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	Author	Patricia Marquez; H. Kause; A. Fuster; Aura Hernandez-Sabate; L. Florack; Debora Gil; Hans van Assen
	Title	Factors Affecting Optical Flow Performance in Tagging Magnetic Resonance Imaging			Type	Conference Article
	Year	2014	Publication	17th International Conference on Medical Image Computing and Computer Assisted Intervention	Abbreviated Journal
	Volume	8896	Issue		Pages	231-238
	Keywords	Optical flow; Performance Evaluation; Synthetic Database; ANOVA; Tagging Magnetic Resonance Imaging
	Abstract	Changes in cardiac deformation patterns are correlated with cardiac pathologies. Deformation can be extracted from tagging Magnetic Resonance Imaging (tMRI) using Optical Flow (OF) techniques. For applications of OF in a clinical setting it is important to assess to what extent the performance of a particular OF method is stable across dierent clinical acquisition artifacts. This paper presents a statistical validation framework, based on ANOVA, to assess the motion and appearance factors that have the largest in uence on OF accuracy drop. In order to validate this framework, we created a database of simulated tMRI data including the most common artifacts of MRI and test three dierent OF methods, including HARP.
	Address	Boston; USA; September 2014
	Corporate Author				Thesis
	Publisher	Springer International Publishing	Place of Publication		Editor
	Language		Summary Language		Original Title
	Series Editor		Series Title		Abbreviated Series Title	LNCS
	Series Volume		Series Issue		Edition
	ISSN	0302-9743	ISBN	978-3-319-14677-5	Medium
	Area		Expedition		Conference	STACOM
	Notes	IAM; ADAS; 600.060; 601.145; 600.076; 600.075			Approved	no
	Call Number	Admin @ si @ MKF2014			Serial	2495
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	Author	Aura Hernandez-Sabate; Debora Gil; Petia Radeva; E.N.Nofrerias
	Title	Anisotropic processing of image structures for adventitia detection in intravascular ultrasound images			Type	Conference Article
	Year	2004	Publication	Proc. Computers in Cardiology	Abbreviated Journal
	Volume	31	Issue		Pages	229-232
	Keywords
	Abstract	The adventitia layer appears as a weak edge in IVUS images with a non-uniform grey level, which difficulties its detection. In order to enhance edges, we apply an anisotropic filter that homogenizes the grey level along the image significant structures (ridges, valleys and edges). A standard edge detector applied to the filtered image yields a set of candidate points prone to be unconnected. The final model is obtained by interpolating the former line segments along the tangent direction to the level curves of the filtered image with an anisotropic contour closing technique based on functional extension principles
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	Chicago (USA)	Editor
	Language		Summary Language		Original Title
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN		ISBN		Medium
	Area		Expedition		Conference
	Notes	IAM; MILAB			Approved	no
	Call Number	IAM @ iam @ HGR2004			Serial	1555
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	Author	Sergio Vera; Debora Gil; Agnes Borras; F. Javier Sanchez; Frederic Perez; Marius G. Linguraru; Miguel Angel Gonzalez Ballester
	Title	Computation and Evaluation of Medial Surfaces for Shape Representation of Abdominal Organs			Type	Book Chapter
	Year	2012	Publication	Workshop on Computational and Clinical Applications in Abdominal Imaging	Abbreviated Journal
	Volume	7029	Issue		Pages	223–230
	Keywords	medial manifolds, abdomen.
	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.
	Address	Toronto; Canada;
	Corporate Author				Thesis
	Publisher	Springer Link	Place of Publication	Berlin	Editor	H. Yoshida et al
	Language	English	Summary Language	English	Original Title
	Series Editor		Series Title	Lecture Notes in Computer Science	Abbreviated Series Title	LNCS
	Series Volume		Series Issue		Edition
	ISSN	0302-9743	ISBN	978-3-642-28556-1	Medium
	Area		Expedition		Conference	ABDI
	Notes	IAM;MV			Approved	no
	Call Number	IAM @ iam @ VGB2012			Serial	1834
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	Author	Sergio Vera; Debora Gil; Agnes Borras; F. Javier Sanchez; Frederic Perez; Marius G. Linguraru
	Title	Computation and Evaluation of Medial Surfaces for Shape Representation of Abdominal Organs			Type	Conference Article
	Year	2011	Publication	Workshop on Computational and Clinical Applications in Abdominal Imaging	Abbreviated Journal
	Volume	7029	Issue		Pages	223-230
	Keywords
	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.
	Address	Nice, France
	Corporate Author				Thesis
	Publisher	Springer Berlin Heidelberg	Place of Publication		Editor	In H. Yoshida et al
	Language		Summary Language		Original Title
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN		ISBN		Medium
	Area		Expedition		Conference	ABDI
	Notes	IAM; MV			Approved	no
	Call Number	VGB2011			Serial	2036
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	Author	David Roche; Debora Gil; Jesus Giraldo
	Title	An inference model for analyzing termination conditions of Evolutionary Algorithms			Type	Conference Article
	Year	2011	Publication	14th Congrès Català en Intel·ligencia Artificial	Abbreviated Journal
	Volume		Issue		Pages	216-225
	Keywords	Evolutionary Computation Convergence, Termination Conditions, Statistical Inference
	Abstract	In real-world problems, it is mandatory to design a termination condition for Evolutionary Algorithms (EAs) ensuring stabilization close to the unknown optimum. Distribution-based quantities are good candidates as far as suitable parameters are used. A main limitation for application to real-world problems is that such parameters strongly depend on the topology of the objective function, as well as, the EA paradigm used. We claim that the termination problem would be fully solved if we had a model measuring to what extent a distribution-based quantity asymptotically behaves like the solution accuracy. We present a regression-prediction model that relates any two given quantities and reports if they can be statistically swapped as termination conditions. Our framework is applied to two issues. First, exploring if the parameters involved in the computation of distribution-based quantities influence their asymptotic behavior. Second, to what extent existing distribution-based quantities can be asymptotically exchanged for the accuracy of the EA solution.
	Address	Lleida, Catalonia (Spain)
	Corporate Author	Associació Catalana Intel·ligència Artificial			Thesis
	Publisher		Place of Publication		Editor
	Language		Summary Language		Original Title
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN		ISBN	978-1-60750-841-0	Medium
	Area		Expedition		Conference	CCIA
	Notes	IAM			Approved	no
	Call Number	IAM @ iam @ RGG2011a			Serial	1677
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	Author	Debora Gil; Oriol Rodriguez-Leon; Petia Radeva; Aura Hernandez-Sabate
	Title	Assessing Artery Motion Compensation in IVUS			Type	Book Chapter
	Year	2007	Publication	Computer Analysis Of Images And Patterns	Abbreviated Journal	LNCS
	Volume	4673	Issue		Pages	213-220
	Keywords	validation standards; quality measures; IVUS motion compensation; conservation laws; Fourier development
	Abstract	Cardiac dynamics suppression is a main issue for visual improvement and computation of tissue mechanical properties in IntraVascular UltraSound (IVUS). Although in recent times several motion compensation techniques have arisen, there is a lack of objective evaluation of motion reduction in in vivo pullbacks. We consider that the assessment protocol deserves special attention for the sake of a clinical applicability as reliable as possible. Our work focuses on defining a quality measure and a validation protocol assessing IVUS motion compensation. On the grounds of continuum mechanics laws we introduce a novel score measuring motion reduction in in vivo sequences. Synthetic experiments validate the proposed score as measure of motion parameters accuracy; while results in in vivo pullbacks show its reliability in clinical cases.
	Address
	Corporate Author				Thesis
	Publisher	Springerlink	Place of Publication	Heidelberg	Editor
	Language		Summary Language		Original Title
	Series Editor		Series Title	Lecture Notes in Computer Science	Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN		ISBN	978-3-540-74271-5	Medium
	Area		Expedition		Conference
	Notes	IAM;MILAB			Approved	no
	Call Number	IAM @ iam @ GRR2007			Serial	1540
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	Author	Debora Gil; Petia Radeva
	Title	Shape Restoration via a Regularized Curvature Flow			Type	Journal Article
	Year	2004	Publication	Journal of Mathematical Imaging and Vision	Abbreviated Journal
	Volume	21	Issue	3	Pages	205-223
	Keywords
	Abstract	Any image filtering operator designed for automatic shape restoration should satisfy robustness (whatever the nature and degree of noise is) as well as non-trivial smooth asymptotic behavior. Moreover, a stopping criterion should be determined by characteristics of the evolved image rather than dependent on the number of iterations. Among the several PDE based techniques, curvature flows appear to be highly reliable for strongly noisy images compared to image diffusion processes. In the present paper, we introduce a regularized curvature flow (RCF) that admits non-trivial steady states. It is based on a measure of the local curve smoothness that takes into account regularity of the curve curvature and serves as stopping term in the mean curvature flow. We prove that this measure decreases over the orbits of RCF, which endows the method with a natural stop criterion in terms of the magnitude of this measure. Further, in its discrete version it produces steady states consisting of piece-wise regular curves. Numerical experiments made on synthetic shapes corrupted with different kinds of noise show the abilities and limitations of each of the current geometric flows and the benefits of RCF. Finally, we present results on real images that illustrate the usefulness of the present approach in practical applications.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Summary Language		Original Title
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN		ISBN		Medium
	Area		Expedition		Conference
	Notes	IAM;MILAB			Approved	no
	Call Number	IAM @ iam @ GiR2004c			Serial	1532
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	Author	Aura Hernandez-Sabate; Debora Gil
	Title	The Benefits of IVUS Dynamics for Retrieving Stable Models of Arteries			Type	Book Chapter
	Year	2012	Publication	Intravascular Ultrasound	Abbreviated Journal
	Volume		Issue		Pages	185-206
	Keywords
	Abstract
	Address
	Corporate Author				Thesis
	Publisher	Intech	Place of Publication		Editor	Yasuhiro Honda
	Language	English	Summary Language	english	Original Title
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN		ISBN	978-953-307-900-4	Medium
	Area		Expedition		Conference
	Notes	IAM; ADAS			Approved	no
	Call Number	IAM @ iam @ HeG2012			Serial	1684
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	Author	Patricia Marquez; Debora Gil ; Aura Hernandez-Sabate
	Title	Error Analysis for Lucas-Kanade Based Schemes			Type	Conference Article
	Year	2012	Publication	9th International Conference on Image Analysis and Recognition	Abbreviated Journal
	Volume	7324	Issue	I	Pages	184-191
	Keywords	Optical flow, Confidence measure, Lucas-Kanade, Cardiac Magnetic Resonance
	Abstract	Optical flow is a valuable tool for motion analysis in medical imaging sequences. A reliable application requires determining the accuracy of the computed optical flow. This is a main challenge given the absence of ground truth in medical sequences. This paper presents an error analysis of Lucas-Kanade schemes in terms of intrinsic design errors and numerical stability of the algorithm. Our analysis provides a confidence measure that is naturally correlated to the accuracy of the flow field. Our experiments show the higher predictive value of our confidence measure compared to existing measures.
	Address	Aveiro, Portugal
	Corporate Author				Thesis
	Publisher	Springer-Verlag Berlin Heidelberg	Place of Publication		Editor
	Language	english	Summary Language		Original Title
	Series Editor	Campilho, Aurélio and Kamel, Mohamed	Series Title	Lecture Notes in Computer Science	Abbreviated Series Title	LNCS
	Series Volume		Series Issue		Edition
	ISSN	0302-9743	ISBN	978-3-642-31294-6	Medium
	Area		Expedition		Conference	ICIAR
	Notes	IAM			Approved	no
	Call Number	IAM @ iam @ MGH2012a			Serial	1899
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	Author	Antoni Rosell; Sonia Baeza; S. Garcia-Reina; JL. Mate; Ignasi Guasch; I. Nogueira; I. Garcia-Olive; Guillermo Torres; Carles Sanchez; Debora Gil
	Title	EP01.05-001 Radiomics to Increase the Effectiveness of Lung Cancer Screening Programs. Radiolung Preliminary Results			Type	Journal Article
	Year	2022	Publication	Journal of Thoracic Oncology	Abbreviated Journal	JTO
	Volume	17	Issue	9	Pages	S182
	Keywords
	Abstract
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Summary Language		Original Title
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN		ISBN		Medium
	Area		Expedition		Conference
	Notes	IAM			Approved	no
	Call Number	Admin @ si @ RBG2022b			Serial	3834
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	Author	Esmitt Ramirez; Carles Sanchez; Agnes Borras; Marta Diez-Ferrer; Antoni Rosell; Debora Gil
	Title	BronchoX: bronchoscopy exploration software for biopsy intervention planning			Type	Journal
	Year	2018	Publication	Healthcare Technology Letters	Abbreviated Journal	HTL
	Volume	5	Issue	5	Pages	177–182
	Keywords
	Abstract	Virtual bronchoscopy (VB) is a non-invasive exploration tool for intervention planning and navigation of possible pulmonary lesions (PLs). A VB software involves the location of a PL and the calculation of a route, starting from the trachea, to reach it. The selection of a VB software might be a complex process, and there is no consensus in the community of medical software developers in which is the best-suited system to use or framework to choose. The authors present Bronchoscopy Exploration (BronchoX), a VB software to plan biopsy interventions that generate physician-readable instructions to reach the PLs. The authors’ solution is open source, multiplatform, and extensible for future functionalities, designed by their multidisciplinary research and development group. BronchoX is a compound of different algorithms for segmentation, visualisation, and navigation of the respiratory tract. Performed results are a focus on the test the effectiveness of their proposal as an exploration software, also to measure its accuracy as a guiding system to reach PLs. Then, 40 different virtual planning paths were created to guide physicians until distal bronchioles. These results provide a functional software for BronchoX and demonstrate how following simple instructions is possible to reach distal lesions from the trachea.
	Address
	Corporate Author	rank (SJR)			Thesis
	Publisher		Place of Publication		Editor
	Language		Summary Language		Original Title
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN		ISBN		Medium
	Area		Expedition		Conference
	Notes	IAM; 600.096; 600.075; 601.323; 601.337; 600.145			Approved	no
	Call Number	Admin @ si @ RSB2018a			Serial	3132
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	Author	Antoni Gurgui; Debora Gil; Enric Marti; Vicente Grau
	Title	Left-Ventricle Basal Region Constrained Parametric Mapping to Unitary Domain			Type	Conference Article
	Year	2016	Publication	7th International Workshop on Statistical Atlases & Computational Modelling of the Heart	Abbreviated Journal
	Volume	10124	Issue		Pages	163-171
	Keywords	Laplacian; Constrained maps; Parameterization; Basal ring
	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.
	Address	Athens; October 2016
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Summary Language		Original Title
	Series Editor		Series Title		Abbreviated Series Title	LNCS
	Series Volume		Series Issue		Edition
	ISSN		ISBN		Medium
	Area		Expedition		Conference	STACOM
	Notes	IAM;			Approved	no
	Call Number	Admin @ si @ GGM2016			Serial	2884
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	Author	Mireia Sole; Joan Blanco; Debora Gil; Oliver Valero; Alvaro Pascual; B. Cardenas; G. Fonseka; E. Anton; Richard Frodsham; Francesca Vidal; Zaida Sarrate
	Title	Chromosomal positioning in spermatogenic cells is influenced by chromosomal factors associated with gene activity, bouquet formation, and meiotic sex-chromosome inactivation			Type	Journal Article
	Year	2021	Publication	Chromosoma	Abbreviated Journal
	Volume	130	Issue		Pages	163-175
	Keywords
	Abstract	Chromosome territoriality is not random along the cell cycle and it is mainly governed by intrinsic chromosome factors and gene expression patterns. Conversely, very few studies have explored the factors that determine chromosome territoriality and its influencing factors during meiosis. In this study, we analysed chromosome positioning in murine spermatogenic cells using three-dimensionally fluorescence in situ hybridization-based methodology, which allows the analysis of the entire karyotype. The main objective of the study was to decipher chromosome positioning in a radial axis (all analysed germ-cell nuclei) and longitudinal axis (only spermatozoa) and to identify the chromosomal factors that regulate such an arrangement. Results demonstrated that the radial positioning of chromosomes during spermatogenesis was cell-type specific and influenced by chromosomal factors associated to gene activity. Chromosomes with specific features that enhance transcription (high GC content, high gene density and high numbers of predicted expressed genes) were preferentially observed in the inner part of the nucleus in virtually all cell types. Moreover, the position of the sex chromosomes was influenced by their transcriptional status, from the periphery of the nucleus when its activity was repressed (pachytene) to a more internal position when it is partially activated (spermatid). At pachytene, chromosome positioning was also influenced by chromosome size due to the bouquet formation. Longitudinal chromosome positioning in the sperm nucleus was not random either, suggesting the importance of ordered longitudinal positioning for the release and activation of the paternal genome after fertilisation.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Summary Language		Original Title
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN		ISBN		Medium
	Area		Expedition		Conference
	Notes	IAM; 600.145			Approved	no
	Call Number	Admin @ si @ SBG2021			Serial	3592
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	Author	David Roche; Debora Gil; Jesus Giraldo
	Title	Mathematical modeling of G protein-coupled receptor function: What can we learn from empirical and mechanistic models?			Type	Book Chapter
	Year	2014	Publication	G Protein-Coupled Receptors – Modeling and Simulation Advances in Experimental Medicine and Biology	Abbreviated Journal
	Volume	796	Issue	3	Pages	159-181
	Keywords	β-arrestin; biased agonism; curve fitting; empirical modeling; evolutionary algorithm; functional selectivity; G protein; GPCR; Hill coefficient; intrinsic efficacy; inverse agonism; mathematical modeling; mechanistic modeling; operational model; parameter optimization; receptor dimer; receptor oligomerization; receptor constitutive activity; signal transduction; two-state model
	Abstract	Empirical and mechanistic models differ in their approaches to the analysis of pharmacological effect. Whereas the parameters of the former are not physical constants those of the latter embody the nature, often complex, of biology. Empirical models are exclusively used for curve fitting, merely to characterize the shape of the E/[A] curves. Mechanistic models, on the contrary, enable the examination of mechanistic hypotheses by parameter simulation. Regretfully, the many parameters that mechanistic models may include can represent a great difficulty for curve fitting, representing, thus, a challenge for computational method development. In the present study some empirical and mechanistic models are shown and the connections, which may appear in a number of cases between them, are analyzed from the curves they yield. It may be concluded that systematic and careful curve shape analysis can be extremely useful for the understanding of receptor function, ligand classification and drug discovery, thus providing a common language for the communication between pharmacologists and medicinal chemists.
	Address
	Corporate Author				Thesis
	Publisher	Springer Netherlands	Place of Publication		Editor
	Language		Summary Language		Original Title
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0065-2598	ISBN	978-94-007-7422-3	Medium
	Area		Expedition		Conference
	Notes	IAM; 600.075			Approved	no
	Call Number	IAM @ iam @ RGG2014			Serial	2197
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	Author	Debora Gil; Antonio Esteban Lansaque; Sebastian Stefaniga; Mihail Gaianu; Carles Sanchez
	Title	Data Augmentation from Sketch			Type	Conference Article
	Year	2019	Publication	International Workshop on Uncertainty for Safe Utilization of Machine Learning in Medical Imaging	Abbreviated Journal
	Volume	11840	Issue		Pages	155-162
	Keywords	Data augmentation; cycleGANs; Multi-objective optimization
	Abstract	State of the art machine learning methods need huge amounts of data with unambiguous annotations for their training. In the context of medical imaging this is, in general, a very difficult task due to limited access to clinical data, the time required for manual annotations and variability across experts. Simulated data could serve for data augmentation provided that its appearance was comparable to the actual appearance of intra-operative acquisitions. Generative Adversarial Networks (GANs) are a powerful tool for artistic style transfer, but lack a criteria for selecting epochs ensuring also preservation of intra-operative content. We propose a multi-objective optimization strategy for a selection of cycleGAN epochs ensuring a mapping between virtual images and the intra-operative domain preserving anatomical content. Our approach has been applied to simulate intra-operative bronchoscopic videos and chest CT scans from virtual sketches generated using simple graphical primitives.
	Address	Shenzhen; China; October 2019
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Summary Language		Original Title
	Series Editor		Series Title		Abbreviated Series Title	LNCS
	Series Volume		Series Issue		Edition
	ISSN		ISBN		Medium
	Area		Expedition		Conference	CLIP
	Notes	IAM; 600.145; 601.337; 600.139; 600.145			Approved	no
	Call Number	Admin @ si @ GES2019			Serial	3359
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