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Publicações

Publicações por João Manuel Pedrosa

2022

Attention-driven Spatial Transformer Network for Abnormality Detection in Chest X-Ray Images

Autores
Rocha, J; Pereira, SC; Pedrosa, J; Campilho, A; Mendonca, AM;

Publicação
2022 IEEE 35TH INTERNATIONAL SYMPOSIUM ON COMPUTER-BASED MEDICAL SYSTEMS (CBMS)

Abstract
Backed by more powerful computational resources and optimized training routines, deep learning models have attained unprecedented performance in extracting information from chest X-ray data. Preceding other tasks, an automated abnormality detection stage can be useful to prioritize certain exams and enable a more efficient clinical workflow. However, the presence of image artifacts such as lettering often generates a harmful bias in the classifier, leading to an increase of false positive results. Consequently, healthcare would benefit from a system that selects the thoracic region of interest prior to deciding whether an image is possibly pathologic. The current work tackles this binary classification exercise using an attention-driven and spatially unsupervised Spatial Transformer Network (STN). The results indicate that the STN achieves similar results to using YOLO-cropped images, with fewer computational expenses and without the need for localization labels. More specifically, the system is able to distinguish between normal and abnormal CheXpert images with a mean AUC of 84.22%.

2022

Leveraging CMR for 3D echocardiography: an annotated multimodality dataset for AI

Autores
Zhao, D; Ferdian, E; Maso Talou, GD; Gilbert, K; Quill, GM; Wang, VY; Pedrosa, J; D'hooge, J; Sutton, T; Lowe, BS; Legget, ME; Ruygrok, PN; Doughty, RN; Young, AA; Nash, MP;

Publicação
European Heart Journal - Cardiovascular Imaging

Abstract
Abstract Funding Acknowledgements: Type of funding sources: Public grant(s) – National budget only. Main funding source(s): Health Research Council of New Zealand (HRC) National Heart Foundation of New Zealand (NHF) Segmentation of the left ventricular myocardium and cavity in 3D echocardiography (3DE) is a critical task for the quantification of systolic function in heart disease. Continuing advances in 3DE have considerably improved image quality, prompting increased clinical uptake in recent years, particularly for volumetric measurements. Nevertheless, analysis of 3DE remains a difficult problem due to inherently complex noise characteristics, anisotropic image resolution, and regions of acoustic dropout. One of the primary challenges associated with the development of automated methods for 3DE analysis is the requirement of a sufficiently large training dataset. Historically, ground truth annotations have been difficult to obtain due to the high degree of inter- and intra-observer variability associated with manual 3DE segmentation, thus, limiting the scope of AI-based solutions. To address the lack of expert consensus, we instead used labels derived from cardiac magnetic resonance (CMR) images of the same subjects. By spatiotemporally registering CMR labels to corresponding 3DE image data on a per subject basis (Figure 1), we collated 520 annotated 3DE images from a mixed cohort of 130 human subjects (2 independent single-beat acquisitions per subject at end-diastole and end-systole) consisting of healthy controls and patients with acquired cardiac disease. Comprising images acquired across a range of patient demographics, this curated dataset exhibits variation in image quality, 3DE acquisition parameters, as well as left ventricular shape and pose within the 3D image volume. To demonstrate the utility of such a dataset, nn-UNet, a self-configuring deep learning method for semantic segmentation was employed. An 80/20 split of the dataset was used for training and testing, respectively, and data augmentations were applied in the form of scaling, rotation, and reflection. The trained network was capable of reproducing measurements derived from CMR for end-diastolic volume, end-systolic volume, ejection fraction, and mass, while outperforming an expert human observer in terms of accuracy as well as scan-rescan reproducibility (Table I). As part of ongoing efforts to improve the accuracy and efficiency of 3DE analysis, we have leveraged the high resolution and signal-to-noise-ratio of CMR (relative to 3DE), to create a novel, publicly available benchmark dataset for developing and evaluating 3DE labelling methods. This approach not only significantly reduces the effects of observer-specific bias and variability in training data arising from conventional manual 3DE analysis methods, but also improves the agreement between cardiac indices derived from 3DE and CMR. Figure 1. Data annotation workflow Table I. Results

2022

Detection of COVID-19 in Point of Care Lung Ultrasound

Autores
Maximino, J; Coimbra, MT; Pedrosa, J;

Publicação
44th Annual International Conference of the IEEE Engineering in Medicine & Biology Society, EMBC 2022, Glasgow, Scotland, United Kingdom, July 11-15, 2022

Abstract

2022

A hybrid approach for tracking borders in echocardiograms

Autores
Ali, Y; Beheshti, S; Janabi Sharifi, F; Rezaii, TY; Cheema, AN; Pedrosa, J;

Publicação
SIGNAL IMAGE AND VIDEO PROCESSING

Abstract
Echocardiography-based cardiac boundary tracking provides valuable information about the heart condition for interventional procedures and intensive care applications. Nevertheless, echocardiographic images come with several issues, making it a challenging task to develop a tracking and segmentation algorithm that is robust to shadows, occlusions, and heart rate changes. We propose an autonomous tracking method to improve the robustness and efficiency of echocardiographic tracking. A method denoted by hybrid Condensation and adaptive Kalman filter (HCAKF) is proposed to overcome tracking challenges of echocardiograms, such as variable heart rate and sensitivity to the initialization stage. The tracking process is initiated by utilizing active shape model, which provides the tracking methods with a number of tracking features. The procedure tracks the endocardium borders, and it is able to adapt to changes in the cardiac boundaries velocity and visibility. HCAKF enables one to use a much smaller number of samples that is used in Condensation without sacrificing tracking accuracy. Furthermore, despite combining the two methods, our complexity analysis shows that HCAKF can produce results in real-time. The obtained results demonstrate the robustness of the proposed method to the changes in the heart rate, yielding an Hausdorff distance of 1.032 +/- 0.375 while providing adequate efficiency for real-time operations.

2022

A Generalization Study of Automatic Pericardial Segmentation in Computed Tomography Images

Autores
Baeza, R; Santos, C; Nunes, F; Mancio, J; Carvalho, RF; Coimbra, MT; Renna, F; Pedrosa, J;

Publicação
Wireless Mobile Communication and Healthcare - 11th EAI International Conference, MobiHealth 2022, Virtual Event, November 30 - December 2, 2022, Proceedings

Abstract
The pericardium is a thin membrane sac that covers the heart. As such, the segmentation of the pericardium in computed tomography (CT) can have several clinical applications, namely as a preprocessing step for extraction of different clinical parameters. However, manual segmentation of the pericardium can be challenging, time-consuming and subject to observer variability, which has motivated the development of automatic pericardial segmentation methods. In this study, a method to automatically segment the pericardium in CT using a U-Net framework is proposed. Two datasets were used in this study: the publicly available Cardiac Fat dataset and a private dataset acquired at the hospital centre of Vila Nova de Gaia e Espinho (CHVNGE). The Cardiac Fat database was used for training with two different input sizes - 512 512 and 256 256. A superior performance was obtained with the 256 256 image size, with a mean Dice similarity score (DCS) of 0.871 ± 0.01 and 0.807 ± 0.06 on the Cardiac Fat test set and the CHVNGE dataset, respectively. Results show that reasonable performance can be achieved with a small number of patients for training and an off-the-shelf framework, with only a small decrease in performance in an external dataset. Nevertheless, additional data will increase the robustness of this approach for difficult cases and future approaches must focus on the integration of 3D information for a more accurate segmentation of the lower pericardium. © 2023, ICST Institute for Computer Sciences, Social Informatics and Telecommunications Engineering.

2023

Assisted probe guidance in cardiac ultrasound: A review

Autores
Ferraz, S; Coimbra, M; Pedrosa, J;

Publicação
FRONTIERS IN CARDIOVASCULAR MEDICINE

Abstract
Echocardiography is the most frequently used imaging modality in cardiology. However, its acquisition is affected by inter-observer variability and largely dependent on the operator's experience. In this context, artificial intelligence techniques could reduce these variabilities and provide a user independent system. In recent years, machine learning (ML) algorithms have been used in echocardiography to automate echocardiographic acquisition. This review focuses on the state-of-the-art studies that use ML to automate tasks regarding the acquisition of echocardiograms, including quality assessment (QA), recognition of cardiac views and assisted probe guidance during the scanning process. The results indicate that performance of automated acquisition was overall good, but most studies lack variability in their datasets. From our comprehensive review, we believe automated acquisition has the potential not only to improve accuracy of diagnosis, but also help novice operators build expertise and facilitate point of care healthcare in medically underserved areas.

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