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About

João Pedrosa was born in Figueira da Foz, Portugal, in 1990. He received the M.Sc. degree in biomedical engineering from the University of Porto, Porto, Portugal, in 2013 and the Ph.D. degree in biomedical sciences with KU Leuven, Leuven, Belgium, in 2018. He is currently a postdoctoral researcher at INESC TEC, Porto Portugal working on image processing and computer-aided diagnosis in lung cancer CT screening and diabetic retinopathy. His research interests include medical imaging acquisition and processing, machine learning and applied research for improved patient care.

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Details

Details

004
Publications

2021

LNDb Challenge on automatic lung cancer patient management

Authors
Pedrosa, J; Aresta, G; Ferreira, C; Atwal, G; Phoulady, HA; Chen, XY; Chen, RZ; Li, JL; Wang, LS; Galdran, A; Bouchachia, H; Kaluva, KC; Vaidhya, K; Chunduru, A; Tarai, S; Nadimpalli, SPP; Vaidya, S; Kim, I; Rassadin, A; Tian, ZH; Sun, ZW; Jia, YZ; Men, XJ; Ramos, I; Cunha, A; Campilho, A;

Publication
Medical Image Analysis

Abstract

2021

Extracting neuronal activity signals from microscopy recordings of contractile tissue using B-spline Explicit Active Surfaces (BEAS) cell tracking

Authors
Kazwiny, Y; Pedrosa, J; Zhang, ZQ; Boesmans, W; D'hooge, J; Vanden Berghe, P;

Publication
SCIENTIFIC REPORTS

Abstract
Ca2+ imaging is a widely used microscopy technique to simultaneously study cellular activity in multiple cells. The desired information consists of cell-specific time series of pixel intensity values, in which the fluorescence intensity represents cellular activity. For static scenes, cellular signal extraction is straightforward, however multiple analysis challenges are present in recordings of contractile tissues, like those of the enteric nervous system (ENS). This layer of critical neurons, embedded within the muscle layers of the gut wall, shows optical overlap between neighboring neurons, intensity changes due to cell activity, and constant movement. These challenges reduce the applicability of classical segmentation techniques and traditional stack alignment and regions-of-interest (ROIs) selection workflows. Therefore, a signal extraction method capable of dealing with moving cells and is insensitive to large intensity changes in consecutive frames is needed. Here we propose a b-spline active contour method to delineate and track neuronal cell bodies based on local and global energy terms. We develop both a single as well as a double-contour approach. The latter takes advantage of the appearance of GCaMP expressing cells, and tracks the nucleus' boundaries together with the cytoplasmic contour, providing a stable delineation of neighboring, overlapping cells despite movement and intensity changes. The tracked contours can also serve as landmarks to relocate additional and manually-selected ROIs. This improves the total yield of efficacious cell tracking and allows signal extraction from other cell compartments like neuronal processes. Compared to manual delineation and other segmentation methods, the proposed method can track cells during large tissue deformations and high-intensity changes such as during neuronal firing events, while preserving the shape of the extracted Ca2+ signal. The analysis package represents a significant improvement to available Ca2+ imaging analysis workflows for ENS recordings and other systems where movement challenges traditional Ca2+ signal extraction workflows.

2021

A multi-task CNN approach for lung nodule malignancy classification and characterization

Authors
Marques, S; Schiavo, F; Ferreira, CA; Pedrosa, J; Cunha, A; Campilho, A;

Publication
Expert Systems with Applications

Abstract

2021

Automated analysis of 3D-echocardiography using spatially registered patient-specific CMR meshes

Authors
Zhao, D; Ferdian, E; Maso Talou, G; Quill, G; Gilbert, K; Babarenda Gamage, T; Wang, V; Pedrosa, J; D"hooge, J; Legget, M; Ruygrok, P; Doughty, R; Camara, O; Young, A; Nash, M;

Publication
European Heart Journal - Cardiovascular Imaging

Abstract
Abstract Funding Acknowledgements Type of funding sources: Public grant(s) – National budget only. Main funding source(s): National Heart Foundation (NHF) of New Zealand Health Research Council (HRC) of New Zealand Artificial intelligence shows considerable promise for automated analysis and interpretation of medical images, particularly in the domain of cardiovascular imaging. While application to cardiac magnetic resonance (CMR) has demonstrated excellent results, automated analysis of 3D echocardiography (3D-echo) remains challenging, due to the lower signal-to-noise ratio (SNR), signal dropout, and greater interobserver variability in manual annotations. As 3D-echo is becoming increasingly widespread, robust analysis methods will substantially benefit patient evaluation.  We sought to leverage the high SNR of CMR to provide training data for a convolutional neural network (CNN) capable of analysing 3D-echo. We imaged 73 participants (53 healthy volunteers, 20 patients with non-ischaemic cardiac disease) under both CMR and 3D-echo (<1 hour between scans). 3D models of the left ventricle (LV) were independently constructed from CMR and 3D-echo, and used to spatially align the image volumes using least squares fitting to a cardiac template. The resultant transformation was used to map the CMR mesh to the 3D-echo image. Alignment of mesh and image was verified through volume slicing and visual inspection (Fig. 1) for 120 paired datasets (including 47 rescans) each at end-diastole and end-systole. 100 datasets (80 for training, 20 for validation) were used to train a shallow CNN for mesh extraction from 3D-echo, optimised with a composite loss function consisting of normalised Euclidian distance (for 290 mesh points) and volume. Data augmentation was applied in the form of rotations and tilts (<15 degrees) about the long axis. The network was tested on the remaining 20 datasets (different participants) of varying image quality (Tab. I). For comparison, corresponding LV measurements from conventional manual analysis of 3D-echo and associated interobserver variability (for two observers) were also estimated. Initial results indicate that the use of embedded CMR meshes as training data for 3D-echo analysis is a promising alternative to manual analysis, with improved accuracy and precision compared with conventional methods. Further optimisations and a larger dataset are expected to improve network performance. (n?=?20) LV EDV (ml) LV ESV (ml) LV EF (%) LV mass (g) Ground truth CMR 150.5 ± 29.5 57.9 ± 12.7 61.5 ± 3.4 128.1 ± 29.8 Algorithm error -13.3 ± 15.7 -1.4 ± 7.6 -2.8 ± 5.5 0.1 ± 20.9 Manual error -30.1 ± 21.0 -15.1 ± 12.4 3.0 ± 5.0 Not available Interobserver error 19.1 ± 14.3 14.4 ± 7.6 -6.4 ± 4.8 Not available Tab. 1. LV mass and volume differences (means ± standard deviations) for 20 test cases. Algorithm: CNN – CMR (as ground truth). Abstract Figure. Fig 1. CMR mesh registered to 3D-echo.

2021

Can shear wave imaging distinguish between diffuse interstitial and replacement myocardial fibrosis?

Authors
Petrescu, A; Cvijic, M; Bezy, S; Santos, P; Duchenne, J; Orlowska, M; Pedrosa, J; Degtiarova, G; Van Keer, J; Von Bardeleben, S; Droogne, W; Van Cleemput, J; Bogaert, J; D"hooge, J; Voigt, J;

Publication
European Heart Journal - Cardiovascular Imaging

Abstract
Abstract Funding Acknowledgements Type of funding sources: None. Background   Diffuse interstitial or myocardial replacement fibrosis are common features of a large variety of cardiomyopathies. These alterations contribute to functional changes, particularly to an increased myocardial stiffness (MS). Histological examination is the gold standard for myocardial fibrosis quantification, however, it requires endomyocardial biopsy which is invasive and not without risks. Cardiac magnetic resonance (CMR) can characterize the extent of both diffuse and replacement fibrosis and may have prognostic value in various cardiomyopathies. Echocardiographic shear wave (SW) elastography is an emerging approach for measuring MS in vivo. SWs occur after mechanical excitation of the myocardium, e.g. after mitral valve closure (MVC), and their propagation velocity is directly related to MS, thus providing an opportunity to assess stiffness at end-diastole. Purpose The aim was to investigate if velocities of natural SW can distinguish between interstitial and replacement fibrosis.  Methods We prospectively enrolled 47 patients (22 patients after heart transplant [54.2?±?15.8 years, 82.6% male] and 25 patients with established hypertrophic cardiomyopathy [54.0?±?13.5 years, 80.0% male]) undergoing CMR during their check-up. We performed SW elastography in parasternal long axis views of the LV using a fully programmable experimental scanner (HD-PULSE) equipped with a clinical phased array transducer (Samsung Medison P2-5AC) at 1100?±?250 frames per second. Tissue acceleration maps were extracted from an anatomical M-mode line along the midline of the LV septum. The SW propagation velocity at MVC was measured as the slope in the M-mode image. All patients underwent T1 mapping as well as late gadolinium enhancement (LGE) cardiac magnetic resonance at 1.5 T to assess the presence of diffuse or replacement fibrosis (Figure A). Therefore, patients were divided in three groups: no fibrosis, diffuse fibrosis and replacement fibrosis. Results Mechanical SW’s were observed in 46 subjects starting immediately after MVC and propagating from the LV base to the apex. SW propagation velocity at MVC correlated well with native myocardial T1 values (r?=?0.65, p?<?0.0001) and differed significantly among groups (p?<?0.0001), with a significant post-test between any pair of groups (Figure B). SW velocities below a cut-off of 6.01 m/s showed the highest accuracy to identify patients without any type of fibrosis (sensitivity 88 %, specificity 89%, area under the curve?=?0.93) (Figure C). A cut-off of 8.11 m/s could distinguish replacement fibrosis from diffuse fibrosis with a sensitivity and specificity of 59% and 92 %, respectively (area under the curve?=?0.80) (Figure D). Conclusions   Shear wave velocities after mitral valve closure can distinguish between normal and pathological myocardium and can detect differences between diffuse and replacement fibrosis. Abstract Figure.

Supervised
thesis

2020

Generative Adversarial Networks in Automated Chest Radiography Screening

Author
Martim Quintas e Sousa

Institution
UP-FEUP