Cookies Policy
The website need some cookies and similar means to function. If you permit us, we will use those means to collect data on your visits for aggregated statistics to improve our service. Find out More
Accept Reject
  • Menu
Publications

Publications by BIO

2019

BACH: Grand challenge on breast cancer histology images

Authors
Aresta, G; Araujo, T; Kwok, S; Chennamsetty, SS; Safwan, M; Alex, V; Marami, B; Prastawa, M; Chan, M; Donovan, M; Fernandez, G; Zeineh, J; Kohl, M; Walz, C; Ludwig, F; Braunewell, S; Baust, M; Vu, QD; To, MNN; Kim, E; Kwak, JT; Galal, S; Sanchez Freire, V; Brancati, N; Frucci, M; Riccio, D; Wang, YQ; Sun, LL; Ma, KQ; Fang, JN; Kone, ME; Boulmane, LS; Campilho, ARLO; Eloy, CTRN; Polonia, AONO; Aguiar, PL;

Publication
MEDICAL IMAGE ANALYSIS

Abstract
Breast cancer is the most common invasive cancer in women, affecting more than 10% of women worldwide. Microscopic analysis of a biopsy remains one of the most important methods to diagnose the type of breast cancer. This requires specialized analysis by pathologists, in a task that i) is highly time and cost-consuming and ii) often leads to nonconsensual results. The relevance and potential of automatic classification algorithms using hematoxylin-eosin stained histopathological images has already been demonstrated, but the reported results are still sub-optimal for clinical use. With the goal of advancing the state-of-the-art in automatic classification, the Grand Challenge on BreAst Cancer Histology images (BACH) was organized in conjunction with the 15th International Conference on Image Analysis and Recognition (ICIAR 2018). BACH aimed at the classification and localization of clinically relevant histopathological classes in microscopy and whole-slide images from a large annotated dataset, specifically compiled and made publicly available for the challenge. Following a positive response from the scientific community, a total of 64 submissions, out of 677 registrations, effectively entered the competition. The submitted algorithms improved the state-of-the-art in automatic classification of breast cancer with microscopy images to an accuracy of 87%. Convolutional neuronal networks were the most successful methodology in the BACH challenge. Detailed analysis of the collective results allowed the identification of remaining challenges in the field and recommendations for future developments. The BACH dataset remains publicly available as to promote further improvements to the field of automatic classification in digital pathology.

2019

Expert Crowdsourcing for Semantic Annotation of Atmospheric Phenomena

Authors
Liberato, M; Paredes, H; Ramos, A; Reis, A; Hénin, R; Barroso, J;

Publication

Abstract

2019

TTR-FAP Progression Evaluation Based on Gait Analysis Using a Single RGB-D Camera

Authors
Vilas Boas, MD; Rocha, AP; Pereira Choupina, HMP; Cardoso, M; Fernandes, JM; Coelho, T; Silva Cunha, JPS;

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

Abstract
Transthyretin Familial Amyloid Polyneuropathy (TTR-FAP) is a rare and disabling neurological disorder caused by, a mutation of the transthyretin gene. One of the disease's characteristics that mostly affects patients' quality of life is its influence on locomotion, with a variable evolution timing. Quantitative motion analysis is useful for assessing motor function, including gait, in diseases affecting movement. However, it is still an evolving field, especially in TTR-FAP, with only a few available studies. A single markerless RGB-D camera pros ides 3-D body joint data in a less expensive, more portable and less intrusive way than reference multi-camera marker-based systems for motion capture. In this contribution, we investigate if a gait analysis system based on a RGB-D camera can be used to detect gait changes over time for a given TTR-FAP patient. 3-D data provided by that system and a reference system were acquired from six TTR-FAP patients, while performing a simple gait task, once and then a year and a half later. For each gait cycle and system, several gait parameters were computed. For each patient, we investigated if the RBG-D camera system is able to detect the existence or not of statistically significant differences between the two different acquisitions (separated by 1.5 years of disease evolution), in a similar way to the reference system. The obtained results show the potential of using a single RGB-D camera to detect relevant changes in spatiotemporal gait parameters (e.g., stride duration and stride length), during TTR-FAP patient follow-up.

2019

Humidity sensor based on optical fiber coated with agarose gel

Authors
Novais, S; Ferreira, MS; Pinto, JL;

Publication
OPTICAL SENSORS 2019

Abstract
A reflective fiber optic sensor based on multimode interference for the measurement of relative humidity (RH) is proposed and experimentally demonstrated. The proposed probe is fabricated by fusion-splicing, approximately 30 mm long coreless fiber section to a single mode fiber. A hydrophilic agarose gel is coated on the coreless fiber, using the dip coating technique. When the incident light comes from the SMF to the CSF, the high-order modes are excited and propagate within the CSF. These excited modes interfere with one another as they propagate along whole CSF length, giving rise to a multimode interference (MMI). Since the effective refractive index of the agarose gel changes with the ambient relative humidity, as the environmental refractive index changes, the propagation constants for each guided mode within the CSF will change too, which leads to shifts in the output spectra. The proposed sensor has a great potential in real time RH monitoring, exhibiting a large range of operation with good stability. For RH variations in the range between 60 %RH and 98.5 %RH, the sensor presents a maximum sensitivity of 44.2 pm/%RH, and taking in consideration the interrogation system, a resolution of 1.1%RH is acquired. This sensor can be of interest for applications where a control of high levels of relative humidity is required.

2019

A Dynamic Mode Decomposition Approach With Hankel Blocks to Forecast Multi-Channel Temporal Series

Authors
Vasconcelos, E; dos Santos, PL;

Publication
IEEE CONTROL SYSTEMS LETTERS

Abstract
Forecasting is a task with many concerns, such as the size, quality, and behavior of the data, the computing power to do it, etc. This letter proposes the dynamic mode decomposition (DMD) as a tool to predict the annual air temperature and the sales of a stores' chain. The DMD decomposes the data into its principal modes, which are estimated from a training data set. It is assumed that the data is generated by a linear time-invariant high order autonomous system. These modes are useful to find the way the system behaves and to predict its future states, without using all the available data, even in a noisy environment. The Hankel block allows the estimation of hidden oscillatory modes, by increasing the order of the underlying dynamical system. The proposed method was tested in a case study consisting of the long term prediction of the weekly sales of a chain of stores. The performance assessment was based on the best fit percentage index. The proposed method is compared with three neural networkbased predictors.

2019

Full-body motion assessment: Concurrent validation of two body tracking depth sensors versus a gold standard system during gait

Authors
Vilas Boas, MD; Pereira Choupina, HMP; Rocha, AP; Fernandes, JM; Silva Cunha, JPS;

Publication
JOURNAL OF BIOMECHANICS

Abstract
RGB-D cameras provide 3-D body joint data in a low-cost, portable and non-intrusive way, when compared with reference motion capture systems used in laboratory settings. In this contribution, we evaluate the validity of both Microsoft Kinect versions (v1 and v2) for motion analysis against a Qualisys system in a simultaneous protocol. Two different walking directions in relation to the Kinect (towards - WT, and away - WA) were explored. For each gait trial, measures related with all body parts were computed: velocity of all joints, distance between symmetrical joints, and angle at some joints. For each measure, we compared each Kinect version and Qualisys by obtaining the mean true error and mean absolute error, Pearson's correlation coefficient, and optical-to-depth ratio. Although both Kinect v1 and v2 and/or WT and WA data present similar accuracy for some measures, better results were achieved, overall, when using WT data provided by the Kinect v2, especially for velocity measures. Moreover, the velocity and distance presented better results than angle measures. Our results show that both Kinect versions can be an alternative to more expensive systems such as Qualisys, for obtaining distance and velocity measures as well as some angles metrics (namely the knee angles). This conclusion is important towards the off-lab non-intrusive assessment of motor function in different areas, including sports and healthcare.

  • 43
  • 113