A Multi-Grid Iterative Method for Photoacoustic Tomography

Inspired by the recent advances on minimizing nonsmooth or bound-constrained convex functions on models using varying degrees of fidelity, we propose a line search multigrid (MG) method for full-wave iterative image reconstruction in photoacoustic tomography (PAT) in heterogeneous media. To compute the search direction at each iteration, we decide between the gradient at the target level, or alternatively an approximate error correction at a coarser level, relying on some predefined criteria. To incorporate absorption and dispersion, we derive the analytical adjoint directly from the first-order acoustic wave system. The effectiveness of the proposed method is tested on a total-variation penalized Iterative Shrinkage Thresholding algorithm (ISTA) and its accelerated variant (FISTA), which have been used in many studies of image reconstruction in PAT. The results show the great potential of the proposed method in improving speed of iterative image reconstruction

Hessian-inversion-free ray-born inversion for quantitative ultrasound tomography

This study proposes a Hessian-inversion-free ray-born inversion approach for biomedical ultrasound tomography. The proposed approach is a more efficient version of the ray-born inversion approach proposed in [1]. Using these approaches, the propagation of acoustic waves are modelled using a ray approximation to heterogeneous Green's function. The inverse problem is solved in the frequency domain by iteratively linearisation and minimisation of the objective function from low to high frequencies. In [1], the linear subproblem associated with each frequency interval is solved by an implicit and iterative inversion of the Hessian matrix (inner iterations). Instead, this study applies a preconditioning approach on each linear subproblem so that the Hessian matrix becomes diagonalised, and can thus be inverted in a single step. Using the proposed preconditioning approach, the computational cost of solving each linear subproblem of the proposed ray-Born inversion approach becomes almost the same as solving one linear subproblem associated with a radon-type time-of-flight-based approach using bent rays. More importantly, the smoothness assumptions made for diagonalising the Hessian matrix make the image reconstruction more stable than the inversion approach in [1] to noise

On inclusion of source in the system of first-order linear acoustic wave equations

Simulating propagation of acoustic waves via solving a system of three-coupled first-order linear differential equations using a k-space pseudo-spectral method is popular for biomedical applications, firstly because of availability of an open-source toolbox for implementation of this numerical approach, and secondly because of its efficiency. The k-space pseudo-spectral method is efficient, because it allows coarser computational grids and larger time steps than finite difference and finite element methods for the same accuracy. The goal of this study is to compare this numerical wave solver with an analytical solution to the wave equation using the Green's function for computing propagation of acoustic waves in homogeneous media. This comparison is done in the frequency domain. Using the k-Wave solver, a match to the Green's function is obtained after modifying the approach taken for including mass source in the linearised equation of continuity (conservation of mass) in the associated system of wave equations.Comment: List of changes: 1) In version 1, there was a mistake in displaying figures 3(d), 3(e), 3(f), 6(d), 6(e) and 6(f). Those figures are corrected. 2) The word "acoustic" was added to the titl

Refraction-corrected ray-based inversion for three-dimensional ultrasound tomography of the breast

Ultrasound Tomography has seen a revival of interest in the past decade, especially for breast imaging, due to improvements in both ultrasound and computing hardware. In particular, three-dimensional ultrasound tomography, a fully tomographic method in which the medium to be imaged is surrounded by ultrasound transducers, has become feasible. In this paper, a comprehensive derivation and study of a robust framework for large-scale bent-ray ultrasound tomography in 3D for a hemispherical detector array is presented. Two ray-tracing approaches are derived and compared. More significantly, the problem of linking the rays between emitters and receivers, which is challenging in 3D due to the high number of degrees of freedom for the trajectory of rays, is analysed both as a minimisation and as a root-finding problem. The ray-linking problem is parameterised for a convex detection surface and three robust, accurate, and efficient ray-linking algorithms are formulated and demonstrated. To stabilise these methods, novel adaptive-smoothing approaches are proposed that control the conditioning of the update matrices to ensure accurate linking. The nonlinear UST problem of estimating the sound speed was recast as a series of linearised subproblems, each solved using the above algorithms and within a steepest descent scheme. The whole imaging algorithm was demonstrated to be robust and accurate on realistic data simulated using a full-wave acoustic model and an anatomical breast phantom, and incorporating the errors due to time-of-flight picking that would be present with measured data. This method can used to provide a low-artefact, quantitatively accurate, 3D sound speed maps. In addition to being useful in their own right, such 3D sound speed maps can be used to initialise full-wave inversion methods, or as an input to photoacoustic tomography reconstructions

A continuous adjoint for photo-acoustic tomography of the brain

We present an optimization framework for photo-acoustic tomography of brain based on a system of coupled equations that describe the propagation of sound waves in linear isotropic inhomogeneous and lossy elastic media with the absorption and physical dispersion following a frequency power law using fractional Laplacian operators. The adjoint of the associated continuous forward operator is derived, and a numerical framework for computing this adjoint based on a k- space pseudospectral method is presented. We analytically show that the derived continuous adjoint matches the adjoint of an associated discretised operator. We include this adjoint in a first-order positivity constrained optimization algorithm that is regularized by total variation minimization, and show that the iterates monotonically converge to a minimizer of an objective function, even in the presence of some error in estimating the physical parameters of the medium.Comment: 28 pages, 24 figure (eps

Ray-based inversion accounting for scattering for biomedical ultrasound computed tomography

An efficient and accurate image reconstruction algorithm for ultrasound tomography (UST) is described and demonstrated, which can recover accurate sound speed distribution from acoustic time series measurements made in soft tissue. The approach is based on a second-order iterative minimisation of the difference between the measurements and a model based on a ray-approximation to the heterogeneous Green's function. It overcomes the computational burden of full-wave solvers while avoiding the drawbacks of time-of-flight methods. Through the use of a second-order iterative minimisation scheme, applied stepwise from low to high frequencies, the effects of scattering are incorporated into the inversion

Refraction-corrected ray-based inversion for three-dimensional ultrasound tomography of the breast

Ultrasound tomography (UST) has seen a revival of interest in the past decade, especially for breast imaging, due to improvements in both ultrasound and computing hardware. In particular, three-dimensional UST, a fully tomographic method in which the medium to be imaged is surrounded by ultrasound transducers, has become feasible. This has led to renewed attention on UST image reconstruction algorithms. In this paper, a comprehensive derivation and study of a robust framework for large-scale bent-ray UST in 3D for a hemispherical detector array is presented. Two ray

Automated four-dimensional long term imaging enables single cell tracking within organotypic brain slices to study neurodevelopment and degeneration.

Current approaches for dynamic profiling of single cells rely on dissociated cultures, which lack important biological features existing in tissues. Organotypic slice cultures preserve aspects of structural and synaptic organisation within the brain and are amenable to microscopy, but established techniques are not well adapted for high throughput or longitudinal single cell analysis. Here we developed a custom-built, automated confocal imaging platform, with improved organotypic slice culture and maintenance. The approach enables fully automated image acquisition and four-dimensional tracking of morphological changes within individual cells in organotypic cultures from rodent and human primary tissues for at least 3 weeks. To validate this system, we analysed neurons expressing a disease-associated version of huntingtin (HTT586Q138-EGFP), and observed that they displayed hallmarks of Huntington's disease and died sooner than controls. By facilitating longitudinal single-cell analyses of neuronal physiology, our system bridges scales necessary to attain statistical power to detect developmental and disease phenotypes

DIRECT QUANTITATIVE PHOTOACOUSTIC TOMOGRAPHY FOR REALISTIC ACOUSTIC MEDIA

Quantitative photo-acoustic tomography (QPAT) seeks to reconstruct a distribution of optical attenuation coefficients inside a sample from a set of time series of pressure data that is measured outside the sample. The associated inverse problems involve two steps, namely acoustic and optical, which can be solved separately or as a direct composite problem. We adopt the latter approach for realistic acoustic media that possess heterogeneous and often not accurately known distributions for sound speed and ambient density, as well as an attenuation following a frequency power law that is evident in tissue media. We use a diffusion approximation (DA) model for the optical portion of the problem. We solve the corresponding composite inverse problem using three total variation (TV) regularised optimisation approaches. Accordingly, we develop two Krylov-subspace inexact-Newton algorithms that utilise the Jacobian matrix in a matrix-free manner in order to handle the computational cost. Additionally, we use a gradient-based algorithm that computes a search direction using the L-BFGS method, and applies a TV regularisation based on the alternating direction method of multipliers (ADMM) as a benchmark, because this method is popular for QPAT and direct QPAT. The results indicate the superiority of the developed inexact Newton algorithms over gradientbased quasi-Newton approaches for a comparable computational complexity