References of "Marée, Raphaël"
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See detailTowards generic image classification: an extensive empirical study
Marée, Raphaël ULg; Geurts, Pierre ULg; Wehenkel, Louis ULg

E-print/Working paper (2014)

This paper considers the general problem of image classification without using any prior knowledge about image classes. We study variants of a method based on supervised learning whose common steps are ... [more ▼]

This paper considers the general problem of image classification without using any prior knowledge about image classes. We study variants of a method based on supervised learning whose common steps are the extraction of random subwindows described by raw pixel intensity values and the use of ensemble of extremely randomized trees to directly classify images or to learn image features. The influence of method parameters and variants is thoroughly evaluated so as to provide baselines and guidelines for future studies. Detailed results are provided on 80 publicly available datasets that depict very diverse types of images (more than 3800 image classes and over 1.5 million images). [less ▲]

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See detailHistoWeb - Toward a new learning ecology for histology
Vincke, Grégoire ULg; Marée, Raphaël ULg; Wehenkel, Louis ULg et al

Conference (2014, December 16)

HistoWeb targets the transformation of the professional tool Cytomineinto a comprehensive and innovative teaching platform, valuing the notions of learning ecology and new learning dimensions seeking for ... [more ▼]

HistoWeb targets the transformation of the professional tool Cytomineinto a comprehensive and innovative teaching platform, valuing the notions of learning ecology and new learning dimensions seeking for lifelong competencies. The poster was released at the Digital Learning round table, organized by the European Commission around H2020 funding instruments and call 2 "ICT-20 Technologies for better human learning" [less ▲]

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See detailHistoWeb - Transforming a professional bioimages platform into a learning tool for histology
QUATRESOOZ, Pascale ULg; Defaweux, Valérie ULg; Rollus, Loïc ULg et al

Scientific conference (2014, October 30)

In 2012, medical studies in Belgium has undergone an important reform that leads to a rocketing rise of the number of students. The University of Liège took this renewed context as an opportunity to ... [more ▼]

In 2012, medical studies in Belgium has undergone an important reform that leads to a rocketing rise of the number of students. The University of Liège took this renewed context as an opportunity to thoroughly revamp its teaching methods in histology, extending CYTOMINE [1] (http://cytomine.be : a web-based, image storage, annotation, and analysis platform) with new pedagogical features. [less ▲]

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See detailA hybrid human-computer approach for large-scale image-based measurements using web services and machine learning
Marée, Raphaël ULg; Rollus, Loïc ULg; Stevens, Benjamin ULg et al

in Proceedings IEEE International Symposium on Biomedical Imaging (2014, May)

We present a novel methodology combining web-based software development practices, machine learning, and spatial databases for computer-aided quantification of regions of interest (ROIs) in large-scale ... [more ▼]

We present a novel methodology combining web-based software development practices, machine learning, and spatial databases for computer-aided quantification of regions of interest (ROIs) in large-scale imaging data. We describe our main methodological choices, and then illustrate the benefits of the approach (workload reduction, improved precision, scalability, and traceability) on hundreds of whole-slide images of biological tissue slices in cancer research. [less ▲]

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See detailPhenotype Classification of Zebrafish Embryos by Supervised Learning
Jeanray, Nathalie ULg; Marée, Raphaël ULg; Pruvot, Benoist et al

in PLoS ONE (2014), soumis

Zebrafish is increasingly used to assess biological properties of chemical substances and thus is becoming a specific tool for toxicological and pharmacological studies. The effects of chemical substances ... [more ▼]

Zebrafish is increasingly used to assess biological properties of chemical substances and thus is becoming a specific tool for toxicological and pharmacological studies. The effects of chemical substances on embryo survival and development are generally evaluated manually through microscopic observation by an expert and documented by several typical photographs. Here, we present a methodology to automatically classify brightfield images of wildtype zebrafish embryos according to their defects by using an image analysis approach based on supervised machine learning. We show that, compared to manual classification, automatic classification results in 90 to 100 % agreement with consensus voting of biological experts in nine out of eleven considered defects in 3 days old zebrafish larvae. Automation of the analysis and classification of zebrafish embryo pictures reduces the workload and time required for the biological expert and increases the reproducibility and objectivity of this classification. [less ▲]

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See detailEvaluation of CellSolutions BestPrep(R) Automated Thin-Layer Liquid-Based Cytology Papanicolaou Slide Preparation and BestCyte(R) Cell Sorter Imaging System.
Delga, Agnes; GOFFIN, Frédéric ULg; Kridelka, Frédéric ULg et al

in Acta cytologica (2014)

Objective: A double-blind study was conducted to compare the performance of the new BestPrep(R) (CellSolutions) liquid-based thin-layer Papanicolaou (Pap) test with ThinPrep(R) (Hologic). Study Design ... [more ▼]

Objective: A double-blind study was conducted to compare the performance of the new BestPrep(R) (CellSolutions) liquid-based thin-layer Papanicolaou (Pap) test with ThinPrep(R) (Hologic). Study Design: Samples from the study patients (n = 105) were collected twice in the same encounter with the ThinPrep sample always taken first and the BestPrep sample collected second. Slides were prepared according to both manufacturers' protocols and evaluated using manual microscopic review and the BestCyte(R) cell sorter imaging system (CellSolutions). Diagnostic truth for each case was determined by independent manual review of both slides by multiple pathologists and histology when available. The presence of atypical squamous cells of undetermined significance was the threshold for positive for sensitivity and specificity calculations. Results: BestPrep and ThinPrep, by manual review, had sensitivities for high-grade squamous intraepithelial lesion (HSIL) cases of 100 and 95.6%, respectively. Using the BestCyte cell sorter, both had 100% sensitivity. For the same HSIL cases, the digene HC2 high-risk human papillomavirus DNA test had sensitivities of 100% (BestPrep) and 95.6% (ThinPrep). Specificities were 71.4% (BestPrep) and 54.8% (ThinPrep). Conclusions: BestPrep was equivalent to ThinPrep for manual review even though BestPrep was always the second sample collected. The BestCyte cell sorter provides a practical alternative to manual review for both BestPrep and ThinPrep slides. (c) 2014 S. Karger AG, Basel. [less ▲]

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See detailA rich internet application for remote visualization and collaborative annotation of digital slide images in histology and cytology
Marée, Raphaël ULg; Stevens, Benjamin ULg; Rollus, Loïc ULg et al

in Diagnostic Pathology (2013), 8(S1), 26

This work proposes a new web-based tool to ease collaborative projects in digital histology and cytology.

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See detailAutomated Processing of Zebrafish Imaging Data: A Survey
Mikut, Ralf; Dickmeis, Thomas; Driever, Wolfgang et al

in Zebrafish (2013), 10(3), 401-421

Due to the relative transparency of its embryos and larvae, the zebrafish is an ideal model organism for bioimaging approaches in vertebrates. Novel microscope technologies allow the imaging of ... [more ▼]

Due to the relative transparency of its embryos and larvae, the zebrafish is an ideal model organism for bioimaging approaches in vertebrates. Novel microscope technologies allow the imaging of developmental processes in unprecedented detail, and they enable the use of complex image-based read-outs for high-throughput/high-content screening. Such applications can easily generate Terabytes of image data, the handling and analysis of which becomes a major bottleneck in extracting the targeted information. Here, we describe the current state of the art in computational image analysis in the zebrafish system. We discuss the challenges encountered when handling high-content image data, especially with regard to data quality, annotation, and storage. We survey methods for preprocessing image data for further analysis, and describe selected examples of automated image analysis, including the tracking of cells during embryogenesis, heartbeat detection, identification of dead embryos, recognition of tissues and anatomical landmarks, and quantification of behavioral patterns of adult fish. We review recent examples for applications using such methods, such as the comprehensive analysis of cell lineages during early development, the generation of a three-dimensional brain atlas of zebrafish larvae, and high-throughput drug screens based on movement patterns. Finally, we identify future challenges for the zebrafish image analysis community, notably those concerning the compatibility of algorithms and data formats for the assembly of modular analysis pipelines. [less ▲]

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See detailExtremely Randomized Trees and Random Subwindows for Image Classification, Annotation, and Retrieval
Marée, Raphaël ULg; Wehenkel, Louis ULg; Geurts, Pierre ULg

in Criminisi, A; Shotton, J (Eds.) Decision Forests in Computer Vision and Medical Image Analysis, Advances in Computer Vision and Pattern Recognition (2013)

We present a unified framework involving the extraction of random subwindows within images and the induction of ensembles of extremely randomized trees. We discuss the specialization of this framework for ... [more ▼]

We present a unified framework involving the extraction of random subwindows within images and the induction of ensembles of extremely randomized trees. We discuss the specialization of this framework for solving several general problems in computer vision, ranging from image classification and segmentation to content-based image retrieval and interest point detection. The methods are illustrated on various applications and datasets from the biomedical domain [less ▲]

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See detailIdentification of protein biomarkers associated with cardiac ischemia by a proteomic approach.
Fillet, Marianne ULg; Deroyer, Céline ULg; COBRAIVILLE, G. et al

in Biomarkers : biochemical indicators of exposure, response, and susceptibility to chemicals (2013), 18(7), 614-24

Angina is chest pain induced by ischemia of the heart muscle, generally due to obstruction or spasm of the coronary arteries. People that suffer from average to severe cases of angina have an increased ... [more ▼]

Angina is chest pain induced by ischemia of the heart muscle, generally due to obstruction or spasm of the coronary arteries. People that suffer from average to severe cases of angina have an increased percentage of death before the age of 55, usually around 60%. Therefore, prevention of major complications, optimizing diagnosis, prognosis and therapeutics are of primary importance. The main objective of this study was to uncover biomarkers by comparing serum protein profiles of patients suffering from stable or unstable angina and controls. We identified by non-targeted proteomic approach and confirmed by the means of independent techniques, the differential expression of several proteins indicating significantly increased vascular inflammation response, disturbance in the lipid metabolism and in atherogenic plaques stability. [less ▲]

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See detailStructural Determinants of Specificity and Catalytic Mechanism in mammalian 25-kDa Thiamine Triphosphatase
Delvaux, David; Kerff, Frédéric ULg; Murty, Mamidanna R.V.S. et al

in Biochimica et Biophysica Acta - General Subjects (2013), 1830

Background: Thiamine triphosphate (ThTP) is present in most organisms and might be involved in intracellular signaling. In mammalian cells, the cytosolic ThTP level is controlled by a specific thiamine ... [more ▼]

Background: Thiamine triphosphate (ThTP) is present in most organisms and might be involved in intracellular signaling. In mammalian cells, the cytosolic ThTP level is controlled by a specific thiamine triphosphatase (ThTPase), belonging to the CYTH superfamily of proteins. CYTH proteins are present in all superkingdoms of life and act on various triphosphorylated substrates. Methods: Using crystallography, mass spectrometry and mutational analysis, we identified the key structural determinants of the high specificity and catalytic efficiency of mammalian ThTPase. Results: Triphosphate binding requires three conserved arginines while the catalytic mechanism relies on an unusual lysine-tyrosine dyad. By docking of the ThTP molecule in the active site, we found that Trp-53 should interact with the thiazole part of the substrate molecule, thus playing a key role in substrate recognition and specificity. Sea anemone and zebrafish CYTH proteins, which retain the corresponding Trp residue, are also specific ThTPases. Surprisingly, the whole chromosome region containing the ThTPase gene is lost in birds. Conclusion: The specificity for ThTP is linked to a stacking interaction between the thiazole heterocycle of thiamine and a tryptophan residue. The latter likely plays a key role in the secondary acquisition of ThTPase activity in early metazoan CYTH enzymes, in the lineage leading from cnidarians to mammals. General significance: We show that ThTPase activity is not restricted to mammals as previously thought but is an acquisition of early metazoans. This, and the identification of critically important residues, allows us to draw an evolutionary perspective of the CYTH family of proteins. [less ▲]

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See detailPhenotype Classification of Zebrafish Embryos by Supervised Learning
Jeanray, Nathalie ULg; Marée, Raphaël ULg; Pruvot, Benoist ULg et al

Conference (2011, September 02)

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See detailHigh-density lipoprotein proteome dynamics in human endotoxemia.
Levels, Johannes Hm; Geurts, Pierre ULg; Karlsson, Helen et al

in Proteome science (2011), 9(1), 34

BACKGROUND: A large variety of proteins involved in inflammation, coagulation, lipid-oxidation and lipid metabolism have been associated with high-density lipoprotein (HDL) and it is anticipated that ... [more ▼]

BACKGROUND: A large variety of proteins involved in inflammation, coagulation, lipid-oxidation and lipid metabolism have been associated with high-density lipoprotein (HDL) and it is anticipated that changes in the HDL proteome have implications for the multiple functions of HDL. Here, SELDI-TOF mass spectrometry (MS) was used to study the dynamic changes of HDL protein composition in a human experimental low-dose endotoxemia model. Ten healthy men with low HDL cholesterol (0.7+/-0.1 mmol/L) and 10 men with high HDL cholesterol levels (1.9+/-0.4 mmol/L) were challenged with endotoxin (LPS) intravenously (1 ng/kg bodyweight). We previously showed that subjects with low HDL cholesterol are more susceptible to an inflammatory challenge. The current study tested the hypothesis that this discrepancy may be related to differences in the HDL proteome. RESULTS: Plasma drawn at 7 time-points over a 24 hour time period after LPS challenge was used for direct capture of HDL using antibodies against apolipoprotein A-I followed by subsequent SELDI-TOF MS profiling. Upon LPS administration, profound changes in 21 markers (adjusted p-value < 0.05) were observed in the proteome in both study groups. These changes were observed 1 hour after LPS infusion and sustained up to 24 hours, but unexpectedly were not different between the 2 study groups. Hierarchical clustering of the protein spectra at all time points of all individuals revealed 3 distinct clusters, which were largely independent of baseline HDL cholesterol levels but correlated with paraoxonase 1 activity. The acute phase protein serum amyloid A-1/2 (SAA-1/2) was clearly upregulated after LPS infusion in both groups and comprised both native and N-terminal truncated variants that were identified by two-dimensional gel electrophoresis and mass spectrometry. Individuals of one of the clusters were distinguished by a lower SAA-1/2 response after LPS challenge and a delayed time-response of the truncated variants. CONCLUSIONS: This study shows that the semi-quantitative differences in the HDL proteome as assessed by SELDI-TOF MS cannot explain why subjects with low HDL cholesterol are more susceptible to a challenge with LPS than those with high HDL cholesterol. Instead the results indicate that hierarchical clustering could be useful to predict HDL functionality in acute phase responses towards LPS. [less ▲]

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