arXiv subjects

Simon Arridge

Publications and source records attributed to Simon Arridge.

At least 19 recordsLinked to original sources

arXiv2026

Deep Image Prior for Computed Tomography Reconstruction

We present a comprehensive overview of the Deep Image Prior (DIP) framework and its applications to image reconstruction in computed tomography. Unlike conventional deep learning methods that rely on large, supervised datasets, the DIP exploits the implicit bias of convolutional neural networks and operates in a fully unsupervised setting, requiring only a single measurement, even in the presence of noise. We describe the standard DIP formulation, outline key algorithmic design choices, and review several strategies to mitigate overfitting, including early stopping, explicit regularisation, and self-guided methods that adapt the network input. In addition, we examine computational improvements such as warm-start and stochastic optimisation methods to reduce the reconstruction time. The discussed methods are tested on real $\mu$CT measurements, which allows examination of trade-offs among the different modifications and extensions.

eess.IV↗

arXiv2025

Learning Binary Sampling Patterns for Single-Pixel Imaging using Bilevel Optimisation

Single-Pixel Imaging (SPI) enables the reconstruction of objects using a single detector through sequential illuminations with structured light patterns. The choice of illumination patterns is critical, particularly in highly undersampled regimes, where it directly determines reconstruction quality and acquisition speed. Instead of relying on handcrafted or fixed patterns, we propose to learn task-specific patterns directly from data. Practical SPI hardware only supports binary patterns, making binary pattern design a necessary consideration. We propose a bilevel optimisation method for learning task-specific binary illumination patterns optimised for applications such as single-pixel fluorescence microscopy. We address the non-differentiable nature of binary optimisation using the Straight-Through Estimator. In addition, we incorporate learned variational regularisation, improving reconstruction quality and robustness. We demonstrate our method on the CytoImageNet microscopy dataset. We show that our learned patterns achieve superior reconstruction performance compared to baseline methods and end-to-end deep learning, particularly in highly undersampled regimes and in scarce-data settings.

cs.CV↗

arXiv2025

Learned Single-Pixel Fluorescence Microscopy

Single-pixel imaging has emerged as a key technique in fluorescence microscopy, where fast acquisition and reconstruction are crucial. In this context, images are reconstructed from linearly compressed measurements. In practice, total variation minimisation is still used to reconstruct the image from noisy measurements of the inner product between orthogonal sampling pattern vectors and the original image data. However, data can be leveraged to learn the measurement vectors and the reconstruction process, thereby enhancing compression, reconstruction quality, and speed. We train an autoencoder through self-supervision to learn an encoder (or measurement matrix) and a decoder. We then test it on physically acquired multispectral and intensity data. During acquisition, the learned encoder becomes part of the physical device. Our approach can enhance single-pixel imaging in fluorescence microscopy by reducing reconstruction time by two orders of magnitude, achieving superior image quality, and enabling multispectral reconstructions. Ultimately, learned single-pixel fluorescence microscopy could advance diagnosis and biological research, providing multispectral imaging at a fraction of the cost.

eess.IV↗

arXiv2025

Reconstructing initial pressure and speed of sound distributions simultaneously in photoacoustic tomography

Image reconstruction in photoacoustic tomography relies on an accurate knowledge of the speed of sound in the target. However, the speed of sound distribution is not generally known, which may result in artefacts in the reconstructed distribution of initial pressure. Therefore, reconstructing the speed of sound simultaneously with the initial pressure would be valuable for accurate imaging in photoacoustic tomography. Furthermore, the speed of sound distribution could provide additional valuable information about the imaged target. In this work, simultaneous reconstruction of initial pressure and speed of sound in photoacoustic tomography is studied. This inverse problem is known to be highly ill-posed. To overcome this, we study an approach where the ill-posedness is alleviated by utilising multiple photoacoustic data sets that are generated by different initial pressure distributions within the same imaged target. Then, these initial pressure distributions are reconstructed simultaneously with the speed of sound distribution. A methodology for solving this minimisation problem is formulated using a gradient-based iterative approach equipped with bound constraints and a multigrid approach. The methodology was evaluated with numerical simulations. Different approaches for generating multiple initial pressure distributions and their effect on the solution of the image reconstruction problem were studied. The results show that initial pressure and speed of sound can be simultaneously reconstructed from photoacoustic data. Furthermore, utilising multiple initial pressure distributions improves the reconstructions such that the locations of initial pressure and speed of sound inhomogeneities can be better distinguished and image artifacts are reduced.

physics.med-ph↗

arXiv2024

Plug-and-Play Half-Quadratic Splitting for Ptychography

Ptychography is a coherent diffraction imaging method that uses phase retrieval techniques to reconstruct complex-valued images. It achieves this by sequentially illuminating overlapping regions of a sample with a coherent beam and recording the diffraction pattern. Although this addresses traditional imaging system challenges, it is computationally intensive and highly sensitive to noise, especially with reduced illumination overlap. Data-driven regularisation techniques have been applied in phase retrieval to improve reconstruction quality. In particular, plug-and-play (PnP) offers flexibility by integrating data-driven denoisers as implicit priors. In this work, we propose a half-quadratic splitting framework for using PnP and other data-driven priors for ptychography. We evaluate our method both on natural images and real test objects to validate its effectiveness for ptychographic image reconstruction.

eess.IV↗

arXiv2024

Equidistribution-based training of Free Knot Splines and ReLU Neural Networks

We consider the problem of univariate nonlinear function approximation using shallow neural networks (NN) with a rectified linear unit (ReLU) activation function. We show that the $L_2$ based approximation problem is ill-conditioned and the behaviour of optimisation algorithms used in training these networks degrades rapidly as the width of the network increases. This can lead to significantly poorer approximation in practice than expected from the theoretical expressivity of the ReLU architecture and traditional methods such as univariate Free Knot Splines (FKS). Univariate shallow ReLU NNs and FKS span the same function space, and thus have the same theoretical expressivity. However, the FKS representation remains well-conditioned as the number of knots increases. We leverage the theory of optimal piecewise linear interpolants to improve the training procedure for ReLU NNs. Using the equidistribution principle, we propose a two-level procedure for training the FKS by first solving the nonlinear problem of finding the optimal knot locations of the interpolating FKS, and then determine the optimal weights and knots of the FKS by solving a nearly linear, well-conditioned problem. The training of the FKS gives insights into how we can train a ReLU NN effectively, with an equally accurate approximation. We combine the training of the ReLU NN with an equidistribution-based loss to find the breakpoints of the ReLU functions. This is then combined with preconditioning the ReLU NN approximation to find the scalings of the ReLU functions. This fast, well-conditioned and reliable method finds an accurate shallow ReLU NN approximation to a univariate target function. We test this method on a series of regular, singular, and rapidly varying target functions and obtain good results, realising the expressivity of the shallow ReLU network in all cases. We then extend our results to deeper networks.

cs.LG↗

arXiv2024

Data-driven approaches for electrical impedance tomography image segmentation from partial boundary data

Electrical impedance tomography (EIT) plays a crucial role in non-invasive imaging, with both medical and industrial applications. In this paper, we present three data-driven reconstruction methods for EIT imaging. These three approaches were originally submitted to the Kuopio tomography challenge 2023 (KTC2023). First, we introduce a post-processing approach, which achieved first place at KTC2023. Further, we present a fully learned and a conditional diffusion approach. All three methods are based on a similar neural network as a backbone and were trained using a synthetically generated data set, providing with an opportunity for a fair comparison of these different data-driven reconstruction methods.

eess.IV↗

arXiv2024

Learning Governing Equations of Unobserved States in Dynamical Systems

Data-driven modelling and scientific machine learning have been responsible for significant advances in determining suitable models to describe data. Within dynamical systems, neural ordinary differential equations (ODEs), where the system equations are set to be governed by a neural network, have become a popular tool for this challenge in recent years. However, less emphasis has been placed on systems that are only partially-observed. In this work, we employ a hybrid neural ODE structure, where the system equations are governed by a combination of a neural network and domain-specific knowledge, together with symbolic regression (SR), to learn governing equations of partially-observed dynamical systems. We test this approach on two case studies: A 3-dimensional model of the Lotka-Volterra system and a 5-dimensional model of the Lorenz system. We demonstrate that the method is capable of successfully learning the true underlying governing equations of unobserved states within these systems, with robustness to measurement noise.

cs.LG↗

arXiv2023

Investigating the use of publicly available natural videos to learn Dynamic MR image reconstruction

Purpose: To develop and assess a deep learning (DL) pipeline to learn dynamic MR image reconstruction from publicly available natural videos (Inter4K). Materials and Methods: Learning was performed for a range of DL architectures (VarNet, 3D UNet, FastDVDNet) and corresponding sampling patterns (Cartesian, radial, spiral) either from true multi-coil cardiac MR data (N=692) or from pseudo-MR data simulated from Inter4K natural videos (N=692). Real-time undersampled dynamic MR images were reconstructed using DL networks trained with cardiac data and natural videos, and compressed sensing (CS). Differences were assessed in simulations (N=104 datasets) in terms of MSE, PSNR, and SSIM and prospectively for cardiac (short axis, four chambers, N=20) and speech (N=10) data in terms of subjective image quality ranking, SNR and Edge sharpness. Friedman Chi Square tests with post-hoc Nemenyi analysis were performed to assess statistical significance. Results: For all simulation metrics, DL networks trained with cardiac data outperformed DL networks trained with natural videos, which outperformed CS (p<0.05). However, in prospective experiments DL reconstructions using both training datasets were ranked similarly (and higher than CS) and presented no statistical differences in SNR and Edge Sharpness for most conditions. Additionally, high SSIM was measured between the DL methods with cardiac data and natural videos (SSIM>0.85). Conclusion: The developed pipeline enabled learning dynamic MR reconstruction from natural videos preserving DL reconstruction advantages such as high quality fast and ultra-fast reconstructions while overcoming some limitations (data scarcity or sharing). The natural video dataset, code and pre-trained networks are made readily available on github. Key Words: real-time; dynamic MRI; deep learning; image reconstruction; machine learning;

eess.IV↗

arXiv2023

Inverse Problems with Learned Forward Operators

Solving inverse problems requires the knowledge of the forward operator, but accurate models can be computationally expensive and hence cheaper variants that do not compromise the reconstruction quality are desired. This chapter reviews reconstruction methods in inverse problems with learned forward operators that follow two different paradigms. The first one is completely agnostic to the forward operator and learns its restriction to the subspace spanned by the training data. The framework of regularisation by projection is then used to find a reconstruction. The second one uses a simplified model of the physics of the measurement process and only relies on the training data to learn a model correction. We present the theory of these two approaches and compare them numerically. A common theme emerges: both methods require, or at least benefit from, training data not only for the forward operator, but also for its adjoint.

math.NA↗

arXiv2023

Steerable Conditional Diffusion for Out-of-Distribution Adaptation in Medical Image Reconstruction

Denoising diffusion models have emerged as the go-to generative framework for solving inverse problems in imaging. A critical concern regarding these models is their performance on out-of-distribution tasks, which remains an under-explored challenge. Using a diffusion model on an out-of-distribution dataset, realistic reconstructions can be generated, but with hallucinating image features that are uniquely present in the training dataset. To address this discrepancy during train-test time and improve reconstruction accuracy, we introduce a novel sampling framework called Steerable Conditional Diffusion. Specifically, this framework adapts the diffusion model, concurrently with image reconstruction, based solely on the information provided by the available measurement. Utilising our proposed method, we achieve substantial enhancements in out-of-distribution performance across diverse imaging modalities, advancing the robust deployment of denoising diffusion models in real-world applications.

cs.CV↗

arXiv2023

Score-Based Generative Models for PET Image Reconstruction

Score-based generative models have demonstrated highly promising results for medical image reconstruction tasks in magnetic resonance imaging or computed tomography. However, their application to Positron Emission Tomography (PET) is still largely unexplored. PET image reconstruction involves a variety of challenges, including Poisson noise with high variance and a wide dynamic range. To address these challenges, we propose several PET-specific adaptations of score-based generative models. The proposed framework is developed for both 2D and 3D PET. In addition, we provide an extension to guided reconstruction using magnetic resonance images. We validate the approach through extensive 2D and 3D $\textit{in-silico}$ experiments with a model trained on patient-realistic data without lesions, and evaluate on data without lesions as well as out-of-distribution data with lesions. This demonstrates the proposed method's robustness and significant potential for improved PET reconstruction.

eess.IV↗

arXiv2022

A Learned Born Series for Highly-Scattering Media

A new method for solving the wave equation is presented, called the learned Born series (LBS), which is derived from a convergent Born Series but its components are found through training. The LBS is shown to be significantly more accurate than the convergent Born series for the same number of iterations, in the presence of high contrast scatterers, while maintaining a comparable computational complexity. The LBS is able to generate a reasonable prediction of the global pressure field with a small number of iterations, and the errors decrease with the number of learned iterations.

physics.comp-ph↗

arXiv2022

Unsupervised denoising for sparse multi-spectral computed tomography

Multi-energy computed tomography (CT) with photon counting detectors (PCDs) enables spectral imaging as PCDs can assign the incoming photons to specific energy channels. However, PCDs with many spectral channels drastically increase the computational complexity of the CT reconstruction, and bespoke reconstruction algorithms need fine-tuning to varying noise statistics. \rev{Especially if many projections are taken, a large amount of data has to be collected and stored. Sparse view CT is one solution for data reduction. However, these issues are especially exacerbated when sparse imaging scenarios are encountered due to a significant reduction in photon counts.} In this work, we investigate the suitability of learning-based improvements to the challenging task of obtaining high-quality reconstructions from sparse measurements for a 64-channel PCD-CT. In particular, to overcome missing reference data for the training procedure, we propose an unsupervised denoising and artefact removal approach by exploiting different filter functions in the reconstruction and an explicit coupling of spectral channels with the nuclear norm. Performance is assessed on both simulated synthetic data and the openly available experimental Multi-Spectral Imaging via Computed Tomography (MUSIC) dataset. We compared the quality of our unsupervised method to iterative total nuclear variation regularized reconstructions and a supervised denoiser trained with reference data. We show that improved reconstruction quality can be achieved with flexibility on noise statistics and effective suppression of streaking artefacts when using unsupervised denoising with spectral coupling.

eess.IV↗

arXiv2022

Neural Network Kalman filtering for 3D object tracking from linear array ultrasound data

Many interventional surgical procedures rely on medical imaging to visualise and track instruments. Such imaging methods not only need to be real-time capable, but also provide accurate and robust positional information. In ultrasound applications, typically only two-dimensional data from a linear array are available, and as such obtaining accurate positional estimation in three dimensions is non-trivial. In this work, we first train a neural network, using realistic synthetic training data, to estimate the out-of-plane offset of an object with the associated axial aberration in the reconstructed ultrasound image. The obtained estimate is then combined with a Kalman filtering approach that utilises positioning estimates obtained in previous time-frames to improve localisation robustness and reduce the impact of measurement noise. The accuracy of the proposed method is evaluated using simulations, and its practical applicability is demonstrated on experimental data obtained using a novel optical ultrasound imaging setup. Accurate and robust positional information is provided in real-time. Axial and lateral coordinates for out-of-plane objects are estimated with a mean error of 0.1mm for simulated data and a mean error of 0.2mm for experimental data. Three-dimensional localisation is most accurate for elevational distances larger than 1mm, with a maximum distance of 6mm considered for a 25mm aperture.

stat.AP↗

arXiv2022

FReSCO: Flow Reconstruction and Segmentation for low latency Cardiac Output monitoring using deep artifact suppression and segmentation

Purpose: Real-time monitoring of cardiac output (CO) requires low latency reconstruction and segmentation of real-time phase contrast MR (PCMR), which has previously been difficult to perform. Here we propose a deep learning framework for 'Flow Reconstruction and Segmentation for low latency Cardiac Output monitoring' (FReSCO). Methods: Deep artifact suppression and segmentation U-Nets were independently trained. Breath hold spiral PCMR data (n=516) was synthetically undersampled using a variable density spiral sampling pattern and gridded to create aliased data for training of the artifact suppression U-net. A subset of the data (n=96) was segmented and used to train the segmentation U-net. Real-time spiral PCMR was prospectively acquired and then reconstructed and segmented using the trained models (FReSCO) at low latency at the scanner in 10 healthy subjects during rest, exercise and recovery periods. CO obtained via FReSCO was compared to a reference rest CO and rest and exercise Compressed Sensing (CS) CO. Results: FReSCO was demonstrated prospectively at the scanner. Beat-to-beat heartrate, stroke volume and CO could be visualized with a mean latency of 622ms. No significant differences were noted when compared to reference at rest (Bias = -0.21+-0.50 L/min, p=0.246) or CS at peak exercise (Bias=0.12+-0.48 L/min, p=0.458). Conclusion: FReSCO was successfully demonstrated for real-time monitoring of CO during exercise and could provide a convenient tool for assessment of the hemodynamic response to a range of stressors.

cs.CV↗

arXiv2022

Phase-insensitive versus phase-sensitive ultrasound absorption tomography in the frequency domain

The sensitivity of phase-sensitive detectors, such as piezoelectric detectors, becomes increasingly directional as the detector element size increases. In contrast, pyroelectric sensors, which are phase-insensitive, retain their omni-directionality even for large element sizes, although they have significantly poorer temporal resolution. This study uses numerical models to examine whether phase-insensitive detectors can be used advantageously in ultrasound tomography, specifically absorption tomography, when the number of detectors is sparse. We present measurement models for phase-sensitive and phase-insensitive sensors and compare the quality of the absorption reconstructions between these sensor types based on image contrast metrics. We perform the inversion using synthetic data with a Jacobian-based linearised matrix inversion approach.

math.NA↗

arXiv2021

Stochastic EM methods with Variance Reduction for Penalised PET Reconstructions

Expectation-maximization (EM) is a popular and well-established method for image reconstruction in positron emission tomography (PET) but it often suffers from slow convergence. Ordered subset EM (OSEM) is an effective reconstruction algorithm that provides significant acceleration during initial iterations, but it has been observed to enter a limit cycle. In this work, we investigate two classes of algorithms for accelerating OSEM based on variance reduction for penalised PET reconstructions. The first is a stochastic variance reduced EM algorithm, termed as SVREM, an extension of the classical EM to the stochastic context, by combining classical OSEM with insights from variance reduction techniques for gradient descent. The second views OSEM as a preconditioned stochastic gradient ascent, and applies variance reduction techniques, i.e., SAGA and SVRG, to estimate the update direction. We present several numerical experiments to illustrate the efficiency and accuracy of the approaches. The numerical results show that these approaches significantly outperform existing OSEM type methods for penalised PET reconstructions, and hold great potential.

physics.med-ph↗