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Publications

Publications by Ana Maria Mendonça

2018

UOLO - Automatic Object Detection and Segmentation in Biomedical Images

Authors
Araujo, T; Aresta, G; Galdran, A; Costa, P; Mendonca, AM; Campilho, A;

Publication
DEEP LEARNING IN MEDICAL IMAGE ANALYSIS AND MULTIMODAL LEARNING FOR CLINICAL DECISION SUPPORT, DLMIA 2018

Abstract
We propose UOLO, a novel framework for the simultaneous detection and segmentation of structures of interest in medical images. UOLO consists of an object segmentation module which intermediate abstract representations are processed and used as input for object detection. The resulting system is optimized simultaneously for detecting a class of objects and segmenting an optionally different class of structures. UOLO is trained on a set of bounding boxes enclosing the objects to detect, as well as pixel-wise segmentation information, when available. A new loss function is devised, taking into account whether a reference segmentation is accessible for each training image, in order to suitably backpropagate the error. We validate UOLO on the task of simultaneous optic disc (OD) detection, fovea detection, and OD segmentation from retinal images, achieving state-of-the-art performance on public datasets.

2018

Calculation and mapping of choroidal thickness in OCT images

Authors
Mendonca, L; Faria, S; Penas, S; Silva, J; Mendonca, AM;

Publication
INVESTIGATIVE OPHTHALMOLOGY & VISUAL SCIENCE

Abstract

2018

Automatic Characterization of the Serous Retinal Detachment Associated with the Subretinal Fluid Presence in Optical Coherence Tomography Images

Authors
Moura, Jd; Novo, J; Penas, S; Ortega, M; Silva, JA; Mendonça, AM;

Publication
Knowledge-Based and Intelligent Information & Engineering Systems: Proceedings of the 22nd International Conference KES-2018, Belgrade, Serbia, 3-5 September 2018.

Abstract
An accurate detection of the macular edema (ME) presence constitutes a crucial ophthalmological issue as it provides useful information for the identification, diagnosis and treatment of different relevant ocular and Systemic diseaseS. serous Retinal Detachment (sRD) is a particular type of ME, which is characterized by the leakage of fluid that has a propensity of being accumulated in the macular region. This paper proposes a new methodology for the automatic identification and characterization of the sRD edema using Optical Coherence Tomography (OCT) imageS. The subretinal fluids and the External Limiting Membrane (ELM) retinal layers are identified and characterized to measure the disease severity. Four different visualization modules were designed including representative derived parameters to facilitate the doctor's work in the diagnostic evaluation of ME. The different steps of this method were validated using the manual labelling provided by an expert clinician. The validation of the proposed method offered satisfactory results, constituting a suitable scenario with intuitive visual representations that also include different relevant biomarkerS. © 2018 The Author(s).

2019

An unsupervised metaheuristic search approach for segmentation and volume measurement of pulmonary nodules in lung CT scans

Authors
Shakibapour, E; Cunha, A; Aresta, G; Mendonca, AM; Campilho, A;

Publication
EXPERT SYSTEMS WITH APPLICATIONS

Abstract
This paper proposes a new methodology to automatically segment and measure the volume of pulmonary nodules in lung computed tomography (CT) scans. Estimating the malignancy likelihood of a pulmonary nodule based on lesion characteristics motivated the development of an unsupervised pulmonary nodule segmentation and volume measurement as a preliminary stage for pulmonary nodule characterization. The idea is to optimally cluster a set of feature vectors composed by intensity and shape-related features in a given feature data space extracted from a pre-detected nodule. For that purpose, a metaheuristic search based on evolutionary computation is used for clustering the corresponding feature vectors. The proposed method is simple, unsupervised and is able to segment different types of nodules in terms of location and texture without the need for any manual annotation. We validate the proposed segmentation and volume measurement on the Lung Image Database Consortium and Image Database Resource Initiative - LIDC-IDRI dataset. The first dataset is a group of 705 solid and sub-solid (assessed as part-solid and non-solid) nodules located in different regions of the lungs, and the second, more challenging, is a group of 59 sub-solid nodules. The average Dice scores of 82.35% and 71.05% for the two datasets show the good performance of the segmentation proposal. Comparisons with previous state-of-the-art techniques also show acceptable and comparable segmentation results. The volumes of the segmented nodules are measured via ellipsoid approximation. The correlation and statistical significance between the measured volumes of the segmented nodules and the ground-truth are obtained by Pearson correlation coefficient value, obtaining an R-value >= 92.16% with a significance level of 5%.

2018

Convolutional Neural Network Architectures for Texture Classification of Pulmonary Nodules

Authors
Ferreira, CA; Cunha, A; Mendonça, AM; Campilho, A;

Publication
Progress in Pattern Recognition, Image Analysis, Computer Vision, and Applications - 23rd Iberoamerican Congress, CIARP 2018, Madrid, Spain, November 19-22, 2018, Proceedings

Abstract
Lung cancer is one of the most common causes of death in the world. The early detection of lung nodules allows an appropriate follow-up, timely treatment and potentially can avoid greater damage in the patient health. The texture is one of the nodule characteristics that is correlated with the malignancy. We developed convolutional neural network architectures to classify automatically the texture of nodules into the non-solid, part-solid and solid classes. The different architectures were tested to determine if the context, the number of slices considered as input and the relation between slices influence on the texture classification performance. The architecture that obtained better performance took into account different scales, different rotations and the context of the nodule, obtaining an accuracy of 0.833 ± 0.041. © Springer Nature Switzerland AG 2019.

2019

Wide Residual Network for Lung-Rads (TM) Screening Referral

Authors
Ferreira, CA; Aresta, G; Cunha, A; Mendonca, AM; Campilho, A;

Publication
2019 6TH IEEE PORTUGUESE MEETING IN BIOENGINEERING (ENBENG)

Abstract
Lung cancer has an increasing preponderance in worldwide mortality, demanding for the development of efficient screening methods. With this in mind, a binary classification method using Lung-RADS (TM) guidelines to warn changes in the screening management is proposed. First, having into account the lack of public datasets for this task, the lung nodules in the LIDC-IDRI dataset were re-annotated to include a Lung-RADS (TM)-based referral label. Then, a wide residual network is used for automatically assessing lung nodules in 3D chest computed tomography exams. Unlike the standard malignancy prediction approaches, the proposed method avoids the need to segment and characterize lung nodules, and instead directly defines if a patient should be submitted for further lung cancer tests. The system achieves a nodule-wise accuracy of 0.87 +/- 0.02.

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