Phase reconstruction from velocity-encoded MRI measurements--a survey of sparsity-promoting variational approaches

Physics-informed compressed sensing for PC-MRI: an inverse Navier-Stokes problem

We formulate a physics-informed compressed sensing (PICS) method for the reconstruction of velocity fields from noisy and sparse phase-contrast magnetic resonance signals. The method solves an inverse Navier-Stokes boundary value problem, which permits us to jointly reconstruct and segment the velocity field, and at the same time infer hidden quantities such as the hydrodynamic pressure and the wall shear stress. Using a Bayesian framework, we regularize the problem by introducing a priori information about the unknown parameters in the form of Gaussian random fields. This prior information is updated using the Navier-Stokes problem, an energy-based segmentation functional, and by requiring that the reconstruction is consistent with the k-space signals. We create an algorithm that solves this inverse problem, and test it for noisy and sparse k-space signals of the flow through a converging nozzle. We find that the method is capable of reconstructing and segmenting the velocity fields from sparsely-sampled (15% k-space coverage), low (~10) signal-to-noise ratio (SNR) signals, and that the reconstructed velocity field compares well with that derived from fully-sampled (100% k-space coverage) high (>40) SNR signals of the same flow.

Integrating Pore-Scale Flow MRI and X-ray μCT for Validation of Numerical Flow Simulations in Porous Sedimentary Rocks

Single-phase fluid flow velocity maps in Ketton and Estaillades carbonate rock core plugs are computed at a pore scale, using the lattice Boltzmann method (LBM) simulations performed directly on three-dimensional (3D) X-ray micro-computed tomography (µCT) images (≤ 7 µm spatial resolution) of the core plugs. The simulations are then benchmarked on a voxel-by-voxel and pore-by-pore basis to quantitative, 3D spatially resolved magnetic resonance imaging (MRI) flow velocity maps, acquired at 35 µm isotropic spatial resolution for flow of water through the same rock samples. Co-registration of the 3D experimental and simulated velocity maps and coarse-graining of the simulation to the same resolution as the experimental data allowed the data to be directly compared. First, the results are demonstrated for Ketton limestone rock, for which good qualitative and quantitative agreement was found between the simulated and experimental velocity maps. The flow-carrying microstructural features in Ketton rock are mostly larger than the spatial resolution of the µCT images, so that the segmented images are an adequate representation of the pore space. Second, the flow data are presented for Estaillades limestone, which presents a more heterogeneous case with microstructural features below the spatial resolution of the µCT images. Still, many of the complex flow patterns were qualitatively reproduced by the LBM simulation in this rock, although in some pores, noticeable differences between the LBM and MRI velocity maps were observed. It was shown that 80% of the flow (fractional summed z-velocities within pores) in the Estaillades rock sample is carried by just 10% of the number of macropores, which is an indication of the high structural heterogeneity of the rock; in the more homogeneous Ketton rock, 50% of the flow is carried by 10% of the macropores. By analysing the 3D MRI velocity map, it was found that approximately one-third of the total flow rate through the Estaillades rock is carried by microporosity—a porosity that is not captured at the spatial resolution of the µCT image.

Characterizing pore-scale structure-flow correlations in sedimentary rocks using magnetic resonance imaging

Quantitative, three-dimensional (3D) spatially resolved magnetic resonance flow imaging (flow MRI) methods are presented to characterize structure-flow correlations in a 4-mm-diameter plug of Ketton limestone rock using undersampled k- and q-space data acquisition methods combined with compressed sensing (CS) data reconstruction techniques. The acquired MRI data are coregistered with an X-ray microcomputed tomography (μCT) image of the same rock sample, allowing direct correlation of the structural features of the rock with local fluid transport characteristics. First, 3D velocity maps acquired at 35 μm isotropic spatial resolution showed that the flow was highly heterogeneous, with ∼10% of the pores carrying more than 50% of the flow. Structure-flow correlations were found between the local flow velocities through pores and the size and topology (coordination number) associated with these pores. These data show consistent trends with analogous data acquired for flow through a packing of 4-mm-diameter spheres, which may be due to the microstructure of Ketton rock being a consolidation of approximately spherical grains. Using two-dimensional and 3D visualization of coregistered μCT images and velocity maps, complex pore-scale flow patterns were identified. Second, 3D spatially resolved propagators were acquired at 94 μm isotropic spatial resolution. Flow dispersion within the rock was examined by analyzing each of the 331 776 local propagators as a function of observation time. Again, the heterogeneity of flow within the rock was shown. Quantification of the mean and standard deviation of each of the local propagators showed enhanced mixing occurring within the pore space at longer observation times. These spatially resolved measurements also enable investigation of the length scale of a representative elementary volume. It is shown that for a 4-mm-diameter plug this length scale is not reached.

Learning the Sampling Pattern for MRI

The discovery of the theory of compressed sensing brought the realisation that many inverse problems can be solved even when measurements are "incomplete". This is particularly interesting in magnetic resonance imaging (MRI), where long acquisition times can limit its use. In this work, we consider the problem of learning a sparse sampling pattern that can be used to optimally balance acquisition time versus quality of the reconstructed image. We use a supervised learning approach, making the assumption that our training data is representative enough of new data acquisitions. We demonstrate that this is indeed the case, even if the training data consists of just 7 training pairs of measurements and ground-truth images; with a training set of brain images of size 192 by 192, for instance, one of the learned patterns samples only 35% of k-space, however results in reconstructions with mean SSIM 0.914 on a test set of similar images. The proposed framework is general enough to learn arbitrary sampling patterns, including common patterns such as Cartesian, spiral and radial sampling.

Identification of sampling patterns for high-resolution compressed sensing MRI of porous materials: 'learning' from X-ray microcomputed tomography data

There exists a strong motivation to increase the spatial resolution of magnetic resonance imaging (MRI) acquisitions so that MRI can be used as a microscopy technique in the study of porous materials. This work introduces a method for identifying novel data sampling patterns to achieve undersampling schemes for compressed sensing MRI (CS-MRI) acquisitions, enabling 3D spatial resolutions of 17.6 µm to be achieved. A data-driven learning approach is used to derive k-space undersampling schemes for 3D MRI acquisitions from 3D X-ray microcomputed tomography (µCT) datasets acquired at a higher spatial resolution than can be acquired using MRI. The performance of the new sampling approach was compared to other, well-established sampling strategies using simulated MRI data obtained from high-resolution µCT images of rock core plugs. These simulations were performed for a range of different k-space sampling fractions (0.125-0.375) using images of Ketton limestone. The method was then extended to consideration of imaging Estaillades limestone and Fontainebleau sandstone. The results show that the new sampling approach performs as well as or better than conventional variable density sampling and without need for time-consuming parameter optimisation. Further, a bespoke sampling pattern is produced for each rock type. The novel undersampling strategy was employed to acquire 3D magnetic resonance images of a Ketton limestone rock at spatial resolutions of 35 and 17.6 µm. The ability of the k-space sampling scheme produced using the new approach in enabling reconstruction of the pore space characteristics of the rock was then demonstrated by benchmarking against the pore space statistics obtained from high-resolution µCT data. The MRI data acquired at 17.6 µm resolution gave excellent agreement with the pore size distribution obtained from the X-ray microcomputed tomography dataset, while the pore coordination number distribution obtained from the MRI data was slightly skewed to lower coordination numbers. This approach provides a method of producing a k-space undersampling pattern for MRI acquisition at a spatial resolution for which a fully sampled acquisition at that spatial resolution would be impractically long. The approach can be easily extended to other CS-MRI techniques, such as spatially resolved flow and relaxation time mapping. LAY DESCRIPTION: Magnetic resonance imaging (MRI) is widely used to study the microstructure of, and fluid transport phenomena in porous media relevant for engineering applications. A major application is the study of water and hydrocarbon transport in porous sedimentary rocks, which typically have pore sizes smaller than 100 µm. The spatial resolution of routine MRI acquisitions, however, is limited to several hundred µm due to the relatively low sensitivity of the magnetic resonance method. Therefore, there exists a strong motivation to increase the spatial resolution of MRI by one to two orders of magnitude to be able to study these rocks at a pore scale. This work reports the initial step towards achieving this. Three-dimensional images of rock pore structure are acquired at both 35 and 17.6 µm spatial resolution. In ongoing work, these methods are now being incorporated into magnetic resonance velocity imaging methods, thereby enabling imaging of both pore structure and hydrodynamics at these much higher spatial resolutions than were hitherto possible. Although X-ray microcomputed tomography (µCT) produces high spatial resolution images, it is far more limited in being able to spatially map transport processes (i.e. flow) in porous media. This work reports a strategy for accelerating the image acquisition time such that sufficient signal-to-noise ratio (SNR) is achieved to increase the spatial resolution, that is, the voxel size within which there is sufficient SNR within the resulting image. To achieve this, a technique known as compressed sensing is used which exploits undersampling of the acquired data relative to the standard fully sampled image. In MRI, data are acquired in so-called k-space and Fourier transformed to yield the real space image. The challenge, when undersampling, is to optimise the specific points in k-space that are acquired because these will influence the quality of the resulting image. This work reports a straightforward, robust strategy for identifying the optimal sets of k-space points to acquire. The method introduced uses simulated MRI images calculated from high-resolution µCT images of the rocks of interest, from which optimised MRI sampling patterns are obtained. The method does not require any optimisation of parameters for its implementation, which is a significant advantage compared to other strategies. Moreover, we show that the pore space characteristics of the acquired MRI images are in excellent agreement with the same characteristics obtained from a high-resolution µCT image.

Accelerating the estimation of 3D spatially resolved T2 distributions

Obtaining quantitative, 3D spatially-resolved T₂ distributions (T₂ maps) from magnetic resonance data is of importance in both medical and porous media applications. Due to the long acquisition time, there is considerable interest in accelerating the experiments by applying undersampling schemes during the acquisition and developing reconstruction techniques for obtaining the 3D T₂ maps from the undersampled data. A multi-echo spin echo pulse sequence is used in this work to acquire the undersampled data according to two different sampling patterns: a conventional coherent sampling pattern where the same set of lines in k-space is sampled for all equally-spaced echoes in the echo train, and a proposed incoherent sampling pattern where an independent set of k-space lines is sampled for each echo. The conventional reconstruction technique of total variation regularization is compared to the more recent techniques of nuclear norm regularization and Nuclear Total Generalized Variation (NTGV) regularization. It is shown that best reconstructions are obtained when the data acquired using an incoherent sampling scheme are processed using NTGV regularization. Using an incoherent sampling pattern and NTGV regularization as the reconstruction technique, quantitative results are obtained at sampling percentages as low as 3.1% of k-space, corresponding to a 32-fold decrease in the acquisition time, compared to a fully sampled dataset.

Acquisition of spatially-resolved displacement propagators using compressed sensing APGSTE-RARE MRI

A method is presented for accelerating the acquisition of spatially-resolved displacement propagators via under-sampling of an Alternating Pulsed Gradient Stimulated Echo - Rapid Acquisition with Relaxation Enhancement (APGSTE-RARE) data acquisition with compressed sensing image reconstruction. The method was demonstrated with respect to the acquisition of 2D spatially-resolved displacement propagators of water flowing through a packed bed of hollow cylinders. The q,k-space was under-sampled according to variable-density pseudo-random sampling patterns. The quality of compressed sensing reconstructions of spatially-resolved propagators at a range of sampling fractions was assessed using the peak signal-to-noise ratio (PSNR) as a quality metric. Propagators of good quality (PSNR 33.2 dB) were reconstructed from only 6.25% of all data points in q,k-space, resulting in a reduction in the data acquisition time from 4 h to 14 min. The spatially-resolved propagators were reconstructed using both the total variation and nuclear norm sparsifying transforms; use of total variation resulted in a slightly higher quality of the reconstructed image in most cases. To illustrate the power of this method to characterise heterogeneous flow in porous media, the method is applied to the characterisation of flow in a vuggy carbonate rock.

In Situ Chemically-Selective Monitoring of Multiphase Displacement Processes in a Carbonate Rock Using 3D Magnetic Resonance Imaging

Accurate monitoring of multiphase displacement processes is essential for the development, validation and benchmarking of numerical models used for reservoir simulation and for asset characterization. Here we demonstrate the first application of a chemically-selective 3D magnetic resonance imaging (MRI) technique which provides high-temporal resolution, quantitative, spatially resolved information of oil and water saturations during a dynamic imbibition core flood experiment in an Estaillades carbonate rock. Firstly, the relative saturations of dodecane (\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$S_{\mathrm{o}})$$\end{document}So) and water (\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$S_{\mathrm{w}})$$\end{document}Sw), as determined from the MRI measurements, have been benchmarked against those obtained from nuclear magnetic resonance (NMR) spectroscopy and volumetric analysis of the core flood effluent. Excellent agreement between both the NMR and MRI determinations of \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$S_{\mathrm{o}}$$\end{document}So and \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$S_{\mathrm{w}}$$\end{document}Sw was obtained. These values were in agreement to 4 and 9% of the values determined by volumetric analysis, with absolute errors in the measurement of saturation determined by NMR and MRI being 0.04 or less over the range of relative saturations investigated. The chemically-selective 3D MRI method was subsequently applied to monitor the displacement of dodecane in the core plug sample by water under continuous flow conditions at an interstitial velocity of \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$1.27\times 10^{-6}\,\hbox {m}\,\hbox {s}^{-1}$$\end{document}1.27×10-6ms-1 (\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$0.4\,\hbox {ft}\,\hbox {day}^{-1})$$\end{document}0.4ftday-1). During the core flood, independent images of water and oil distributions within the rock core plug at a spatial resolution of \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$0.31\,\hbox {mm}\times 0.39\,\hbox {mm} \times 0.39\,\hbox {mm}$$\end{document}0.31mm×0.39mm×0.39mm were acquired on a timescale of 16 min per image. Using this technique the spatial and temporal dynamics of the displacement process have been monitored. This MRI technique will provide insights to structure–transport relationships associated with multiphase displacement processes in complex porous materials, such as those encountered in petrophysics research.

Retaining both discrete and smooth features in 1D and 2D NMR relaxation and diffusion experiments

A new method of regularization of 1D and 2D NMR relaxation and diffusion experiments is proposed and a robust algorithm for its implementation is introduced. The new form of regularization, termed the Modified Total Generalized Variation (MTGV) regularization, offers a compromise between distinguishing discrete and smooth features in the reconstructed distributions. The method is compared to the conventional method of Tikhonov regularization and the recently proposed method of L₁ regularization, when applied to simulated data of 1D spin-lattice relaxation, T₁, 1D spin-spin relaxation, T₂, and 2D T₁-T₂ NMR experiments. A range of simulated distributions composed of two lognormally distributed peaks were studied. The distributions differed with regard to the variance of the peaks, which were designed to investigate a range of distributions containing only discrete, only smooth or both features in the same distribution. Three different signal-to-noise ratios were studied: 2000, 200 and 20. A new metric is proposed to compare the distributions reconstructed from the different regularization methods with the true distributions. The metric is designed to penalise reconstructed distributions which show artefact peaks. Based on this metric, MTGV regularization performs better than Tikhonov and L₁ regularization in all cases except when the distribution is known to only comprise of discrete peaks, in which case L₁ regularization is slightly more accurate than MTGV regularization.

Obtaining sparse distributions in 2D inverse problems

The mathematics of inverse problems has relevance across numerous estimation problems in science and engineering. L₁ regularization has attracted recent attention in reconstructing the system properties in the case of sparse inverse problems; i.e., when the true property sought is not adequately described by a continuous distribution, in particular in Compressed Sensing image reconstruction. In this work, we focus on the application of L₁ regularization to a class of inverse problems; relaxation-relaxation, T₁-T₂, and diffusion-relaxation, D-T₂, correlation experiments in NMR, which have found widespread applications in a number of areas including probing surface interactions in catalysis and characterizing fluid composition and pore structures in rocks. We introduce a robust algorithm for solving the L₁ regularization problem and provide a guide to implementing it, including the choice of the amount of regularization used and the assignment of error estimates. We then show experimentally that L₁ regularization has significant advantages over both the Non-Negative Least Squares (NNLS) algorithm and Tikhonov regularization. It is shown that the L₁ regularization algorithm stably recovers a distribution at a signal to noise ratio<20 and that it resolves relaxation time constants and diffusion coefficients differing by as little as 10%. The enhanced resolving capability is used to measure the inter and intra particle concentrations of a mixture of hexane and dodecane present within porous silica beads immersed within a bulk liquid phase; neither NNLS nor Tikhonov regularization are able to provide this resolution. This experimental study shows that the approach enables discrimination between different chemical species when direct spectroscopic discrimination is impossible, and hence measurement of chemical composition within porous media, such as catalysts or rocks, is possible while still being stable to high levels of noise.

Magnetic Resonance Imaging and Velocity Mapping in Chemical Engineering Applications

This review aims to illustrate the diversity of measurements that can be made using magnetic resonance techniques, which have the potential to provide insights into chemical engineering systems that cannot readily be achieved using any other method. Perhaps the most notable advantage in using magnetic resonance methods is that both chemistry and transport can be followed in three dimensions, in optically opaque systems, and without the need for tracers to be introduced into the system. Here we focus on hydrodynamics and, in particular, applications to rheology, pipe flow, and fixed-bed and gas-solid fluidized bed reactors. With increasing development of industrially relevant sample environments and undersampling data acquisition strategies that can reduce acquisition times to <1 s, magnetic resonance is finding increasing application in chemical engineering research.

Acceleration of the PDHGM on Partially Strongly Convex Functions

We propose several variants of the primal-dual method due to Chambolle and Pock. Without requiring full strong convexity of the objective functions, our methods are accelerated on subspaces with strong convexity. This yields mixed rates, O ( 1 / N 2 ) with respect to initialisation and O(1 / N) with respect to the dual sequence, and the residual part of the primal sequence. We demonstrate the efficacy of the proposed methods on image processing problems lacking strong convexity, such as total generalised variation denoising and total variation deblurring.

Accelerated high-resolution photoacoustic tomography via compressed sensing

Current 3D photoacoustic tomography (PAT) systems offer either high image quality or high frame rates but are not able to deliver high spatial and temporal resolution simultaneously, which limits their ability to image dynamic processes in living tissue (4D PAT). A particular example is the planar Fabry-Pérot (FP) photoacoustic scanner, which yields high-resolution 3D images but takes several minutes to sequentially map the incident photoacoustic field on the 2D sensor plane, point-by-point. However, as the spatio-temporal complexity of many absorbing tissue structures is rather low, the data recorded in such a conventional, regularly sampled fashion is often highly redundant. We demonstrate that combining model-based, variational image reconstruction methods using spatial sparsity constraints with the development of novel PAT acquisition systems capable of sub-sampling the acoustic wave field can dramatically increase the acquisition speed while maintaining a good spatial resolution: first, we describe and model two general spatial sub-sampling schemes. Then, we discuss how to implement them using the FP interferometer and demonstrate the potential of these novel compressed sensing PAT devices through simulated data from a realistic numerical phantom and through measured data from a dynamic experimental phantom as well as from in vivo experiments. Our results show that images with good spatial resolution and contrast can be obtained from highly sub-sampled PAT data if variational image reconstruction techniques that describe the tissues structures with suitable sparsity-constraints are used. In particular, we examine the use of total variation (TV) regularization enhanced by Bregman iterations. These novel reconstruction strategies offer new opportunities to dramatically increase the acquisition speed of photoacoustic scanners that employ point-by-point sequential scanning as well as reducing the channel count of parallelized schemes that use detector arrays.

Development of ultrafast UTE imaging for granular systems

Ultrashort echo time (UTE) imaging is commonly used in medical MRI to image 'solid' types of tissue; to date it has not been widely used in engineering or materials science, in part due to the relatively long imaging times required. Here we show how the acquisition time for UTE can be reduced to enable a preliminary study of a fluidized bed, a type of reactor commonly used throughout industry containing short T₂^∗ material and requiring fast imaging. We demonstrate UTE imaging of particles with a T₂^∗ of only 185μs, and an image acquisition time of only 25ms. The images are obtained using compressed sensing (CS) and by exploiting the Hermitian symmetry of k-space, to increase the resolution beyond that predicted by the Nyquist theorem. The technique is demonstrated by obtaining one- and two-dimensional images of bubbles rising in a model fluidized bed reactor.

Fast imaging of laboratory core floods using 3D compressed sensing RARE MRI

Three-dimensional (3D) imaging of the fluid distributions within the rock is essential to enable the unambiguous interpretation of core flooding data. Magnetic resonance imaging (MRI) has been widely used to image fluid saturation in rock cores; however, conventional acquisition strategies are typically too slow to capture the dynamic nature of the displacement processes that are of interest. Using Compressed Sensing (CS), it is possible to reconstruct a near-perfect image from significantly fewer measurements than was previously thought necessary, and this can result in a significant reduction in the image acquisition times. In the present study, a method using the Rapid Acquisition with Relaxation Enhancement (RARE) pulse sequence with CS to provide 3D images of the fluid saturation in rock core samples during laboratory core floods is demonstrated. An objective method using image quality metrics for the determination of the most suitable regularisation functional to be used in the CS reconstructions is reported. It is shown that for the present application, Total Variation outperforms the Haar and Daubechies3 wavelet families in terms of the agreement of their respective CS reconstructions with a fully-sampled reference image. Using the CS-RARE approach, 3D images of the fluid saturation in the rock core have been acquired in 16min. The CS-RARE technique has been applied to image the residual water saturation in the rock during a water-water displacement core flood. With a flow rate corresponding to an interstitial velocity of vi=1.89±0.03ftday(-1), 0.1 pore volumes were injected over the course of each image acquisition, a four-fold reduction when compared to a fully-sampled RARE acquisition. Finally, the 3D CS-RARE technique has been used to image the drainage of dodecane into the water-saturated rock in which the dynamics of the coalescence of discrete clusters of the non-wetting phase are clearly observed. The enhancement in the temporal resolution that has been achieved using the CS-RARE approach enables dynamic transport processes pertinent to laboratory core floods to be investigated in 3D on a time-scale and with a spatial resolution that, until now, has not been possible.

Sparse Reconstruction Techniques in Magnetic Resonance Imaging: Methods, Applications, and Challenges to Clinical Adoption

The family of sparse reconstruction techniques, including the recently introduced compressed sensing framework, has been extensively explored to reduce scan times in magnetic resonance imaging (MRI). While there are many different methods that fall under the general umbrella of sparse reconstructions, they all rely on the idea that a priori information about the sparsity of MR images can be used to reconstruct full images from undersampled data. This review describes the basic ideas behind sparse reconstruction techniques, how they could be applied to improve MRI, and the open challenges to their general adoption in a clinical setting. The fundamental principles underlying different classes of sparse reconstructions techniques are examined, and the requirements that each make on the undersampled data outlined. Applications that could potentially benefit from the accelerations that sparse reconstructions could provide are described, and clinical studies using sparse reconstructions reviewed. Lastly, technical and clinical challenges to widespread implementation of sparse reconstruction techniques, including optimization, reconstruction times, artifact appearance, and comparison with current gold standards, are discussed.

Bilevel Parameter Learning for Higher-Order Total Variation Regularisation Models

We consider a bilevel optimisation approach for parameter learning in higher-order total variation image reconstruction models. Apart from the least squares cost functional, naturally used in bilevel learning, we propose and analyse an alternative cost based on a Huber-regularised TV seminorm. Differentiability properties of the solution operator are verified and a first-order optimality system is derived. Based on the adjoint information, a combined quasi-Newton/semismooth Newton algorithm is proposed for the numerical solution of the bilevel problems. Numerical experiments are carried out to show the suitability of our approach and the improved performance of the new cost functional. Thanks to the bilevel optimisation framework, also a detailed comparison between TGV 2 and ICTV is carried out, showing the advantages and shortcomings of both regularisers, depending on the structure of the processed images and their noise level.

Quantitative mapping of chemical compositions with MRI using compressed sensing

In this work, a magnetic resonance (MR) imaging method for accelerating the acquisition time of two dimensional concentration maps of different chemical species in mixtures by the use of compressed sensing (CS) is presented. Whilst 2D-concentration maps with a high spatial resolution are prohibitively time-consuming to acquire using full k-space sampling techniques, CS enables the reconstruction of quantitative concentration maps from sub-sampled k-space data. First, the method was tested by reconstructing simulated data. Then, the CS algorithm was used to reconstruct concentration maps of binary mixtures of 1,4-dioxane and cyclooctane in different samples with a field-of-view of 22mm and a spatial resolution of 344μm×344μm. Spiral based trajectories were used as sampling schemes. For the data acquisition, eight scans with slightly different trajectories were applied resulting in a total acquisition time of about 8min. In contrast, a conventional chemical shift imaging experiment at the same resolution would require about 17h. To get quantitative results, a careful weighting of the regularisation parameter (via the L-curve approach) or contrast-enhancing Bregman iterations are applied for the reconstruction of the concentration maps. Both approaches yield relative errors of the concentration map of less than 2mol-% without any calibration prior to the measurement. The accuracy of the reconstructed concentration maps deteriorates when the reconstruction model is biased by systematic errors such as large inhomogeneities in the static magnetic field. The presented method is a powerful tool for the fast acquisition of concentration maps that can provide valuable information for the investigation of many phenomena in chemical engineering applications.

Reduced-dose and high-speed acquisition strategies for multi-dimensional electron microscopy

Multi-dimensional electron microscopy has recently gained considerable interest thanks to the advent of microscopes with unprecedented analytical and in situ capabilities. These information-rich imaging modes, though, are often subject to long acquisition times and large data generation. In this paper, we explore novel acquisition strategies and reconstruction algorithms to retrieve reliable reconstructions from datasets that are limited in terms of both per image and tilt series angular sampling. We show that inpainting techniques are capable of restoring scanning transmission electron microscopy images in which a very restricted number of pixels are scanned, while compressed sensing tomographic reconstruction is capable of minimising artefacts due to angular subsampling. An example of robust reconstruction from data constituting a dose reduction of 10× is presented, using an organic/inorganic core-shell nanowire as a test sample. The combination of these novel acquisition schemes and image recovery strategies provides new avenues to reduced-dose and high-speed imaging.

Accelerated three-dimensional cine phase contrast imaging using randomly undersampled echo planar imaging with compressed sensing reconstruction

The aim of this study was to implement and evaluate an accelerated three-dimensional (3D) cine phase contrast MRI sequence by combining a randomly sampled 3D k-space acquisition sequence with an echo planar imaging (EPI) readout. An accelerated 3D cine phase contrast MRI sequence was implemented by combining EPI readout with randomly undersampled 3D k-space data suitable for compressed sensing (CS) reconstruction. The undersampled data were then reconstructed using low-dimensional structural self-learning and thresholding (LOST). 3D phase contrast MRI was acquired in 11 healthy adults using an overall acceleration of 7 (EPI factor of 3 and CS rate of 3). For comparison, a single two-dimensional (2D) cine phase contrast scan was also performed with sensitivity encoding (SENSE) rate 2 and approximately at the level of the pulmonary artery bifurcation. The stroke volume and mean velocity in both the ascending and descending aorta were measured and compared between two sequences using Bland-Altman plots. An average scan time of 3 min and 30 s, corresponding to an acceleration rate of 7, was achieved for 3D cine phase contrast scan with one direction flow encoding, voxel size of 2 × 2 × 3 mm(3) , foot-head coverage of 6 cm and temporal resolution of 30 ms. The mean velocity and stroke volume in both the ascending and descending aorta were statistically equivalent between the proposed 3D sequence and the standard 2D cine phase contrast sequence. The combination of EPI with a randomly undersampled 3D k-space sampling sequence using LOST reconstruction allows a seven-fold reduction in scan time of 3D cine phase contrast MRI without compromising blood flow quantification.

Ultrashort echo time (UTE) imaging using gradient pre-equalization and compressed sensing

Ultrashort echo time (UTE) imaging is a well-known technique used in medical MRI, however, the implementation of the sequence remains non-trivial. This paper introduces UTE for non-medical applications and outlines a method for the implementation of UTE to enable accurate slice selection and short acquisition times. Slice selection in UTE requires fast, accurate switching of the gradient and r.f. pulses. Here a gradient "pre-equalization" technique is used to optimize the gradient switching and achieve an effective echo time of 10μs. In order to minimize the echo time, k-space is sampled radially. A compressed sensing approach is used to minimize the total acquisition time. Using the corrections for slice selection and acquisition along with novel image reconstruction techniques, UTE is shown to be a viable method to study samples of cork and rubber with a shorter signal lifetime than can typically be measured. Further, the compressed sensing image reconstruction algorithm is shown to provide accurate images of the samples with as little as 12.5% of the full k-space data set, potentially permitting real time imaging of short T2(*) materials.