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About

About

Carlos Ferreira is passionate about health, technology and entrepreneurship since child age. In this way, he started the Bioengineering degree at Faculty of Engineering of the University of Porto in 2012, ending the same in 2017. During his degree, he had inroads by research groups of INESC-TEC and I3S. He also founded a student branch chapter of the EMBS in UP in the year 2015, being chair of the same for two years, and vice chair of NEB FEUP / ICBAS during 2016/2017. In 2017, he worked at U. Porto Inovação as a technology analyst before joining INESC TEC as a researcher in the field of medical image analysis for the classification of pulmonary nodules in computed tomography. In 2019, he received funding from the FCT for PhD and became Business Development Manager on TEC4Health at INESC TEC. Finally, Carlos has been elected treasurer in the IEEE, first from 2018-2021 in the EMBS PT chapter and since 2022 in the Portugal section.

Interest
Topics
Details

Details

  • Name

    Carlos Alexandre Ferreira
  • Role

    Business Developer
  • Since

    06th September 2017
  • Nationality

    Portugal
  • Contacts

    +351222094000
    carlos.a.ferreira@inesctec.pt
004
Publications

2024

LNDb v4: pulmonary nodule annotation from medical reports

Authors
Ferreira, CA; Sousa, C; Marques, ID; Sousa, P; Ramos, I; Coimbra, M; Campilho, A;

Publication
SCIENTIFIC DATA

Abstract
Given the high prevalence of lung cancer, an accurate diagnosis is crucial. In the diagnosis process, radiologists play an important role by examining numerous radiology exams to identify different types of nodules. To aid the clinicians' analytical efforts, computer-aided diagnosis can streamline the process of identifying pulmonary nodules. For this purpose, medical reports can serve as valuable sources for automatically retrieving image annotations. Our study focused on converting medical reports into nodule annotations, matching textual information with manually annotated data from the Lung Nodule Database (LNDb)-a comprehensive repository of lung scans and nodule annotations. As a result of this study, we have released a tabular data file containing information from 292 medical reports in the LNDb, along with files detailing nodule characteristics and corresponding matches to the manually annotated data. The objective is to enable further research studies in lung cancer by bridging the gap between existing reports and additional manual annotations that may be collected, thereby fostering discussions about the advantages and disadvantages between these two data types.

2024

Towards automatic forecasting of lung nodule diameter with tabular data and CT imaging

Authors
Ferreira, ICA; Venkadesh, KV; Jacobs, C; Coimbra, M; Campilho, A;

Publication
BIOMEDICAL SIGNAL PROCESSING AND CONTROL

Abstract
Objective: This study aims to forecast the progression of lung cancer by estimating the future diameter of lung nodules. Methods: This approach uses as input the tabular data, axial images from tomography scans, and both data types, employing a ResNet50 model for image feature extraction and direct analysis of patient information for tabular data. The data are processed through a neural network before prediction. In the training phase, class weights are assigned based on the rarity of different types of nodules within the dataset, in alignment with nodule management guidelines. Results: Tabular data alone yielded the most accurate results, with a mean absolute deviation of 0.99 mm. For malignant nodules, the best performance, marked by a deviation of 2.82 mm, was achieved using tabular data applying Lung-RADS class weights during training. The tabular data results highlight the influence of using the initial nodule size as an input feature. These results surpass the literature reference of 348-day volume doubling time for malignant nodules. Conclusion: The developed predictive model is optimized for integration into a clinical workflow after detecting, segmenting, and classifying nodules. It provides accurate growth forecasts, establishing a more objective basis for determining follow-up intervals. Significance: With lung cancer's low survival rates, the capacity for precise nodule growth prediction represents a significant breakthrough. This methodology promises to revolutionize patient care and management, enhancing the chances for early risk assessment and effective intervention.

2024

A Comparative Study of Feature-Based and End-to-End Approaches for Lung Nodule Classification in CT Volumes to Lung-RADS Follow-up Recommendation

Authors
Ferreira, CA; Ramos, I; Coimbra, M; Campilho, A;

Publication
2024 IEEE 22ND MEDITERRANEAN ELECTROTECHNICAL CONFERENCE, MELECON 2024

Abstract
Lung cancer represents a significant health concern necessitating diligent monitoring of individuals at risk. While the detection of pulmonary nodules warrants clinical attention, not all cases require immediate surgical intervention, often calling for a strategic approach to follow-up decisions. The Lung-RADS guideline serves as a cornerstone in clinical practice, furnishing structured recommendations based on various nodule characteristics, including size, calcification, and texture, outlined within established reference tables. However, the reliance on labor-intensive manual measurements underscores the potential advantages of integrating decision support systems into this process. Herein, we propose a feature-based methodology aimed at enhancing clinical decision-making by automating the assessment of nodules in computed tomography scans. Leveraging algorithms tailored for nodule calcification, texture analysis, and segmentation, our approach facilitates the automated classification of follow-up recommendations aligned with Lung-RADS criteria. Comparison with a previously reported end-to-end image-based classification method revealed competitive performance, with the feature-based approach achieving an accuracy of 0.701 +/- 0.026, while the end-to-end method attained 0.727 +/- 0.020. The inherent explainability of the feature-based approach offers distinct advantages, allowing clinicians to scrutinize and modify individual features to address disagreements or rectify inaccuracies, thereby tailoring follow-up recommendations to patient profiles.

2024

MedShapeNet - a large-scale dataset of 3D medical shapes for computer vision

Authors
Li, J; Zhou, Z; Yang, J; Pepe, A; Gsaxner, C; Luijten, G; Qu, C; Zhang, T; Chen, X; Li, W; Wodzinski, M; Friedrich, P; Xie, K; Jin, Y; Ambigapathy, N; Nasca, E; Solak, N; Melito, GM; Vu, VD; Memon, R; Schlachta, C; De Ribaupierre, S; Patel, R; Eagleson, R; Chen, X; Mächler, H; Kirschke, JS; La Rosa, E; Christ, PF; Li, HB; Ellis, G; Aizenberg, R; Gatidis, S; Küstner, T; Shusharina, N; Heller, N; Andrearczyk, V; Depeursinge, A; Hatt, M; Sekuboyina, A; Löffler, T; Liebl, H; Dorent, R; Vercauteren, T; Shapey, J; Kujawa, A; Cornelissen, S; Langenhuizen, P; Ben Hamadou, A; Rekik, A; Pujades, S; Boyer, E; Bolelli, F; Grana, C; Lumetti, L; Salehi, H; Ma, J; Zhang, Y; Gharleghi, R; Beier, S; Sowmya, A; Garza Villarreal, A; Balducci, T; Angeles Valdez, D; Souza, R; Rittner, L; Frayne, R; Ji, Y; Ferrari, V; Chatterjee, S; Dubost, F; Schreiber, S; Mattern, H; Speck, O; Haehn, D; John, C; Nürnberger, A; Pedrosa, J; Ferreira, C; Aresta, G; Cunha, A; Campilho, A; Suter, Y; Garcia, J; Lalande, A; Vandenbossche, V; Van Oevelen, A; Duquesne, K; Mekhzoum, H; Vandemeulebroucke, J; Audenaert, E; Krebs, C; Van Leeuwen, T; Vereecke, E; Heidemeyer, H; Röhrig, R; Hölzle, F; Badeli, V; Krieger, K; Gunzer, M; Chen, J; Van Meegdenburg, T; Dada, A; Balzer, M; Fragemann, J; Jonske, F; Rempe, M; Malorodov, S; Bahnsen, H; Seibold, C; Jaus, A; Marinov, Z; Jaeger, F; Stiefelhagen, R; Santos, AS; Lindo, M; Ferreira, A; Alves, V; Kamp, M; Abourayya, A; Nensa, F; Hörst, F; Brehmer, A; Heine, L; Hanusrichter, Y; Weßling, M; Dudda, M; Podleska, E; Fink, A; Keyl, J; Tserpes, K; Kim, M; Elhabian, S; Lamecker, H; Zukic, De; Paniagua, B; Wachinger, C; Urschler, M; Duong, L; Wasserthal, J; Hoyer, F; Basu, O; Maal, T; Witjes, JH; Schiele, G; Chang, T; Ahmadi, S; Luo, P; Menze, B; Reyes, M; Deserno, M; Davatzikos, C; Puladi, B; Fua, P; Yuille, L; Kleesiek, J; Egger, J;

Publication
Biomedizinische Technik

Abstract
The shape is commonly used to describe the objects. State-of-the-art algorithms in medical imaging are predominantly diverging from computer vision, where voxel grids, meshes, point clouds, and implicit surface models are used. This is seen from the growing popularity of ShapeNet (51,300 models) and Princeton ModelNet (127,915 models). However, a large collection of anatomical shapes (e.g., bones, organs, vessels) and 3D models of surgical instruments is missing. We present MedShapeNet to translate data-driven vision algorithms to medical applications and to adapt state-of-the-art vision algorithms to medical problems. As a unique feature, we directly model the majority of shapes on the imaging data of real patients. We present use cases in classifying brain tumors, skull reconstructions, multi-class anatomy completion, education, and 3D printing. By now, MedShapeNet includes 23 datasets with more than 100,000 shapes that are paired with annotations (ground truth). Our data is freely accessible via a web interface and a Python application programming interface and can be used for discriminative, reconstructive, and variational benchmarks as well as various applications in virtual, augmented, or mixed reality, and 3D printing. MedShapeNet contains medical shapes from anatomy and surgical instruments and will continue to collect data for benchmarks and applications. © 2024 Walter de Gruyter GmbH, Berlin/Boston.

2024

Automated Visceral and Subcutaneous Fat Segmentation in Computed Tomography

Authors
Castro, R; Sousa, I; Nunes, F; Mancio, J; Fontes Carvalho, R; Ferreira, C; Pedrosa, J;

Publication
Proceedings - International Symposium on Biomedical Imaging

Abstract
Cardiovascular diseases are the leading causes of death worldwide. While there are a number of cardiovascular risk indicators, recent studies have found a connection between cardiovascular risk and the accumulation and characteristics of visceral adipose tissue in the ventral cavity. The quantification of visceral adipose tissue can be easily performed in computed tomography scans but the manual delineation of these structures is a time consuming process subject to variability. This has motivated the development of automatic tools to achieve a faster and more precise solution. This paper explores the use of a U-Net architecture to perform ventral cavity segmentation followed by the use of threshold-based approaches for visceral and subcutaneous adipose tissue segmentation. Experiments with different learning rates, input image sizes and types of loss functions were employed to assess the hyperparameters most suited to this problem. In an external test set, the ventral cavity segmentation model with the best performance achieved a 0.967 Dice Score Coefficient, while the visceral and subcutaneous adipose tissue achieve Dice Score Coefficients of 0.986 and 0.995. Not only are these competitive results when compared to state of the art, the interobserver variability measured in this external dataset was similar to these results confirming the robustness and reliability of the proposed segmentation. © 2024 IEEE.

Supervised
thesis

2024

Automatic Visceral/Abdominal Fat Segmentation in Computed Tomography

Author
Rui Castro

Institution
UP-FEUP