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Publicações

Publicações por Tomé Mendes Albuquerque

2022

Quality Control in Digital Pathology: Automatic Fragment Detection and Counting

Autores
Albuquerque, T; Moreira, A; Barros, B; Montezuma, D; Oliveira, SP; Neto, PC; Monteiro, JC; Ribeiro, L; Gonçalves, S; Monteiro, A; Pinto, IM; Cardoso, JS;

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

Abstract
Manual assessment of fragments during the pro-cessing of pathology specimens is critical to ensure that the material available for slide analysis matches that captured during grossing without losing valuable material during this process. However, this step is still performed manually, resulting in lost time and delays in making the complete case available for evaluation by the pathologist. To overcome this limitation, we developed an autonomous system that can detect and count the number of fragments contained on each slide. We applied and compared two different methods: conventional machine learning methods and deep convolutional network methods. For conventional machine learning methods, we tested a two-stage approach with a supervised classifier followed by unsupervised hierarchical clustering. In addition, Fast R-CNN and YOLOv5, two state-of-the-art deep learning models for detection, were used and compared. All experiments were performed on a dataset comprising 1276 images of colorec-tal biopsy and polypectomy specimens manually labeled for fragment/set detection. The best results were obtained with the YOLOv5 architecture with a map@0.5 of 0.977 for fragment/set detection.

2023

Rethinking low-cost microscopy workflow: Image enhancement using deep based Extended Depth of Field methods

Autores
Albuquerque, T; Rosado, L; Cruz, RPM; Vasconcelos, MJM; Oliveira, T; Cardoso, JS;

Publicação
Intell. Syst. Appl.

Abstract
Microscopic techniques in low-to-middle income countries are constrained by the lack of adequate equipment and trained operators. Since light microscopy delivers crucial methods for the diagnosis and screening of numerous diseases, several efforts have been made by the scientific community to develop low-cost devices such as 3D-printed portable microscopes. Nevertheless, these devices present some drawbacks that directly affect image quality: the capture of the samples is done via mobile phones; more affordable lenses are usually used, leading to poorer physical properties and images with lower depth of field; misalignments in the microscopic set-up regarding optical, mechanical, and illumination components are frequent, causing image distortions such as chromatic aberrations. This work investigates several pre-processing methods to tackle the presented issues and proposed a new workflow for low-cost microscopy. Additionally, two new deep learning models based on Convolutional Neural Networks are also proposed (EDoF-CNN-Fast and EDoF-CNN-Pairwise) to generate Extended Depth of Field (EDoF) images, and compared against state-of-the-art approaches. The models were tested using two different datasets of cytology microscopic images: public Cervix93 and a new dataset that has been made publicly available containing images captured with µSmartScope. Experimental results demonstrate that the proposed workflow can achieve state-of-the-art performance when generating EDoF images from low-cost microscopes. © 2022 The Author(s)

2023

Fill in the blank for fashion complementary outfit product Retrieval: VISUM summer school competition

Autores
Castro, E; Ferreira, PM; Rebelo, A; Rio-Torto, I; Capozzi, L; Ferreira, MF; Goncalves, T; Albuquerque, T; Silva, W; Afonso, C; Sousa, RG; Cimarelli, C; Daoudi, N; Moreira, G; Yang, HY; Hrga, I; Ahmad, J; Keswani, M; Beco, S;

Publicação
MACHINE VISION AND APPLICATIONS

Abstract
Every year, the VISion Understanding and Machine intelligence (VISUM) summer school runs a competition where participants can learn and share knowledge about Computer Vision and Machine Learning in a vibrant environment. 2021 VISUM's focused on applying those methodologies in fashion. Recently, there has been an increase of interest within the scientific community in applying computer vision methodologies to the fashion domain. That is highly motivated by fashion being one of the world's largest industries presenting a rapid development in e-commerce mainly since the COVID-19 pandemic. Computer Vision for Fashion enables a wide range of innovations, from personalized recommendations to outfit matching. The competition enabled students to apply the knowledge acquired in the summer school to a real-world problem. The ambition was to foster research and development in fashion outfit complementary product retrieval by leveraging vast visual and textual data with domain knowledge. For this, a new fashion outfit dataset (acquired and curated by FARFETCH) for research and benchmark purposes is introduced. Additionally, a competitive baseline with an original negative sampling process for triplet mining was implemented and served as a starting point for participants. The top 3 performing methods are described in this paper since they constitute the reference state-of-the-art for this particular problem. To our knowledge, this is the first challenge in fashion outfit complementary product retrieval. Moreover, this joint project between academia and industry brings several relevant contributions to disseminating science and technology, promoting economic and social development, and helping to connect early-career researchers to real-world industry challenges.

2023

Unimodal Distributions for Ordinal Regression

Autores
Cardoso, JS; Cruz, R; Albuquerque, T;

Publicação
CoRR

Abstract

2024

A systematic review of machine learning-based tumor-infiltrating lymphocytes analysis in colorectal cancer: Overview of techniques, performance metrics, and clinical outcomes

Autores
Kazemi, A; Rasouli Saravani, A; Gharib, M; Albuquerque, T; Eslami, S; Schüffler, J;

Publicação
Computers in Biology and Medicine

Abstract
The incidence of colorectal cancer (CRC), one of the deadliest cancers around the world, is increasing. Tissue microenvironment (TME) features such as tumor-infiltrating lymphocytes (TILs) can have a crucial impact on diagnosis or decision-making for treating patients with CRC. While clinical studies showed that TILs improve the host immune response, leading to a better prognosis, inter-observer agreement for quantifying TILs is not perfect. Incorporating machine learning (ML) based applications in clinical routine may promote diagnosis reliability. Recently, ML has shown potential for making progress in routine clinical procedures. We aim to systematically review the TILs analysis based on ML in CRC histological images. Deep learning (DL) and non-DL techniques can aid pathologists in identifying TILs, and automated TILs are associated with patient outcomes. However, a large multi-institutional CRC dataset with a diverse and multi-ethnic population is necessary to generalize ML methods. © 2024 Elsevier Ltd

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