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Publications

Publications by João Pedro Teixeira

2018

Three-dimensional planning tool for breast conserving surgery: A technological review

Authors
Oliveira, SP; Morgado, P; Gouveia, PF; Teixeira, JF; Bessa, S; Monteiro, JP; Zolfagharnasab, H; Reis, M; Silva, NL; Veiga, D; Cardoso, MJ; Oliveira, HP; Ferreira, MJ;

Publication
Critical Reviews in Biomedical Engineering

Abstract
Breast cancer is one of the most common malignanciesaffecting women worldwide. However, despite its incidence trends have increased, the mortality rate has significantly decreased. The primary concern in any cancer treatment is the oncological outcome but, in the case of breast cancer, the surgery aesthetic result has become an important quality indicator for breast cancer patients. In this sense, an adequate surgical planning and prediction tool would empower the patient regarding the treatment decision process, enabling a better communication between the surgeon and the patient and a better understanding of the impact of each surgical option. To develop such tool, it is necessary to create complete 3D model of the breast, integrating both inner and outer breast data. In this review, we thoroughly explore and review the major existing works that address, directly or not, the technical challenges involved in the development of a 3D software planning tool in the field of breast conserving surgery. © 2018 by Begell House, Inc.

2018

Automatic Quality Assessment of Smart Device Microphone Spirometry

Authors
Pinho, B; Almeida, R; Jácome, C; Teixeira, JF; Amaral, R; Lopes, F; Jacinto, T; Guedes, R; Pereira, M; Gonçalves, I; Fonseca, J;

Publication
Proceedings of the 8th International Joint Conference on Pervasive and Embedded Computing and Communication Systems, PECCS 2018, Porto, Portugal, July 29-30, 2018.

Abstract
Lung function tests are critical for diagnosis and monitoring of asthma and other respiratory diseases. Monitoring of lung function, in the absence of a healthcare professional, is very challenging but may be obtained through Smart Devices if_automated quality assessment systems guarantee the proper technique during the forced expiratory manoeuvre. This paper describes the evaluation of one such system that uses the microphone of smart devices, regarding the initial effort of forced expiratory manoeuvres using the Back Extrapolated Volume. A health professional recorded microphone spirometry in 55 children (5-10 years), using a mobile game engineered for the purpose, and registered its quality. At least one acceptable manoeuvre was achieved for 96% of the children using a featured threshold. Using a stricter threshold of 5% of forced vital capacity, it was possible to ensure at least one acceptable manoeuvre for 69%. While the obtained results are comparable to findings in literature for regular spirometry in this age group, further work is required before we can determine whether the proposed algorithm is effective in real life. Copyright

2019

Lightweight Deep Learning Pipeline for Detection, Segmentation and Classification of Breast Cancer Anomalies

Authors
Oliveira, HS; Teixeira, JF; Oliveira, HP;

Publication
IMAGE ANALYSIS AND PROCESSING - ICIAP 2019, PT II

Abstract
The small amount of public available medical images hinders the use of deep learning techniques for mammogram automatic diagnosis. Deep learning methods require large annotated training sets to be effective, however medical datasets are costly to obtain and suffer from large variability. In this work, a lightweight deep learning pipeline to detect, segment and classify anomalies in mammogram images is presented. First, data augmentation using the ground-truth annotation is performed and used by a cascade segmentation and classification methods. Results are obtained using the INbreast public database in the context of lesion detection and BI-RADS classification. Moreover, a pre-trained Convolutional Neural Network using ResNet50 is modified to generate the lesion regions proposals followed by a false positive reduction and contour refinement stages while a pre-trained VGG16 network is fine-tuned to classify mammograms. The detection and segmentation stage results show that the cascade configuration achieves a DICE of 0.83 without massive training while the multi-class classification exhibits an MAE of 0.58 with data augmentation.

2020

Automatic Quality Assessment of a Forced Expiratory Manoeuvre Acquired with the Tablet Microphone

Authors
Almeida, R; Pinho, B; Jacome, C; Teixeira, JF; Amaral, R; Goncalves, I; Lopes, F; Pinheiro, AC; Jacinto, T; Paixao, C; Pereira, M; Marques, A; Fonseca, JA;

Publication
XV MEDITERRANEAN CONFERENCE ON MEDICAL AND BIOLOGICAL ENGINEERING AND COMPUTING - MEDICON 2019

Abstract
Evaluation of lung function is central to the management of chronic obstructive respiratory diseases. It is typically evaluated with a spirometer by a specialized health professional, who ensures the correct execution of a forced expiratory manoeuvre (FEM). Audio recording of a FEM using a smart device embedded microphone can be used to self-monitor lung function between clinical visits. The challenge of microphone spirometry is to ensure the validity and reliability of the FEM, in the absence of a health professional. In particular, the absence of a mouthpiece may allow excessive mouth closure, leading to an incorrect manoeuvre. In this work, a strategy to automatically assess the correct execution of the FEM is proposed and validated. Using 498 FEM recordings, both specificity and sensitivity attained were above 90%. This method provides immediate feedback to the user, by grading the manoeuvre in a visual scale, promoting the repetition of the FEM when needed.

2019

Automatic Sternum Segmentation in Thoracic MRI

Authors
Dias, M; Rocha, B; Teixeira, JF; Oliveira, HP;

Publication
2019 41ST ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY (EMBC)

Abstract
The Sternum is a human bone located in the anterior area of the thoracic cage. It is present in most of the axial cuts provided from the Magnetic Resonance Imaging (MRI) acquisitions. used in the medical field. Detecting the Sternum is relevant as it contains rigid key-points for 3D model reconstructions, assisting in the planning and evaluation of several surgical procedures, and for atlas development by segmenting structures in anatomical proximity. In the absence of applicable approaches for this specific problem. this paper focuses on two distinct automated methods for Sternum segmentation in MRI. The first. relies on K-Means (Clustering) to perform the segmentation, while the second encompasses the closed Minimum Path over the elliptical transformation of Gradient images. A dataset of 14 annotated acquisitions was used for evaluation. The results favored the Gradient approach over Clustering.

2020

B-Mode Ultrasound Breast Anatomy Segmentation

Authors
Teixeira, JF; Carreiro, AM; Santos, RM; Oliveira, HP;

Publication
Image Analysis and Recognition - 17th International Conference, ICIAR 2020, Póvoa de Varzim, Portugal, June 24-26, 2020, Proceedings, Part II

Abstract
Breast Ultrasound has long been used to support diagnostic and exploratory procedures concerning breast cancer, with an interesting success rate, specially when complemented with other radiology information. This usability can further enhance visualization tasks during pre-treatment clinical analysis by coupling the B-Mode images to 3D space, as found in Magnetic Resonance Imaging (MRI) per instance. In fact, Lesions in B-mode are visible and present high detail when comparing with other 3D sequences. This coupling, however, would be largely benefited from the ability to match the various structures present in the B-Mode, apart from the broadly studied lesion. In this work we focus on structures such as skin, subcutaneous fat, mammary gland and thoracic region. We provide a preliminary insight to several structure segmentation approaches in the hopes of obtaining a functional and dependable pipeline for delineating these potential reference regions that will assist in multi-modal radiological data alignment. For this, we experiment with pre-processing stages that include Anisotropic Diffusion guided by Log-Gabor filters (ADLG) and main segmentation steps using K-Means, Meanshift and Watershed. Among the pipeline configurations tested, the best results were found using the ADLG filter that ran for 50 iterations and H-Maxima suppression of 20% and the K-Means method with $$K=6$$. The results present several cases that closely approach the ground truth despite overall having larger average errors. This encourages the experimentation of other approaches that could withstand the innate data variability that makes this task very challenging. © Springer Nature Switzerland AG 2020.

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