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Author |
Albert Andaluz |
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Title |
LV Contour Segmentation in TMR images using Semantic Description of Tissue and Prior Knowledge Correction |
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Report |
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2009 |
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CVC Technical Report |
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142 |
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Active Contour Models; Snakes; Active Shape Models; Deformable Templates; Left Ventricle Segmentation; Generalized Orthogonal Procrustes Analysis; Harmonic Phase Flow; Principal Component Analysis; Tagged Magnetic Resonance |
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Abstract |
The Diagnosis of Left Ventricle (LV) pathologies is related to regional wall motion analysis. Health indicator scores such as the rotation and the torsion are useful for the diagnose of the Left Ventricle (LV) function. However, this requires proper identification of LV segments. On one hand, manual segmentation is robust, but it is slow and requires medical expertise. On the other hand, the tag pattern in Tagged Magnetic Resonance (TMR) sequences is a problem for the automatic segmentation of the LV boundaries. Consequently, we propose a method based in the classical formulation of parametric Snakes, combined with Active Shape models. Our semantic definition of the LV is tagged tissue that experiences motion in the systolic cycle. This defines two energy potentials for the Snake convergence. Additionally, the mean shape corrects excessive deviation from the anatomical shape. We have validated our approach in 15 healthy volunteers and two short axis cuts. In this way, we have compared the automatic segmentations to manual shapes outlined by medical experts. Also, we have explored the accuracy of clinical scores computed using automatic contours. The results show minor divergence in the approximation and the manual segmentations as well as robust computation of clinical scores in all cases. From this we conclude that the proposed method is a promising support tool for clinical analysis. |
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Master's thesis |
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Bellaterra 08193, Barcelona, Spain |
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IAM @ iam @ And2009 |
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1667 |
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Mireia Sole; Joan Blanco; Debora Gil; Oliver Valero; Alvaro Pascual; B. Cardenas; G. Fonseka; E. Anton; Richard Frodsham; Francesca Vidal; Zaida Sarrate |
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Chromosomal positioning in spermatogenic cells is influenced by chromosomal factors associated with gene activity, bouquet formation, and meiotic sex-chromosome inactivation |
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2021 |
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Chromosoma |
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130 |
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163-175 |
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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. |
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IAM; 600.145 |
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Admin @ si @ SBG2021 |
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3592 |
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Fernando Vilariño; Debora Gil; Petia Radeva |
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Title |
A Novel FLDA Formulation for Numerical Stability Analysis |
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2004 |
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Recent Advances in Artificial Intelligence Research and Development |
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113 |
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77-84 |
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Supervised Learning; Linear Discriminant Analysis; Numerical Stability; Computer Vision |
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Fisher Linear Discriminant Analysis (FLDA) is one of the most popular techniques used in classification applying dimensional reduction. The numerical scheme involves the inversion of the within-class scatter matrix, which makes FLDA potentially ill-conditioned when it becomes singular. In this paper we present a novel explicit formulation of FLDA in terms of the eccentricity ratio and eigenvector orientations of the within-class scatter matrix. An analysis of this function will characterize those situations where FLDA response is not reliable because of numerical instability. This can solve common situations of poor classification performance in computer vision. |
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IOS Press |
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J. Vitrià, P. Radeva and I. Aguiló |
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978-1-58603-466-5 |
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MV;IAM;MILAB;SIAI |
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IAM @ iam @ VGR2004 |
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1663 |
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Debora Gil; Petia Radeva |
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Title |
Extending anisotropic operators to recover smooth shapes |
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2005 |
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Computer Vision and Image Understanding |
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99 |
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1 |
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110-125 |
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Contour completion; Functional extension; Differential operators; Riemmanian manifolds; Snake segmentation |
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Anisotropic differential operators are widely used in image enhancement processes. Recently, their property of smoothly extending functions to the whole image domain has begun to be exploited. Strong ellipticity of differential operators is a requirement that ensures existence of a unique solution. This condition is too restrictive for operators designed to extend image level sets: their own functionality implies that they should restrict to some vector field. The diffusion tensor that defines the diffusion operator links anisotropic processes with Riemmanian manifolds. In this context, degeneracy implies restricting diffusion to the varieties generated by the vector fields of positive eigenvalues, provided that an integrability condition is satisfied. We will use that any smooth vector field fulfills this integrability requirement to design line connection algorithms for contour completion. As application we present a segmenting strategy that assures convergent snakes whatever the geometry of the object to be modelled is. |
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1077-3142 |
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IAM;MILAB |
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IAM @ iam @ GIR2005 |
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1530 |
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Maurizio Mencuccini; Jordi Martinez-Vilalta; Josep Piñol; Lasse Loepfe; Mireia Burnat ; Xavier Alvarez; Juan Camacho; Debora Gil |
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Title |
A quantitative and statistically robust method for the determination of xylem conduit spatial distribution |
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Journal Article |
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2010 |
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American Journal of Botany |
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AJB |
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97 |
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8 |
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1247-1259 |
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Geyer; hydraulic conductivity; point pattern analysis; Ripley; Spatstat; vessel clusters; xylem anatomy; xylem network |
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Premise of the study: Because of their limited length, xylem conduits need to connect to each other to maintain water transport from roots to leaves. Conduit spatial distribution in a cross section plays an important role in aiding this connectivity. While indices of conduit spatial distribution already exist, they are not well defined statistically. * Methods: We used point pattern analysis to derive new spatial indices. One hundred and five cross-sectional images from different species were transformed into binary images. The resulting point patterns, based on the locations of the conduit centers-of-area, were analyzed to determine whether they departed from randomness. Conduit distribution was then modeled using a spatially explicit stochastic model. * Key results: The presence of conduit randomness, uniformity, or aggregation depended on the spatial scale of the analysis. The large majority of the images showed patterns significantly different from randomness at least at one spatial scale. A strong phylogenetic signal was detected in the spatial variables. * Conclusions: Conduit spatial arrangement has been largely conserved during evolution, especially at small spatial scales. Species in which conduits were aggregated in clusters had a lower conduit density compared to those with uniform distribution. Statistically sound spatial indices must be employed as an aid in the characterization of distributional patterns across species and in models of xylem water transport. Point pattern analysis is a very useful tool in identifying spatial patterns. |
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IAM; |
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IAM @ iam @ MMG2010 |
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1623 |
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Marta Diez-Ferrer; Arturo Morales; Rosa Lopez Lisbona; Noelia Cubero; Cristian Tebe; Susana Padrones; Samantha Aso; Jordi Dorca; Debora Gil; Antoni Rosell |
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Title |
Ultrathin Bronchoscopy with and without Virtual Bronchoscopic Navigation: Influence of Segmentation on Diagnostic Yield |
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Journal Article |
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2019 |
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Respiration |
Abbreviated Journal |
RES |
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97 |
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3 |
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252-258 |
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Lung cancer; Peripheral lung lesion; Diagnosis; Bronchoscopy; Ultrathin bronchoscopy; Virtual bronchoscopic navigation |
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Background: Bronchoscopy is a safe technique for diagnosing peripheral pulmonary lesions (PPLs), and virtual bronchoscopic navigation (VBN) helps guide the bronchoscope to PPLs. Objectives: We aimed to compare the diagnostic yield of VBN-guided and unguided ultrathin bronchoscopy (UTB) and explore clinical and technical factors associated with better results. We developed a diagnostic algorithm for deciding whether to use VBN to reach PPLs or choose an alternative diagnostic approach. Methods: We compared diagnostic yield between VBN-UTB (prospective cases) and unguided UTB (historical controls) and analyzed the VBN-UTB subgroup to identify clinical and technical variables that could predict the success of VBN-UTB. Results: Fifty-five cases and 110 controls were included. The overall diagnostic yield did not differ between the VBN-guided and unguided arms (47 and 40%, respectively; p = 0.354). Although the yield was slightly higher for PPLs ≤20 mm in the VBN-UTB arm, the difference was not significant (p = 0.069). No other clinical characteristics were associated with a higher yield in a subgroup analysis, but an 85% diagnostic yield was observed when segmentation was optimal and the PPL was endobronchial (vs. 30% when segmentation was suboptimal and 20% when segmentation was optimal but the PPL was extrabronchial). Conclusions: VBN-guided UTB is not superior to unguided UTB. A greater impact of VBN-guided over unguided UTB is highly dependent on both segmentation quality and an endobronchial location of the PPL. Segmentation quality should be considered before starting a procedure, when an alternative technique that may improve yield can be chosen, saving time and resources. |
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IAM; 600.145; 600.139 |
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Admin @ si @ DML2019 |
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3134 |
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Marta Diez-Ferrer; Debora Gil; Cristian Tebe; Carles Sanchez |
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Title |
Positive Airway Pressure to Enhance Computed Tomography Imaging for Airway Segmentation for Virtual Bronchoscopic Navigation |
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Journal Article |
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2018 |
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Respiration |
Abbreviated Journal |
RES |
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96 |
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6 |
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525-534 |
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Multidetector computed tomography; Bronchoscopy; Continuous positive airway pressure; Image enhancement; Virtual bronchoscopic navigation |
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Abstract
RATIONALE:
Virtual bronchoscopic navigation (VBN) guidance to peripheral pulmonary lesions is often limited by insufficient segmentation of the peripheral airways.
OBJECTIVES:
To test the effect of applying positive airway pressure (PAP) during CT acquisition to improve segmentation, particularly at end-expiration.
METHODS:
CT acquisitions in inspiration and expiration with 4 PAP protocols were recorded prospectively and compared to baseline inspiratory acquisitions in 20 patients. The 4 protocols explored differences between devices (flow vs. turbine), exposures (within seconds vs. 15-min) and pressure levels (10 vs. 14 cmH2O). Segmentation quality was evaluated with the number of airways and number of endpoints reached. A generalized mixed-effects model explored the estimated effect of each protocol.
MEASUREMENTS AND MAIN RESULTS:
Patient characteristics and lung function did not significantly differ between protocols. Compared to baseline inspiratory acquisitions, expiratory acquisitions after 15 min of 14 cmH2O PAP segmented 1.63-fold more airways (95% CI 1.07-2.48; p = 0.018) and reached 1.34-fold more endpoints (95% CI 1.08-1.66; p = 0.004). Inspiratory acquisitions performed immediately under 10 cmH2O PAP reached 1.20-fold (95% CI 1.09-1.33; p < 0.001) more endpoints; after 15 min the increase was 1.14-fold (95% CI 1.05-1.24; p < 0.001).
CONCLUSIONS:
CT acquisitions with PAP segment more airways and reach more endpoints than baseline inspiratory acquisitions. The improvement is particularly evident at end-expiration after 15 min of 14 cmH2O PAP. Further studies must confirm that the improvement increases diagnostic yield when using VBN to evaluate peripheral pulmonary lesions. |
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IAM; 600.145 |
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Admin @ si @ DGT2018 |
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3135 |
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Debora Gil; Rosa Maria Ortiz; Carles Sanchez; Antoni Rosell |
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Objective endoscopic measurements of central airway stenosis. A pilot study |
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2018 |
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Respiration |
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RES |
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95 |
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63–69 |
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Bronchoscopy; Tracheal stenosis; Airway stenosis; Computer-assisted analysis |
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Endoscopic estimation of the degree of stenosis in central airway obstruction is subjective and highly variable. Objective: To determine the benefits of using SENSA (System for Endoscopic Stenosis Assessment), an image-based computational software, for obtaining objective stenosis index (SI) measurements among a group of expert bronchoscopists and general pulmonologists. Methods: A total of 7 expert bronchoscopists and 7 general pulmonologists were enrolled to validate SENSA usage. The SI obtained by the physicians and by SENSA were compared with a reference SI to set their precision in SI computation. We used SENSA to efficiently obtain this reference SI in 11 selected cases of benign stenosis. A Web platform with three user-friendly microtasks was designed to gather the data. The users had to visually estimate the SI from videos with and without contours of the normal and the obstructed area provided by SENSA. The users were able to modify the SENSA contours to define the reference SI using morphometric bronchoscopy. Results: Visual SI estimation accuracy was associated with neither bronchoscopic experience (p = 0.71) nor the contours of the normal and the obstructed area provided by the system (p = 0.13). The precision of the SI by SENSA was 97.7% (95% CI: 92.4-103.7), which is significantly better than the precision of the SI by visual estimation (p < 0.001), with an improvement by at least 15%. Conclusion: SENSA provides objective SI measurements with a precision of up to 99.5%, which can be calculated from any bronchoscope using an affordable scalable interface. Providing normal and obstructed contours on bronchoscopic videos does not improve physicians' visual estimation of the SI. |
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IAM; 600.075; 600.096; 600.145 |
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Admin @ si @ GOS2018 |
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3043 |
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H.Martin Kjer; Jens Fagertuna; Sergio Vera; Debora Gil; Miguel Angel Gonzalez Ballester; Rasmus R. Paulsena |
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Free-form image registration of human cochlear uCT data using skeleton similarity as anatomical prior |
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2016 |
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Patter Recognition Letters |
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PRL |
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76 |
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1 |
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76-82 |
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IAM; 600.060 |
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Admin @ si @ MFV2017b |
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2941 |
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Ferran Poveda; Debora Gil; Enric Marti; Albert Andaluz; Manel Ballester;Francesc Carreras Costa |
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Helical structure of the cardiac ventricular anatomy assessed by Diffusion Tensor Magnetic Resonance Imaging multi-resolution tractography |
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2013 |
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Revista Española de Cardiología |
Abbreviated Journal |
REC |
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66 |
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10 |
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782-790 |
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Heart;Diffusion magnetic resonance imaging;Diffusion tractography;Helical heart;Myocardial ventricular band. |
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Deep understanding of myocardial structure linking morphology and function of the heart would unravel crucial knowledge for medical and surgical clinical procedures and studies. Several conceptual models of myocardial fiber organization have been proposed but the lack of an automatic and objective methodology prevented an agreement. We sought to deepen in this knowledge through advanced computer graphic representations of the myocardial fiber architecture by diffusion tensor magnetic resonance imaging (DT-MRI).
We performed automatic tractography reconstruction of unsegmented DT-MRI canine heart datasets coming from the public database of the Johns Hopkins University. Full scale tractographies have been build with 200 seeds and are composed by streamlines computed on the vectorial field of primary eigenvectors given at the diffusion tensor volumes. Also, we introduced a novel multi-scale visualization technique in order to obtain a simplified tractography. This methodology allowed to keep the main geometric features of the fiber tracts, making easier to decipher the main properties of the architectural organization of the heart.
On the analysis of the output from our tractographic representations we found exact correlation with low-level details of myocardial architecture, but also with the more abstract conceptualization of a continuous helical ventricular myocardial fiber array.
Objective analysis of myocardial architecture by an automated method, including the entire myocardium and using several 3D levels of complexity, reveals a continuous helical myocardial fiber arrangement of both right and left ventricles, supporting the anatomical model of the helical ventricular myocardial band described by Torrent-Guasp. |
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Elsevier |
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IAM; 600.044; 600.060 |
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IAM @ iam @ PGM2013 |
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2194 |
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