva técnica para segmentar las vías aéreas superiores. Esta propuesta permite la extracción de estructuras curvilíneas usando curvaturas principales. La propuesta permite la extracción de éstas estructuras en imágenes 2D y 3D. Entre las principales novedades se encuentra la propuesta de un nuevo criterio de parada en la propagación del algoritmo de realce de contraste (operador multi-escala de tipo sombrero alto). De la misma forma, el criterio de parada propuesto es usado para detener los algoritmos de difusión anisotrópica. Además, un nuevo criterio es propuesto para seleccionar las curvaturas principales que conforman las estructuras curvilíneas, que se basa en los criterios propuestos por Steger, Deng et. al. y Armande et. al. Además, se propone un nuevo algoritmo para realizar la supresión de nomáximos que permite reducir la presencia de discontinuidades en el borde de las estructuras curvilíneas. Para extraer los bordes de las estructuras curvilíneas, se utiliza un algoritmo de enlace que incluye un nuevo criterio de distancia para reducir la aparición de agujeros en la estructura final. Finalmente, con base en los resultados obtenidos, se utiliza un algoritmo morfológico para cerrar los agujeros y se aplica un algoritmo de crecimiento de regiones para obtener la segmentación final de las vías respiratorias superiores.This dissertation proposes a new approach to segment the upper airways. This proposal allows the extraction of curvilinear structures based on the principal curvatures. The proposal allows extracting these structures from 2D and 3D images. Among the main novelties is the proposal of a new stopping criterion to stop the propagation of the contrast enhancement algorithm (multiscale top-hat morphological operator). In the same way, the proposed stopping criterion is used to stop the anisotropic diffusion algorithms. In addition, a new criterion is proposed to select the principal curvatures that make up the curvilinear structures, which is based on the criteria proposed by Steger, Deng et. al. and Armande et. al. Furthermore, a new algorithm to perform the non-maximum suppression that allows reducing the presence of discontinuities in the border of curvilinear structures is proposed. To extract the edges of the curvilinear structures, a linking algorithm is used that includes a new distance criterion to reduce the appearance of gaps in the final structure. Finally, based on the obtained results, a morphological algorithm is used to close the gaps and a region growing algorithm to obtain the final upper airways segmentation is applied.Doctor en IngenieríaDoctorad

Variational Multi-Task Models for Image Analysis: Applications to Magnetic Resonance Imaging

This thesis deals with the study and development of several variational multi-task models for solving inverse problems in imaging, with a particular focus on Magnetic Resonance Imaging (MRI). In most image processing problems, one usually deals with the reconstruction task, i.e., the task of reconstructing an image from indirect measurements, and then performs various operations, one after the other (i.e. sequentially), to improve the quality of the reconstruction and to extract useful information. However, recent developments in a variational context, have shown that performing those tasks jointly (i.e. in a multi-task framework) offers great benefits, and this is the perspective that we follow in this thesis. We go beyond traditional sequential approaches and set a new basis for variational multi-task methods for MRI analysis. We demonstrate that by sharing representation between tasks and carefully interconnecting them, one can create synergies across challenging problems and reduce error propagation. More precisely, firstly we propose a multi-task variational model to tackle the problems of image reconstruction and image segmentation using non-convex Bregman iteration. We describe theoretical and numerical details of the problem and its optimisation scheme. Moreover, we show that our multi-task model achieves better results in several examples and MRI applications than existing approaches in the same context. Secondly, we show that our approach can be extended to a multi-task reconstruction and segmentation model for the nonlinear inverse problem of velocity-encoded MRI. In this context, the aim is to estimate not only the magnitude from MRI data, but also the phase and its flow information, whilst simultaneously identify regions of interest through the segmentation task. Finally, we go beyond two-task frameworks and introduce for the first time a variational multi-task model to handle three imaging tasks. To this end, we design a variational multi-task framework addressing reconstruction, super-resolution and registration for improving the quality of MRI reconstruction. We demonstrate that our model is theoretically well-motivated and it outperforms sequential models whilst requiring less computational cost. Furthermore, we show through experimental results the potential of this approach for clinical applications

Computational Methods for Segmentation of Multi-Modal Multi-Dimensional Cardiac Images

Segmentation of the heart structures helps compute the cardiac contractile function quantified via the systolic and diastolic volumes, ejection fraction, and myocardial mass, representing a reliable diagnostic value. Similarly, quantification of the myocardial mechanics throughout the cardiac cycle, analysis of the activation patterns in the heart via electrocardiography (ECG) signals, serve as good cardiac diagnosis indicators. Furthermore, high quality anatomical models of the heart can be used in planning and guidance of minimally invasive interventions under the assistance of image guidance. The most crucial step for the above mentioned applications is to segment the ventricles and myocardium from the acquired cardiac image data. Although the manual delineation of the heart structures is deemed as the gold-standard approach, it requires significant time and effort, and is highly susceptible to inter- and intra-observer variability. These limitations suggest a need for fast, robust, and accurate semi- or fully-automatic segmentation algorithms. However, the complex motion and anatomy of the heart, indistinct borders due to blood flow, the presence of trabeculations, intensity inhomogeneity, and various other imaging artifacts, makes the segmentation task challenging. In this work, we present and evaluate segmentation algorithms for multi-modal, multi-dimensional cardiac image datasets. Firstly, we segment the left ventricle (LV) blood-pool from a tri-plane 2D+time trans-esophageal (TEE) ultrasound acquisition using local phase based filtering and graph-cut technique, propagate the segmentation throughout the cardiac cycle using non-rigid registration-based motion extraction, and reconstruct the 3D LV geometry. Secondly, we segment the LV blood-pool and myocardium from an open-source 4D cardiac cine Magnetic Resonance Imaging (MRI) dataset by incorporating average atlas based shape constraint into the graph-cut framework and iterative segmentation refinement. The developed fast and robust framework is further extended to perform right ventricle (RV) blood-pool segmentation from a different open-source 4D cardiac cine MRI dataset. Next, we employ convolutional neural network based multi-task learning framework to segment the myocardium and regress its area, simultaneously, and show that segmentation based computation of the myocardial area is significantly better than that regressed directly from the network, while also being more interpretable. Finally, we impose a weak shape constraint via multi-task learning framework in a fully convolutional network and show improved segmentation performance for LV, RV and myocardium across healthy and pathological cases, as well as, in the challenging apical and basal slices in two open-source 4D cardiac cine MRI datasets. We demonstrate the accuracy and robustness of the proposed segmentation methods by comparing the obtained results against the provided gold-standard manual segmentations, as well as with other competing segmentation methods

An investigation of real time ultrasound Doppler techniques for tissue motion and deformation analysis

Cardiovascular disease accounts for more than 50% of all deaths in the Western world. Atherosclerosis is responsible for the vast majority of these diseases. There are a range of risk factors for atherosclerosis that affect the endothelial lining vessel wall cells to cause endothelial dysfunction, which then predisposes to a localized build-up of 'plaque' tissue that narrows the lumen of the arteries. Plaque rupture promotes localized vasospasm, thrombosis and embolism causing downstream tissue death, resulting in severe disability or death from, for instance, heart attack (in the coronary circulation) or stroke (in the cerebral circulation). Narrowing of the lumen and plaque rupture are associated with high tissue stresses and tissue under perfusion, which will alter local arterial and myocardial wall dynamics and elastic properties. Hence visualization of tissue dynamic and deformation property changes is crucial to detect atherosclerosis in the earliest stages to prevent acute events.The objective of this dissertation research is to develop new techniques based on Doppler ultrasound to investigate and visualize changes in tissue dynamic and deformation properties due to atherosclerosis in cardiac and vascular applications. A new technique, to correct for the Doppler angle dependence for tissue motion analysis has been developed. It is based on multiple ultrasound beams, and has been validated in vitro to study tissue dynamic properties. It can measure tissue velocity magnitude with low bias (5%) and standard deviation (10%), and tissue velocity orientation with a bias less than 5 degrees and a standard deviation below 5 degrees. A new Doppler based method, called strain rate, has also been developed and validated in vitro for the quantification of regional vessel or myocardial wall deformation. Strain rate is derived from the velocity information and can assess tissue deformation with an accuracy of 5% and a standard deviation less than 10%. Some examples of cardiac strain rate imaging have been gathered and are described in this thesis. Strain rate, as all Doppler based techniques, suffers from angle dependence limitation. A method to estimate one-component strain rate in any direction in the two-dimensional image not necessarily along the ultrasound beam has been developed. The method allows correcting for the strain rate bias along any user-defined direction. It is also shown that the full strain rate tensor can theoretically be extracted from the velocity vector field acquired by multiple beam tissue vector velocity technique. In vitro experiments have shown that qualitative two-component strain rate tensor can be derived. Two-component vector velocity from the moving tissue was acquired and two two-component strain rate images were derived. The images showed agreement with the expected deformation pattern

Exploiting Spatio-Temporal Coherence for Video Object Detection in Robotics

This paper proposes a method to enhance video object detection for indoor environments in robotics. Concretely, it exploits knowledge about the camera motion between frames to propagate previously detected objects to successive frames. The proposal is rooted in the concepts of planar homography to propose regions of interest where to find objects, and recursive Bayesian filtering to integrate observations over time. The proposal is evaluated on six virtual, indoor environments, accounting for the detection of nine object classes over a total of ∼ 7k frames. Results show that our proposal improves the recall and the F1-score by a factor of 1.41 and 1.27, respectively, as well as it achieves a significant reduction of the object categorization entropy (58.8%) when compared to a two-stage video object detection method used as baseline, at the cost of small time overheads (120 ms) and precision loss (0.92).</p

Study of Computational Image Matching Techniques: Improving Our View of Biomedical Image Data

Image matching techniques are proven to be necessary in various fields of science and engineering, with many new methods and applications introduced over the years. In this PhD thesis, several computational image matching methods are introduced and investigated for improving the analysis of various biomedical image data. These improvements include the use of matching techniques for enhancing visualization of cross-sectional imaging modalities such as Computed Tomography (CT) and Magnetic Resonance Imaging (MRI), denoising of retinal Optical Coherence Tomography (OCT), and high quality 3D reconstruction of surfaces from Scanning Electron Microscope (SEM) images. This work greatly improves the process of data interpretation of image data with far reaching consequences for basic sciences research. The thesis starts with a general notion of the problem of image matching followed by an overview of the topics covered in the thesis. This is followed by introduction and investigation of several applications of image matching/registration in biomdecial image processing: a) registration-based slice interpolation, b) fast mesh-based deformable image registration and c) use of simultaneous rigid registration and Robust Principal Component Analysis (RPCA) for speckle noise reduction of retinal OCT images. Moving towards a different notion of image matching/correspondence, the problem of view synthesis and 3D reconstruction, with a focus on 3D reconstruction of microscopic samples from 2D images captured by SEM, is considered next. Starting from sparse feature-based matching techniques, an extensive analysis is provided for using several well-known feature detector/descriptor techniques, namely ORB, BRIEF, SURF and SIFT, for the problem of multi-view 3D reconstruction. This chapter contains qualitative and quantitative comparisons in order to reveal the shortcomings of the sparse feature-based techniques. This is followed by introduction of a novel framework using sparse-dense matching/correspondence for high quality 3D reconstruction of SEM images. As will be shown, the proposed framework results in better reconstructions when compared with state-of-the-art sparse-feature based techniques. Even though the proposed framework produces satisfactory results, there is room for improvements. These improvements become more necessary when dealing with higher complexity microscopic samples imaged by SEM as well as in cases with large displacements between corresponding points in micrographs. Therefore, based on the proposed framework, a new approach is proposed for high quality 3D reconstruction of microscopic samples. While in case of having simpler microscopic samples the performance of the two proposed techniques are comparable, the new technique results in more truthful reconstruction of highly complex samples. The thesis is concluded with an overview of the thesis and also pointers regarding future directions of the research using both multi-view and photometric techniques for 3D reconstruction of SEM images

Forum Bildverarbeitung 2020

Image processing plays a key role for fast and contact-free data acquisition in many technical areas, e.g., in quality control or robotics. These conference proceedings of the “Forum Bildverarbeitung”, which took place on 26.-27.11.202 in Karlsruhe as a common event of the Karlsruhe Institute of Technology and the Fraunhofer Institute of Optronics, System Technologies and Image Exploitation, contain the articles of the contributions

Q(sqrt(-3))-Integral Points on a Mordell Curve

We use an extension of quadratic Chabauty to number fields,recently developed by the author with Balakrishnan, Besser and M ̈uller,combined with a sieving technique, to determine the integral points overQ(√−3) on the Mordell curve y2 = x3 − 4