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	Author	Debora Gil
	Title	Geometric Differential Operators for Shape Modelling			Type	Book Whole
	Year	2004	Publication	PhD Thesis, Universitat Autonoma de Barcelona-CVC	Abbreviated Journal
	Volume		Issue		Pages
	Keywords
	Abstract	Medical imaging feeds research in many computer vision and image processing fields: image filtering, segmentation, shape recovery, registration, retrieval and pattern matching. Because of their low contrast changes and large variety of artifacts and noise, medical imaging processing techniques relying on an analysis of the geometry of image level sets rather than on intensity values result in more robust treatment. From the starting point of treatment of intravascular images, this PhD thesis ad- dresses the design of differential image operators based on geometric principles for a robust shape modelling and restoration. Among all fields applying shape recovery, we approach filtering and segmentation of image objects. For a successful use in real images, the segmentation process should go through three stages: noise removing, shape modelling and shape recovery. This PhD addresses all three topics, but for the sake of algorithms as automated as possible, techniques for image processing will be designed to satisfy three main principles: a) convergence of the iterative schemes to non-trivial states avoiding image degeneration to a constant image and representing smooth models of the originals; b) smooth asymptotic behav- ior ensuring stabilization of the iterative process; c) fixed parameter values ensuring equal (domain free) performance of the algorithms whatever initial images/shapes. Our geometric approach to the generic equations that model the different processes approached enables defining techniques satisfying all the former requirements. First, we introduce a new curvature-based geometric flow for image filtering achieving a good compromise between noise removing and resemblance to original images. Sec- ond, we describe a new family of diffusion operators that restrict their scope to image level curves and serve to restore smooth closed models from unconnected sets of points. Finally, we design a regularization of snake (distance) maps that ensures its smooth convergence towards any closed shape. Experiments show that performance of the techniques proposed overpasses that of state-of-the-art algorithms.
	Address
	Corporate Author				Thesis	Ph.D. thesis
	Publisher	Ediciones Graficas Rey	Place of Publication	Barcelona (Spain)	Editor	Jordi Saludes i Closa;Petia Radeva
	Language		Summary Language		Original Title
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN		ISBN	84-933652-0-3	Medium	prit
	Area		Expedition		Conference
	Notes	IAM;			Approved	no
	Call Number	IAM @ iam @ GIL2004			Serial	1517
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	Author	Aura Hernandez-Sabate
	Title	Exploring Arterial Dynamics and Structures in IntraVascular Ultrasound Sequences			Type	Book Whole
	Year	2009	Publication	PhD Thesis, Universitat Autonoma de Barcelona-CVC	Abbreviated Journal
	Volume		Issue		Pages
	Keywords
	Abstract	Cardiovascular diseases are a leading cause of death in developed countries. Most of them are caused by arterial (specially coronary) diseases, mainly caused by plaque accumulation. Such pathology narrows blood flow (stenosis) and affects artery bio- mechanical elastic properties (atherosclerosis). In the last decades, IntraVascular UltraSound (IVUS) has become a usual imaging technique for the diagnosis and follow up of arterial diseases. IVUS is a catheter-based imaging technique which shows a sequence of cross sections of the artery under study. Inspection of a single image gives information about the percentage of stenosis. Meanwhile, inspection of longitudinal views provides information about artery bio-mechanical properties, which can prevent a fatal outcome of the cardiovascular disease. On one hand, dynamics of arteries (due to heart pumping among others) is a major artifact for exploring tissue bio-mechanical properties. On the other one, manual stenosis measurements require a manual tracing of vessel borders, which is a time-consuming task and might suffer from inter-observer variations. This PhD thesis proposes several image processing tools for exploring vessel dy- namics and structures. We present a physics-based model to extract, analyze and correct vessel in-plane rigid dynamics and to retrieve cardiac phase. Furthermore, we introduce a deterministic-statistical method for automatic vessel borders detection. In particular, we address adventitia layer segmentation. An accurate validation pro- tocol to ensure reliable clinical applicability of the methods is a crucial step in any proposal of an algorithm. In this thesis we take special care in designing a valida- tion protocol for each approach proposed and we contribute to the in vivo dynamics validation with a quantitative and objective score to measure the amount of motion suppressed.
	Address
	Corporate Author				Thesis	Ph.D. thesis
	Publisher	Ediciones Graficas Rey	Place of Publication		Editor	Debora Gil
	Language		Summary Language		Original Title
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN		ISBN	978-84-937261-6-4	Medium
	Area		Expedition		Conference
	Notes	IAM;			Approved	no
	Call Number	IAM @ iam @ Her2009			Serial	1543
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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	Carles Sanchez
	Title	Tracheal Structure Characterization using Geometric and Appearance Models for Efficient Assessment of Stenosis in Videobronchoscopy			Type	Book Whole
	Year	2014	Publication	PhD Thesis, Universitat Autonoma de Barcelona-CVC	Abbreviated Journal
	Volume		Issue		Pages
	Keywords
	Abstract	Recent advances in endoscopic devices have increased their use for minimal invasive diagnostic and intervention procedures. Among all endoscopic modalities, bronchoscopy is one of the most frequent with around 261 millions of procedures per year. Although the use of bronchoscopy is spread among clinical facilities it presents some drawbacks, being the visual inspection for the assessment of anatomical measurements the most prevalent of them. In particular, inaccuracies in the estimation of the degree of stenosis (the percentage of obstructed airway) decreases its diagnostic yield and might lead to erroneous treatments. An objective computation of tracheal stenosis in bronchoscopy videos would constitute a breakthrough for this non-invasive technique and a reduction in treatment cost. This thesis settles the first steps towards on-line reliable extraction of anatomical information from videobronchoscopy for computation of objective measures. In particular, we focus on the computation of the degree of stenosis, which is obtained by comparing the area delimited by a healthy tracheal ring and the stenosed lumen. Reliable extraction of airway structures in interventional videobronchoscopy is a challenging task. This is mainly due to the large variety of acquisition conditions (positions and illumination), devices (different digitalizations) and in videos acquired at the operating room the unpredicted presence of surgical devices (such as probe ends). This thesis contributes to on-line stenosis assessment in several ways. We propose a parametric strategy for the extraction of lumen and tracheal rings regions based on the characterization of their geometry and appearance that guide a deformable model. The geometric and appearance characterization is based on a physical model describing the way bronchoscopy images are obtained and includes local and global descriptions. In order to ensure a systematic applicability we present a statistical framework to select the optimal parameters of our method. Experiments perform on the first public annotated database, show that the performance of our method is comparable to the one provided by clinicians and its computation time allows for a on-line implementation in the operating room.
	Address
	Corporate Author				Thesis	Ph.D. thesis
	Publisher	Ediciones Graficas Rey	Place of Publication		Editor	F. Javier Sanchez;Debora Gil;Jorge Bernal
	Language		Summary Language		Original Title
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN		ISBN	978-84-940902-9-5	Medium
	Area		Expedition		Conference
	Notes	IAM; 600.075			Approved	no
	Call Number	Admin @ si @ San2014			Serial	2575
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	Author	David Roche
	Title	A Statistical Framework for Terminating Evolutionary Algorithms at their Steady State			Type	Book Whole
	Year	2015	Publication	PhD Thesis, Universitat Autonoma de Barcelona-CVC	Abbreviated Journal
	Volume		Issue		Pages
	Keywords
	Abstract	As any iterative technique, it is a necessary condition a stop criterion for terminating Evolutionary Algorithms (EA). In the case of optimization methods, the algorithm should stop at the time it has reached a steady state so it can not improve results anymore. Assessing the reliability of termination conditions for EAs is of prime importance. A wrong or weak stop criterion can negatively aect both the computational eort and the nal result. In this Thesis, we introduce a statistical framework for assessing whether a termination condition is able to stop EA at its steady state. In one hand a numeric approximation to steady states to detect the point in which EA population has lost its diversity has been presented for EA termination. This approximation has been applied to dierent EA paradigms based on diversity and a selection of functions covering the properties most relevant for EA convergence. Experiments show that our condition works regardless of the search space dimension and function landscape and Dierential Evolution (DE) arises as the best paradigm. On the other hand, we use a regression model in order to determine the requirements ensuring that a measure derived from EA evolving population is related to the distance to the optimum in xspace. Our theoretical framework is analyzed across several benchmark test functions and two standard termination criteria based on function improvement in f-space and EA population x-space distribution for the DE paradigm. Results validate our statistical framework as a powerful tool for determining the capability of a measure for terminating EA and select the x-space distribution as the best-suited for accurately stopping DE in real-world applications.
	Address	July 2015
	Corporate Author				Thesis	Ph.D. thesis
	Publisher	Ediciones Graficas Rey	Place of Publication		Editor	Debora Gil;Jesus Giraldo
	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; 600.075			Approved	no
	Call Number	Admin @ si @ Roc2015			Serial	2686
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	Author	Patricia Marquez
	Title	A Confidence Framework for the Assessment of Optical Flow Performance			Type	Book Whole
	Year	2015	Publication	PhD Thesis, Universitat Autonoma de Barcelona-CVC	Abbreviated Journal
	Volume		Issue		Pages
	Keywords
	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.
	Address	July 2015
	Corporate Author				Thesis	Ph.D. thesis
	Publisher	Ediciones Graficas Rey	Place of Publication		Editor	Debora Gil;Aura Hernandez
	Language		Summary Language		Original Title
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN		ISBN	978-84-943427-2-1	Medium
	Area		Expedition		Conference
	Notes	IAM; 600.075			Approved	no
	Call Number	Admin @ si @ Mar2015			Serial	2687
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	Author	Sergio Vera
	Title	Anatomic Registration based on Medial Axis Parametrizations			Type	Book Whole
	Year	2015	Publication	PhD Thesis, Universitat Autonoma de Barcelona-CVC	Abbreviated Journal
	Volume		Issue		Pages
	Keywords
	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 specic 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 specic 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 denition 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.
	Address	November 2015
	Corporate Author				Thesis	Ph.D. thesis
	Publisher	Ediciones Graficas Rey	Place of Publication		Editor	Debora Gil;Miguel Angel Gonzalez Ballester
	Language		Summary Language		Original Title
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN		ISBN	978-84-943427-8-3	Medium
	Area		Expedition		Conference
	Notes	IAM; 600.075			Approved	no
	Call Number	Admin @ si @ Ver2015			Serial	2708
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	Author	H. Martin ; Jens Fagertun; Sergio Vera; Debora Gil
	Title	Medial structure generation for registration of anatomical structures			Type	Book Chapter
	Year	2017	Publication	Skeletonization, Theory, Methods and Applications	Abbreviated Journal
	Volume	11	Issue		Pages
	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; 600.096; 600.075; 600.145			Approved	no
	Call Number	Admin @ si @ MFV2017a			Serial	2935
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	Author	Antonio Esteban Lansaque
	Title	An Endoscopic Navigation System for Lung Cancer Biopsy			Type	Book Whole
	Year	2019	Publication	PhD Thesis, Universitat Autonoma de Barcelona-CVC	Abbreviated Journal
	Volume		Issue		Pages
	Keywords
	Abstract	Lung cancer is one of the most diagnosed cancers among men and women. Actually, lung cancer accounts for 13% of the total cases with a 5-year global survival rate in patients. Although Early detection increases survival rate from 38% to 67%, accurate diagnosis remains a challenge. Pathological confirmation requires extracting a sample of the lesion tissue for its biopsy. The preferred procedure for tissue biopsy is called bronchoscopy. A bronchoscopy is an endoscopic technique for the internal exploration of airways which facilitates the performance of minimal invasive interventions with low risk for the patient. Recent advances in bronchoscopic devices have increased their use for minimal invasive diagnostic and intervention procedures, like lung cancer biopsy sampling. Despite the improvement in bronchoscopic device quality, there is a lack of intelligent computational systems for supporting in-vivo clinical decision during examinations. Existing technologies fail to accurately reach the lesion due to several aspects at intervention off-line planning and poor intra-operative guidance at exploration time. Existing guiding systems radiate patients and clinical staff,might be expensive and achieve a suboptimlal 70% of yield boost. Diagnostic yield could be improved reducing radiation and costs by developing intra-operative support systems able to guide the bronchoscopist to the lesion during the intervention. The goal of this PhD thesis is to develop an image-based navigation systemfor intra-operative guidance of bronchoscopists to a target lesion across a path previously planned on a CT-scan. We propose a 3D navigation system which uses the anatomy of video bronchoscopy frames to locate the bronchoscope within the airways. Once the bronchoscope is located, our navigation system is able to indicate the bifurcation which needs to be followed to reach the lesion. In order to facilitate an off-line validation as realistic as possible, we also present a method for augmenting simulated virtual bronchoscopies with the appearance of intra-operative videos. Experiments performed on augmented and intra-operative videos, prove that our algorithm can be speeded up for an on-line implementation in the operating room.
	Address	October 2019
	Corporate Author				Thesis	Ph.D. thesis
	Publisher	Ediciones Graficas Rey	Place of Publication		Editor	Debora Gil;Carles Sanchez
	Language		Summary Language		Original Title
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN		ISBN	978-84-121011-0-2	Medium
	Area		Expedition		Conference
	Notes	IAM; 600.139; 600.145			Approved	no
	Call Number	Admin @ si @ Est2019			Serial	3392
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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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