|
Records |
Links |
|
Author |
Pau Cano; Alvaro Caravaca; Debora Gil; Eva Musulen |
|
|
Title |
Diagnosis of Helicobacter pylori using AutoEncoders for the Detection of Anomalous Staining Patterns in Immunohistochemistry Images |
Type |
Miscellaneous |
|
Year |
2023 |
Publication |
Arxiv |
Abbreviated Journal |
|
|
|
Volume |
|
Issue |
|
Pages |
107241 |
|
|
Keywords |
|
|
|
Abstract |
This work addresses the detection of Helicobacter pylori a bacterium classified since 1994 as class 1 carcinogen to humans. By its highest specificity and sensitivity, the preferred diagnosis technique is the analysis of histological images with immunohistochemical staining, a process in which certain stained antibodies bind to antigens of the biological element of interest. This analysis is a time demanding task, which is currently done by an expert pathologist that visually inspects the digitized samples.
We propose to use autoencoders to learn latent patterns of healthy tissue and detect H. pylori as an anomaly in image staining. Unlike existing classification approaches, an autoencoder is able to learn patterns in an unsupervised manner (without the need of image annotations) with high performance. In particular, our model has an overall 91% of accuracy with 86\% sensitivity, 96% specificity and 0.97 AUC in the detection of H. pylori. |
|
|
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 @ CCG2023 |
Serial |
3855 |
|
Permanent link to this record |
|
|
|
|
Author |
Aura Hernandez-Sabate; Petia Radeva; Antonio Tovar; Debora Gil |
|
|
Title |
Vessel structures alignment by spectral analysis of ivus sequences |
Type |
Conference Article |
|
Year |
2006 |
Publication |
Proc. of CVII, MICCAI Workshop |
Abbreviated Journal |
|
|
|
Volume |
|
Issue |
|
Pages |
39-36 |
|
|
Keywords |
|
|
|
Abstract |
Three-dimensional intravascular ultrasound (IVUS) allows to visualize and obtain volumetric measurements of coronary lesions through an exploration of the cross sections and longitudinal views of arteries. However, the visualization and subsequent morpho-geometric measurements in IVUS longitudinal cuts are subject to distortion caused by periodic image/vessel motion around the IVUS catheter. Usually, to overcome the image motion artifact ECG-gating and image-gated approaches are proposed, leading to slowing the pullback acquisition or disregarding part of IVUS data. In this paper, we argue that the image motion is due to 3-D vessel geometry as well as cardiac dynamics, and propose a dynamic model based on the tracking of an elliptical vessel approximation to recover the rigid transformation and align IVUS images without loosing any IVUS data. We report an extensive validation with synthetic simulated data and in vivo IVUS sequences of 30 patients achieving an average reduction of the image artifact of 97% in synthetic data and 79% in real-data. Our study shows that IVUS alignment improves longitudinal analysis of the IVUS data and is a necessary step towards accurate reconstruction and volumetric measurements of 3-D IVUS. |
|
|
Address |
|
|
|
Corporate Author |
|
Thesis |
|
|
|
Publisher |
|
Place of Publication |
Copenhaguen (Denmark), |
Editor |
|
|
|
Language |
|
Summary Language |
|
Original Title |
|
|
|
Series Editor |
|
Series Title |
1st International Wokshop on Computer Vision for Intravascular and Intracardiac Imaging (CVII’06) |
Abbreviated Series Title |
|
|
|
Series Volume |
|
Series Issue |
|
Edition |
|
|
|
ISSN |
|
ISBN |
|
Medium |
|
|
|
Area |
|
Expedition |
|
Conference |
|
|
|
Notes |
IAM; MILAB |
Approved |
no |
|
|
Call Number |
IAM @ iam @ HRT2006 |
Serial |
1552 |
|
Permanent link to this record |
|
|
|
|
Author |
Misael Rosales; Petia Radeva; Oriol Rodriguez-Leor; Debora Gil |
|
|
Title |
Modelling of image-catheter motion for 3-D IVUS |
Type |
Journal Article |
|
Year |
2009 |
Publication |
Medical image analysis |
Abbreviated Journal |
MIA |
|
|
Volume |
13 |
Issue |
1 |
Pages |
91-104 |
|
|
Keywords |
Intravascular ultrasound (IVUS); Motion estimation; Motion decomposition; Fourier |
|
|
Abstract |
Three-dimensional intravascular ultrasound (IVUS) allows to visualize and obtain volumetric measurements of coronary lesions through an exploration of the cross sections and longitudinal views of arteries. However, the visualization and subsequent morpho-geometric measurements in IVUS longitudinal cuts are subject to distortion caused by periodic image/vessel motion around the IVUS catheter. Usually, to overcome the image motion artifact ECG-gating and image-gated approaches are proposed, leading to slowing the pullback acquisition or disregarding part of IVUS data. In this paper, we argue that the image motion is due to 3-D vessel geometry as well as cardiac dynamics, and propose a dynamic model based on the tracking of an elliptical vessel approximation to recover the rigid transformation and align IVUS images without loosing any IVUS data. We report an extensive validation with synthetic simulated data and in vivo IVUS sequences of 30 patients achieving an average reduction of the image artifact of 97% in synthetic data and 79% in real-data. Our study shows that IVUS alignment improves longitudinal analysis of the IVUS data and is a necessary step towards accurate reconstruction and volumetric measurements of 3-D IVUS. |
|
|
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 @ RRR2009 |
Serial |
1646 |
|
Permanent link to this record |
|
|
|
|
Author |
Aura Hernandez-Sabate; Debora Gil;Eduard Fernandez-Nofrerias;Petia Radeva; Enric Marti |
|
|
Title |
Approaching Artery Rigid Dynamics in IVUS |
Type |
Journal Article |
|
Year |
2009 |
Publication |
IEEE Transactions on Medical Imaging |
Abbreviated Journal |
TMI |
|
|
Volume |
28 |
Issue |
11 |
Pages |
1670-1680 |
|
|
Keywords |
Fourier analysis; intravascular ultrasound (IVUS) dynamics; longitudinal motion; quality measures; tissue deformation. |
|
|
Abstract |
Tissue biomechanical properties (like strain and stress) are playing an increasing role in diagnosis and long-term treatment of intravascular coronary diseases. Their assessment strongly relies on estimation of vessel wall deformation. Since intravascular ultrasound (IVUS) sequences allow visualizing vessel morphology and reflect its dynamics, this technique represents a useful tool for evaluation of tissue mechanical properties. Image misalignment introduced by vessel-catheter motion is a major artifact for a proper tracking of tissue deformation. In this work, we focus on compensating and assessing IVUS rigid in-plane motion due to heart beating. Motion parameters are computed by considering both the vessel geometry and its appearance in the image. Continuum mechanics laws serve to introduce a novel score measuring motion reduction in in vivo sequences. Synthetic experiments validate the proposed score as measure of motion parameters accuracy; whereas results in in vivo pullbacks show the reliability of the presented methodologies in clinical cases. |
|
|
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 |
0278-0062 |
ISBN |
|
Medium |
|
|
|
Area |
|
Expedition |
|
Conference |
|
|
|
Notes |
IAM; MILAB |
Approved |
no |
|
|
Call Number |
IAM @ iam @ HGF2009 |
Serial |
1545 |
|
Permanent link to this record |
|
|
|
|
Author |
David Roche; Debora Gil; Jesus Giraldo |
|
|
Title |
Mechanistic analysis of the function of agonists and allosteric modulators: Reconciling two-state and operational models |
Type |
Journal Article |
|
Year |
2013 |
Publication |
British Journal of Pharmacology |
Abbreviated Journal |
BJP |
|
|
Volume |
169 |
Issue |
6 |
Pages |
1189-202 |
|
|
Keywords |
|
|
|
Abstract |
Two-state and operational models of both agonism and allosterism are compared to identify and characterize common pharmacological parameters. To account for the receptor-dependent basal response, constitutive receptor activity is considered in the operational models. By arranging two-state models as the fraction of active receptors and operational models as the fractional response relative to the maximum effect of the system, a one-by-one correspondence between parameters is found. The comparative analysis allows a better understanding of complex allosteric interactions. In particular, the inclusion of constitutive receptor activity in the operational model of allosterism allows the characterization of modulators able to lower the basal response of the system; that is, allosteric modulators with negative intrinsic efficacy. Theoretical simulations and overall goodness of fit of the models to simulated data suggest that it is feasible to apply the models to experimental data and constitute one step forward in receptor theory formalism. |
|
|
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; 600.044; 605.203 |
Approved |
no |
|
|
Call Number |
IAM @ iam @ RGG2013b |
Serial |
2195 |
|
Permanent link to this record |
|
|
|
|
Author |
Debora Gil; Aura Hernandez-Sabate; Oriol Rodriguez; J. Mauri; Petia Radeva |
|
|
Title |
Statistical Strategy for Anisotropic Adventitia Modelling in IVUS |
Type |
Journal Article |
|
Year |
2006 |
Publication |
IEEE Transactions on Medical Imaging |
Abbreviated Journal |
|
|
|
Volume |
25 |
Issue |
6 |
Pages |
768-778 |
|
|
Keywords |
Corners; T-junctions; Wavelets |
|
|
Abstract |
Vessel plaque assessment by analysis of intravascular ultrasound sequences is a useful tool for cardiac disease diagnosis and intervention. Manual detection of luminal (inner) and mediaadventitia (external) vessel borders is the main activity of physicians in the process of lumen narrowing (plaque) quantification. Difficult definition of vessel border descriptors, as well as, shades, artifacts, and blurred signal response due to ultrasound physical properties trouble automated adventitia segmentation. In order to efficiently approach such a complex problem, we propose blending advanced anisotropic filtering operators and statistical classification techniques into a vessel border modelling strategy. Our systematic statistical analysis shows that the reported adventitia detection achieves an accuracy in the range of interobserver variability regardless of plaque nature, vessel geometry, and incomplete vessel borders. Index Terms–-Anisotropic processing, intravascular ultrasound (IVUS), vessel border segmentation, vessel structure classification. |
|
|
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 @ GHR2006 |
Serial |
1525 |
|
Permanent link to this record |
|
|
|
|
Author |
Carles Sanchez; Debora Gil; Antoni Rosell; Albert Andaluz; F. Javier Sanchez |
|
|
Title |
Segmentation of Tracheal Rings in Videobronchoscopy combining Geometry and Appearance |
Type |
Conference Article |
|
Year |
2013 |
Publication |
Proceedings of the International Conference on Computer Vision Theory and Applications |
Abbreviated Journal |
|
|
|
Volume |
1 |
Issue |
|
Pages |
153--161 |
|
|
Keywords |
Video-bronchoscopy, tracheal ring segmentation, trachea geometric and appearance model |
|
|
Abstract |
Videobronchoscopy is a medical imaging technique that allows interactive navigation inside the respiratory pathways and minimal invasive interventions. Tracheal procedures are ordinary interventions that require measurement of the percentage of obstructed pathway for injury (stenosis) assessment. Visual assessment of stenosis in videobronchoscopic sequences requires high expertise of trachea anatomy and is prone to human error. Accurate detection of tracheal rings is the basis for automated estimation of the size of stenosed trachea. Processing of videobronchoscopic images acquired at the operating room is a challenging task due to the wide range of artifacts and acquisition conditions. We present a model of the geometric-appearance of tracheal rings for its detection in videobronchoscopic videos. Experiments on sequences acquired at the operating room, show a performance close to inter-observer variability |
|
|
Address |
Barcelona; February 2013 |
|
|
Corporate Author |
|
Thesis |
|
|
|
Publisher |
SciTePress |
Place of Publication |
Portugal |
Editor |
Sebastiano Battiato and José Braz |
|
|
Language |
|
Summary Language |
|
Original Title |
|
|
|
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
LNCS |
|
|
Series Volume |
|
Series Issue |
|
Edition |
|
|
|
ISSN |
|
ISBN |
978-989-8565-47-1 |
Medium |
|
|
|
Area |
800 |
Expedition |
|
Conference |
VISAPP |
|
|
Notes |
IAM;MV; 600.044; 600.047; 600.060; 605.203 |
Approved |
no |
|
|
Call Number |
IAM @ iam @ SGR2013 |
Serial |
2123 |
|
Permanent link to this record |
|
|
|
|
Author |
Carles Sanchez;F. Javier Sanchez; Antoni Rosell; Debora Gil |
|
|
Title |
An illumination model of the trachea appearance in videobronchoscopy images |
Type |
Book Chapter |
|
Year |
2012 |
Publication |
Image Analysis and Recognition |
Abbreviated Journal |
LNCS |
|
|
Volume |
7325 |
Issue |
|
Pages |
313-320 |
|
|
Keywords |
Bronchoscopy, tracheal ring, stenosis assesment, trachea appearance model, segmentation |
|
|
Abstract |
Videobronchoscopy is a medical imaging technique that allows interactive navigation inside the respiratory pathways. This imaging modality provides realistic images and allows non-invasive minimal intervention procedures. Tracheal procedures are routinary interventions that require assessment of the percentage of obstructed pathway for injury (stenosis) detection. Visual assessment in videobronchoscopic sequences requires high expertise of trachea anatomy and is prone to human error.
This paper introduces an automatic method for the estimation of steneosed trachea percentage reduction in videobronchoscopic images. We look for tracheal rings , whose deformation determines the degree of obstruction. For ring extraction , we present a ring detector based on an illumination and appearance model. This model allows us to parametrise the ring detection. Finally, we can infer optimal estimation parameters for any video resolution. |
|
|
Address |
Aveiro, Portugal |
|
|
Corporate Author |
|
Thesis |
|
|
|
Publisher |
Springer Berlin Heidelberg |
Place of Publication |
|
Editor |
|
|
|
Language |
|
Summary Language |
|
Original Title |
|
|
|
Series Editor |
|
Series Title |
Lecture Notes in Computer Science |
Abbreviated Series Title |
LNCS |
|
|
Series Volume |
|
Series Issue |
|
Edition |
|
|
|
ISSN |
0302-9743 |
ISBN |
978-3-642-31297-7 |
Medium |
|
|
|
Area |
800 |
Expedition |
|
Conference |
ICIAR |
|
|
Notes |
MV;IAM |
Approved |
no |
|
|
Call Number |
IAM @ iam @ SSR2012 |
Serial |
1898 |
|
Permanent link to this record |
|
|
|
|
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 |
|
Permanent link to this record |
|
|
|
|
Author |
Juan Borrego-Carazo; Carles Sanchez; David Castells; Jordi Carrabina; Debora Gil |
|
|
Title |
BronchoPose: an analysis of data and model configuration for vision-based bronchoscopy pose estimation |
Type |
Journal Article |
|
Year |
2023 |
Publication |
Computer Methods and Programs in Biomedicine |
Abbreviated Journal |
CMPB |
|
|
Volume |
228 |
Issue |
|
Pages |
107241 |
|
|
Keywords |
Videobronchoscopy guiding; Deep learning; Architecture optimization; Datasets; Standardized evaluation framework; Pose estimation |
|
|
Abstract |
Vision-based bronchoscopy (VB) models require the registration of the virtual lung model with the frames from the video bronchoscopy to provide effective guidance during the biopsy. The registration can be achieved by either tracking the position and orientation of the bronchoscopy camera or by calibrating its deviation from the pose (position and orientation) simulated in the virtual lung model. Recent advances in neural networks and temporal image processing have provided new opportunities for guided bronchoscopy. However, such progress has been hindered by the lack of comparative experimental conditions.
In the present paper, we share a novel synthetic dataset allowing for a fair comparison of methods. Moreover, this paper investigates several neural network architectures for the learning of temporal information at different levels of subject personalization. In order to improve orientation measurement, we also present a standardized comparison framework and a novel metric for camera orientation learning. Results on the dataset show that the proposed metric and architectures, as well as the standardized conditions, provide notable improvements to current state-of-the-art camera pose estimation in video bronchoscopy. |
|
|
Address |
|
|
|
Corporate Author |
|
Thesis |
|
|
|
Publisher |
Elsevier |
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 @ BSC2023 |
Serial |
3702 |
|
Permanent link to this record |