Abstract: Colorectal cancer is the fourth most common cause of cancer death worldwide and its survival rate depends on the stage in which it is detected on hence the necessity for an early colon screening. There are several screening techniques but colonoscopy is still nowadays the gold standard, although it has some drawbacks such as the miss rate. Our contribution, in the field of intelligent systems for colonoscopy, aims at providing a polyp localization and a polyp segmentation system based on a model of appearance for polyps. To develop both methods we define a model of appearance for polyps, which describes a polyp as enclosed by intensity valleys. The novelty of our contribution resides on the fact that we include in our model aspects of the image formation and we also consider the presence of other elements from the endoluminal scene such as specular highlights and blood vessels, which have an impact on the performance of our methods. In order to develop our polyp localization method we accumulate valley information in order to generate energy maps, which are also used to guide the polyp segmentation. Our methods achieve promising results in polyp localization and segmentation. As we want to explore the usability of our methods we present a comparative analysis between physicians fixations obtained via an eye tracking device and our polyp localization method. The results show that our method is indistinguishable to novice physicians although it is far from expert physicians.

Abstract: Handwritten documents are not only preserved in historical archives but also widely used in administrative documents such as cheques and claims. With the rise of the deep learning era, many state-of-the-art approaches have achieved good performance on specific datasets for Handwritten Text Recognition (HTR). However, it is still challenging to solve real use cases because of the varied handwriting styles across different writers and the limited labeled data. Thus, both explorin a more robust handwriting recognition architectures and proposing methods to diminish the gap between the source and target data in an unsupervised way are
demanded.
In this thesis, firstly, we explore novel architectures for HTR, from Sequence-to-Sequence (Seq2Seq) method with attention mechanism to non-recurrent Transformer-based method. Secondly, we focus on diminishing the performance gap between source and target data in an unsupervised way. Finally, we propose a group of generative methods for handwritten text images, which could be utilized to increase the training set to obtain a more robust recognizer. In addition, by simply modifying the generative method and joining it with a recognizer, we end up with an effective disentanglement method to distill textual content from handwriting styles so as to achieve a generalized recognition performance.
We outperform state-of-the-art HTR performances in the experimental results among different scientific and industrial datasets, which prove the effectiveness of the proposed methods. To the best of our knowledge, the non-recurrent recognizer and the disentanglement method are the first contributions in the handwriting recognition field. Furthermore, we have outlined the potential research lines, which would be interesting to explore in the future.

Abstract: In this thesis, we propose different contributions with the goal of enhancing and recognizing historical handwritten document images, especially the ones with rare scripts, such as cipher documents.
In the first part, some effective end-to-end models for Document Image Enhancement (DIE) using deep learning models were presented. First, Generative Adversarial Networks (cGAN) for different tasks (document clean-up, binarization, deblurring, and watermark removal) were explored. Next, we further improve the results by recovering the degraded document images into a clean and readable form by integrating a text recognizer into the cGAN model to promote the generated document image to be more readable. Afterward, we present a new encoder-decoder architecture based on vision transformers to enhance both machine-printed and handwritten document images, in an end-to-end fashion.
The second part of the thesis addresses Handwritten Text Recognition (HTR) in low resource scenarios, i.e. when only few labeled training data is available. We propose novel methods for recognizing ciphers with rare scripts. First, a few-shot object detection based method was proposed. Then, we incorporate a progressive learning strategy that automatically assignspseudo-labels to a set of unlabeled data to reduce the human labor of annotating few pages while maintaining the good performance of the model. Secondly, a data generation technique based on Bayesian Program Learning (BPL) is proposed to overcome the lack of data in such rare scripts. Thirdly, we propose a Text-Degradation Invariant Auto Encoder (Text-DIAE). This latter self-supervised model is designed to tackle two tasks, text recognition and document image enhancement. The proposed model does not exhibit limitations of previous state-of-the-art methods based on contrastive losses, while at the same time, it requires substantially fewer data samples to converge.
In the third part of the thesis, we analyze, from the user perspective, the usage of HTR systems in low resource scenarios. This contrasts with the usual research on HTR, which often focuses on technical aspects only and rarely devotes efforts on implementing software tools for scholars in Humanities.

Abstract: Medial representations are powerful tools for describing and parameterizing the volumetric shape of anatomical structures. Existing methods show excellent results when applied to 2D objects, but their quality drops across dimensions. This paper contributes to the computation of medial manifolds in two aspects. First, we provide a standard scheme for the computation of medial manifolds that avoid degenerated medial axis segments; second, we introduce an energy based method which performs independently of the dimension. We evaluate quantitatively the performance of our method with respect to existing approaches, by applying them to synthetic shapes of known medial geometry. Finally, we show results on shape representation of multiple abdominal organs, exploring the use of medial manifolds for the representation of multi-organ relations.

Abstract: Motion perception is one of the most important attributes of the human brain. Visual motion perception consists in inferring speed and direction of elements in a scene based on visual inputs. Analogously, computer vision is assisted by motion cues in the scene. Motion detection in computer vision is useful in solving problems such as segmentation, depth from motion, structure from motion, compression, navigation and many others. These problems are common in several applications, for instance, video surveillance, robot navigation and advanced driver assistance systems (ADAS). One of the most widely used techniques for motion detection is the optical flow estimation. The work in this thesis attempts to make optical flow suitable for the requirements and conditions of driving scenarios. In this context, a novel space-variant representation called reverse log-polar representation is proposed that is shown to be better than the traditional log-polar space-variant representation for ADAS. The space-variant representations reduce the amount of data to be processed. Another major contribution in this research is related to the analysis of the influence of specific characteristics from driving scenarios on the optical flow accuracy. Characteristics such as vehicle speed and
road texture are considered in the aforementioned analysis. From this study, it is inferred that the regularization weight has to be adapted according to the required error measure and for different speeds and road textures. It is also shown that polar represented optical flow suits driving scenarios where predominant motion is translation. Due to the requirements of such a study and by the lack of needed datasets a new synthetic dataset is presented; it contains: i) sequences of different speeds and road textures in an urban scenario; ii) sequences with complex motion of an on-board camera; and iii) sequences with additional moving vehicles in the scene. The ground-truth optical flow is generated by the ray-tracing technique. Further, few applications of optical flow in ADAS are shown. Firstly, a robust RANSAC based technique to estimate horizon line is proposed. Then, an egomotion estimation is presented to compare the proposed space-variant representation with the classical one. As a final contribution, a modification in the regularization term is proposed that notably improves the results
in the ADAS applications. This adaptation is evaluated using a state of the art optical flow technique. The experiments on a public dataset (KITTI) validate the advantages of using the proposed modification.

Abstract: The image sensor, nowadays, is rolling the smartphone industry. While some phone brands explore equipping more image sensors, others, like Google, maintain their smartphones with just one sensor; but this sensor is equipped with Deep Learning to enhance the image quality. However, what all brands agree on is the need to research new image sensors; for instance, in 2015 Omnivision and PixelTeq presented new CMOS based image sensors defined as multispectral Single Sensor Camera (SSC), which are capable of capturing multispectral bands. This dissertation presents the benefits of using a multispectral SSCs that, as aforementioned, simultaneously acquires images in the visible and near-infrared (NIR) bands. The principal benefits while addressing problems related to image bands in the spectral range of 400 to 1100 nanometers, there are cost reductions in the hardware and software setup because only one SSC is needed instead of two, and the images alignment are not required any more. Concerning to the NIR spectrum, many works in literature have proven the benefits of working with NIR to enhance RGB images (e.g., image enhancement, remove shadows, dehazing, etc.). In spite of the advantage of using SSC (e.g., low latency), there are some drawback to be solved. One of this drawback corresponds to the nature of the silicon-based sensor, which in addition to capture the RGB image, when the infrared cut off filter is not installed it also acquires NIR information into the visible image. This phenomenon is called RGB and NIR crosstalking. This thesis firstly faces this problem in challenging images and then it shows the benefit of using multispectral images in the edge detection task.
The RGB color restoration from RGBN image is the topic tackled in RGB and NIR crosstalking. Even though in the literature a set of processes have been proposed to face this issue, in this thesis novel approaches, based on DL, are proposed to subtract the additional NIR included in the RGB channel. More precisely, an Artificial Neural Network (NN) and two Convolutional Neural Network (CNN) models are proposed. As the DL based models need a dataset with a large collection of image pairs, a large dataset is collected to address the color restoration. The collected images are from challenging scenes where the sunlight radiation is sufficient to give absorption/reflectance properties to the considered scenes. An extensive evaluation has been conducted on the CNN models, differences from most of the restored images are almost imperceptible to the human eye. The next proposal of the thesis is the validation of the usage of SSC images in the edge detection task. Three methods based on CNN have been proposed. While the first one is based on the most used model, holistically-nested edge detection (HED) termed as multispectral HED (MS-HED), the other two have been proposed observing the drawbacks of MS-HED. These two novel architectures have been designed from scratch (training from scratch); after the first architecture is validated in the visible domain a slight redesign is proposed to tackle the multispectral domain. Again, another dataset is collected to face this problem with SSCs. Even though edge detection is confronted in the multispectral domain, its qualitative and quantitative evaluation demonstrates the generalization in other datasets used for edge detection, improving state-of-the-art results.

Abstract: Human vision is restricted to the visual-optical spectrum. Machine vision is not.
Cameras sensitive to diverse infrared spectral bands can improve the capacities of
autonomous systems and provide a comprehensive view. Relevant scene content
can be made visible, particularly in situations when sensors of other modalities,
such as a visual-optical camera, require a source of illumination. As a result, increasing the level of automation not only avoids human errors but also reduces
machine-induced errors. Furthermore, multi-spectral sensor systems with infrared
imagery as one modality are a rich source of information and can conceivably
increase the robustness of many autonomous systems. Robotics, automobiles,
biometrics, security, surveillance, and the military are some examples of fields
that can profit from the use of infrared imagery in their respective applications.
Although multimodal spectral sensors have come a long way, there are still several
bottlenecks that prevent us from combining their output information and using
them as comprehensive images. The primary issue with infrared imaging is the lack
of potential benefits due to their cost influence on sensor resolution, which grows
exponentially with greater resolution. Due to the more costly sensor technology
required for their development, their resolutions are substantially lower than thoseof regular digital cameras.
This thesis aims to improve beyond-visible-spectrum machine vision by integrating multi-modal spectral sensors. The emphasis is on transforming the produced images to enhance their resolution to match expected human perception, bring the color representation close to human understanding of natural color, and improve machine vision application performance. This research focuses mainly on two tasks, image Colorization and Image Super resolution for both single- and cross-domain problems. We first start with an extensive review of the state of the art in both tasks, point out the shortcomings of existing approaches, and then present our solutions to address their limitations. Our solutions demonstrate that low-cost channel information (i.e., visible image) can be used to improve expensive channel
information (i.e., infrared image), resulting in images with higher quality and closer to human perception at a lower cost than a high-cost infrared camera.