An application of neighbourhoods in digraphs to the classification of binary dynamics

A binary state on a graph means an assignment of binary values to its vertices. A time dependent sequence of binary states is referred to as binary dynamics. We describe a method for the classification of binary dynamics of digraphs, using particular choices of closed neighbourhoods. Our motivation and application comes from neuroscience, where a directed graph is an abstraction of neurons and their connections, and where the simplification of large amounts of data is key to any computation. We present a topological/graph theoretic method for extracting information out of binary dynamics on a graph, based on a selection of a relatively small number of vertices and their neighbourhoods. We consider existing and introduce new real-valued functions on closed neighbourhoods, comparing them by their ability to accurately classify different binary dynamics. We describe a classification algorithm that uses two parameters and sets up a machine learning pipeline. We demonstrate the effectiveness of the method on simulated activity on a digital reconstruction of cortical tissue of a rat, and on a non-biological random graph with similar density.

A new interactive gazetteer of Perczel’s globe

As a result of the Perczel Project outlined by Mátyás Márton in 2007 at the Department of Cartography and Geoinformatics of Eötvös Loránd University (ELTE), the complete digital restoration and then reconstruction of the 127.5 cm diameter manuscript globe was completed in 2019. The final cartographic completion of the ongoing task at the department by 2013 – led by Mátyás Márton, the project manager, who carried out this work with the help of Judit Paksi –, which included the work of many lecturers and students, aimed at saving the globe.Using this augmented digital processing, it was also possible to create three artistic copies of Perczel’s globe, which was originally made in 1862. This unique work of art, which has suffered irreparable damage due to the ordeals of the 20th century, is of great cultural value and also very important for our cartographic heritage, has been reborn.Following the digital reconstruction, there was a good opportunity to revive another related project. The website, “The interactive gazetteer of Perczel’s globe”, which was born as a result of the work of Zsuzsanna Ungvári and Tibor Tokai earlier, was also created with a new, expanded content. The present study presents the antecedents of gazetteer creation and describes the most important steps of current processing.

Modelling mixed matrix membranes and ceramic foams with application to separation processes

Τα ετερογενή πορώδη υλικά είναι παρόντα σε πολλές πρακτικές και σύγχρονες εφαρμογές, όπως στη διήθηση αιωρημάτων και αεροκολλοειδών, τις διεργασίες βιομετατροπής άνθρακα, τη γεωλογική αποθήκευση CO2 και τις βιοϊατρικές διεργασίες, Οι εφαρμογές αυτές βασίζονται σε συγκεκριμένους φυσικούς, χημικούς ή βιοχημικούς μηχανισμούς για τη λειτουργία τους, όπως είναι η μεταφορά μάζας, ορμής ή ενέργειας, η ρόφηση καθώς και οι χημικές/βιοχημικές αντιδράσεις. Οι μηχανισμοί αυτοί στο εσωτερικό των πορωδών μέσων συναρτώνται σε μεγάλο βαθμό με τη δομή και τη μορφολογία του πορώδους μέσου. Ως εκ τούτου, απαιτείται λεπτομερής μελέτη της εσωτερικής δομής αυτών των πορωδών μέσων για την κατανόηση και τη βελτίωση των διεργασιών στις οποίες χρησιμοποιούνται. Μια λεπτομερής περιγραφή της μικροδομής μπορεί να χρησιμοποιηθεί για την εξακρίβωση των φυσικών ιδιοτήτων και την εκτίμηση και βελτίωση της απόδοσής τους. Η παρούσα διατριβή χρησιμοποιεί στατιστικές ιδιότητες που εξάγονται από εικόνες ηλεκτρονικής μικροσκοπίας σάρωσης (SEM) για τη διερεύνηση και την ψηφιακή αναδημιουργία δομών πορωδών μέσων. Αρχικά, επιλέγεται μια στοχαστική προσέγγιση για την ανακατασκευή πορωδών μέσων επειδή αποτυπώνει τη στοχαστική φύση τους σε λογικά εύρη υπολογιστικού κόστους και χρόνου. Στη συνέχεια, δημιουργείται ένα ψηφιακό μοντέλο ανακατασκευής και ένα πρόγραμμα υπολογιστή για την αναδημιουργία δομών πορωδών μέσων αξιοποιώντας τις διάφορες στατιστικές ιδιότητές τους. Μια ειδική εφαρμογή που μελετάται στην παρούσα διατριβή είναι ο ψηφιακός χαρακτηρισμός των μεμβρανών PES/ PVP που χρησιμοποιούνται σε διαδικασίες αιμοκάθαρσης και η ανάπτυξη ενός μοντέλου που μπορεί να προβλέψει την απόδοσή τους στον καθαρισμό του αίματος. Οι εν λόγω μεμβράνες αποτελούνται από πολλαπλά στρώματα και, συνήθως, μια δομή που μοιάζει με αφρό σχηματίζεται στο εσωτερικό τους, επηρεάζοντας την απόδοση διαχωρισμού και βελτιώνοντας τις μηχανικές ιδιότητες της μεμβράνης.Σε αυτό το πλαίσιο, αναπτύχθηκε μια νέα μέθοδος για την ψηφιακή ανακατασκευή αφρών χρησιμοποιώντας την προσέγγιση Laguerre Tessellation, η οποία παρουσιάζει αξιοσημείωτη ικανότητα να περιγράφει αφρώδη υλικά που αποτελούνται από μακροκοιλότητες με πολυεδρική μορφή. [1]. Επιπλέον, για να περιγραφούν αφρώδη υλικά με μακροκοιλότητες σφαιρικού σχήματος και αυξημένη συνδεσιμότητα, αναπτύχθηκε μια εναλλακτική μέθοδος που βασίζεται στη δημιουργία συσσωρεύσεων κοίλων σφαιρών. [2]. Τέλος, αναπτύχθηκε ένα μοντέλο για την περιγραφή της απομάκρυνσης των δεσμευμένων σε πρωτεΐνες τοξινών κατά τη διάρκεια της διαδικασίας αιμοκάθαρσης με τη χρήση μεμβρανών μικτής μήτρας και επικυρώθηκε με πειραματικά δεδομένα. [3]. Αυτό το μοντέλο επεκτάθηκε περαιτέρω και χρησιμοποιήθηκε για την πρόβλεψη της απόδοσης μιας πολυστρωματικής μεμβράνης μικτής μήτρας κατά την απομάκρυνση της τοξίνης κρεατινίνη. [4]. Επιπλέον, η ενσωμάτωση των διαδικασιών ανακατασκευής που αναπτύχθηκαν στο μοντέλο μείωσε περαιτέρω τα απαιτούμενα πειραματικά δεδομένα.Η χρήση αυτών των μεθόδων ανακατασκευής στο νέο μοντέλο που αναπτύχθηκε παρείχε πληροφορίες για τα χαρακτηριστικά της μεμβράνης και τις συνθήκες της διεργασίας. Έτσι, θα μπορούσε να βοηθήσει στη βελτιστοποίηση της μεταφοράς μάζας μέσω της μεμβράνης αιμοκάθαρσης. Επιπλέον, η διαδικασία αυτή μπορεί να επεκταθεί σε διαφορετικές τεχνολογίες διαχωρισμού ανοίγοντας το δρόμο προς το σχεδιασμό προσαρμοσμένων δομών πορωδών μέσων με επιθυμητές ιδιότητες μεταφοράς αποφεύγοντας χρονοβόρα και συχνά ακριβά φυσικά πειράματα. 1. Stiapis, C.S.; Skouras, E.D.; Burganos, V.N. Advanced Laguerre Tessellation for the Reconstruction of Ceramic Foams and Prediction of Transport Properties. Materials 2019, 12, 1137.2. Stiapis, C.S.; Skouras, E.D.; Burganos, V.N. Three-Dimensional Digital Reconstruction of Ti2AlC Ceramic Foams Produced by the Gelcast Method. Materials 2019, 12, 4085.3. Stiapis, C.; Skouras, E.; Pavlenko, D.; Stamatialis, D.; Burganos, V. Evaluation of the Toxin-to-Protein Binding Rates during Hemodialysis Using Sorbent-Loaded Mixed-Matrix Membranes. Applied Sciences 2018, 8, 536.4. Stiapis, C.S.; Skouras, E.D.; Burganos, V.N. Prediction of Toxin Removal Efficiency of Novel Hemodialysis Multilayered Mixed-Matrix Membranes. Separation and Purification Technology 2020, 250, 117272.

The Benefits of 3D and 4D Synthesis of Marine Geophysical Datasets for Analysis and Visualisation of Shipwrecks, and for Interpretation of Physical Processes over Shipwreck Sites: A Case Study off Methoni, Greece

Through the study of three wreck sites over the Methoni Bay (Greece), this article presents the benefits of spatio-temporal integration and correlation of marine geophysical data in a common three-dimensional (3D) geographical platform for analysis, and visualisation of shipwreck ruins and for interpretation of physical processes over wreck sites. The integration of 3D datasets has been proven to support identification of archaeological features over and under the seafloor, evaluation of the wreck structure state, and assessment on the wrecking event and the wreck site arrangement at that time, due to interactive cross-examination of datasets acquired in separate planes. Data synthesis is fundamental for 3D digital reconstruction of scattered and partially buried shipwreck ruins in complex geology as every dataset acts as interpretive and complimentary to each other. It is also shown that data synthesis highlights the signatures of physical processes over the wreck sites, and the interaction between the processes and the shipwrecks. The analysis of spatio-temporal, four-dimensional (4D) integrated datasets has proved to provide knowledge on the wreck site evolution through time, and highlights the disturbance of underwater archaeological resources due to human activities. The study has also shown that the creation of a shoalest depth true position bathymetric surface supports the realistic 3D wreck representation over the seafloor.

The digital reconstruction of degraded ancient temple murals using dynamic mask generation and an extended exemplar-based region-filling algorithm

A mural is any piece of artwork sculpted or applied directly on a wall, ceiling or other permanent surface. This artwork symbolizes various culture’s, traditions, historical events, spiritual stories, and civilizations of respective societies of ancient times. But these mural paintings are subjected to degradation either by various natural causes as well as pollution or by human beings without knowing their value. Restoring these paintings requires skilled artisans who are hard to find these days. Consequently, an efficient image restoration technique is required to meet the particular needs of the paintings. Existing in-painting algorithms largely use pixel-based textural reconstruction. The technique, however, does not work well for images with large, degraded portions. and also fails in the restoration of the structure. To resolve these drawbacks, we propose a combined technique for the textural and structural reconstruction of ancient murals. The proposed Extended Exemplar-based Region-Filling Algorithm uses a patch-based reconstruction procedure and masked images are created automatically using the Dynamic Mask Generation Algorithm. The deteriorated portions are identified by creating masks, and masks are created in such a way that degraded portions have a pixel intensity value of one and the remaining part has a value of zero, and filling is done by analyzing the surrounding pixel values of the degraded pixel. The algorithm reconstructs the structure of the paintings efficiently by generating sketches. The proposed technique reconstructs both the structure and textural information, and ensures efficient reconstructed results, compared to existing in-painting techniques. Performance is evaluated by metrics such as the Mean Square Error (MSE), Peak Signal-to-Noise Ratio (PSNR), and Structural Similarity Index (SSIM).

Depth-camera-based rebar detection and digital reconstruction for robotic concrete spraying

In this paper, we tackle the challenge of detection and accurate digital reconstruction of steel rebar meshes using a set of industrial depth cameras. A construction example under investigation in this paper is robotic concrete spraying, where material is sprayed onto double-curved single layered rebar meshes. Before the spraying process can start, the location and geometry of the rebar mesh needs to be accurately know. We present an automatic image-based processing approach of depth images for grid point extraction at an accuracy of a few mm. Furthermore, we propose a sequence of execution steps in a robotic setup, including the hand–eye calibration, which enables the direct georeferencing of multiple data sets acquired from various poses into a common coordinate system. With the proposed approach we are able to digitally reconstruct a mesh of an unknown geometry in under 10 min with an accuracy better than 5 mm. The digitally reconstructed mesh allows for computation of material needed for its construction, enabling sustainable use of concrete in digital fabrication. The accurately reconstructed digital mesh, generated based on the proposed approach in this paper, is the input for the following spraying step, allowing for generation of accurate spray trajectories.

TRACER: A toolkit to register and visualize anatomical coordinates in the rat brain

The need for anatomical registration and visualization tools is greater than ever thanks to novel technologies that allow users to record from thousands of neurons across multiple brain regions simultaneously. The vast majority of digital reconstruction toolkits for rodent models were developed using mouse brain atlases, leaving few options for those using rats. Retrofitting rat atlases into extant software is possible, but this demands effort and programming skills which most end-users lack. We therefore developed an open-source, python-based Toolkit for Reconstructing Anatomical CoordinatEs in Rats, TRACER, which allows users to reconstruct the trajectories of recording electrodes (e.g Neuropixels) or to visualize virus expression or other features in a comprehensively annotated 3D volume, the Waxholm Space (WHS) rat brain atlas. The WHS atlas is made from high-resolution magnetic resonance imaging (MRI) and diffusion tensor imaging (DTI) scans, and contains >200 regional delineations. Beyond post-hoc reconstructions of electrodes or virus expression, TRACER can be used to generate coordinates for targeting brain regions prior to surgery. TRACER is available openly on GitHub and is compatible with Windows, macOS and Linux operating systems.

A Comprehensive, FAIR File Format for Neuroanatomical Structure Modeling

With advances in microscopy and computer science, the technique of digitally reconstructing, modeling, and quantifying microscopic anatomies has become central to many fields of biological research. MBF Bioscience has chosen to openly document their digital reconstruction file format, the Neuromorphological File Specification, available at www.mbfbioscience.com/filespecification (Angstman et al., 2020). The format, created and maintained by MBF Bioscience, is broadly utilized by the neuroscience community. The data format’s structure and capabilities have evolved since its inception, with modifications made to keep pace with advancements in microscopy and the scientific questions raised by worldwide experts in the field. More recent modifications to the neuromorphological file format ensure it abides by the Findable, Accessible, Interoperable, and Reusable (FAIR) data principles promoted by the International Neuroinformatics Coordinating Facility (INCF; Wilkinson et al., Scientific Data, 3, 160018,, 2016). The incorporated metadata make it easy to identify and repurpose these data types for downstream applications and investigation. This publication describes key elements of the file format and details their relevant structural advantages in an effort to encourage the reuse of these rich data files for alternative analysis or reproduction of derived conclusions.