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- ItemDenoising for Improved Parametric MRI of the Kidney: Protocol for Nonlocal Means Filtering(Totowa, NJ : Humana Press, 2021) Starke, Ludger; Tabelow, Karsten; Niendorf, Thoralf; Pohlmann, Andreas; Pohlmann, Andreas; Niendorf, ThoralfIn order to tackle the challenges caused by the variability in estimated MRI parameters (e.g., T2* and T2) due to low SNR a number of strategies can be followed. One approach is postprocessing of the acquired data with a filter. The basic idea is that MR images possess a local spatial structure that is characterized by equal, or at least similar, noise-free signal values in vicinities of a location. Then, local averaging of the signal reduces the noise component of the signal. In contrast, nonlocal means filtering defines the weights for averaging not only within the local vicinity, bur it compares the image intensities between all voxels to define “nonlocal” weights. Furthermore, it generally compares not only single-voxel intensities but small spatial patches of the data to better account for extended similar patterns. Here we describe how to use an open source NLM filter tool to denoise 2D MR image series of the kidney used for parametric mapping of the relaxation times T2* and T2. This chapter is based upon work from the COST Action PARENCHIMA, a community-driven network funded by the European Cooperation in Science and Technology (COST) program of the European Union, which aims to improve the reproducibility and standardization of renal MRI biomarkers.
- ItemSpin pumping at interfaces with ferro- and paramagnetic Fe60Al40films acting as spin source and spin sink(Melville, NY : American Inst. of Physics, 2022) Strusch, T.; Lenz, K.; Meckenstock, R.; Bali, R.; Ehrler, J.; Lindner, J.; Fassbender, J.; Farle, M.; Potzger, K.; Semisalova, A.We present a study of spin pumping efficiency and determine the spin mixing conductance and spin diffusion length in thin bilayer films based on 3d transition metal alloy Fe60Al40. Due to its magnetostructural phase transition, Fe60Al40 can be utilized as a ferromagnetic (FM) or paramagnetic (PM) material at the same temperature depending on its structural order; thus a thin Fe60Al40 film can act as a spin source or a spin sink when interfaced with a paramagnet or a ferromagnet, respectively. Ferromagnetic resonance measurements were performed in a frequency range of 5-35 GHz on bilayer films composed of FM-Fe60Al40/Pd and PM-Fe60Al40/Ni80Fe20 (permalloy). The increase in damping with the thickness of the paramagnetic layer was interpreted as a result of spin pumping into the paramagnet. We determine the spin mixing conductance g P d ↑↓ = (3.8 ± 0.5) × 10 18 m - 2 at the FM-Fe60Al40/Pd interface and the spin diffusion length λ P d = 9.1 ± 2.0 nm in Pd. For the PM-Fe60Al40/permalloy interface, we find a spin mixing conductance g F e A l ↑↓ = (2.1 ± 0.2) × 10 18 m - 2 and a spin diffusion length λ F e A l = 11.9 ± 0.2 nm for PM-Fe60Al40. The demonstrated bi-functionality of the Fe60Al40 alloy in spin pumping structures may be promising for spintronic applications.
- ItemHigh photon count rates improve the quality of super-resolution fluorescence fluctuation spectroscopy(Bristol : IOP Publ., 2020) Schneider, Falk; Hernandez-Varas, Pablo; Lagerholm, B. Christoffer; Shrestha, Dilip; Sezgin, Erdinc; Roberti, M. Julia; Ossato, Giulia; Hecht, Frank; Eggeling, Christian; Urbančič, IztokProbing the diffusion of molecules has become a routine measurement across the life sciences, chemistry and physics. It provides valuable insights into reaction dynamics, oligomerisation, molecular (re-)organisation or cellular heterogeneities. Fluorescence correlation spectroscopy (FCS) is one of the widely applied techniques to determine diffusion dynamics in two and three dimensions. This technique relies on the temporal autocorrelation of intensity fluctuations but recording these fluctuations has thus far been limited by the detection electronics, which could not efficiently and accurately time-tag photons at high count rates. This has until now restricted the range of measurable dye concentrations, as well as the data quality of the FCS recordings, especially in combination with super-resolution stimulated emission depletion (STED) nanoscopy. Here, we investigate the applicability and reliability of (STED-)FCS at high photon count rates (average intensities of more than 1 MHz) using novel detection equipment, namely hybrid detectors and real-time gigahertz sampling of the photon streams implemented on a commercial microscope. By measuring the diffusion of fluorophores in solution and cytoplasm of live cells, as well as in model and cellular membranes, we show that accurate diffusion and concentration measurements are possible in these previously inaccessible high photon count regimes. Specifically, it offers much greater flexibility of experiments with biological samples with highly variable intensity, e.g. due to a wide range of expression levels of fluorescent proteins. In this context, we highlight the independence of diffusion properties of cytosolic GFP in a concentration range of approx. 0.01-1 µm. We further show that higher photon count rates also allow for much shorter acquisition times, and improved data quality. Finally, this approach also pronouncedly increases the robustness of challenging live cell STED-FCS measurements of nanoscale diffusion dynamics, which we testify by confirming a free diffusion pattern for a fluorescent lipid analogue on the apical membrane of adherent cells. © The Author(s). Published by IOP Publishing Ltd.
- ItemCarbon and Neon Ion Bombardment Induced Smoothing and Surface Relaxation of Titania Nanotubes(Basel : MDPI, 2021) Kupferer, Astrid; Mensing, Michael; Lehnert, Jan; Mändl, Stephan; Mayr, Stefan G.Titania nanotube arrays with their enormous surface area are the subject of much attention in diverse fields of research. In the present work, we show that not only 60 keV and 150 keV ion bombardment of amorphous titania nanotube arrays yields defect creation within the tube walls, but it also changes the surface morphology: the surface relaxes and smoothens in accordance with a curvature-driven surface material’s transport mechanism, which is mediated by radiation-induced viscous flow or radiation-enhanced surface diffusion, while the nanotubes act as additional sinks for the particle surface currents. These effects occur independently of the ion species: both carbon and neon ion bombardments result in comparable surface relaxation responses initiated by an ion energy of 60 keV at a fluence of 1 × 1016 ions/cm2. Using atomic force microscopy and contact angle measurements, we thoroughly study the relaxation effects on the surface topography and surface free energy, respectively. Moreover, surface relaxation is accompanied by further amorphization in surface-near regions and a reduction in the mass density, as demonstrated by Raman spectroscopy and X-ray reflectivity. Since ion bombardment can be performed on global and local scales, it constitutes a versatile tool to achieve well-defined and tunable topographies and distinct surface characteristics. Hence, different types of nanotube arrays can be modified for various applications.
- ItemTRAIT2D: a Software for Quantitative Analysis of Single Particle Diffusion Data(London : F1000 Research Ltd, 2021) Reina, Francesco; Wigg, John M.A.; Dmitrieva, Mariia; Lefebvre, Joël; Rittscher, Jens; Eggeling, ChristianSingle particle tracking (SPT) is one of the most widely used tools in optical microscopy to evaluate particle mobility in a variety of situations, including cellular and model membrane dynamics. Recent technological developments, such as Interferometric Scattering microscopy, have allowed recording of long, uninterrupted single particle trajectories at kilohertz framerates. The resulting data, where particles are continuously detected and do not displace much between observations, thereby do not require complex linking algorithms. Moreover, while these measurements offer more details into the short-term diffusion behaviour of the tracked particles, they are also subject to the influence of localisation uncertainties, which are often underestimated by conventional analysis pipelines. we thus developed a Python library, under the name of TRAIT2D (Tracking Analysis Toolbox – 2D version), in order to track particle diffusion at high sampling rates, and analyse the resulting trajectories with an innovative approach. The data analysis pipeline introduced is more localisation-uncertainty aware, and also selects the most appropriate diffusion model for the data provided on a statistical basis. A trajectory simulation platform also allows the user to handily generate trajectories and even synthetic time-lapses to test alternative tracking algorithms and data analysis approaches. A high degree of customisation for the analysis pipeline, for example with the introduction of different diffusion modes, is possible from the source code. Finally, the presence of graphical user interfaces lowers the access barrier for users with little to no programming experience.
- ItemPseudo-chemotaxis of active Brownian particles competing for food(San Francisco, California, US : PLOS, 2020) Merlitz, Holger; Vuijk, Hidde D.; Wittmann, René; Sharma, Abhinav; Sommer, Jens-UweActive Brownian particles (ABPs) are physical models for motility in simple life forms and easily studied in simulations. An open question is to what extent an increase of activity by a gradient of fuel, or food in living systems, results in an evolutionary advantage of actively moving systems such as ABPs over non-motile systems, which rely on thermal diffusion only. It is an established fact that within confined systems in a stationary state, the activity of ABPs generates density profiles that are enhanced in regions of low activity, which is thus referred to as ‘anti-chemotaxis’. This would suggest that a rather complex sensoric subsystem and information processing is a precondition to recognize and navigate towards a food source. We demonstrate in this work that in non-stationary setups, for instance as a result of short bursts of fuel/food, ABPs do in fact exhibit chemotactic behavior. In direct competition with inactive, but otherwise identical Brownian particles (BPs), the ABPs are shown to fetch a larger amount of food. We discuss this result based on simple physical arguments. From the biological perspective, the ability of primitive entities to move in direct response to the available amount of external energy would, even in absence of any sensoric devices, encompass an evolutionary advantage.