A. Marcal - Academia.edu (original) (raw)

Papers by A. Marcal

World Journal of Emergency Surgery

Introduction The concept of “weekend effect”, that is, substandard healthcare during weekends, ha... more Introduction The concept of “weekend effect”, that is, substandard healthcare during weekends, has never been fully demonstrated, and the different outcomes of emergency surgical patients admitted during weekends may be due to different conditions at admission and/or different therapeutic approaches. Aim of this international audit was to identify any change of pattern of emergency surgical admissions and treatments during weekends. Furthermore, we aimed at investigating the impact of the COVID-19 pandemic on the alleged “weekend effect”. Methods The database of the CovidICE-International Study was interrogated, and 6263 patients were selected for analysis. Non-trauma, 18+ yo patients admitted to 45 emergency surgery units in Europe in the months of March–April 2019 and March–April 2020 were included. Demographic and clinical data were anonymised by the referring centre and centrally collected and analysed with a statistical package. This study was endorsed by the Association of Ita...

British Journal of Surgery, 2020

For centuries, music has been shared and remembered by two traditions: aural transmission and in ... more For centuries, music has been shared and remembered by two traditions: aural transmission and in the form of written documents normally called musical scores. Many of these scores exist in the form of unpublished manuscripts and hence they are in danger of being lost through the normal ravages of time. To preserve the music some form of typesetting or, ideally, a computer system that can automatically decode the symbolic images and create new scores is required. Programs analogous to optical character recognition systems called optical music recognition (OMR) systems have been under intensive development for many years. However, the results to date are far from ideal. Each of the proposed methods emphasizes different properties and therefore makes it difficult to effectively evaluate its competitive advantages. This article provides an overview of the literature concerning the automatic analysis of images of printed and handwritten musical scores. For self-containment and for the benefit of the reader, an introduction to OMR processing systems precedes the literature overview. The following study

Lecture Notes in Computer Science, 2012

Dermoscopy is a non-invasive diagnostic technique for the in vivo observation of pigmented skin l... more Dermoscopy is a non-invasive diagnostic technique for the in vivo observation of pigmented skin lesions used in dermatology. There is currently a great interest in the prospects of automatic image analysis methods for dermoscopy, both to provide quantitative information about a lesion, which can be of relevance for the clinician, and as a stand alone early warning tool. The standard approach in automatic dermoscopic image analysis has usually three stages: (i) segmentation, (ii) feature extraction and selection, (iii) lesion classification. This paper evaluates the potential of an alternative approach based on the Menzies methodpresence of 1 or more of 6 color classes, indicating that the lesion should be considered a potential melanoma. This method does not require stages (i) and (ii)-lesion segmentation and feature extraction. The Jeffries-Matusita and Transformed Divergence metrics were used to evaluate the color class separability. The preliminary results presented in this paper suggest that a system based on the Menzies method could provide valuable information for automatic dermoscopic image analysis.

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Dermoscopy is a non-invasive diagnosis technique for in vivo observation of pigmented skin lesion... more Dermoscopy is a non-invasive diagnosis technique for in vivo observation of pigmented skin lesions used in dermatology. There is currently a great interest in the development of computer assisted diagnosis systems, given their great potential to this area of medicine. The standard approach in automatic dermoscopic image analysis can be divided in three stages: image segmentation, feature extraction/selection and lesion classification. In order to validate the algorithms developed for each stage, a great number of reliable images and clinical diagnosis are required. This paper presents a software tool to collect and organize dermoscopic data from hospital databases. It is suitable for clinical daily routine and simultaneously has a data structure to support the development and validation of algorithms created by the researchers to construct the computer assisted diagnosis system. This tool is composed by a database with three related but independent modules: Clinical Module, Processing Module and Statistical Module.

International Journal of Remote Sensing, 2008

The use of black & white air photographs for the production of historic land cover maps can be do... more The use of black & white air photographs for the production of historic land cover maps can be done by image classification, using additional texture features. In this paper we evaluate the importance of a number of parameters in the image classification process based on texture, such as the quantization level, the window size used to produce the texture features, the feature selection criteria and the image spatial resolution. The evaluation was performed using 4 photographs from the 1950s. The influence of the classification method, the number of classes searched for in the images and the post-processing tasks were also investigated. The importance of each of these parameters for the classification accuracy was evaluated by cross validation. The selection of the best parameters was performed based on the validation results, and also on the computation load involved for each case and the end user requirements. An average accuracy of 85.2% was achieved for 4 land cover classes. New Developments and Challenges in Remote Sensing, Z. Bochenek (ed.) ß2007 Millpress, Rotterdam,

IEEE Transactions on Geoscience and Remote Sensing, 2011

This paper presents a new Bayesian approach to hyperspectral image segmentation that boosts the p... more This paper presents a new Bayesian approach to hyperspectral image segmentation that boosts the performance of the discriminative classifiers. This is achieved by combining class densities based on discriminative classifiers with a Multi-Level Logistic Markov-Gibs prior. This density favors neighbouring labels of the same class. The adopted discriminative classifier is the Fast Sparse Multinomial Regression. The discrete optimization problem one is led to is solved efficiently via graph cut tools. The effectiveness of the proposed method is evaluated, with simulated and real AVIRIS images, in two directions: 1) to improve the classification performance and 2) to decrease the size of the training sets.

IEEE Journal of Selected Topics in Signal Processing, 2009

In this paper, we propose and evaluate six methods for the segmentation of skin lesions in dermos... more In this paper, we propose and evaluate six methods for the segmentation of skin lesions in dermoscopic images. This set includes some state of the art techniques which have been successfully used in many medical imaging problems (gradient vector flow (GVF) and the level set method of Chan et al. [(C-LS)]. It also includes a set of methods developed by the authors which were tailored to this particular application (adaptive thresholding (AT), adaptive snake (AS), EM level set [(EM-LS), and fuzzy-based splitand-merge algorithm (FBSM)]. The segmentation methods were applied to 100 dermoscopic images and evaluated with four different metrics, using the segmentation result obtained by an experienced dermatologist as the ground truth. The best results were obtained by the AS and EM-LS methods, which are semi-supervised methods. The best fully automatic method was FBSM, with results only slightly worse than AS and EM-LS.

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... Analysis of the Portuguese West Coast Morphology and Morphodynamics Correlation. A GIS Tool f... more ... Analysis of the Portuguese West Coast Morphology and Morphodynamics Correlation. A GIS Tool for Coastal Erosion Management. Artigo em Livro de Actas de Conferência Internacional. Autores: Joaquim Barbosa Fernando Veloso Gomes Francisco Taveira Pinto. ...

Applied and Environmental Microbiology, 2011

ABSTRACTPhytosanitary regulations and the provision of plant health certificates still rely mainl... more ABSTRACTPhytosanitary regulations and the provision of plant health certificates still rely mainly on long and laborious culture-based methods of diagnosis, which are frequently inconclusive. DNA-based methods of detection can circumvent many of the limitations of currently used screening methods, allowing a fast and accurate monitoring of samples. The genusXanthomonasincludes 13 phytopathogenic quarantine organisms for which improved methods of diagnosis are needed. In this work, we propose 21 newXanthomonas-specific molecular markers, within loci coding forXanthomonas-specific protein domains, useful for DNA-based methods of identification of xanthomonads. The specificity of these markers was assessed by a dot blot hybridization array using 23 non-Xanthomonasspecies, mostly soil dwelling and/or phytopathogens for the same host plants. In addition, the validation of these markers on 15Xanthomonasspp. suggested species-specific hybridization patterns, which allowed discrimination am...

Optical Music Recognition (OMR) systems are an important tool for the automatic recognition of di... more Optical Music Recognition (OMR) systems are an important tool for the automatic recognition of digitized music scores. However, handwritten musical scores are especially problematic for an automatic recognition. They have irregularities that go from heterogeneous illumination to variability in symbols shape and complexity inherent to music structure. These issues cause serious difficulties when one wants a robust OMR system facilitating search, retrieval and analysis operations. To transform the paper-based music scores and manuscripts into a machine-readable symbolic format several consistent algorithms are needed. In this paper a method for music symbols extraction in handwritten and printed scores is presented. This technique tries to incorporate musical rules as prior knowledge in the segmentation process in order to overcome the state of the art results.

International Journal of Remote Sensing, 2000

An attempt has been made to assess the e ciency of image data compression by wavelet transform en... more An attempt has been made to assess the e ciency of image data compression by wavelet transform encoding using National Oceanic and Atmospheric Administration (NOAA) Advanced Very High Resolution Radiometer (AVHRR) images. Raw and derived images were compressed to various levels and a number of parameters in the decompressed images compared with those obtained using raw data as a yardstick against which to measure the loss of information due to compression. Unsupervised classi cation, Normalized Di erence Vegetation Index (NDVI) values and brightness temperatures appeared to su er little degradation and only for fractal dimensions was there signi cant loss of integrity at compression rates of up to a factor of 32. The general conclusion from a visual inspection of the e ect of such compressions on arti cially generated geometrical imagettes con rms the e ectiveness of this method of compression.

Plant Pathology, 2015

ABSTRACT Ralstonia solanacearum (Rs) is a quarantine phytopathogenic bacterium accountable for he... more ABSTRACT Ralstonia solanacearum (Rs) is a quarantine phytopathogenic bacterium accountable for heavy economic losses worldwide. Monitoring and eradication programs required for this pathogen are dependent on the availability of time- and cost-efficient detection and typing methods. However, members of the Rs species complex are characterized by a high phenotypic and genetic diversity, which requires improved diagnostics methods.The currently available full genome sequences of several Rs strains allow for the selection of novel specific DNA markers using comparative genomics tools. In this work, seventeen novel markers were selected based on Rs-specific protein domains and thoroughly validated for specificity and stability, both in silico and using “wet lab” assays. PCR- and hybridization-based validation assays revealed that the DNA regions selected as markers were unevenly distributed amongst the tested strains, with nine markers present throughout the species complex. The distribution of the remaining eight markers was highly variable between the different analyzed strains and allowed to obtain strain-specific dot blot hybridization patterns particularly informative for typing. The average probability value of each strain being positive for each of the seventeen markers was calculated by an algorithm and used to obtain a dendrogram representing the hierarchical clustering analysis of Rs, according to the similarity of their hybridization patterns. We believe that this method can be a robust contribution for the straightforward genotyping of members from the Rs species complex. Furthermore, this quantitative hybridization approach would allow to construct databases increasingly informative to determine new Rs genotypes and infer epidemiological patterns.This article is protected by copyright. All rights reserved.

SMCia/08 - Proceedings of the 2008 IEEE Conference on Soft Computing on Industrial Applications, 2008

This paper proposes perceptual segmentation of natural color images using a fuzzy-based hierarchi... more This paper proposes perceptual segmentation of natural color images using a fuzzy-based hierarchical algorithm and its application to the segmentation of dermoscopy images. A fuzzy-based homogeneity measure makes a fusion of the color features and the texture features. The proposed hierarchical segmentation method is performed in four stages: simple splitting, local merging, global merging and boundary refinement. The effectiveness of the proposed method is confirmed through computer simulations that demonstrate the applicability of the proposed method to the segmentation of natural color images and dermoscopy images.

International Geoscience and Remote Sensing Symposium (IGARSS), 2009

The segmentation stage is a key aspect of an object-based image analysis system. However, the seg... more The segmentation stage is a key aspect of an object-based image analysis system. However, the segmentation quality is usually difficult to evaluate for satellite images. The Synthetic Image TEsting Framework (SITEF) is a tool to evaluate and compare image segmentation results. This paper presents the SITEF with an extension to model adjacency effects between neighboring parcels, using the sensor's point spread function and a grid offset. A practical application of SITEF is presented using a SPOT HRG satellite image, with 6 vegetation land cover classes identified on a mountainous area. The segmentation results were evaluated under various perspectives, including the parcel size and shape, the land cover types, the sensor grid offset and one parameter used in the segmentation algorithm.

Remote Sensing of the Ocean and Sea Ice 2004, 2004

Remote sensing techniques are a powerful tool for monitoring littoral zones. Optical sensors can ... more Remote sensing techniques are a powerful tool for monitoring littoral zones. Optical sensors can be used to quantify water quality parameters such as suspended sediments. It is possible to estimate the Total Suspended Matter (TSM) concentration using multi-spectral satellite images. In order to extract meaningful information, the satellite data needs to be validated with in situ measurements. The main objective of this work was to quantify the TSM in sea breaking zone, using multi-spectral satellite images. A part of the northwest coast of Portugal, centered around Aveiro, was chosen as a test area. Several methodologies have been used to establish a relationship between the above sea water reflectance and the TSM concentration. Various field trips were done in order to simultaneously obtain water samples and reflectance measurements. A relationship between TSM concentration and reflectance was established for the range 400-900 nm. Data from Landsat TM, SPOT HRVIR and ASTER were calibrated and geometric corrected. The reflectance values were used to estimate the TSM concentration using the relationships established using the field measurements. The model coefficients and correlation factors, for identical bands on different sensors, presented a high similarity. The results have been incorporated in a Geographical Information System (GIS).

Proceedings - 4th International Congress on Image and Signal Processing, CISP 2011, 2011

Counting the number of Collembola in digital images is a routine task in laboratories of soil eco... more Counting the number of Collembola in digital images is a routine task in laboratories of soil ecotoxicology. This process is based on a direct visual identification of Collembola, and is consequently a time consuming task. This paper present a fully automatic system for counting the number of Collembola in digital images. The system selects the interest area of the image, detects and removes the specular reflection of the incident light, as well as the foam developed during laboratory experiment and finally identifies and counts the number of Collembola. The system performance was tested using 5 treatments with 9 or 10 replicates and 13 treatments with 4 or 5 replicates. A total of 111 images were tested and the results were compared with those obtained by manual identification. The average relative error between automatic and manual counts from multiple observations of the same treatment was 2.1%, which can be considered a good result, given that this value is below the standard deviation between multiple replicate counts.

Proceedings of the 31st Annual International Conference of the IEEE Engineering in Medicine and Biology Society: Engineering the Future of Biomedicine, EMBC 2009, 2009

This paper presents a system for the automatic processing of Digital Images obtained from Gel Ele... more This paper presents a system for the automatic processing of Digital Images obtained from Gel Electrophoresis. The system identifies automatically the number and the location of lanes in the digital image, as well as the location of bands on each lane, without any intervention from the user. A reference lane with a know substance is used to compute the molecular weight of the observed (unknown) bands. The system performance was tested using 12 images, obtained from 4 gels with 3 different exposures. A total of 5443 bands were tested in 12 images, 672 reference / observed lane pairs. The average error in the estimation of molecular weight of 9.2%.

Image Analysis and Recognition, 2010

This paper presents a method (GEIAS) for the automatic processing of digital images obtained from... more This paper presents a method (GEIAS) for the automatic processing of digital images obtained from Gel Electrophoresis. The performance of GEIAS was tested using 12 images, obtained from 4 gels with 3 different exposures with a total of 1082 bands, comparing the results provided by GEIAS and 3 other software tools. The GEIAS is able to fully automatically detect DNA