Visual attention models and arse representations for morphometrical image analysis

Abstract. Medical diagnosis, treatment, follow-up and research activities are nowadays strongly supported on different types of diagnostic images, whose main goal is to provide an useful exchange of medical knowledge. This multi-modal information needs to be processed in order to extract information exploitable within the context of a particular medical task. In despite of the relevance of these complementary sources of medical knowledge, medical images are rarely further processed in actual clinical practice, so the specialists take decisions only based in the raw data. A new trend in the development of medical image processing and analysis tools follows the idea of biologically-inspired methods, which resemble the performance of the human vision system. Visual attention models and sparse representations are examples of this tendency. Based on this, the aim of this thesis was the development of a set of computational methods for automatic morph metrical analysis, combining the relevant region extraction power of visual attention models with the incorporation of a priori information capabilities of sparse representations. The combination of these biologically inspired tools with common machine learning techniques allowed the identification of visual patterns relevant for pathology discrimination, improving the accuracy and interpretability of morph metric measures and comparisons. After extensive validations with different image data sets, the computational methods proposed in this thesis seems to be promising tools for the definition of anatomical biomarkers, based on visual pattern analysis, and suitable for patient's diagnosis, prognosis and follow-up.Las actividades de diagnóstico, tratamiento, seguimiento e investigación en medicina están actualmente soportadas en diferentes clases de imágenes diagnósticas, cuyo objetivo principal es el de proveer un intercambio efectivo de conocimiento médico. Esta información multimodal necesita ser procesada con el objetivo de extraer información aprovechable en el contexto de una tarea médica particular. A pesar de la relevancia de estas fuentes complementarias de información clínica, las imágenes médicas son raramente procesadas en la práctica clínica actual, de forma que los especialistas sólo toman decisiones basados en los datos crudos. Una nueva tendencia en el desarrollo de herramientas de análisis y procesamiento de imágenes médicas persigue la idea de métodos biológicamente inspirados, que se asemejan al sistema de visión humana. Son ejemplos de esta tendencia los modelos de atención visual y las representaciones escasas (sparse representations). Con base en esto, el objetivo de esta tesis fue el desarrollo de un conjunto de métodos computacionales para soportar automáticamente los análisis morfo métricos, combinando el poder de extracción de regiones relevantes de los modelos de atención visual junto con la capacidad de incorporación de información a priori de las representaciones escasas. La combinación de estos métodos biológicamente inspirados con técnicas de aprendizaje de maquina facilito la identificación de patrones visuales relevantes para discriminar patologías cerebrales, mejorando la precisión e interpretabilidad de las medidas y comparaciones morfo métricas. Después de extensivas validaciones con diferentes conjuntos de imágenes, los métodos computacionales propuestos en esta tesis se perfilan como herramientas prometedoras para la definición de biomarcadores anatómicos, basados en el análisis visual de patrones, y convenientes para el diagnóstico, pronóstico y seguimiento del paciente.Doctorad

Joint super-resolution and synthesis of 1 mm isotropic MP-RAGE volumes from clinical MRI exams with scans of different orientation, resolution and contrast

Most existing algorithms for automatic 3D morphometry of human brain MRI scans are designed for data with near-isotropic voxels at approximately 1 mm resolution, and frequently have contrast constraints as well-typically requiring T1-weighted images (e.g., MP-RAGE scans). This limitation prevents the analysis of millions of MRI scans acquired with large inter-slice spacing in clinical settings every year. In turn, the inability to quantitatively analyze these scans hinders the adoption of quantitative neuro imaging in healthcare, and also precludes research studies that could attain huge sample sizes and hence greatly improve our understanding of the human brain. Recent advances in convolutional neural networks (CNNs) are producing outstanding results in super-resolution and contrast synthesis of MRI. However, these approaches are very sensitive to the specific combination of contrast, resolution and orientation of the input images, and thus do not generalize to diverse clinical acquisition protocols - even within sites. In this article, we present SynthSR, a method to train a CNN that receives one or more scans with spaced slices, acquired with different contrast, resolution and orientation, and produces an isotropic scan of canonical contrast (typically a 1 mm MP-RAGE). The presented method does not require any preprocessing, beyond rigid coregistration of the input scans. Crucially, SynthSR trains on synthetic input images generated from 3D segmentations, and can thus be used to train CNNs for any combination of contrasts, resolutions and orientations without high-resolution real images of the input contrasts. We test the images generated with SynthSR in an array of common downstream analyses, and show that they can be reliably used for subcortical segmentation and volumetry, image registration (e.g., for tensor-based morphometry), and, if some image quality requirements are met, even cortical thickness morphometry. The source code is publicly available at https://github.com/BBillot/SynthSR

Real-time Ultrasound Signals Processing: Denoising and Super-resolution

Ultrasound acquisition is widespread in the biomedical field, due to its properties of low cost, portability, and non-invasiveness for the patient. The processing and analysis of US signals, such as images, 2D videos, and volumetric images, allows the physician to monitor the evolution of the patient's disease, and support diagnosis, and treatments (e.g., surgery). US images are affected by speckle noise, generated by the overlap of US waves. Furthermore, low-resolution images are acquired when a high acquisition frequency is applied to accurately characterise the behaviour of anatomical features that quickly change over time. Denoising and super-resolution of US signals are relevant to improve the visual evaluation of the physician and the performance and accuracy of processing methods, such as segmentation and classification. The main requirements for the processing and analysis of US signals are real-time execution, preservation of anatomical features, and reduction of artefacts. In this context, we present a novel framework for the real-time denoising of US 2D images based on deep learning and high-performance computing, which reduces noise while preserving anatomical features in real-time execution. We extend our framework to the denoise of arbitrary US signals, such as 2D videos and 3D images, and we apply denoising algorithms that account for spatio-temporal signal properties into an image-to-image deep learning model. As a building block of this framework, we propose a novel denoising method belonging to the class of low-rank approximations, which learns and predicts the optimal thresholds of the Singular Value Decomposition. While previous denoise work compromises the computational cost and effectiveness of the method, the proposed framework achieves the results of the best denoising algorithms in terms of noise removal, anatomical feature preservation, and geometric and texture properties conservation, in a real-time execution that respects industrial constraints. The framework reduces the artefacts (e.g., blurring) and preserves the spatio-temporal consistency among frames/slices; also, it is general to the denoising algorithm, anatomical district, and noise intensity. Then, we introduce a novel framework for the real-time reconstruction of the non-acquired scan lines through an interpolating method; a deep learning model improves the results of the interpolation to match the target image (i.e., the high-resolution image). We improve the accuracy of the prediction of the reconstructed lines through the design of the network architecture and the loss function. %The design of the deep learning architecture and the loss function allow the network to improve the accuracy of the prediction of the reconstructed lines. In the context of signal approximation, we introduce our kernel-based sampling method for the reconstruction of 2D and 3D signals defined on regular and irregular grids, with an application to US 2D and 3D images. Our method improves previous work in terms of sampling quality, approximation accuracy, and geometry reconstruction with a slightly higher computational cost. For both denoising and super-resolution, we evaluate the compliance with the real-time requirement of US applications in the medical domain and provide a quantitative evaluation of denoising and super-resolution methods on US and synthetic images. Finally, we discuss the role of denoising and super-resolution as pre-processing steps for segmentation and predictive analysis of breast pathologies

Generative Models for Preprocessing of Hospital Brain Scans

I will in this thesis present novel computational methods for processing routine clinical brain scans. Such scans were originally acquired for qualitative assessment by trained radiologists, and present a number of difficulties for computational models, such as those within common neuroimaging analysis software. The overarching objective of this work is to enable efficient and fully automated analysis of large neuroimaging datasets, of the type currently present in many hospitals worldwide. The methods presented are based on probabilistic, generative models of the observed imaging data, and therefore rely on informative priors and realistic forward models. The first part of the thesis will present a model for image quality improvement, whose key component is a novel prior for multimodal datasets. I will demonstrate its effectiveness for super-resolving thick-sliced clinical MR scans and for denoising CT images and MR-based, multi-parametric mapping acquisitions. I will then show how the same prior can be used for within-subject, intermodal image registration, for more robustly registering large numbers of clinical scans. The second part of the thesis focusses on improved, automatic segmentation and spatial normalisation of routine clinical brain scans. I propose two extensions to a widely used segmentation technique. First, a method for this model to handle missing data, which allows me to predict entirely missing modalities from one, or a few, MR contrasts. Second, a principled way of combining the strengths of probabilistic, generative models with the unprecedented discriminative capability of deep learning. By introducing a convolutional neural network as a Markov random field prior, I can model nonlinear class interactions and learn these using backpropagation. I show that this model is robust to sequence and scanner variability. Finally, I show examples of fitting a population-level, generative model to various neuroimaging data, which can model, e.g., CT scans with haemorrhagic lesions

Sparse and low-rank techniques for the efficient restoration of images

Image reconstruction is a key problem in numerous applications of computer vision and medical imaging. By removing noise and artifacts from corrupted images, or by enhancing the quality of low-resolution images, reconstruction methods are essential to provide high-quality images for these applications. Over the years, extensive research efforts have been invested toward the development of accurate and efficient approaches for this problem. Recently, considerable improvements have been achieved by exploiting the principles of sparse representation and nonlocal self-similarity. However, techniques based on these principles often suffer from important limitations that impede their use in high-quality and large-scale applications. Thus, sparse representation approaches consider local patches during reconstruction, but ignore the global structure of the image. Likewise, because they average over groups of similar patches, nonlocal self-similarity methods tend to over-smooth images. Such methods can also be computationally expensive, requiring a hour or more to reconstruct a single image. Furthermore, existing reconstruction approaches consider either local patch-based regularization or global structure regularization, due to the complexity of combining both regularization strategies in a single model. Yet, such combined model could improve upon existing techniques by removing noise or reconstruction artifacts, while preserving both local details and global structure in the image. Similarly, current approaches rarely consider external information during the reconstruction process. When the structure to reconstruct is known, external information like statistical atlases or geometrical priors could also improve performance by guiding the reconstruction. This thesis addresses limitations of the prior art through three distinct contributions. The first contribution investigates the histogram of image gradients as a powerful prior for image reconstruction. Due to the trade-off between noise removal and smoothing, image reconstruction techniques based on global or local regularization often over-smooth the image, leading to the loss of edges and textures. To alleviate this problem, we propose a novel prior for preserving the distribution of image gradients modeled as a histogram. This prior is combined with low-rank patch regularization in a single efficient model, which is then shown to improve reconstruction accuracy for the problems of denoising and deblurring. The second contribution explores the joint modeling of local and global structure regularization for image restoration. Toward this goal, groups of similar patches are reconstructed simultaneously using an adaptive regularization technique based on the weighted nuclear norm. An innovative strategy, which decomposes the image into a smooth component and a sparse residual, is proposed to preserve global image structure. This strategy is shown to better exploit the property of structure sparsity than standard techniques like total variation. The proposed model is evaluated on the problems of completion and super-resolution, outperforming state-of-the-art approaches for these tasks. Lastly, the third contribution of this thesis proposes an atlas-based prior for the efficient reconstruction of MR data. Although popular, image priors based on total variation and nonlocal patch similarity often over-smooth edges and textures in the image due to the uniform regularization of gradients. Unlike natural images, the spatial characteristics of medical images are often restricted by the target anatomical structure and imaging modality. Based on this principle, we propose a novel MRI reconstruction method that leverages external information in the form of an probabilistic atlas. This atlas controls the level of gradient regularization at each image location, via a weighted total-variation prior. The proposed method also exploits the redundancy of nonlocal similar patches through a sparse representation model. Experiments on a large scale dataset of T1-weighted images show this method to be highly competitive with the state-of-the-art

Robust computational intelligence techniques for visual information processing

The third part is exclusively dedicated to the super-resolution of Magnetic Resonance Images. In one of these works, an algorithm based on the random shifting technique is developed. Besides, we studied noise removal and resolution enhancement simultaneously. To end, the cost function of deep networks has been modified by different combinations of norms in order to improve their training. Finally, the general conclusions of the research are presented and discussed, as well as the possible future research lines that are able to make use of the results obtained in this Ph.D. thesis.This Ph.D. thesis is about image processing by computational intelligence techniques. Firstly, a general overview of this book is carried out, where the motivation, the hypothesis, the objectives, and the methodology employed are described. The use and analysis of different mathematical norms will be our goal. After that, state of the art focused on the applications of the image processing proposals is presented. In addition, the fundamentals of the image modalities, with particular attention to magnetic resonance, and the learning techniques used in this research, mainly based on neural networks, are summarized. To end up, the mathematical framework on which this work is based on, ₚ-norms, is defined. Three different parts associated with image processing techniques follow. The first non-introductory part of this book collects the developments which are about image segmentation. Two of them are applications for video surveillance tasks and try to model the background of a scenario using a specific camera. The other work is centered on the medical field, where the goal of segmenting diabetic wounds of a very heterogeneous dataset is addressed. The second part is focused on the optimization and implementation of new models for curve and surface fitting in two and three dimensions, respectively. The first work presents a parabola fitting algorithm based on the measurement of the distances of the interior and exterior points to the focus and the directrix. The second work changes to an ellipse shape, and it ensembles the information of multiple fitting methods. Last, the ellipsoid problem is addressed in a similar way to the parabola