Abstract: The main objective of this thesis is to highlight the salient object in an image or in a video sequence. We address three important—but in our opinion
insufficiently investigated—aspects of saliency detection. Firstly, we start
by extending previous research on saliency which explicitly models the information provided from the context. Then, we show the importance of
explicit context modelling for saliency estimation. Several important works
in saliency are based on the usage of object proposals. However, these methods
focus on the saliency of the object proposal itself and ignore the context.
To introduce context in such saliency approaches, we couple every object
proposal with its direct context. This allows us to evaluate the importance
of the immediate surround (context) for its saliency. We propose several
saliency features which are computed from the context proposals including
features based on omni-directional and horizontal context continuity. Secondly,
we investigate the usage of top-downmethods (high-level semantic
information) for the task of saliency prediction since most computational
methods are bottom-up or only include few semantic classes. We propose
to consider a wider group of object classes. These objects represent important
semantic information which we will exploit in our saliency prediction
approach. Thirdly, we develop a method to detect video saliency by computing
saliency from supervoxels and optical flow. In addition, we apply the
context features developed in this thesis for video saliency detection. The
method combines shape and motion features with our proposed context
features. To summarize, we prove that extending object proposals with their
direct context improves the task of saliency detection in both image and
video data. Also the importance of the semantic information in saliency
estimation is evaluated. Finally, we propose a newmotion feature to detect
saliency in video data. The three proposed novelties are evaluated on standard
saliency benchmark datasets and are shown to improve with respect to
state-of-the-art.

Abstract: Over the last few years, the number of consumer computer vision applications has increased dramatically. Today, computer vision solutions can be found in video game consoles, smartphone applications, driving assistance – just to name a few. Ideally, we require the performance of those applications, particularly those that are safety critical to remain constant under any external environment factors, such as changes in illumination or weather conditions. However, this is not always possible or very difficult to obtain by only using visible imagery, due to the inherent limitations of the images from that spectral band. For that reason, the use of images from different or multiple spectral bands is becoming more appealing.
The aforementioned possible advantages of using images from multiples spectral bands on various vision applications make multi-spectral image processing a relevant topic for research and development. Like in visible image processing, multi-spectral image processing needs tools and algorithms to handle information from various spectral bands. Furthermore, traditional tools such as local feature detection, which is the basis of many vision tasks such as visual odometry, image registration, or structure from motion, must be adjusted or reformulated to operate under new conditions. Traditional feature detection, description, and matching methods tend to underperform in multi-spectral settings, in comparison to mono-spectral settings, due to the natural differences between each spectral band.
The work in this thesis is focused on the local feature description problem when cross-spectral images are considered. In this context, this dissertation has three main contributions. Firstly, the work starts by proposing the usage of a combination of frequency and spatial information, in a multi-scale scheme, as feature description. Evaluations of this proposal, based on classical hand-made feature descriptors, and comparisons with state of the art cross-spectral approaches help to find and understand limitations of such strategy. Secondly, different convolutional neural network (CNN) based architectures are evaluated when used to describe cross-spectral image patches. Results showed that CNN-based methods, designed to work with visible monocular images, could be successfully applied to the description of images from two different spectral bands, with just minor modifications. In this framework, a novel CNN-based network model, specifically intended to describe image patches from two different spectral bands, is proposed. This network, referred to as Q-Net, outperforms state of the art in the cross-spectral domain, including both previous hand-made solutions as well as L2 CNN-based architectures. The third contribution of this dissertation is in the cross-spectral feature description application domain. The multispectral odometry problem is tackled showing a real application of cross-spectral descriptors
In addition to the three main contributions mentioned above, in this dissertation, two different multi-spectral datasets are generated and shared with the community to be used as benchmarks for further studies.

Abstract: The original idea of this project was to study the role of colour in the challenging task of object recognition. We started by extending previous research on colour naming showing that it is feasible to capture colour terms through parsimonious ellipsoids. Although, the results of our model exceeded state-of-the-art in two benchmark datasets, we realised that the two phenomena of metameric lights and colour constancy must be addressed prior to any further colour processing. Our investigation of metameric pairs reached the conclusion that they are infrequent in real world scenarios. Contrary to that, the illumination of a scene often changes dramatically. We addressed this issue by proposing a colour constancy model inspired by the dynamical centre-surround adaptation of neurons in the visual cortex. This was implemented through two overlapping asymmetric Gaussians whose variances and heights are adjusted according to the local contrast of pixels. We complemented this model with a generic contrast-variant pooling mechanism that inversely connect the percentage of pooled signal to the local contrast of a region. The results of our experiments on four benchmark datasets were indeed promising: the proposed model, although simple, outperformed even learning-based approaches in many cases. Encouraged by the success of our contrast-variant surround modulation, we extended this approach to detect boundaries of objects. We proposed an edge detection model based on the first derivative of the Gaussian kernel. We incorporated four types of surround: full, far, iso- and orthogonal-orientation. Furthermore, we accounted for the pooling mechanism at higher cortical areas and the shape feedback sent to lower areas. Our results in three benchmark datasets showed significant improvement over non-learning algorithms.
To summarise, we demonstrated that biologically-inspired models offer promising solutions to computer vision problems, such as, colour naming, colour constancy and edge detection. We believe that the greatest contribution of this Ph.D dissertation is modelling the concept of dynamic surround modulation that shows the significance of contrast-variant surround integration. The models proposed here are grounded on only a portion of what we know about the human visual system. Therefore, it is only natural to complement them accordingly in future works.

Abstract: Latest advances in digitization techniques have fostered the interest in creating digital copies of collections of documents. Digitized documents permit an easy maintenance, loss-less storage, and efficient ways for transmission and to perform information retrieval processes. This situation has opened a new market niche to develop systems able to automatically extract and analyze information contained in these collections, specially in the ambit of the business activity.
Due to the great variety of types of documents this is not a trivial task. For instance, the automatic extraction of numerical data from invoices differs substantially from a task of text recognition in historical documents. However, in order to extract the information of interest, is always necessary to identify the area of the document where it is located. In the area of Document Analysis we refer to this process as layout analysis, which aims at identifying and categorizing the different entities that compose the document, such as text regions, pictures, text lines, or tables, among others. To perform this task it is usually necessary to incorporate a prior knowledge about the task into the analysis process, which can be modeled by defining a set of contextual relations between the different entities of the document. The use of context has proven to be useful to reinforce the recognition process and improve the results on many computer vision tasks. It presents two fundamental questions: What kind of contextual information is appropriate for a given task, and how to incorporate this information into the models.
In this thesis we study several ways to incorporate contextual information to the task of document layout analysis, and to the particular case of handwritten text line segmentation. We focus on the study of Probabilistic Graphical Models and other mechanisms for this purpose, and propose several solutions to these problems. First, we present a method for layout analysis based on Conditional Random Fields. With this model we encode local contextual relations between variables, such as pair-wise constraints. Besides, we encode a set of structural relations between different classes of regions at feature level. Second, we present a method based on 2D-Probabilistic Context-free Grammars to encode structural and hierarchical relations. We perform a comparative study between Probabilistic Graphical Models and this syntactic approach. Third, we propose a method for structured documents based on Bayesian Networks to represent the document structure, and an algorithm based in the Expectation-Maximization to find the best configuration of the page. We perform a thorough evaluation of the proposed methods on two particular collections of documents: a historical collection composed of ancient structured documents, and a collection of contemporary documents. In addition, we present a general method for the task of handwritten text line segmentation. We define a probabilistic framework where we combine the EM algorithm with variational approaches for computing inference and parameter learning on a Markov Random Field. We evaluate our method on several collections of documents, including a general dataset of annotated administrative documents. Results demonstrate the applicability of our method to real problems, and the contribution of the use of contextual information to this kind of problems.

Abstract: Image registration has been for many years the gold standard method to bring two images into correspondence. It has been used extensively in the eld of medical imaging in order to put images of dierent patients into a common overlapping spatial position. However, medical image registration is a slow, iterative optimization process, where many variables and prone to fall into the pit traps local minima.
A coordinate system parameterizing the interior of organs is a powerful tool for a systematic localization of injured tissue. If the same coordinate values are assigned to specic anatomical sites, parameterizations ensure integration of data across different medical image modalities. Harmonic mappings have been used to produce parametric meshes over the surface of anatomical shapes, given their ability to set values at specic locations through boundary conditions. However, most of the existing implementations in medical imaging restrict to either anatomical surfaces, or the depth coordinate with boundary conditions is given at discrete sites of limited geometric diversity.
The medial surface of the shape can be used to provide a continuous basis for the denition of a depth coordinate. However, given that dierent methods for generation of medial surfaces generate dierent manifolds, not all of them are equally suited to be the basis of radial coordinate for a parameterization. It would be desirable that the medial surface will be smooth, and robust to surface shape noise, with low number of spurious branches or surfaces.
In this thesis we present methods for computation of smooth medial manifolds and apply them to the generation of for anatomical volumetric parameterization that extends current harmonic parameterizations to the interior anatomy using information provided by the volume medial surface. This reference system sets a solid base for creating anatomical models of the anatomical shapes, and allows comparing several patients in a common framework of reference.

Abstract: Colorectal cancer is the third most common cancer worldwide and the second most common malignant tumor in Europe. Screening tests have shown to be very eective in increasing the survival rates since they allow an early detection of polyps. Among the dierent screening techniques, colonoscopy is considered the gold standard although clinical studies mention several problems that have an impact in the quality of the procedure. The navigation through the rectum and colon track can be challenging for the physicians which can increase polyp miss rates. The thorough visualization of the colon track must be ensured so that
the chances of missing lesions are minimized. The visual analysis of colonoscopy images can provide important information to the physicians and support their navigation during the procedure.
Blood vessels and their branching patterns can provide descriptive power to potentially develop biometric markers. Anatomical markers based on blood vessel patterns could be used to identify a particular scene in colonoscopy videos and to support endoscope navigation by generating a sequence of ordered scenes through the dierent colon sections. By verifying the presence of vascular content in the endoluminal scene it is also possible to certify a proper
inspection of the colon mucosa and to improve polyp localization. Considering the potential uses of blood vessel description, this contribution studies the characterization of the vascular content and the analysis of the descriptive power of its branching patterns.
Blood vessel characterization in colonoscopy images is shown to be a challenging task. The endoluminal scene is conformed by several elements whose similar characteristics hinder the development of particular models for each of them. To overcome such diculties we propose the use of the blood vessel branching characteristics as key features for pattern description. We present a model to characterize junctions in binary patterns. The implementation
of the junction model allows us to develop a junction localization method. We
created two data sets including manually labeled vessel information as well as manual ground truths of two types of keypoint landmarks: junctions and endpoints. The proposed method outperforms the available algorithms in the literature in experiments in both, our newly created colon vessel data set, and in DRIVE retinal fundus image data set. In the latter case, we created a manual ground truth of junction coordinates. Since we want to explore the descriptive potential of junctions and vessels, we propose a graph-based approach to
create anatomical markers. In the context of polyp localization, we present a new method to inhibit the in uence of blood vessels in the extraction valley-prole information. The results show that our methodology decreases vessel in
uence, increases polyp information and leads to an improvement in state-of-the-art polyp localization performance. We also propose a polyp-specic segmentation method that outperforms other general and specic approaches.

Abstract: Optical Flow (OF) is the input of a wide range of decision support systems such as car driver assistance, UAV guiding or medical diagnose. In these real situations, the absence of ground truth forces to assess OF quality using quantities computed from either sequences or the computed optical flow itself. These quantities are generally known as Confidence Measures, CM. Even if we have a proper confidence measure we still need a way to evaluate its ability to discard pixels with an OF prone to have a large error. Current approaches only provide a descriptive evaluation of the CM performance but such approaches are not capable to fairly compare different confidence measures and optical flow algorithms. Thus, it is of prime importance to define a framework and a general road map for the evaluation of optical flow performance.
This thesis provides a framework able to decide which pairs “ optical flow – confidence measure” (OF-CM) are best suited for optical flow error bounding given a confidence level determined by a decision support system. To design this framework we cover the following points:
Descriptive scores. As a first step, we summarize and analyze the sources of inaccuracies in the output of optical flow algorithms. Second, we present several descriptive plots that visually assess CM capabilities for OF error bounding. In addition to the descriptive plots, given a plot representing OF-CM capabilities to bound the error, we provide a numeric score that categorizes the plot according to its decreasing profile, that is, a score assessing CM performance.
Statistical framework. We provide a comparison framework that assesses the best suited OF-CM pair for error bounding that uses a two stage cascade process. First of all we assess the predictive value of the confidence measures by means of a descriptive plot. Then, for a sample of descriptive plots computed over training frames, we obtain a generic curve that will be used for sequences with no ground truth. As a second step, we evaluate the obtained general curve and its capabilities to really reflect the predictive value of a confidence measure using the variability across train frames by means of ANOVA.
The presented framework has shown its potential in the application on clinical decision support systems. In particular, we have analyzed the impact of the different image artifacts such as noise and decay to the output of optical flow in a cardiac diagnose system and we have improved the navigation inside the bronchial tree on bronchoscopy.

Abstract: In this work, we develop a generic framework that is able to handle the document retrieval problem in various scenarios such as searching for full page matches or retrieving the counterparts for specific document areas, focusing on their structural similarity or letting their visual resemblance to play a dominant role. Based on the spatial indexing technique, we propose to search for matches of local key-region pairs carrying both structural and visual information from the collection while a scheme allowing to adjust the relative contribution of structural and visual similarity is presented.
Based on the fact that the structure of documents is tightly linked with the distance among their elements, we firstly introduce an efficient detector named Distance Transform based Maximally Stable Extremal Regions (DTMSER). We illustrate that this detector is able to efficiently extract the structure of a document image as a dendrogram (hierarchical tree) of multi-scale key-regions that roughly correspond to letters, words and paragraphs. We demonstrate that, without benefiting from the structure information, the key-regions extracted by the DTMSER algorithm achieve better results comparing with state-of-the-art methods while much less amount of key-regions are employed.
We subsequently propose a pair-wise Bag of Words (BoW) framework to efficiently embed the explicit structure extracted by the DTMSER algorithm. We represent each document as a list of key-region pairs that correspond to the edges in the dendrogram where inclusion relationship is encoded. By employing those structural key-region pairs as the pooling elements for generating the histogram of features, the proposed method is able to encode the explicit inclusion relations into a BoW representation. The experimental results illustrate that the pair-wise BoW, powered by the embedded structural information, achieves remarkable improvement over the conventional BoW and spatial pyramidal BoW methods.
To handle various retrieval scenarios in one framework, we propose to directly query a series of key-region pairs, carrying both structure and visual information, from the collection. We introduce the spatial indexing techniques to the document retrieval community to speed up the structural relationship computation for key-region pairs. We firstly test the proposed framework in a full page retrieval scenario where structurally similar matches are expected. In this case, the pair-wise querying method achieves notable improvement over the BoW and spatial pyramidal BoW frameworks. Furthermore, we illustrate that the proposed method is also able to handle focused retrieval situations where the queries are defined as a specific interesting partial areas of the images. We examine our method on two types of focused queries: structure-focused and exact queries. The experimental results show that, the proposed generic framework obtains nearly perfect precision on both types of focused queries while it is the first framework able to tackle structure-focused queries, setting a new state of the art in the field.
Besides, we introduce a line verification method to check the spatial consistency among the matched key-region pairs. We propose a computationally efficient version of line verification through a two step implementation. We first compute tentative localizations of the query and subsequently employ them to divide the matched key-region pairs into several groups, then line verification is performed within each group while more precise bounding boxes are computed. We demonstrate that, comparing with the standard approach (based on RANSAC), the line verification proposed generally achieves much higher recall with slight loss on precision on specific queries.