Adaptive Segmentation of Knee Radiographs for Selecting the Optimal ROI in Texture Analysis

The purposes of this study were to investigate: 1) the effect of placement of region-of-interest (ROI) for texture analysis of subchondral bone in knee radiographs, and 2) the ability of several texture descriptors to distinguish between the knees with and without radiographic osteoarthritis (OA). Bilateral posterior-anterior knee radiographs were analyzed from the baseline of OAI and MOST datasets. A fully automatic method to locate the most informative region from subchondral bone using adaptive segmentation was developed. We used an oversegmentation strategy for partitioning knee images into the compact regions that follow natural texture boundaries. LBP, Fractal Dimension (FD), Haralick features, Shannon entropy, and HOG methods were computed within the standard ROI and within the proposed adaptive ROIs. Subsequently, we built logistic regression models to identify and compare the performances of each texture descriptor and each ROI placement method using 5-fold cross validation setting. Importantly, we also investigated the generalizability of our approach by training the models on OAI and testing them on MOST dataset.We used area under the receiver operating characteristic (ROC) curve (AUC) and average precision (AP) obtained from the precision-recall (PR) curve to compare the results. We found that the adaptive ROI improves the classification performance (OA vs. non-OA) over the commonly used standard ROI (up to 9% percent increase in AUC). We also observed that, from all texture parameters, LBP yielded the best performance in all settings with the best AUC of 0.840 [0.825, 0.852] and associated AP of 0.804 [0.786, 0.820]. Compared to the current state-of-the-art approaches, our results suggest that the proposed adaptive ROI approach in texture analysis of subchondral bone can increase the diagnostic performance for detecting the presence of radiographic OA

Scene understanding for interactive applications

Para interactuar con el entorno, es necesario entender que está ocurriendo en la escena donde se desarrolla la acción. Décadas de investigación en el campo de la visión por computador han contribuido a conseguir sistemas que permiten interpretar de manera automática el contenido en una escena a partir de información visual. Se podría decir el objetivo principal de estos sistemas es replicar la capacidad humana para extraer toda la información a partir solo de datos visuales. Por ejemplo, uno de sus objetivos es entender como percibimosel mundo en tres dimensiones o como podemos reconocer sitios y objetos a pesar de la gran variación en su apariencia. Una de las tareas básicas para entender una escena es asignar un significado semántico a cada elemento (píxel) de una imagen. Esta tarea se puede formular como un problema de etiquetado denso el cual especifica valores (etiquetas) a cada pixel o región de una imagen. Dependiendo de la aplicación, estas etiquetas puedenrepresentar conceptos muy diferentes, desde magnitudes físicas como la información de profundidad, hasta información semántica, como la categoría de un objeto. El objetivo general en esta tesis es investigar y desarrollar nuevas técnicas para incorporar automáticamente una retroalimentación por parte del usuario, o un conocimiento previo en sistemas inteligente para conseguir analizar automáticamente el contenido de una escena. en particular,esta tesis explora dos fuentes comunes de información previa proporcionado por los usuario: interacción humana y etiquetado manual de datos de ejemplo.La primera parte de esta tesis esta dedicada a aprendizaje de información de una escena a partir de información proporcionada de manera interactiva por un usuario. Las soluciones que involucran a un usuario imponen limitaciones en el rendimiento, ya que la respuesta que se le da al usuario debe obtenerse en un tiempo interactivo. Esta tesis presenta un paradigma eficiente que aproxima cualquier magnitud por píxel a partir de unos pocos trazos del usuario. Este sistema propaga los escasos datos de entrada proporcionados por el usuario a cada píxel de la imagen. El paradigma propuesto se ha validado a través detres aplicaciones interactivas para editar imágenes, las cuales requieren un conocimiento por píxel de una cierta magnitud, con el objetivo de simular distintos efectos.Otra estrategia común para aprender a partir de información de usuarios es diseñar sistemas supervisados de aprendizaje automático. En los últimos años, las redes neuronales convolucionales han superado el estado del arte de gran variedad de problemas de reconocimiento visual. Sin embargo, para nuevas tareas, los datos necesarios de entrenamiento pueden no estar disponibles y recopilar suficientes no es siempre posible. La segunda parte de esta tesis explora como mejorar los sistema que aprenden etiquetado denso semántico a partir de imágenes previamente etiquetadas por los usuarios. En particular, se presenta y validan estrategias, basadas en los dos principales enfoques para transferir modelos basados en deep learning, para segmentación semántica, con el objetivo de poder aprender nuevas clases cuando los datos de entrenamiento no son suficientes en cantidad o precisión.Estas estrategias se han validado en varios entornos realistas muy diferentes, incluyendo entornos urbanos, imágenes aereas y imágenes submarinas.In order to interact with the environment, it is necessary to understand what is happening on it, on the scene where the action is ocurring. Decades of research in the computer vision field have contributed towards automatically achieving this scene understanding from visual information. Scene understanding is a very broad area of research within the computer vision field. We could say that it tries to replicate the human capability of extracting plenty of information from visual data. For example, we would like to understand how the people perceive the world in three dimensions or can quickly recognize places or objects despite substantial appearance variation. One of the basic tasks in scene understanding from visual data is to assign a semantic meaning to every element of the image, i.e., assign a concept or object label to every pixel in the image. This problem can be formulated as a dense image labeling problem which assigns specific values (labels) to each pixel or region in the image. Depending on the application, the labels can represent very different concepts, from a physical magnitude, such as depth information, to high level semantic information, such as an object category. The general goal in this thesis is to investigate and develop new ways to automatically incorporate human feedback or prior knowledge in intelligent systems that require scene understanding capabilities. In particular, this thesis explores two common sources of prior information from users: human interactions and human labeling of sample data. The first part of this thesis is focused on learning complex scene information from interactive human knowledge. Interactive user solutions impose limitations on the performance where the feedback to the user must be at interactive rates. This thesis presents an efficient interaction paradigm that approximates any per-pixel magnitude from a few user strokes. It propagates the sparse user input to each pixel of the image. We demonstrate the suitability of the proposed paradigm through three interactive image editing applications which require per-pixel knowledge of certain magnitude: simulate the effect of depth of field, dehazing and HDR tone mapping. Other common strategy to learn from user prior knowledge is to design supervised machine-learning approaches. In the last years, Convolutional Neural Networks (CNNs) have pushed the state-of-the-art on a broad variety of visual recognition problems. However, for new tasks, enough training data is not always available and therefore, training from scratch is not always feasible. The second part of this thesis investigates how to improve systems that learn dense semantic labeling of images from user labeled examples. In particular, we present and validate strategies, based on common transfer learning approaches, for semantic segmentation. The goal of these strategies is to learn new specific classes when there is not enough labeled data to train from scratch. We evaluate these strategies across different environments, such as autonomous driving scenes, aerial images or underwater ones.<br /

Accurate segmentation and registration of skin lesion images to evaluate lesion change

Skin cancer is a major health problem. There are several techniques to help diagnose skin lesions from a captured image. Computer-aided diagnosis (CAD) systems operate on single images of skin lesions, extracting lesion features to further classify them and help the specialists. Accurate feature extraction, which later on depends on precise lesion segmentation, is key for the performance of these systems. In this paper, we present a skin lesion segmentation algorithm based on a novel adaptation of superpixels techniques and achieve the best reported results for the ISIC 2017 challenge dataset. Additionally, CAD systems have paid little attention to a critical criterion in skin lesion diagnosis: the lesion's evolution. This requires operating on two or more images of the same lesion, captured at different times but with a comparable scale, orientation, and point of view; in other words, an image registration process should first be performed. We also propose in this work, an image registration approach that outperforms top image registration techniques. Combined with the proposed lesion segmentation algorithm, this allows for the accurate extraction of features to assess the evolution of the lesion. We present a case study with the lesion-size feature, paving the way for the development of automatic systems to easily evaluate skin lesion evolutionThis work was supported in part by the Spanish Government (HAVideo, TEC2014-53176-R) and in part by the TEC department (Universidad Autonoma de Madrid

Combining local features and region segmentation: methods and applications

Tesis doctoral inédita leída en la Universidad Autónoma de Madrid, Escuela Politécnica Superior, Departamento de Tecnología Electrónica y de las Comunicaciones. Fecha de lectura: 23-01-2020Esta tesis tiene embargado el acceso al texto completo hasta el 23-07-2021Muchas y muy diferentes son las propuestas que se han desarrollado en el área de la visión artificial para la extracción de información de las imágenes y su posterior uso. Entra las más destacadas se encuentran las conocidas como características locales, del inglés local features, que detectan puntos o áreas de la imagen con ciertas características de interés, y las describen usando información de su entorno (local). También destacan las regiones en este área, y en especial este trabajo se ha centrado en los segmentadores en regiones, cuyo objetivo es agrupar la información de la imagen atendiendo a diversos criterios. Pese al enorme potencial de estas técnicas, y su probado éxito en diversas aplicaciones, su definición lleva implícita una serie de limitaciones funcionales que les han impedido exportar sus capacidades a otras áreas de aplicación. Se pretende impulsar el uso de estas herramientas en dichas aplicaciones, y por tanto mejorar los resultados del estado del arte, mediante la propuesta de un marco de desarrollo de nuevas soluciones. En concreto, la hipótesis principal del proyecto es que las capacidades de las características locales y los segmentadores en regiones son complementarias, y que su combinación, realizada de la forma adecuada, las maximiza a la vez que minimiza sus limitaciones. El principal objetivo, y por tanto la principal contribución del proyecto, es validar dicha hipótesis mediante la propuesta de un marco de desarrollo de nuevas soluciones combinando características locales y segmentadores para técnicas con capacidades mejoradas. Al tratarse de un marco de combinación de dos técnicas, el proceso de validación se ha llevado a cabo en dos pasos. En primer lugar se ha planteado el caso del uso de segmentadores en regiones para mejorar las características locales. Para verificar la viabilidad y el éxito de esta combinación se ha desarrollado una propuesta específica, SP-SIFT, que se ha validado tanto a nivel experimental como a nivel de aplicación real, en concreto como técnica principal de algoritmos de seguimiento de objetos. En segundo lugar, se ha planteado el caso de uso de características locales para mejorar los segmentadores en regiones. Para verificar la viabilidad y el éxito de esta combinación se ha desarrollado una propuesta específica, LF-SLIC, que se ha validado tanto a nivel experimental como a nivel de aplicación real, en concreto como técnica principal de un algoritmo de segmentación de lesiones pigmentadas de la piel. Los resultados conceptuales han probado que las técnicas mejoran a nivel de capacidades. Los resultados aplicados han probado que estas mejoras permiten el uso de estas técnicas en aplicaciones donde antes no tenían éxito. Con ello, se ha considerado la hipótesis validada, y por tanto exitosa la definición de un marco para el desarrollo de nuevas técnicas específicas con capacidades mejoradas. En conclusión, la principal aportación de la tesis es el marco de combinación de técnicas, plasmada en sus dos propuestas específicas: características locales mejoradas con segmentadores y segmentadores mejorados con características locales, y en el éxito conseguido en sus aplicaciones.A huge number of proposals have been developed in the area of computer vision for information extraction from images, and its further use. One of the most prevalent solutions are those known as local features. They detect points or areas of the image with certain characteristics of interest, and describe them using information from their (local) environment. The regions also stand out in the area, and especially this work has focused on the region segmentation algorithms, whose objective is to group the information of the image according to di erent criteria. Despite the enormous potential of these techniques, and their proven success in a number of applications, their de nition implies a series of functional limitations that have prevented them from exporting their capabilities to other application areas. In this thesis, it is intended to promote the use of these tools in these applications, and therefore improve the results of the state of the art, by proposing a framework for developing new solutions. Speci cally, the main hypothesis of the project is that the capacities of the local features and the region segmentation algorithms are complementary, and thus their combination, carried out in the right way, maximizes them while minimizing their limitations. The main objective, and therefore the main contribution of the thesis, is to validate this hypothesis by proposing a framework for developing new solutions combining local features and region segmentation algorithms, obtaining solutions with improved capabilities. As the hypothesis is proposing to combine two techniques, the validation process has been carried out in two steps. First, the use case of region segmentation algorithms enhancing local features. In order to verify the viability and success of this combination, a speci c proposal, SP-SIFT, was been developed. This proposal was validated both experimentally and in a real application scenario, speci cally as the main technique of object tracking algorithms. Second, the use case of enhancing region segmentation algorithm with local features. In order to verify the viability and success of this combination, a speci c proposal, LF-SLIC, was developed. The proposal was validated both experimentally and in a real application scenario, speci cally as the main technique of a pigmented skin lesions segmentation algorithm. The conceptual results proved that the techniques improve at the capabilities level. The application results proved that these improvements allow the use of this techniques in applications where they were previously unsuccessful. Thus, the hypothesis can be considered validated, and therefore the de nition of a framework for the development of new techniques with improved capabilities can be considered successful. In conclusion, the main contribution of the thesis is the framework for the combination of techniques, embodied in the two speci c proposals: enhanced local features with region segmentation algorithms, and region segmentation algorithms enhanced with local features; and in the success achieved in their applications.The work described in this Thesis was carried out within the Video Processing and Understanding Lab at the Department of Tecnología Electrónica y de las Comunicaciones, Escuela Politécnica Superior, Universidad Autónoma de Madrid (from 2014 to 2019). It was partially supported by the Spanish Government (TEC2014-53176-R, HAVideo)

A comparative study of algorithms for automatic segmentation of dermoscopic images

Melanoma is the most common as well as the most dangerous type of skin cancer. Nevertheless, it can be effectively treated if detected early. Dermoscopy is one of the major non-invasive imaging techniques for the diagnosis of skin lesions. The computer-aided diagnosis based on the processing of dermoscopic images aims to reduce the subjectivity and time-consuming analysis related to traditional diagnosis. The first step of automatic diagnosis is image segmentation. In this project, the implementation and evaluation of several methods were proposed for the automatic segmentation of lesion regions in dermoscopic images, along with the corresponding implemented phases for image preprocessing and postprocessing. The developed algorithms include methods based on different state of the art techniques. The main groups of techniques which have been selected to be studied and implemented are thresholding-based methods, region-based methods, segmentation based on deformable models, as well as a new proposed approach based on the bag-of-words model. The implemented methods incorporate modifications for a better adaptation to features associated with dermoscopic images. Each implemented method was applied to a database constituted by 724 dermoscopic images. The output of the automatic segmentation procedure for each image was compared with the corresponding manual segmentation in order to evaluate the performance. The comparison between algorithms was carried out regarding the obtained evaluation metrics. The best results were achieved by the combination of region-based segmentation based on the multi-region adaptation of the k-means algorithm and the subIngeniería de Sistemas Audiovisuale

Human shape modelling for carried object detection and segmentation

La détection des objets transportés est un des prérequis pour développer des systèmes qui cherchent à comprendre les activités impliquant des personnes et des objets. Cette thèse présente de nouvelles méthodes pour détecter et segmenter les objets transportés dans des vidéos de surveillance. Les contributions sont divisées en trois principaux chapitres. Dans le premier chapitre, nous introduisons notre détecteur d’objets transportés, qui nous permet de détecter un type générique d’objets. Nous formulons la détection d’objets transportés comme un problème de classification de contours. Nous classifions le contour des objets mobiles en deux classes : objets transportés et personnes. Un masque de probabilités est généré pour le contour d’une personne basé sur un ensemble d’exemplaires (ECE) de personnes qui marchent ou se tiennent debout de différents points de vue. Les contours qui ne correspondent pas au masque de probabilités généré sont considérés comme des candidats pour être des objets transportés. Ensuite, une région est assignée à chaque objet transporté en utilisant la Coupe Biaisée Normalisée (BNC) avec une probabilité obtenue par une fonction pondérée de son chevauchement avec l’hypothèse du masque de contours de la personne et du premier plan segmenté. Finalement, les objets transportés sont détectés en appliquant une Suppression des Non-Maxima (NMS) qui élimine les scores trop bas pour les objets candidats. Le deuxième chapitre de contribution présente une approche pour détecter des objets transportés avec une méthode innovatrice pour extraire des caractéristiques des régions d’avant-plan basée sur leurs contours locaux et l’information des super-pixels. Initiallement, un objet bougeant dans une séquence vidéo est segmente en super-pixels sous plusieurs échelles. Ensuite, les régions ressemblant à des personnes dans l’avant-plan sont identifiées en utilisant un ensemble de caractéristiques extraites de super-pixels dans un codebook de formes locales. Ici, les régions ressemblant à des humains sont équivalentes au masque de probabilités de la première méthode (ECE). Notre deuxième détecteur d’objets transportés bénéficie du nouveau descripteur de caractéristiques pour produire une carte de probabilité plus précise. Les compléments des super-pixels correspondants aux régions ressemblant à des personnes dans l’avant-plan sont considérés comme une carte de probabilité des objets transportés. Finalement, chaque groupe de super-pixels voisins avec une haute probabilité d’objets transportés et qui ont un fort support de bordure sont fusionnés pour former un objet transporté. Finalement, dans le troisième chapitre, nous présentons une méthode pour détecter et segmenter les objets transportés. La méthode proposée adopte le nouveau descripteur basé sur les super-pixels pour iii identifier les régions ressemblant à des objets transportés en utilisant la modélisation de la forme humaine. En utilisant l’information spatio-temporelle des régions candidates, la consistance des objets transportés récurrents, vus dans le temps, est obtenue et sert à détecter les objets transportés. Enfin, les régions d’objets transportés sont raffinées en intégrant de l’information sur leur apparence et leur position à travers le temps avec une extension spatio-temporelle de GrabCut. Cette étape finale sert à segmenter avec précision les objets transportés dans les séquences vidéo. Nos méthodes sont complètement automatiques, et font des suppositions minimales sur les personnes, les objets transportés, et les les séquences vidéo. Nous évaluons les méthodes décrites en utilisant deux ensembles de données, PETS 2006 et i-Lids AVSS. Nous évaluons notre détecteur et nos méthodes de segmentation en les comparant avec l’état de l’art. L’évaluation expérimentale sur les deux ensembles de données démontre que notre détecteur d’objets transportés et nos méthodes de segmentation surpassent de façon significative les algorithmes compétiteurs.Detecting carried objects is one of the requirements for developing systems that reason about activities involving people and objects. This thesis presents novel methods to detect and segment carried objects in surveillance videos. The contributions are divided into three main chapters. In the first, we introduce our carried object detector which allows to detect a generic class of objects. We formulate carried object detection in terms of a contour classification problem. We classify moving object contours into two classes: carried object and person. A probability mask for person’s contours is generated based on an ensemble of contour exemplars (ECE) of walking/standing humans in different viewing directions. Contours that are not falling in the generated hypothesis mask are considered as candidates for carried object contours. Then, a region is assigned to each carried object candidate contour using Biased Normalized Cut (BNC) with a probability obtained by a weighted function of its overlap with the person’s contour hypothesis mask and segmented foreground. Finally, carried objects are detected by applying a Non-Maximum Suppression (NMS) method which eliminates the low score carried object candidates. The second contribution presents an approach to detect carried objects with an innovative method for extracting features from foreground regions based on their local contours and superpixel information. Initially, a moving object in a video frame is segmented into multi-scale superpixels. Then human-like regions in the foreground area are identified by matching a set of extracted features from superpixels against a codebook of local shapes. Here the definition of human like regions is equivalent to a person’s probability map in our first proposed method (ECE). Our second carried object detector benefits from the novel feature descriptor to produce a more accurate probability map. Complement of the matching probabilities of superpixels to human-like regions in the foreground are considered as a carried object probability map. At the end, each group of neighboring superpixels with a high carried object probability which has strong edge support is merged to form a carried object. Finally, in the third contribution we present a method to detect and segment carried objects. The proposed method adopts the new superpixel-based descriptor to identify carried object-like candidate regions using human shape modeling. Using spatio-temporal information of the candidate regions, consistency of recurring carried object candidates viewed over time is obtained and serves to detect carried objects. Last, the detected carried object regions are refined by integrating information of their appearances and their locations over time with a spatio-temporal extension of GrabCut. This final stage is used to accurately segment carried objects in frames. Our methods are fully automatic, and make minimal assumptions about a person, carried objects and videos. We evaluate the aforementioned methods using two available datasets PETS 2006 and i-Lids AVSS. We compare our detector and segmentation methods against a state-of-the-art detector. Experimental evaluation on the two datasets demonstrates that both our carried object detection and segmentation methods significantly outperform competing algorithms