Optical tomography using the SCIRun problem solving environment: Preliminary results for three-dimensional geometries and parallel processing

We present a 3D implementation of the UCL imaging package for absorption and scatter reconstruction from time-resolved data (TOAST), embedded in the SCIRun interactive simulation and visualization package developed at the University of Utah. SCIRun is a scientific programming environment that allows the interactive construction, debugging, and steering of large-scale scientific computations. While the capabilities of SCIRun's interactive approach are not yet fully exploited in the current TOAST implementation, an immediate benefit of the combined TOAST/SCIRun package is the availability of optimized parallel finite element forward solvers, and the use of SCIRun's existing 3D visualisation tools. A reconstruction of a segmented 3D head model is used as an example for demonstrating the capability of TOAST/SCIRun of simulating anatomically shaped meshes

Motion and contrast enhancement separation model reconstruction from partial measurements in dynamic MRI

We propose a motion and contrast enhancement separation model in dynamic magnetic resonance imaging (MRI). Furthermore, the reconstruction is done from partial measurements to achieve faster dynamic MR imaging. The algorithm minimizes a linear combination of three terms, a data fitting functional and two regularization functionals corresponding to the nuclear and ℓ1 norm. The proposed method is tested on simulated and real dynamic datasets. This paper suggests an image reconstruction model that directly induces clinically-relevant informations from partial measurements

Finite element approximation of the radiative transport equation in a medium with piece-wise constant refractive index

The radiative transport equation can be used as a light transport model in a medium with scattering particles, such as biological tissues. In the radiative transport equation, the refractive index is assumed to be constant within the medium. However, in biomedical media, changes in the refractive index can occur between different tissue types. In this work, light propagation in a medium with piece-wise constant refractive index is considered. Light propagation in each sub-domain with a constant refractive index is modeled using the radiative transport equation and the equations are coupled using boundary conditions describing Fresnel reflection and refraction phenomena on the interfaces between the sub-domains. The resulting coupled system of radiative transport equations is numerically solved using a finite element method. The approach is tested with simulations. The results show that this coupled system describes light propagation accurately through comparison with the Monte Carlo method. It is also shown that neglecting the internal changes of the refractive index can lead to erroneous boundary measurements of scattered light

Utilising the radiative transfer equation in quantitative photoacoustic tomography

Quantitative photoacoustic tomography is an emerging imaging technique aimed at estimating optical parameters inside tissue from photoacoustic images. This optical parameter estimation problem is an ill-posed inverse problem, and thus it is sensitive to measurement and modelling errors. Therefore, light propagation in quantitative photoacoustic tomography needs to be accurately modelled. A widely accepted model for light propagation in biological tissue is the radiative transfer equation. In this work, the radiative transfer equation is utilised in quantitative photoacoustic tomography. Estimating absorption and scattering distributions in quantitative photoacoustic tomography using various illuminations is investigated

Simulating optical memory effects and the scanning of foci using wavefront shaping in tissue-like scattering media

Wavefront shaping could enable focussing light deep inside scattering media, increasing the depth and resolution of imaging techniques like optical microscopy and optical coherence tomography. However, factors like rapid decorrelation times due to microscale motion and thermal variation make focusing in living tissue difficult. A way to ease the requirements could be exploiting prior information provided by memory effects. For example, this might allow partially or wholly scanning a focus. To study this and related ideas, a computational model was developed to simulate the generation and correlations of foci formed by WFS in scattering media. Predictions of the angular memory range were consistent with experimental observations. Furthermore, correlations observed between optical phase maps required to focus at different positions suggested correlation-based priors might enable accelerated focussing. This work could pave the way to faster optical focussing and thus deeper imaging in living tissue

j-Wave: An open-source differentiable wave simulator

We present an open-source differentiable acoustic simulator, j-Wave, which can solve time-varying and time-harmonic acoustic problems. It supports automatic differentiation, which is a program transformation technique that has many applications, especially in machine learning and scientific computing. j-Wave is composed of modular components that can be easily customized and reused. At the same time, it is compatible with some of the most popular machine learning libraries, such as JAX and TensorFlow. The accuracy of the simulation results for known configurations is evaluated against the widely used k-Wave toolbox and a cohort of acoustic simulation software. j-Wave is available from https://github.com/ucl-bug/jwave

A computational framework for investigating the feasibility of focusing light in biological tissue via photoacoustic wavefront shaping

Photoacoustic (PA) wavefront shaping (WFS; PAWS) could allow focusing light deep in living tissue, increasing the penetration depth of biomedical optics techniques. PAWS experiments have demonstrated focusing light through rigid scattering media. However, focusing deep in tissue is significantly more challenging. To examine the scale of this challenge, a computational model of the propagation of coherent light in tissue was developed to simulate the focusing of light via PAWS. To demonstrate the model, it was used to simulate focusing in an 800 µm thick tissue-like medium. To show the utility of the model, the focusing was repeated in different conditions illustrative of simplified PAWS experiments involving different spatial resolutions. As expected, a finer spatial resolution led to a brighter focus. By providing a simulation platform for studying PAWS, this work could pave the way to developing systems that can focus light in tissue

Vector-Valued Image Processing by Parallel Level Sets

Vector-valued images such as RGB color images or multimodal medical images show a strong interchannel correlation, which is not exploited by most image processing tools. We propose a new notion of treating vector-valued images which is based on the angle between the spatial gradients of their channels. Through minimizing a cost functional that penalizes large angles, images with parallel level sets can be obtained. After formally introducing this idea and the corresponding cost functionals, we discuss their Gâteaux derivatives that lead to a diffusion-like gradient descent scheme. We illustrate the properties of this cost functional by several examples in denoising and demosaicking of RGB color images. They show that parallel level sets are a suitable concept for color image enhancement. Demosaicking with parallel level sets gives visually perfect results for low noise levels. Furthermore, the proposed functional yields sharper images than the other approaches in comparison

Three dimensional optical imaging of blood volume and oxygenation in the neonatal brain

Optical methods provide a means of monitoring cerebral oxygenation in newborn infants at risk of brain injury. A 32-channel optical imaging system has been developed with the aim of reconstructing three-dimensional images of regional blood volume and oxygenation. Full image data sets were acquired from 14 out of 24 infants studied; successful images have been reconstructed in 8 of these infants. Regional variations in cerebral blood volume and tissue oxygen saturation are present in healthy preterm infants. In an infant with a large unilateral intraventricular haemorrhage, a corresponding region of low oxygen saturation was detected. These results suggest that optical tomography may provide an appropriate technique for investigating regional cerebral haemodynamics and oxygenation at the cotside. (c) 2006 Elsevier Inc. All rights reserved