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Esmitt Ramirez; Carles Sanchez; Agnes Borras; Marta Diez-Ferrer; Antoni Rosell; Debora Gil |
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Title |
BronchoX: bronchoscopy exploration software for biopsy intervention planning |
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2018 |
Publication |
Healthcare Technology Letters |
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HTL |
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5 |
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5 |
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177–182 |
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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. |
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IAM; 600.096; 600.075; 601.323; 601.337; 600.145 |
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Admin @ si @ RSB2018a |
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3132 |
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Author |
Debora Gil; Ruth Aris; Agnes Borras; Esmitt Ramirez; Rafael Sebastian; Mariano Vazquez |
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Title |
Influence of fiber connectivity in simulations of cardiac biomechanics |
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Journal Article |
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Year |
2019 |
Publication |
International Journal of Computer Assisted Radiology and Surgery |
Abbreviated Journal |
IJCAR |
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14 |
Issue |
1 |
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63–72 |
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Cardiac electromechanical simulations; Diffusion tensor imaging; Fiber connectivity |
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PURPOSE:
Personalized computational simulations of the heart could open up new improved approaches to diagnosis and surgery assistance systems. While it is fully recognized that myocardial fiber orientation is central for the construction of realistic computational models of cardiac electromechanics, the role of its overall architecture and connectivity remains unclear. Morphological studies show that the distribution of cardiac muscular fibers at the basal ring connects epicardium and endocardium. However, computational models simplify their distribution and disregard the basal loop. This work explores the influence in computational simulations of fiber distribution at different short-axis cuts.
METHODS:
We have used a highly parallelized computational solver to test different fiber models of ventricular muscular connectivity. We have considered two rule-based mathematical models and an own-designed method preserving basal connectivity as observed in experimental data. Simulated cardiac functional scores (rotation, torsion and longitudinal shortening) were compared to experimental healthy ranges using generalized models (rotation) and Mahalanobis distances (shortening, torsion).
RESULTS:
The probability of rotation was significantly lower for ruled-based models [95% CI (0.13, 0.20)] in comparison with experimental data [95% CI (0.23, 0.31)]. The Mahalanobis distance for experimental data was in the edge of the region enclosing 99% of the healthy population.
CONCLUSIONS:
Cardiac electromechanical simulations of the heart with fibers extracted from experimental data produce functional scores closer to healthy ranges than rule-based models disregarding architecture connectivity. |
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IAM; 600.096; 601.323; 600.139; 600.145 |
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Admin @ si @ GAB2019a |
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3133 |
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Esmitt Ramirez; Carles Sanchez; Agnes Borras; Marta Diez-Ferrer; Antoni Rosell; Debora Gil |
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Title |
Image-Based Bronchial Anatomy Codification for Biopsy Guiding in Video Bronchoscopy |
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Conference Article |
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2018 |
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OR 2.0 Context-Aware Operating Theaters, Computer Assisted Robotic Endoscopy, Clinical Image-Based Procedures, and Skin Image Analysis |
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11041 |
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Biopsy guiding; Bronchoscopy; Lung biopsy; Intervention guiding; Airway codification |
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Bronchoscopy examinations allow biopsy of pulmonary nodules with minimum risk for the patient. Even for experienced bronchoscopists, it is difficult to guide the bronchoscope to most distal lesions and obtain an accurate diagnosis. This paper presents an image-based codification of the bronchial anatomy for bronchoscopy biopsy guiding. The 3D anatomy of each patient is codified as a binary tree with nodes representing bronchial levels and edges labeled using their position on images projecting the 3D anatomy from a set of branching points. The paths from the root to leaves provide a codification of navigation routes with spatially consistent labels according to the anatomy observes in video bronchoscopy explorations. We evaluate our labeling approach as a guiding system in terms of the number of bronchial levels correctly codified, also in the number of labels-based instructions correctly supplied, using generalized mixed models and computer-generated data. Results obtained for three independent observers prove the consistency and reproducibility of our guiding system. We trust that our codification based on viewer’s projection might be used as a foundation for the navigation process in Virtual Bronchoscopy systems. |
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Granada; September 2018 |
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MICCAIW |
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IAM; 600.096; 600.075; 601.323; 600.145 |
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Admin @ si @ RSB2018b |
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3137 |
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Debora Gil; Antonio Esteban Lansaque; Agnes Borras; Carles Sanchez |
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Title |
Enhancing virtual bronchoscopy with intra-operative data using a multi-objective GAN |
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2019 |
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International Journal of Computer Assisted Radiology and Surgery |
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IJCAR |
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7 |
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1 |
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This manuscript has been withdrawn by bioRxiv due to upload of an incorrect version of the manuscript by the authors. Therefore, this manuscript should not be cited as reference for this project. |
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IAM; 600.139; 600.145 |
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Admin @ si @ GEB2019 |
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3307 |
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Author |
Debora Gil; Carles Sanchez; Agnes Borras; Marta Diez-Ferrer; Antoni Rosell |
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Title |
Segmentation of Distal Airways using Structural Analysis |
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Journal Article |
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Year |
2019 |
Publication |
PloS one |
Abbreviated Journal |
Plos |
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14 |
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12 |
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Segmentation of airways in Computed Tomography (CT) scans is a must for accurate support of diagnosis and intervention of many pulmonary disorders. In particular, lung cancer diagnosis would benefit from segmentations reaching most distal airways. We present a method that combines descriptors of bronchi local appearance and graph global structural analysis to fine-tune thresholds on the descriptors adapted for each bronchial level. We have compared our method to the top performers of the EXACT09 challenge and to a commercial software for biopsy planning evaluated in an own-collected data-base of high resolution CT scans acquired under different breathing conditions. Results on EXACT09 data show that our method provides a high leakage reduction with minimum loss in airway detection. Results on our data-base show the reliability across varying breathing conditions and a competitive performance for biopsy planning compared to a commercial solution. |
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IAM; 600.139; 600.145 |
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Admin @ si @ GSB2019 |
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3357 |
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Author |
Carles Sanchez; Miguel Viñas; Coen Antens; Agnes Borras; Debora Gil |
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Back to Front Architecture for Diagnosis as a Service |
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Conference Article |
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2018 |
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20th International Symposium on Symbolic and Numeric Algorithms for Scientific Computing |
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343-346 |
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Software as a Service (SaaS) is a cloud computing model in which a provider hosts applications in a server that customers use via internet. Since SaaS does not require to install applications on customers' own computers, it allows the use by multiple users of highly specialized software without extra expenses for hardware acquisition or licensing. A SaaS tailored for clinical needs not only would alleviate licensing costs, but also would facilitate easy access to new methods for diagnosis assistance. This paper presents a SaaS client-server architecture for Diagnosis as a Service (DaaS). The server is based on docker technology in order to allow execution of softwares implemented in different languages with the highest portability and scalability. The client is a content management system allowing the design of websites with multimedia content and interactive visualization of results allowing user editing. We explain a usage case that uses our DaaS as crowdsourcing platform in a multicentric pilot study carried out to evaluate the clinical benefits of a software for assessment of central airway obstruction. |
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Timisoara; Rumania; September 2018 |
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SYNASC |
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IAM; 600.145 |
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Admin @ si @ SVA2018 |
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3360 |
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Debora Gil; Antonio Esteban Lansaque; Agnes Borras; Esmitt Ramirez; Carles Sanchez |
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Title |
Intraoperative Extraction of Airways Anatomy in VideoBronchoscopy |
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2020 |
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IEEE Access |
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ACCESS |
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8 |
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159696 - 159704 |
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A main bottleneck in bronchoscopic biopsy sampling is to efficiently reach the lesion navigating across bronchial levels. Any guidance system should be able to localize the scope position during the intervention with minimal costs and alteration of clinical protocols. With the final goal of an affordable image-based guidance, this work presents a novel strategy to extract and codify the anatomical structure of bronchi, as well as, the scope navigation path from videobronchoscopy. Experiments using interventional data show that our method accurately identifies the bronchial structure. Meanwhile, experiments using simulated data verify that the extracted navigation path matches the 3D route. |
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IAM; 600.139; 600.145 |
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Admin @ si @ GEB2020 |
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3467 |
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Debora Gil; Agnes Borras; Manuel Ballester; Francesc Carreras; Ruth Aris; Manuel Vazquez; Enric Marti; Ferran Poveda |
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MIOCARDIA: Integrating cardiac function and muscular architecture for a better diagnosis |
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2011 |
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14th International Symposium on Applied Sciences in Biomedical and Communication Technologies |
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Deep understanding of myocardial structure of the heart would unravel crucial knowledge for clinical and medical procedures. The MIOCARDIA project is a multidisciplinary project in cooperation with l'Hospital de la Santa Creu i de Sant Pau, Clinica la Creu Blanca and Barcelona Supercomputing Center. The ultimate goal of this project is defining a computational model of the myocardium. The model takes into account the deep interrelation between the anatomy and the mechanics of the heart. The paper explains the workflow of the MIOCARDIA project. It also introduces a multiresolution reconstruction technique based on DT-MRI streamlining for simplified global myocardial model generation. Our reconstructions can restore the most complex myocardial structures and provides evidences of a global helical organization. |
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Barcelona; Spain |
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Association for Computing Machinery |
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Barcelona, Spain |
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Association for Computing Machinery |
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english |
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english |
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978-1-4503-0913-4 |
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ISABEL |
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IAM |
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IAM @ iam @ GGB2011 |
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1691 |
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Agnes Borras; Josep Llados |
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Similarity-Based Object Retrieval Using Appearance and Geometric Feature Combination |
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2007 |
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3rd Iberian Conference on Pattern Recognition and Image Analysis (IbPRIA 2007), J. Marti et al. (Eds.) LNCS 4477:113–120 |
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LNCS |
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4478 |
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33–39 |
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This work presents a content-based image retrieval system of general purpose that deals with cluttered scenes containing a given query object. The system is flexible enough to handle with a single image of an object despite its rotation, translation and scale variations. The image content is divided in parts that are described with a combination of features based on geometrical and color properties. The idea behind the feature combination is to benefit from a fuzzy similarity computation that provides robustness and tolerance to the retrieval process. The features can be independently computed and the image parts can be easily indexed by using a table structure on every feature value. Finally a process inspired in the alignment strategies is used to check the coherence of the object parts found in a scene. Our work presents a system of easy implementation that uses an open set of features and can suit a wide variety of applications. |
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Girona (Spain) |
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978-3-540-72848-1 |
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DAG; |
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DAG @ dag @ BoL2007a; IAM @ iam @ BoL2007a |
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776 |
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Sergio Vera; Debora Gil; Agnes Borras; F. Javier Sanchez; Frederic Perez; Marius G. Linguraru; Miguel Angel Gonzalez Ballester |
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Computation and Evaluation of Medial Surfaces for Shape Representation of Abdominal Organs |
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2012 |
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Workshop on Computational and Clinical Applications in Abdominal Imaging |
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7029 |
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223–230 |
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medial manifolds, abdomen. |
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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. |
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Toronto; Canada; |
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Springer Link |
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Berlin |
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H. Yoshida et al |
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English |
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English |
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Lecture Notes in Computer Science |
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0302-9743 |
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978-3-642-28556-1 |
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ABDI |
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IAM;MV |
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IAM @ iam @ VGB2012 |
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1834 |
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