Online sharing educational content on biodiversity topics: a case study from organic agriculture and agroecology

E-Learning Technologies and Standards are emerging as the dominant way to make educational content widely available. Approaches to these technologies should be domain-independent and easily adaptable to different contexts. Organic.Edunet aims at making content on Organic Agriculture and Agroecology widely available through a single point of reference. To achieve this, the project has adopted and adapted Open Software solutions and has built upon them to offer the Organic.Edunet Web Federation Portal and the Repository Suite of Tools. This paper presents the tools that were developed in the frame of Organic.Edunet project, serving as a guide for all individuals that aim at establishing similar tools in a field such as the biodiversity

Υπολογιστική επεξεργασία και ανάλυση ακολουθιών εικόνων υπερήχων της καρωτίδας: συσχέτιση με τη μηχανική συμπεριφορά του αρτηριακού τοιχώματος

The purpose of this Ph.D. thesis is to develop and apply advanced image processing and analysis methods to sequences of B-mode ultrasound images of the carotid artery aiming to support the diagnosis of carotid atherosclerosis. The computational methods, presented in the thesis, are applied to both synthetic and real ultrasound data. Based on the findings of a carefully designed study, optimal ultrasound device settings are proposed for reliable motion estimation. Standardized techniques, including image normalization, are also recommended for image processing tasks. Texture analysis of the carotid atheromatous plaque was performed using three transform-based methods (Fourier transform, Wavelet transform and Gabor filters). Texture features estimated using the discrete 2D Wavelet transform and the Gabor filters are found significantly different between symptomatic and asymptomatic subjects. Four different approaches are proposed for the analysis of motion of the carotid artery wall and a validation study is performed using simulated data. The weighted least-squares optical flow method is found to have the best performance. This method is subsequently used to analyze the motion of the healthy carotid artery wall, as well as of the arterial wall with asymptomatic and symptomatic atheromatous plaque. Moreover, an automatic segmentation method based on Hough transform is proposed for the segmentation of the arterial wall from B-mode ultrasound images of longitudinal and transverse sections of the carotid artery. The method can be used for the estimation of widely used diagnostic measures, such as the intima-media thickness and the arterial distension waveforms. The accuracy of the method was reasonably high for longitudinal sections and somewhat lower for transverse sections and diseased arteries. A combination of Hough transform and active contours is proposed to improve the segmentation results in those cases. A mathematical model of the mechanical deformation of the carotid artery wall is also proposed. In an attempt to determine a patient-specific approach, the model is fitted to actual displacement waveforms estimated using the least-squares optical flow method to B-mode ultrasound image sequences of the carotid artery. A number of model parameters are found significantly different between different layers of the arterial wall and between healthy and diseased wall. The previous methods for the processing and analysis of B-mode ultrasound images of the carotid artery are integrated to a modular software system (ANALYSIS). Analysis can be a useful and powerful tool for the diagnosis of carotid atherosclerosis. The computational methods presented in this thesis are expected to contribute not only to the study of the mechanical behavior of the healthy and diseased carotid artery wall but also to the definition of an objective and reliable approach for the diagnosis of carotid atherosclerosis and the optimal selection of patients for carotid endarterectomy.Η παρούσα διδακτορική διατριβή έχει στόχο την υπολογιστική υποβοήθηση της διάγνωσης της αθηρωμάτωσης μέσω της ανάπτυξης και εφαρμογής προηγμένων μεθοδολογιών επεξεργασίας και ανάλυσης ακολουθιών εικόνων υπερήχων β-σάρωσης της καρωτίδας. Οι μέθοδοι που παρουσιάζονται στη διατριβή αξιολογούνται τόσο σε συνθετικά όσο και σε πραγματικά απεικονιστικά δεδομένα. Μετά από διεξοδική μελέτη προτείνονται οι κατάλληλες ρυθμίσεις της υπερηχοτομογραφικής διάταξης καθώς και η εφαρμογή διαδικασίας κανονικοποίησης των λαμβανομένων εικόνων, με στόχο τη βελτιστοποίηση του αποτελέσματος των διαδικασιών επεξεργασίας εικόνας. Για την ανάλυση της υφής της αθηρωματικής πλάκας στην καρωτίδα, προτείνονται και αξιολογούνται συγκριτικά τρεις τεχνικές μετασχηματισμού: μετασχηματισμός Fourier, μετασχηματισμός κυματιδίου και φίλτρα Gabor. Αποδεικνύεται ότι χαρακτηριστικά υφής που υπολογίζονται τόσο με βάση το μετασχηματισμό κυματιδίου όσο και με τα φίλτρα Gabor μπορούν να διαχωρίσουν τους δυο τύπους αθηρωματικών πλακών (συμπτωματικές και ασυμπτωματικές). Για την εκτίμηση της κίνησης του τοιχώματος της καρωτίδας προτείνονται και αξιολογούνται τέσσερις μέθοδοι, από τις οποίες η μέθοδος της οπτικής ροής ελάχιστων τετραγώνων με βάρη βρέθηκε να έχει τη βέλτιστη απόδοση. Η μέθοδος αυτή χρησιμοποιείται για την εκτίμηση της μετατόπισης τόσο του υγιούς τοιχώματος της καρωτίδας, όσο και τοιχώματος με ασυμπτωματική ή συμπτωματική αθηρωματική πλάκα. Επιπλέον, προτείνεται μια αυτόματη μέθοδος κατάτμησης του τοιχώματος της καρωτίδας από διαμήκεις και εγκάρσιες εικόνες υπερήχων, η οποία βασίζεται στο μετασχηματισμό Hough. Η προτεινόμενη μεθοδολογία χρησιμοποιείται για τον υπολογισμό χρήσιμων για τη διάγνωση ποσοτικών δεικτών, όπως το πάχος του έσω-μέσου χιτώνα και οι κυματομορφές μεταβολής της αρτηριακής διαμέτρου. Σύμφωνα με τα αποτελέσματα, η εν γένει υψηλή ακρίβεια της μεθόδου περιορίζεται για την περίπτωση εγκάρσιων τομών και αθηρωμάτωσης. Για τη βελτίωση του αποτελέσματος της κατάτμησης σε αυτές τις περιπτώσεις, προτείνεται ο συνδυασμός του μετασχηματισμού Hough με ενεργές καμπύλες. Η μελέτη της κίνησης του αρτηριακού τοιχώματος συμπληρώνεται με ένα μαθηματικό μοντέλο για την παραμόρφωση του αρτηριακού τοιχώματος κατά την ακτινική και αξονική διεύθυνση. Για την εξατομίκευση του μοντέλου και τον προσδιορισμό των παραμέτρων του, πραγματοποιείται προσαρμογή σε πραγματικές μετρήσεις της παραμόρφωσης, που υπολογίζονται με εφαρμογή της μεθόδου ανάλυσης κίνησης σε ακολουθίες εικόνων συγκεκριμένων ασθενών. Ορισμένες παράμετροι του μαθηματικού μοντέλου βρέθηκαν να διαφοροποιούνται σημαντικά μεταξύ των στρωμάτων του αρτηριακού τοιχώματος αλλά και μεταξύ υγιούς τοιχώματος και τοιχώματος με αθηρωμάτωση. Η υλοποίηση των παραπάνω μεθοδολογιών σε συνδυασμό με κατάλληλη διεπιφάνεια χρήσης οδήγησε στην ανάπτυξη ενός ολοκληρωμένου συστήματος λογισμικού (ANALYSIS), το οποίο στοχεύει στην υποβοήθηση της διάγνωσης της αθηρωμάτωσης της καρωτίδας. Το σύνολο των μεθόδων που παρουσιάζονται στη διδακτορική διατριβή αναμένεται να συμβάλουν αφενός στη μελέτη της μηχανικής συμπεριφοράς του φυσιολογικού και αθηρωματικού αρτηριακού τοιχώματος και αφετέρου στην καθιέρωση μιας πιο αντικειμενικής και αξιόπιστης προσέγγισης για τη διάγνωση της αθηρωμάτωσης και την επιλογή ασθενών υποψήφιων για ενδαρτηρεκτομή

Texture Characterization of Carotid Atherosclerotic Plaque from B-mode Ultrasound Using Gabor Filters

Texture analysis of B-mode ultrasound images of carotid atheromatous plaque can be valuable for the accurate diagnosis of atherosclerosis. In this paper, Gabor filters were used to characterize the texture of carotid artery atherosclerotic tissue. B-mode ultrasound images of 10 symptomatic and 9 asymptomatic plaques were interrogated. A total of 40 texture features were estimated for each plaque. The bootstrap method was used to compare the mean values of the texture features extracted from the two groups. After bootstrapping, the mean value and the standard deviation of the energy estimated using the Gabor filters was found to be significantly different between symptomatic and asymptomatic plaques in the first scale of analysis and for all orientations. In addition, a number of texture features that correspond to larger resolution scales were found to be significantly different between the two types of plaques. It is concluded that Gabor-filter-based texture analysis in combination with a powerful statistical technique, such as bootstrapping, may provide valuable information about the plaque tissue type

Computer aided diagnosis based on medical image processing and artificial intelligence methods

Advances in imaging technology and computer science have greatly enhanced interpretation of medical images, and contributed to early diagnosis. The typical architecture of a Computer Aided Diagnosis (CAD) system includes image pre-processing, definition of region(s) of interest, features extraction and selection, and classification. In this paper, the principles of CAD systems design and development are demonstrated by means of two examples. The first one focuses on the differentiation between symptomatic and asymptomatic carotid atherotnatous plaques. For each plaque, a vector of texture and motion features was estimated, which was then reduced to the most robust ones by means of ANalysis of VAriance (ANOVA). Using fuzzy c-means, the features were then clustered into two classes. Clustering performances of 74%, 79%, and 84%, were achieved for texture only, motion only, and combinations of texture and motion features, respectively. The second CAD system presented in this paper supports the diagnosis of focal liver lesions and is able to characterize liver tissue from Computed Tomography (CT) images as normal, hepatic cyst, hemangioma, and hepatocellular carcinoma. Five texture feature sets were extracted for each lesion, while a genetic algorithm based feature selection method was applied to identify the most robust features. The selected feature set was fed into an ensemble of neural network classifiers. The achieved classification performance was 100%, 93.75% and 90.63% in the training, validation and testing set, respectively. It is concluded that computerized analysis of medical images in combination with artificial intelligence can be used in clinical practice and may contribute to more efficient diagnosis. (c) 2006 Elsevier B.V. All rights reserved

Carotid artery motion estimation from sequences of b-mode ultrasound images: Effect of scanner settings and image normalization

Abstract—The motion of the carotid artery wall can quantita-tively be estimated from sequences of B-mode ultrasound images. In this paper, the effects of dynamic range (DR) and persistence, along with that of image normalization, were studied, in an attempt to suggest optimal values for reliable motion analysis. Image sequences were recorded using four different values for DR, i.e., 0, 48, 66, and 90 dB, and three different values for persistence, i.e., 0, 5.6, and 50. Radial and axial displacements, as well as the correlation coefficients (CCs), were estimated using block matching from recordings with durations of about 3 s. The variances of radial and axial displacements were not significantly affected by changes in DR and persistence. The mean value of the CC, which is an index of the reliability of motion analysis, was also not significantly affected by these settings. However, an increase in persistence increased the delays between peak radial displacements and cardiac systole. Image normalization did not affect the results of motion analysis. It is suggested that high values of DR (66 or 90 dB) and low values of persistence (0 or 5.6) are used for motion analysis based on block matching. Index Terms—Block matching, carotid artery, dynamic range (DR), motion analysis, normalization, persistence, ultrasound imaging. I

Federating natural history museums in natural Europe

Summarization: An impressive abundance of high quality scientific content about Earth’s biodiversity and natural history available in Natural History Museums (NHMs) around Europe remains largely unexploited due to a number of barriers, such as: the lack of interconnection and interoperability between the management systems used by museums, the lack of centralized access through a European point of reference like Europeana, and the inadequacy of the current metadata and content organization. To cope with these problems, the Natural Europe project offers a coordinated solution at European level. Cultural heritage content is collected from six Natural History Museums around Europe into a federation of European Natural History Digital Libraries that is directly connected with Europeana.eu. This paper presents the Natural Europe Cultural Digital Libraries Federation infrastructure consisting of: (a) The Natural Europe Cultural Environment (NECE), i.e. the infrastructure and toolset deployed on each NHM allowing their curators to publish, semantically describe, manage and disseminate the Cultural Heritage Objects (CHOs) they contribute to the project, and (b) the Natural Europe Cultural Heritage Infrastructure (NECHI) interconnecting NHM digital libraries and further exposing their metadata records to Europeana.eu.Παρουσιάστηκε στο: 7th Metadata Semantics and Research Conference (MTSR) 201