SSTRED: A data-processing and metadata-generating pipeline for CHROMIS and CRISP

We present a data pipeline for the newly installed SST/CHROMIS imaging spectrometer, as well as for the older SST/CRISP spectropolarimeter. The aim is to provide observers with a user-friendly data pipeline, that delivers science-ready data with the metadata needed for archival. We generalized the CRISPRED data pipeline for multiple instruments and added metadata according to recommendations worked out as part of the SOLARNET project. We made improvements to several steps in the pipeline, including the MOMFBD image restoration. A part of that is a new fork of the MOMFBD program called REDUX, with several new features that are needed in the new pipeline. The CRISPEX data viewer has been updated to accommodate data cubes stored in this format. The pipeline code, as well as REDUX and CRISPEX are all freely available through git repositories or web download. We derive expressions for combining statistics of individual frames into statistics for a set of frames. We define a new extension to the World Coordinate System, that allow us to specify cavity errors as distortions to the spectral coordinate.Comment: Draf

Estimating individual muscle forces in human movement

If individual muscle forces could be routinely calculated in vivo, non-invasively, considerable insight could be obtained into the etiology of injuries and the training of muscle for rehabilitation and sport. As there are generally more muscles crossing a joint than there are degrees of freedom at the joint, determining the individual forces in the muscles crossing a joint is a non-trivial problem. This study focused on the development of the procedures necessary to estimate the individual muscle forces during a dumbell curl, and the measurement procedures required for the determination of the necessary input parameters. The procedures developed could easily be applied to other body movements. [Continues.

Optical Coherence Tomography guided Laser-Cochleostomy

Despite the high precision of laser, it remains challenging to control the laser-bone ablation without injuring the underlying critical structures. Providing an axial resolution on micrometre scale, OCT is a promising candidate for imaging microstructures beneath the bone surface and monitoring the ablation process. In this work, a bridge connecting these two technologies is established. A closed-loop control of laser-bone ablation under the monitoring with OCT has been successfully realised

Advanced experimental methods for the characterization of welded structures

Welding is one of the most prevalent techniques for mechanical fastening of metals. Recent developments in welding technology have led to welding techniques being more readily employed in safety-critical engineering structures. Since the existence of residual stresses and material property variation around welds affects the mechanical performance and thereby structural integrity, it is essential to improve our knowledge in understanding and modelling the mechanical response of the welded structures. The present work focuses on mechanical characterizations of such structures. This work can be broadly classified into two parts; the first part investigates the residual stress distribution in welded specimens of different metals and the second part presents investigations of mechanical properties in welded specimen using full field optical techniques. A newly invented destructive technique for residual stress measurement, the contour method, was used for the investigations of the residual stress in welded joints in this study. The principle of the contour method is based on a variation of Bueckner's superposition theory. By means of a single straight cut, the 2D residual stress component normal to the region of interest can be determined. In this work, first the numerical simulations of the contour method using two and three dimensional bodies have been demonstrated. The contour method was then applied to one-pass and three-pass groove weld specimens and the results obtained from the contour method were compared to those obtained by the neutron diffraction strain measurement technique. The capability of the contour method to measure multiple residual stress components was also investigated in this project. A recent development of the contour method of stress measurement, the multi-axial contour method, permits measurement of the 3D residual stress distribution in a body, based on the assumption that the residual stresses are due to an inelastic misfit strain (eigenstrain) that does not change when a sample containing residual stresses is sectioned. The eigenstrain is derived from measured displacements due to residual stress relaxation when the specimen is sectioned. By carrying out multiple cuts, the full residual stress tensor in a continuously processed body can then be determined. In this study, finite element simulations of the technique were carried out to verify the method numerically. The method was then used to determine the residual stresses in a VPP A-welded sample, and the results were validated by neutron diffraction measurements. As part of the characterization of the welded structures, a study was undertaken to develop a method of extracting local mechanical properties from weld metal by strain mapping using the digital image correlation (DIC) technique. The feasibility of determining local stress-strain behaviour in the weld zone of a 316H stainless steel pipe with a girth weld was investigated by tensile tests on miniature and standard tensile test specimens. In addition, electron speckle pattern interferometry (ESPI) was utilized to obtain the full-field strain maps of a standard tensile specimen during loading and compared to those obtained in the same specimen by digital image correlation in order to verify the DIC measurements

Automatic reconstruction from serial sections

In many experiments in biological and medical research, serial sectioning of biological material is the only way to reveal the three dimensional (3D) structure and function. For a number of reasons other 3D imaging techniques, such as CT, MRI, and confocal microscopy, are not always adequate because they cannot provide the necessary resolution or contrast, or because the specimen is too large, or because the staining techniques require sectioning. Therefore for the foreseeable future reconstruction from serial sections will remain the only method for 3D investigations in many biomedical fields. Reconstruction is a difficult problem due to the loss of 3D alignment as the sections are cut and, more seriously, the systematic and random distortion caused by the sectioning and preparation processes.Many authors have reported how serial sections can be registered by means of fiducial markers or otherwise, but there have been only a few studies of automated correction of the sectioning distortions. In this thesis solutions to the registration problem are reviewed and discussed, and a solution to the warping problem, based on image pro¬ cessing techniques and the finite element method (FEM), is presented. The aim of this project was to develop a fully automatic method of reconstruction in order to provide a 3D atlas of mouse development as part of a gene expression database. For this purpose it is not necessary to warp the object so that it is identical to the original object, but to correct local distortions in the sections in order to produce a smooth representative mouse embryo. Furthermore the use of fiducial markers was not possible because the reconstructions were from already sectioned material.In this thesis we demonstrate a new method for warping serial sections. The sections are warped by applying forces to each section, where each section is modelled as a thin elastic plate. The deformation forces are determined from correspondences between sections which are calculated by combining match strengths and positional information. The equilibrium state which represents the reconstructed 3D image is calculated using the finite element method. Results of the application of these methods to paraffin wax and resin embedded sections of the mouse embryo are presented

Computed Tomography of Chemiluminescence: A 3D Time Resolved Sensor for Turbulent Combustion

Time resolved 3D measurements of turbulent flames are required to further understanding of combustion and support advanced simulation techniques (LES). Computed Tomography of Chemiluminescence (CTC) allows a flame’s 3D chemiluminescence profile to be obtained by inverting a series of integral measurements. CTC provides the instantaneous 3D flame structure, and can also measure: excited species concentrations, equivalence ratio, heat release rate, and possibly strain rate. High resolutions require simultaneous measurements from many view points, and the cost of multiple sensors has traditionally limited spatial resolutions. However, recent improvements in commodity cameras makes a high resolution CTC sensor possible and is investigated in this work. Using realistic LES Phantoms (known fields), the CT algorithm (ART) is shown to produce low error reconstructions even from limited noisy datasets. Error from selfabsorption is also tested using LES Phantoms and a modification to ART that successfully corrects this error is presented. A proof-of-concept experiment using 48 non-simultaneous views is performed and successfully resolves a Matrix Burner flame to 0.01% of the domain width (D). ART is also extended to 3D (without stacking) to allow 3D camera locations and optical effects to be considered. An optical integral geometry (weighted double-cone) is presented that corrects for limited depth-of-field, and (even with poorly estimated camera parameters) reconstructs the Matrix Burner as well as the standard geometry. CTC is implemented using five PicSight P32M cameras and mirrors to provide 10 simultaneous views. Measurements of the Matrix Burner and a Turbulent Opposed Jet achieve exposure times as low as 62 μs, with even shorter exposures possible. With only 10 views the spatial resolution of the reconstructions is low. However, a cosine Phantom study shows that 20–40 viewing angles are necessary to achieve high resolutions (0.01– 0.04D). With 40 P32M cameras costing £40000, future CTC implementations can achieve high spatial and temporal resolutions

Weak Gravitational Lensing by Large-Scale Structures:A Tool for Constraining Cosmology

There is now very strong evidence that our Universe is undergoing an accelerated expansion period as if it were under the influence of a gravitationally repulsive “dark energy” component. Furthermore, most of the mass of the Universe seems to be in the form of non-luminous matter, the so-called “dark matter”. Together, these “dark” components, whose nature remains unknown today, represent around 96 % of the matter-energy budget of the Universe. Unraveling the true nature of the dark energy and dark matter has thus, obviously, become one of the primary goals of present-day cosmology. Weak gravitational lensing, or weak lensing for short, is the effect whereby light emitted by distant galaxies is slightly deflected by the tidal gravitational fields of intervening foreground structures. Because it only relies on the physics of gravity, weak lensing has the unique ability to probe the distribution of mass in a direct and unbiased way. This technique is at present routinely used to study the dark matter, typical applications being the mass reconstruction of galaxy clusters and the study of the properties of dark halos surrounding galaxies. Another and more recent application of weak lensing, on which we focus in this thesis, is the analysis of the cosmological lensing signal induced by large-scale structures, the so-called “cosmic shear”. This signal can be used to measure the growth of structures and the expansion history of the Universe, which makes it particularly relevant to the study of dark energy. Of all weak lensing effects, the cosmic shear is the most subtle and its detection requires the accurate analysis of the shapes of millions of distant, faint galaxies in the near infrared. So far, the main factor limiting cosmic shear measurement accuracy has been the relatively small sky areas covered. Next-generation of wide-field, multicolor surveys will, however, overcome this hurdle by covering a much larger portion of the sky with improved image quality. The resulting statistical errors will then become subdominant compared to systematic errors, the latter becoming instead the main source of uncertainty. In fact, uncovering key properties of dark energy will only be achievable if these systematics are well understood and reduced to the required level. The major sources of uncertainty resides in the shape measurement algorithm used, the convolution of the original image by the instrumental and possibly atmospheric point spread function (PSF), the pixelation effect caused by the integration of light falling on the detector pixels and the degradation caused by various sources of noise. Measuring the Cosmic shear thus entails solving the difficult inverse problem of recovering the shear signal from blurred, pixelated and noisy galaxy images while keeping errors within the limits demanded by future weak lensing surveys. Reaching this goal is not without challenges. In fact, the best available shear measurement methods would need a tenfold improvement in accuracy to match the requirements of a space mission like Euclid from ESA, scheduled at the end of this decade. Significant progress has nevertheless been made in the last few years, with substantial contributions from initiatives such as GREAT (GRavitational lEnsing Accuracy Testing) challenges. The main objective of these open competitions is to foster the development of new and more accurate shear measurement methods. We start this work with a quick overview of modern cosmology: its fundamental tenets, achievements and the challenges it faces today. We then review the theory of weak gravitational lensing and explains how it can make use of cosmic shear observations to place constraints on cosmology. The last part of this thesis focuses on the practical challenges associated with the accurate measurement of the cosmic shear. After a review of the subject we present the main contributions we have brought in this area: the development of the gfit shear measurement method, new algorithms for point spread function (PSF) interpolation and image denoising. The gfit method emerged as one of the top performers in the GREAT10 Galaxy Challenge. It essentially consists in fitting two-dimensional elliptical Sérsic light profiles to observed galaxy image in order to produce estimates for the shear power spectrum. PSF correction is automatic and an efficient shape-preserving denoising algorithm can be optionally applied prior to fitting the data. PSF interpolation is also an important issue in shear measurement because the PSF is only known at star positions while PSF correction has to be performed at any position on the sky. We have developed innovative PSF interpolation algorithms on the occasion of the GREAT10 Star Challenge, a competition dedicated to the PSF interpolation problem. Our participation was very successful since one of our interpolation method won the Star Challenge while the remaining four achieved the next highest scores of the competition. Finally we have participated in the development of a wavelet-based, shape-preserving denoising method particularly well suited to weak lensing analysis

Three-dimensional morphanalysis of the face.

The aim of the work reported in this thesis was to determine the extent to which orthogonal two-dimensional morphanalytic (universally relatable) craniofacial imaging methods can be extended into the realm of computer-based three-dimensional imaging. New methods are presented for capturing universally relatable laser-video surface data, for inter-relating facial surface scans and for constructing probabilistic facial averages. Universally relatable surface scans are captured using the fixed relations principle com- bined with a new laser-video scanner calibration method. Inter- subject comparison of facial surface scans is achieved using inter- active feature labelling and warping methods. These methods have been extended to groups of subjects to allow the construction of three-dimensional probabilistic facial averages. The potential of universally relatable facial surface data for applications such as growth studies and patient assessment is demonstrated. In addition, new methods for scattered data interpolation, for controlling overlap in image warping and a fast, high-resolution method for simulating craniofacial surgery are described. The results demonstrate that it is not only possible to extend universally relatable imaging into three dimensions, but that the extension also enhances the established methods, providing a wide range of new applications