Bioimage informatics in STED super-resolution microscopy

Optical microscopy is living its renaissance. The diffraction limit, although still physically true, plays a minor role in the achievable resolution in far-field fluorescence microscopy. Super-resolution techniques enable fluorescence microscopy at nearly molecular resolution. Modern (super-resolution) microscopy methods rely strongly on software. Software tools are needed all the way from data acquisition, data storage, image reconstruction, restoration and alignment, to quantitative image analysis and image visualization. These tools play a key role in all aspects of microscopy today – and their importance in the coming years is certainly going to increase, when microscopy little-by-little transitions from single cells into more complex and even living model systems. In this thesis, a series of bioimage informatics software tools are introduced for STED super-resolution microscopy. Tomographic reconstruction software, coupled with a novel image acquisition method STED< is shown to enable axial (3D) super-resolution imaging in a standard 2D-STED microscope. Software tools are introduced for STED super-resolution correlative imaging with transmission electron microscopes or atomic force microscopes. A novel method for automatically ranking image quality within microscope image datasets is introduced, and it is utilized to for example select the best images in a STED microscope image dataset.Siirretty Doriast

An interactive ImageJ plugin for semi-automated image denoising in electron microscopy

The recent advent of 3D in electron microscopy (EM) has allowed for detection of nanometer resolution structures. This has caused an explosion in dataset size, necessitating the development of automated workflows. Moreover, large 3D EM datasets typically require hours to days to be acquired and accelerated imaging typically results in noisy data. Advanced denoising techniques can alleviate this, but tend to be less accessible to the community due to low-level programming environments, complex parameter tuning or a computational bottleneck. We present DenoisEM: an interactive and GPU accelerated denoising plugin for ImageJ that ensures fast parameter tuning and processing through parallel computing. Experimental results show that DenoisEM is one order of magnitude faster than related software and can accelerate data acquisition by a factor of 4 without significantly affecting data quality. Lastly, we show that image denoising benefits visualization and (semi-)automated segmentation and analysis of ultrastructure in various volume EM datasets

Digital Techniques for Documenting and Preserving Cultural Heritage

In this unique collection the authors present a wide range of interdisciplinary methods to study, document, and conserve material cultural heritage. The methods used serve as exemplars of best practice with a wide variety of cultural heritage objects having been recorded, examined, and visualised. The objects range in date, scale, materials, and state of preservation and so pose different research questions and challenges for digitization, conservation, and ontological representation of knowledge. Heritage science and specialist digital technologies are presented in a way approachable to non-scientists, while a separate technical section provides details of methods and techniques, alongside examples of notable applications of spatial and spectral documentation of material cultural heritage, with selected literature and identification of future research. This book is an outcome of interdisciplinary research and debates conducted by the participants of the COST Action TD1201, Colour and Space in Cultural Heritage, 2012–16 and is an Open Access publication available under a CC BY-NC-ND licence.https://scholarworks.wmich.edu/mip_arc_cdh/1000/thumbnail.jp

Coherent X-ray di�ffraction imaging of zinc oxide crystals

Zinc Oxide (ZnO) exhibits a plethora of physical properties potentially advantageous in many roles and is why it one of the most studied semiconductor compounds. When doped or in its intrinsic state ZnO demonstrates a multitude of electronic, optical and magnetic properties in a large variety of manufacturable morphologies. Thus it is inherently important to understand why these properties arise and the impact potentially invasive sample preparation methods have for both the function and durability of the material and its devices. Coherent X-ray Diff�raction Imaging (CXDI) is a recently established non-destructive technique which can probe the whole three dimensional structure of small crystalline materials and has the potential for sub angstrom strain resolution. The iterative methods employed to overcome the `phase problem' are described fully. CXDI studies of wurtzite ZnO crystals in the rod morphology with high aspect ratio are presented. ZnO rods synthesised via Chemical Vapour Transport Deposition were studied in post growth state and during in-situ modifi�cation via metal evaporation processing and annealing. Small variations in post growth state were observed, the physical origin of which remains unidentifi�ed. The doping of a ZnO crystal with Iron, Nickel and Cobalt by thermal evaporation and subsequent annealing was studied. The evolution of diff�using ions into the crystal lattice from was not observed, decomposition was found to be the dominant process. Improvements in experimental technique allowed multiple Bragg reflections from a single ZnO crystal to be measured for the fi�rst time. Large aspect ratio ZnO rods were used to probe the coherence properties of the incident beam. The longitudinal coherence function of the illuminating radiation was mapped using the visibility of the interference pattern at each bragg reflection and an accurate estimate of the longitudinal coherence length obtained, \xi(L) = 0.66\pm 0.02 \mu m. The consequences for data analysis are discussed. The combination of multiple Bragg reflections to realise three dimensional displacement �fields was also approached

Microscopy Conference 2021 (MC 2021) - Proceedings

Das Dokument enthält die Kurzfassungen der Beiträge aller Teilnehmer an der Mikroskopiekonferenz "MC 2021"