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Mireia Sole, Joan Blanco, Debora Gil, Oliver Valero, B. Cardenas, G. Fonseka, et al. (2022). "Time to match; when do homologous chromosomes become closer? " Chromosoma, .
Abstract: In most eukaryotes, pairing of homologous chromosomes is an essential feature of meiosis that ensures homologous recombination and segregation. However, when the pairing process begins, it is still under investigation. Contrasting data exists in Mus musculus, since both leptotene DSB-dependent and preleptotene DSB-independent mechanisms have been described. To unravel this contention, we examined homologous pairing in pre-meiotic and meiotic Mus musculus cells using a threedimensional fuorescence in situ hybridization-based protocol, which enables the analysis of the entire karyotype using DNA painting probes. Our data establishes in an unambiguously manner that 73.83% of homologous chromosomes are already paired at premeiotic stages (spermatogonia-early preleptotene spermatocytes). The percentage of paired homologous chromosomes increases to 84.60% at mid-preleptotene-zygotene stage, reaching 100% at pachytene stage. Importantly, our results demonstrate a high percentage of homologous pairing observed before the onset of meiosis; this pairing does not occur randomly, as the percentage was higher than that observed in somatic cells (19.47%) and between nonhomologous chromosomes (41.1%). Finally, we have also observed that premeiotic homologous pairing is asynchronous and independent of the chromosome size, GC content, or presence of NOR regions.
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Oriol Ramos Terrades, Albert Berenguel, & Debora Gil. (2022). "A Flexible Outlier Detector Based on a Topology Given by Graph Communities " . Big Data Research, 29, 100332.
Abstract: Outlier detection is essential for optimal performance of machine learning methods and statistical predictive models. Their detection is especially determinant in small sample size unbalanced problems, since in such settings outliers become highly influential and significantly bias models. This particular experimental settings are usual in medical applications, like diagnosis of rare pathologies, outcome of experimental personalized treatments or pandemic emergencies. In contrast to population-based methods, neighborhood based local approaches compute an outlier score from the neighbors of each sample, are simple flexible methods that have the potential to perform well in small sample size unbalanced problems. A main concern of local approaches is the impact that the computation of each sample neighborhood has on the method performance. Most approaches use a distance in the feature space to define a single neighborhood that requires careful selection of several parameters, like the number of neighbors.
This work presents a local approach based on a local measure of the heterogeneity of sample labels in the feature space considered as a topological manifold. Topology is computed using the communities of a weighted graph codifying mutual nearest neighbors in the feature space. This way, we provide with a set of multiple neighborhoods able to describe the structure of complex spaces without parameter fine tuning. The extensive experiments on real-world and synthetic data sets show that our approach outperforms, both, local and global strategies in multi and single view settings.
Keywords: Classification algorithms; Detection algorithms; Description of feature space local structure; Graph communities; Machine learning algorithms; Outlier detectors
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Antoni Gurgui, Debora Gil, Enric Marti, & Vicente Grau. (2016). "Left-Ventricle Basal Region Constrained Parametric Mapping to Unitary Domain " In 7th International Workshop on Statistical Atlases & Computational Modelling of the Heart (Vol. 10124, pp. 163–171).
Abstract: Due to its complex geometry, the basal ring is often omitted when putting different heart geometries into correspondence. In this paper, we present the first results on a new mapping of the left ventricle basal rings onto a normalized coordinate system using a fold-over free approach to the solution to the Laplacian. To guarantee correspondences between different basal rings, we imposed some internal constrained positions at anatomical landmarks in the normalized coordinate system. To prevent internal fold-overs, constraints are handled by cutting the volume into regions defined by anatomical features and mapping each piece of the volume separately. Initial results presented in this paper indicate that our method is able to handle internal constrains without introducing fold-overs and thus guarantees one-to-one mappings between different basal ring geometries.
Keywords: Laplacian; Constrained maps; Parameterization; Basal ring
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Antonio Esteban Lansaque, Carles Sanchez, Agnes Borras, Marta Diez-Ferrer, Antoni Rosell, & Debora Gil. (2016). "Stable Anatomical Structure Tracking for video-bronchoscopy Navigation " In 19th International Conference on Medical Image Computing and Computer Assisted Intervention Workshops.
Abstract: Bronchoscopy allows to examine the patient airways for detection of lesions and sampling of tissues without surgery. A main drawback in lung cancer diagnosis is the diculty to check whether the exploration is following the correct path to the nodule that has to be biopsied. The most extended guidance uses uoroscopy which implies repeated radiation of clinical sta and patients. Alternatives such as virtual bronchoscopy or electromagnetic navigation are very expensive and not completely robust to blood, mocus or deformations as to be extensively used. We propose a method that extracts and tracks stable lumen regions at di erent levels of the bronchial tree. The tracked regions are stored in a tree that encodes the anatomical structure of the scene which can be useful to retrieve the path to the lesion that the clinician should follow to do the biopsy. We present a multi-expert validation of our anatomical landmark extraction in 3 intra-operative ultrathin explorations.
Keywords: Lung cancer diagnosis; video-bronchoscopy; airway lumen detection; region tracking
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Sergio Vera, Debora Gil, & Miguel Angel Gonzalez Ballester. (2014). "Anatomical parameterization for volumetric meshing of the liver " In SPIE – Medical Imaging (Vol. 9036).
Abstract: A coordinate system describing the interior of organs is a powerful tool for a systematic localization of injured tissue. If the same coordinate values are assigned to specific anatomical landmarks, the coordinate system allows integration of data across different medical image modalities. Harmonic mappings have been used to produce parametric coordinate systems over the surface of anatomical shapes, given their flexibility to set values
at specific 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 sites
of limited geometric diversity. In this paper we present a method for anatomical volumetric parameterization that extends current harmonic parameterizations to the interior anatomy using information provided by the
volume medial surface. We have applied the methodology to define a common reference system for the liver shape and functional anatomy. This reference system sets a solid base for creating anatomical models of the patient’s liver, and allows comparing livers from several patients in a common framework of reference.
Keywords: Coordinate System; Anatomy Modeling; Parameterization
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Francesco Brughi, Debora Gil, Llorenç Badiella, Eva Jove Casabella, & Oriol Ramos Terrades. (2014). "Exploring the impact of inter-query variability on the performance of retrieval systems " In 11th International Conference on Image Analysis and Recognition (Vol. 8814, 413–420). Springer International Publishing.
Abstract: This paper introduces a framework for evaluating the performance of information retrieval systems. Current evaluation metrics provide an average score that does not consider performance variability across the query set. In this manner, conclusions lack of any statistical significance, yielding poor inference to cases outside the query set and possibly unfair comparisons. We propose to apply statistical methods in order to obtain a more informative measure for problems in which different query classes can be identified. In this context, we assess the performance variability on two levels: overall variability across the whole query set and specific query class-related variability. To this end, we estimate confidence bands for precision-recall curves, and we apply ANOVA in order to assess the significance of the performance across different query classes.
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Sonia Baeza, Debora Gil, I.Garcia Olive, M.Salcedo, J.Deportos, Carles Sanchez, et al. (2022). "A novel intelligent radiomic analysis of perfusion SPECT/CT images to optimize pulmonary embolism diagnosis in COVID-19 patients " . EJNMMI Physics, 9(1, Article 84), 1–17.
Abstract: Background: COVID-19 infection, especially in cases with pneumonia, is associated with a high rate of pulmonary embolism (PE). In patients with contraindications for CT pulmonary angiography (CTPA) or non-diagnostic CTPA, perfusion single-photon emission computed tomography/computed tomography (Q-SPECT/CT) is a diagnostic alternative. The goal of this study is to develop a radiomic diagnostic system to detect PE based only on the analysis of Q-SPECT/CT scans.
Methods: This radiomic diagnostic system is based on a local analysis of Q-SPECT/CT volumes that includes both CT and Q-SPECT values for each volume point. We present a combined approach that uses radiomic features extracted from each scan as input into a fully connected classifcation neural network that optimizes a weighted crossentropy loss trained to discriminate between three diferent types of image patterns (pixel sample level): healthy lungs (control group), PE and pneumonia. Four types of models using diferent confguration of parameters were tested.
Results: The proposed radiomic diagnostic system was trained on 20 patients (4,927 sets of samples of three types of image patterns) and validated in a group of 39 patients (4,410 sets of samples of three types of image patterns). In the training group, COVID-19 infection corresponded to 45% of the cases and 51.28% in the test group. In the test group, the best model for determining diferent types of image patterns with PE presented a sensitivity, specifcity, positive predictive value and negative predictive value of 75.1%, 98.2%, 88.9% and 95.4%, respectively. The best model for detecting
pneumonia presented a sensitivity, specifcity, positive predictive value and negative predictive value of 94.1%, 93.6%, 85.2% and 97.6%, respectively. The area under the curve (AUC) was 0.92 for PE and 0.91 for pneumonia. When the results obtained at the pixel sample level are aggregated into regions of interest, the sensitivity of the PE increases to 85%, and all metrics improve for pneumonia.
Conclusion: This radiomic diagnostic system was able to identify the diferent lung imaging patterns and is a frst step toward a comprehensive intelligent radiomic system to optimize the diagnosis of PE by Q-SPECT/CT.
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David Castells, Vinh Ngo, Juan Borrego-Carazo, Marc Codina, Carles Sanchez, Debora Gil, et al. (2022). "A Survey of FPGA-Based Vision Systems for Autonomous Cars " . IEEE Access, 10, 132525–132563.
Abstract: On the road to making self-driving cars a reality, academic and industrial researchers are working hard to continue to increase safety while meeting technical and regulatory constraints Understanding the surrounding environment is a fundamental task in self-driving cars. It requires combining complex computer vision algorithms. Although state-of-the-art algorithms achieve good accuracy, their implementations often require powerful computing platforms with high power consumption. In some cases, the processing speed does not meet real-time constraints. FPGA platforms are often used to implement a category of latency-critical algorithms that demand maximum performance and energy efficiency. Since self-driving car computer vision functions fall into this category, one could expect to see a wide adoption of FPGAs in autonomous cars. In this paper, we survey the computer vision FPGA-based works from the literature targeting automotive applications over the last decade. Based on the survey, we identify the strengths and weaknesses of FPGAs in this domain and future research opportunities and challenges.
Keywords: Autonomous automobile; Computer vision; field programmable gate arrays; reconfigurable architectures
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Debora Gil, & Petia Radeva. (2004). "A Regularized Curvature Flow Designed for a Selective Shape Restoration " . IEEE Transactions on Image Processing, 13, 1444–1458.
Abstract: Among all filtering techniques, those based exclu- sively on image level sets (geometric flows) have proven to be the less sensitive to the nature of noise and the most contrast preserving. A common feature to existent curvature flows is that they penalize high curvature, regardless of the curve regularity. This constitutes a major drawback since curvature extreme values are standard descriptors of the contour geometry. We argue that an operator designed with shape recovery purposes should include a term penalizing irregularity in the curvature rather than its magnitude. To this purpose, we present a novel geometric flow that includes a function that measures the degree of local irregularity present in the curve. A main advantage is that it achieves non-trivial steady states representing a smooth model of level curves in a noisy image. Performance of our approach is compared to classical filtering techniques in terms of quality in the restored image/shape and asymptotic behavior. We empirically prove that our approach is the technique that achieves the best compromise between image quality and evolution stabilization.
Keywords: Geometric flows, nonlinear filtering, shape recovery.
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Oriol Rodriguez-Leon, Josefina Mauri, Eduard Fernandez-Nofrerias, Antonio Tovar, Vicente del Valle, Aura Hernandez-Sabate, et al. (2004)." Utilizacion de la estructura de los campos vectoriales para la deteccion de la Adventicia en imagenes de Ecografia Intracoronaria" . Revista Española de Cardiología, 57(2), 100.
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