Compressed sensing in fluorescence microscopy.

Compressed sensing (CS) is a signal processing approach that solves ill-posed inverse problems, from under-sampled data with respect to the Nyquist criterium. CS exploits sparsity constraints based on the knowledge of prior information, relative to the structure of the object in the spatial or other domains. It is commonly used in image and video compression as well as in scientific and medical applications, including computed tomography and magnetic resonance imaging. In the field of fluorescence microscopy, it has been demonstrated to be valuable for fast and high-resolution imaging, from single-molecule localization, super-resolution to light-sheet microscopy. Furthermore, CS has found remarkable applications in the field of mesoscopic imaging, facilitating the study of small animals' organs and entire organisms. This review article illustrates the working principles of CS, its implementations in optical imaging and discusses several relevant uses of CS in the field of fluorescence imaging from super-resolution microscopy to mesoscopy

Unraveling the Thousand Word Picture: An Introduction to Super-Resolution Data Analysis

Super-resolution microscopy provides direct insight into fundamental biological processes occurring at length scales smaller than light’s diffraction limit. The analysis of data at such scales has brought statistical and machine learning methods into the mainstream. Here we provide a survey of data analysis methods starting from an overview of basic statistical techniques underlying the analysis of super-resolution and, more broadly, imaging data. We subsequently break down the analysis of super-resolution data into four problems: the localization problem, the counting problem, the linking problem, and what we’ve termed the interpretation problem

Microscopy and Analysis

Microscopes represent tools of the utmost importance for a wide range of disciplines. Without them, it would have been impossible to stand where we stand today in terms of understanding the structure and functions of organelles and cells, tissue composition and metabolism, or the causes behind various pathologies and their progression. Our knowledge on basic and advanced materials is also intimately intertwined to the realm of microscopy, and progress in key fields of micro- and nanotechnologies critically depends on high-resolution imaging systems. This volume includes a series of chapters that address highly significant scientific subjects from diverse areas of microscopy and analysis. Authoritative voices in their fields present in this volume their work or review recent trends, concepts, and applications, in a manner that is accessible to a broad readership audience from both within and outside their specialist area

Methods for analyzing the influence of molecular dynamics on neuronal activity

Magdeburg, Univ., Fak. für Informatik, Diss., 2015von Stefan Sokol

Image Restoration

This book represents a sample of recent contributions of researchers all around the world in the field of image restoration. The book consists of 15 chapters organized in three main sections (Theory, Applications, Interdisciplinarity). Topics cover some different aspects of the theory of image restoration, but this book is also an occasion to highlight some new topics of research related to the emergence of some original imaging devices. From this arise some real challenging problems related to image reconstruction/restoration that open the way to some new fundamental scientific questions closely related with the world we interact with

Appearance Modelling and Reconstruction for Navigation in Minimally Invasive Surgery

Minimally invasive surgery is playing an increasingly important role for patient care. Whilst its direct patient benefit in terms of reduced trauma, improved recovery and shortened hospitalisation has been well established, there is a sustained need for improved training of the existing procedures and the development of new smart instruments to tackle the issue of visualisation, ergonomic control, haptic and tactile feedback. For endoscopic intervention, the small field of view in the presence of a complex anatomy can easily introduce disorientation to the operator as the tortuous access pathway is not always easy to predict and control with standard endoscopes. Effective training through simulation devices, based on either virtual reality or mixed-reality simulators, can help to improve the spatial awareness, consistency and safety of these procedures. This thesis examines the use of endoscopic videos for both simulation and navigation purposes. More specifically, it addresses the challenging problem of how to build high-fidelity subject-specific simulation environments for improved training and skills assessment. Issues related to mesh parameterisation and texture blending are investigated. With the maturity of computer vision in terms of both 3D shape reconstruction and localisation and mapping, vision-based techniques have enjoyed significant interest in recent years for surgical navigation. The thesis also tackles the problem of how to use vision-based techniques for providing a detailed 3D map and dynamically expanded field of view to improve spatial awareness and avoid operator disorientation. The key advantage of this approach is that it does not require additional hardware, and thus introduces minimal interference to the existing surgical workflow. The derived 3D map can be effectively integrated with pre-operative data, allowing both global and local 3D navigation by taking into account tissue structural and appearance changes. Both simulation and laboratory-based experiments are conducted throughout this research to assess the practical value of the method proposed

Material Recognition Meets 3D Reconstruction : Novel Tools for Efficient, Automatic Acquisition Systems

For decades, the accurate acquisition of geometry and reflectance properties has represented one of the major objectives in computer vision and computer graphics with many applications in industry, entertainment and cultural heritage. Reproducing even the finest details of surface geometry and surface reflectance has become a ubiquitous prerequisite in visual prototyping, advertisement or digital preservation of objects. However, today's acquisition methods are typically designed for only a rather small range of material types. Furthermore, there is still a lack of accurate reconstruction methods for objects with a more complex surface reflectance behavior beyond diffuse reflectance. In addition to accurate acquisition techniques, the demand for creating large quantities of digital contents also pushes the focus towards fully automatic and highly efficient solutions that allow for masses of objects to be acquired as fast as possible. This thesis is dedicated to the investigation of basic components that allow an efficient, automatic acquisition process. We argue that such an efficient, automatic acquisition can be realized when material recognition "meets" 3D reconstruction and we will demonstrate that reliably recognizing the materials of the considered object allows a more efficient geometry acquisition. Therefore, the main objectives of this thesis are given by the development of novel, robust geometry acquisition techniques for surface materials beyond diffuse surface reflectance, and the development of novel, robust techniques for material recognition. In the context of 3D geometry acquisition, we introduce an improvement of structured light systems, which are capable of robustly acquiring objects ranging from diffuse surface reflectance to even specular surface reflectance with a sufficient diffuse component. We demonstrate that the resolution of the reconstruction can be increased significantly for multi-camera, multi-projector structured light systems by using overlappings of patterns that have been projected under different projector poses. As the reconstructions obtained by applying such triangulation-based techniques still contain high-frequency noise due to inaccurately localized correspondences established for images acquired under different viewpoints, we furthermore introduce a novel geometry acquisition technique that complements the structured light system with additional photometric normals and results in significantly more accurate reconstructions. In addition, we also present a novel method to acquire the 3D shape of mirroring objects with complex surface geometry. The aforementioned investigations on 3D reconstruction are accompanied by the development of novel tools for reliable material recognition which can be used in an initial step to recognize the present surface materials and, hence, to efficiently select the subsequently applied appropriate acquisition techniques based on these classified materials. In the scope of this thesis, we therefore focus on material recognition for scenarios with controlled illumination as given in lab environments as well as scenarios with natural illumination that are given in photographs of typical daily life scenes. Finally, based on the techniques developed in this thesis, we provide novel concepts towards efficient, automatic acquisition systems