A method for the visualization of high phase gradients in a microscopic image

Holografická mikroskopie je nekonvenční mikroskopická technika, vhodná zvláště pro vzorky s malou optickou hustotou, která umožňuje zviditelnit index lomu pozorovaných objektů. Na Ústavu fyzikálního inženýrství Fakulty strojního inženýrství VUT v Brně byl sestrojen unikátní transmisní digitální holografický mikroskop (TDHM). Pořízené snímky (hologramy) jsou zpracovány metodou založenou na Fourierově ransformaci, čímž je zrekonstruována intenzita a fáze světelné vlny procházející pozorovaným objektem. Fáze popisuje index lomu a tloušťku pozorovaného objektu. V místech, kde se mění index lomu nebo tloušťka, dochází i ke změně fáze. Úkolem této bakalářské práce bylo najít metodu pro zviditelnění míst s vysokým gradientem fáze. Podařilo se vytvořit metodu, která nevyžaduje navazování fáze, a proto je vhodná pro libovolné obrazy pořízené TDHM. Tato metoda byla implementována do počítačového programu Gradient3D, který kromě výpočtu gradientu ve dvou a třech rozměrech umožňuje i vytváření barevných obrazů, jejichž složkami jsou kombinace intenzity, fáze a gradientu. Program též umožňuje odstranění falešných gradientů v místech s nízkou intenzitou, kde je hodnota fáze nespolehlivá. Program byl testován na několika souborech hologramů pořízených TDHM při pozorování biologických vzorků.Holographic microscopy is an unconventional microscopy technique suitable especially for transparent samples. It enables to visualize the refractive index of observed objects. A unique transmitted-light digital holographic microscope (TDHM) has been constructed at Institute of Physical Engineering, Faculty of Mechanical Engineering, Brno University of Technology. Holograms captured by the microscope are processed by means of a technique based on the Fourier transform in order to reconstruct the intensity and phase of the light waves passing through the observed object. The phase describes the object refractive index and thickness. In places where the object refractive index or thickness changes, also the phase does. The task of this bachelor thesis was to find a method for visualizing places with high phase gradient. A gradient computation method which was created does not require phase unwrapping and is therefore suitable generally for any images. The method was implemented in a computer software called Gradient3D, which enables not only to compute the phase gradient in two and three dimensions, but also to create color images composed from combinations of intensity, phase and gradient. It also contains methods for handling places with low reconstructed intensity where the phase value is unreliable and usually causes false phase gradients. The program has been tested on several image sets from the TDHM capturing biological specimens.

The Influence of Magnetic Field on Oscillations in the Solar Chromosphere

Two sequences of solar images obtained by the Transition Region and Coronal Explorer in three UV passbands are studied using wavelet and Fourier analysis and compared to the photospheric magnetic flux measured by the Michelson Doppler Interferometer on the Solar Heliospheric Observatory to study wave behaviour in differing magnetic environments. Wavelet periods show deviations from the theoretical cutoff value and are interpreted in terms of inclined fields. The variation of wave speeds indicates that a transition from dominant fast-magnetoacoustic waves to slow modes is observed when moving from network into plage and umbrae. This implies preferential transmission of slow modes into the upper atmosphere, where they may lead to heating or be detected in coronal loops and plumes.Comment: 8 pages, 6 figures (4 colour online only), accepted for publication in The Astrophysical Journa

PHACT: parallel HOG and correlation tracking

Histogram of Oriented Gradients (HOG) based methods for the detection of humans have become one of the most reliable methods of detecting pedestrians with a single passive imaging camera. However, they are not 100 percent reliable. This paper presents an improved tracker for the monitoring of pedestrians within images. The Parallel HOG and Correlation Tracking (PHACT) algorithm utilises self learning to overcome the drifting problem. A detection algorithm that utilises HOG features runs in parallel to an adaptive and stateful correlator. The combination of both acting in a cascade provides a much more robust tracker than the two components separately could produce. © (2014) COPYRIGHT Society of Photo-Optical Instrumentation Engineers (SPIE). Downloading of the abstract is permitted for personal use only

Observation of force-detected nuclear magnetic resonance in a homogeneous field

We report the experimental realization of BOOMERANG (better observation of magnetization, enhanced resolution, and no gradient), a sensitive and general method of magnetic resonance. The prototype millimeter-scale NMR spectrometer shows signal and noise levels in agreement with the design principles. We present H-1 and F-19 NMR in both solid and liquid samples, including time-domain Fourier transform NMR spectroscopy, multiple-pulse echoes, and heteronuclear J spectroscopy. By measuring a H-1-F-19 J coupling, this last experiment accomplishes chemically specific spectroscopy with force-detected NMR. In BOOMERANG, an assembly of permanent magnets provides a homogeneous field throughout the sample, while a harmonically suspended part of the assembly, a detector, is mechanically driven by spin-dependent forces. By placing the sample in a homogeneous field, signal dephasing by diffusion in a field gradient is made negligible, enabling application to liquids, in contrast to other force-detection methods. The design appears readily scalable to µm-scale samples where it should have sensitivity advantages over inductive detection with microcoils and where it holds great promise for application of magnetic resonance in biology, chemistry, physics, and surface science. We briefly discuss extensions of the BOOMERANG method to the µm and nm scales

The instanton method and its numerical implementation in fluid mechanics

A precise characterization of structures occurring in turbulent fluid flows at high Reynolds numbers is one of the last open problems of classical physics. In this review we discuss recent developments related to the application of instanton methods to turbulence. Instantons are saddle point configurations of the underlying path integrals. They are equivalent to minimizers of the related Freidlin-Wentzell action and known to be able to characterize rare events in such systems. While there is an impressive body of work concerning their analytical description, this review focuses on the question on how to compute these minimizers numerically. In a short introduction we present the relevant mathematical and physical background before we discuss the stochastic Burgers equation in detail. We present algorithms to compute instantons numerically by an efficient solution of the corresponding Euler-Lagrange equations. A second focus is the discussion of a recently developed numerical filtering technique that allows to extract instantons from direct numerical simulations. In the following we present modifications of the algorithms to make them efficient when applied to two- or three-dimensional fluid dynamical problems. We illustrate these ideas using the two-dimensional Burgers equation and the three-dimensional Navier-Stokes equations

Fourier Magnetic Imaging with Nanoscale Resolution and Compressed Sensing Speed-up using Electronic Spins in Diamond

Optically-detected magnetic resonance using Nitrogen Vacancy (NV) color centres in diamond is a leading modality for nanoscale magnetic field imaging, as it provides single electron spin sensitivity, three-dimensional resolution better than 1 nm, and applicability to a wide range of physical and biological samples under ambient conditions. To date, however, NV-diamond magnetic imaging has been performed using real space techniques, which are either limited by optical diffraction to 250 nm resolution or require slow, point-by-point scanning for nanoscale resolution, e.g., using an atomic force microscope, magnetic tip, or super-resolution optical imaging. Here we introduce an alternative technique of Fourier magnetic imaging using NV-diamond. In analogy with conventional magnetic resonance imaging (MRI), we employ pulsed magnetic field gradients to phase-encode spatial information on NV electronic spins in wavenumber or k-space followed by a fast Fourier transform to yield real-space images with nanoscale resolution, wide field-of-view (FOV), and compressed sensing speed-up.Comment: 31 pages, 10 figure

Adjustment of a turbulent boundary layer to a 'canopy' of roughness elements

A model is developed for the adjustment of the spatially averaged time-mean flow of a deep turbulent boundary layer over small roughness elements to a canopy of larger three-dimensional roughness elements. Scaling arguments identify three stages of the adjustment. First, the drag and the finite volumes of the canopy elements decelerate air parcels; the associated pressure gradient decelerates the flow within an impact region upwind of the canopy. Secondly, within an adjustment region of length of order Lc downwind of the leading edge of the canopy, the flow within the canopy decelerates substantially until it comes into a local balance between downward transport of momentum by turbulent stresses and removal of momentum by the drag of the canopy elements. The adjustment length, Lc, is proportional to (i) the reciprocal of the roughness density (defined to be the frontal area of canopy elements per unit floor area) and (ii) the drag coefficient of individual canopy elements. Further downstream, within a roughness-change region, the canopy is shown to affect the flow above as if it were a change in roughness length, leading to the development of an internal boundary layer. A quantitative model for the adjustment of the flow is developed by calculating analytically small perturbations to a logarithmic turbulent velocity profile induced by the drag due to a sparse canopy with L/Lc≪1, where L is the length of the canopy. These linearized solutions are then evaluated numerically with a nonlinear correction to account for the drag varying with the velocity. A further correction is derived to account for the finite volume of the canopy elements. The calculations are shown to agree with experimental measurements in a fine-scale vegetation canopy, when the drag is more important than the finite volume effects, and a canopy of coarse-scale cuboids, when the finite volume effects are of comparable importance to the drag in the impact region. An expression is derived showing how the effective roughness length of the canopy, \z0eff, is related to the drag in the canopy. The value of \z0eff varies smoothly with fetch through the adjustment region from the roughness length of the upstream surface to the equilibrium roughness length of the canopy. Hence, the analysis shows how to resolve the unphysical flow singularities obtained with previous models of flow over sudden changes in surface roughness