3D exemplar-based image inpainting in electron microscopy

In electron microscopy (EM) a common problem is the non-availability of data, which causes artefacts in reconstructions. In this thesis the goal is to generate artificial data where missing in EM by using exemplar-based inpainting (EBI). We implement an accelerated 3D version tailored to applications in EM, which reduces reconstruction times from days to minutes. We develop intelligent sampling strategies to find optimal data as input for reconstruction methods. Further, we investigate approaches to reduce electron dose and acquisition time. Sparse sampling followed by inpainting is the most promising approach. As common evaluation measures may lead to misinterpretation of results in EM and falsify a subsequent analysis, we propose to use application driven metrics and demonstrate this in a segmentation task. A further application of our technique is the artificial generation of projections in tiltbased EM. EBI is used to generate missing projections, such that the full angular range is covered. Subsequent reconstructions are significantly enhanced in terms of resolution, which facilitates further analysis of samples. In conclusion, EBI proves promising when used as an additional data generation step to tackle the non-availability of data in EM, which is evaluated in selected applications. Enhancing adaptive sampling methods and refining EBI, especially considering the mutual influence, promotes higher throughput in EM using less electron dose while not lessening quality.Ein häufig vorkommendes Problem in der Elektronenmikroskopie (EM) ist die Nichtverfügbarkeit von Daten, was zu Artefakten in Rekonstruktionen führt. In dieser Arbeit ist es das Ziel fehlende Daten in der EM künstlich zu erzeugen, was durch Exemplar-basiertes Inpainting (EBI) realisiert wird. Wir implementieren eine auf EM zugeschnittene beschleunigte 3D Version, welche es ermöglicht, Rekonstruktionszeiten von Tagen auf Minuten zu reduzieren. Wir entwickeln intelligente Abtaststrategien, um optimale Datenpunkte für die Rekonstruktion zu erhalten. Ansätze zur Reduzierung von Elektronendosis und Aufnahmezeit werden untersucht. Unterabtastung gefolgt von Inpainting führt zu den besten Resultaten. Evaluationsmaße zur Beurteilung der Rekonstruktionsqualität helfen in der EM oft nicht und können zu falschen Schlüssen führen, weswegen anwendungsbasierte Metriken die bessere Wahl darstellen. Dies demonstrieren wir anhand eines Beispiels. Die künstliche Erzeugung von Projektionen in der neigungsbasierten Elektronentomographie ist eine weitere Anwendung. EBI wird verwendet um fehlende Projektionen zu generieren. Daraus resultierende Rekonstruktionen weisen eine deutlich erhöhte Auflösung auf. EBI ist ein vielversprechender Ansatz, um nicht verfügbare Daten in der EM zu generieren. Dies wird auf Basis verschiedener Anwendungen gezeigt und evaluiert. Adaptive Aufnahmestrategien und EBI können also zu einem höheren Durchsatz in der EM führen, ohne die Bildqualität merklich zu verschlechtern

Book of Abstracts 15th International Symposium on Computer Methods in Biomechanics and Biomedical Engineering and 3rd Conference on Imaging and Visualization

In this edition, the two events will run together as a single conference, highlighting the strong connection with the Taylor & Francis journals: Computer Methods in Biomechanics and Biomedical Engineering (John Middleton and Christopher Jacobs, Eds.) and Computer Methods in Biomechanics and Biomedical Engineering: Imaging and Visualization (JoãoManuel R.S. Tavares, Ed.). The conference has become a major international meeting on computational biomechanics, imaging andvisualization. In this edition, the main program includes 212 presentations. In addition, sixteen renowned researchers will give plenary keynotes, addressing current challenges in computational biomechanics and biomedical imaging. In Lisbon, for the first time, a session dedicated to award the winner of the Best Paper in CMBBE Journal will take place. We believe that CMBBE2018 will have a strong impact on the development of computational biomechanics and biomedical imaging and visualization, identifying emerging areas of research and promoting the collaboration and networking between participants. This impact is evidenced through the well-known research groups, commercial companies and scientific organizations, who continue to support and sponsor the CMBBE meeting series. In fact, the conference is enriched with five workshops on specific scientific topics and commercial software.info:eu-repo/semantics/draf

Sparse Signal Recovery Based on Compressive Sensing and Exploration Using Multiple Mobile Sensors

The work in this dissertation is focused on two areas within the general discipline of statistical signal processing. First, several new algorithms are developed and exhaustively tested for solving the inverse problem of compressive sensing (CS). CS is a recently developed sub-sampling technique for signal acquisition and reconstruction which is more efficient than the traditional Nyquist sampling method. It provides the possibility of compressed data acquisition approaches to directly acquire just the important information of the signal of interest. Many natural signals are sparse or compressible in some domain such as pixel domain of images, time, frequency and so forth. The notion of compressibility or sparsity here means that many coefficients of the signal of interest are either zero or of low amplitude, in some domain, whereas some are dominating coefficients. Therefore, we may not need to take many direct or indirect samples from the signal or phenomenon to be able to capture the important information of the signal. As a simple example, one can think of a system of linear equations with N unknowns. Traditional methods suggest solving N linearly independent equations to solve for the unknowns. However, if many of the variables are known to be zero or of low amplitude, then intuitively speaking, there will be no need to have N equations. Unfortunately, in many real-world problems, the number of non-zero (effective) variables are unknown. In these cases, CS is capable of solving for the unknowns in an efficient way. In other words, it enables us to collect the important information of the sparse signal with low number of measurements. Then, considering the fact that the signal is sparse, extracting the important information of the signal is the challenge that needs to be addressed. Since most of the existing recovery algorithms in this area need some prior knowledge or parameter tuning, their application to real-world problems to achieve a good performance is difficult. In this dissertation, several new CS algorithms are proposed for the recovery of sparse signals. The proposed algorithms mostly do not require any prior knowledge on the signal or its structure. In fact, these algorithms can learn the underlying structure of the signal based on the collected measurements and successfully reconstruct the signal, with high probability. The other merit of the proposed algorithms is that they are generally flexible in incorporating any prior knowledge on the noise, sparisty level, and so on. The second part of this study is devoted to deployment of mobile sensors in circumstances that the number of sensors to sample the entire region is inadequate. Therefore, where to deploy the sensors, to both explore new regions while refining knowledge in aleady visited areas is of high importance. Here, a new framework is proposed to decide on the trajectories of sensors as they collect the measurements. The proposed framework has two main stages. The first stage performs interpolation/extrapolation to estimate the phenomenon of interest at unseen loactions, and the second stage decides on the informative trajectory based on the collected and estimated data. This framework can be applied to various problems such as tuning the constellation of sensor-bearing satellites, robotics, or any type of adaptive sensor placement/configuration problem. Depending on the problem, some modifications on the constraints in the framework may be needed. As an application side of this work, the proposed framework is applied to a surrogate problem related to the constellation adjustment of sensor-bearing satellites

Intelligent Biosignal Processing in Wearable and Implantable Sensors

This reprint provides a collection of papers illustrating the state-of-the-art of smart processing of data coming from wearable, implantable or portable sensors. Each paper presents the design, databases used, methodological background, obtained results, and their interpretation for biomedical applications. Revealing examples are brain–machine interfaces for medical rehabilitation, the evaluation of sympathetic nerve activity, a novel automated diagnostic tool based on ECG data to diagnose COVID-19, machine learning-based hypertension risk assessment by means of photoplethysmography and electrocardiography signals, Parkinsonian gait assessment using machine learning tools, thorough analysis of compressive sensing of ECG signals, development of a nanotechnology application for decoding vagus-nerve activity, detection of liver dysfunction using a wearable electronic nose system, prosthetic hand control using surface electromyography, epileptic seizure detection using a CNN, and premature ventricular contraction detection using deep metric learning. Thus, this reprint presents significant clinical applications as well as valuable new research issues, providing current illustrations of this new field of research by addressing the promises, challenges, and hurdles associated with the synergy of biosignal processing and AI through 16 different pertinent studies. Covering a wide range of research and application areas, this book is an excellent resource for researchers, physicians, academics, and PhD or master students working on (bio)signal and image processing, AI, biomaterials, biomechanics, and biotechnology with applications in medicine