Ander Biguri

Sören Dittmer, Michael Roberts, Julian Gilbey et al.

In this perspective, we argue that despite the democratization of powerful tools for data science and machine learning over the last decade, developing the code for a trustworthy and effective data science system (DSS) is getting harder. Perverse incentives and a lack of widespread software engineering (SE) skills are among many root causes we identify that naturally give rise to the current systemic crisis in reproducibility of DSSs. We analyze why SE and building large complex systems is, in general, hard. Based on these insights, we identify how SE addresses those difficulties and how we can apply and generalize SE methods to construct DSSs that are fit for purpose. We advocate two key development philosophies, namely that one should incrementally grow -- not biphasically plan and build -- DSSs, and one should always employ two types of feedback loops during development: one which tests the code's correctness and another that evaluates the code's efficacy.

Maximilian B. Kiss, Ander Biguri, Carola-Bibiane Schönlieb et al.

Like in many other research fields, recent developments in computational imaging have focused on developing machine learning (ML) approaches to tackle its main challenges. To improve the performance of computational imaging algorithms, machine learning methods are used for image processing tasks such as noise reduction. Generally, these ML methods heavily rely on the availability of high-quality data on which they are trained. This work explores the application of ML methods, specifically convolutional neural networks (CNNs), in the context of noise reduction for computed tomography (CT) imaging. We utilize a large 2D computed tomography dataset for machine learning to carry out for the first time a comprehensive study on the differences between the observed performances of algorithms trained on simulated noisy data and on real-world experimental noisy data. The study compares the performance of two common CNN architectures, U-Net and MSD-Net, that are trained and evaluated on both simulated and experimental noisy data. The results show that while sinogram denoising performed better with simulated noisy data if evaluated in the sinogram domain, the performance did not carry over to the reconstruction domain where training on experimental noisy data shows a higher performance in denoising experimental noisy data. Training the algorithms in an end-to-end fashion from sinogram to reconstruction significantly improved model performance, emphasizing the importance of matching raw measurement data to high-quality CT reconstructions. The study furthermore suggests the need for more sophisticated noise simulation approaches to bridge the gap between simulated and real-world data in CT image denoising applications and gives insights into the challenges and opportunities in leveraging simulated data for machine learning in computational imaging.

Eashrat Jahan Muniya, Gernot Kronreif, Ander Biguri et al.

Soft-tissue deformation remains a major limitation in image-guided neurosurgery, where intra-operative anatomy can deviate substantially from pre-operative imaging due to brain shift, compromising navigation accuracy and surgical safety. Existing compensation methods often rely on intra-operative MRI, CT, or ultrasound, which are disruptive and difficult to integrate repeatedly into the surgical workflow. In contrast, partial 3D cortical surfaces can be reconstructed as point clouds from stereoscopic microscopes or laser range scanners (LRS), capturing only a limited portion of the exposed cortex. This makes point cloud registration a practical alternative without interrupting surgery; however, such partial and noisy observations make deformation estimation highly challenging. In this study, we propose a deep learning-based framework for non-rigid volume-to-surface registration, enabling dense displacement field estimation from sparse intra-operative surface observations without explicit point correspondences or volumetric intra-operative imaging. The network leverages multi-scale point-based feature extraction and a hierarchical deformation decoder to capture both global and local deformations. The key contribution lies in integrating partial intra-operative surface information into the full pre-operative point cloud domain, enabling implicit correspondence learning and dense deformation recovery under limited visibility. Quantitative results demonstrate accurate recovery of fine-scale deformations, achieving an Endpoint Error (EPE) of 1.13 +/- 0.75 mm and RMSE of 1.33 +/- 0.81 mm under challenging partial-surface conditions. The proposed approach supports automatic, workflow-compatible brain-shift compensation from sparse surface observations.

Poorya MohammadiNasab, Ander Biguri, Philipp Steininger et al.

Iterative reconstruction technique's ability to reduce radiation exposure by using fewer projections has attracted significant attention. However, these methods typically require a precise tuning of several hyperparameters, which can have a major impact on reconstruction quality. Manually setting these parameters is time-consuming and increases the workload for human operators. In this paper, we introduce a novel fully automatic parameter optimization framework that can be applied to a wide range of Cone-beam computed tomography (CBCT) iterative reconstruction algorithms to determine optimal parameters without requiring a reference reconstruction. The proposed method incorporates a modified crow search algorithm (CSA) featuring a superior set-dependent local search mechanism, a search-space-aware global search strategy, and an objective-driven balance between local and global search. Additionally, to ensure an effective initial population, we propose a chaotic diagonal linear uniform initialization scheme that accelerates algorithm convergence. The performance of the proposed framework was evaluated on three imaging machines and four real datasets, as well as three different iterative reconstruction methods with the highest number of tunable parameters, representing the most challenging senario. The results indicate that the proposed method could outperform manual settings and CSA, with an 4.19% improvement in average fitness and 4.89% and 3.82% improvements on CHILL@UK and RPI_AXIS, respectively, which are two benchmark no-reference learning-based quality metrics. In addition, the qualitative results clearly show the superiority of the proposed method by maintaining fine details sharply. The overall performance of the proposed framework across different comparison scenarios demonstrates its effectiveness and robustness across all cases.

Maximilian B. Kiss, Ander Biguri, Zakhar Shumaylov et al.

Computed tomography (CT) is a widely used non-invasive diagnostic method in various fields, and recent advances in deep learning have led to significant progress in CT image reconstruction. However, the lack of large-scale, open-access datasets has hindered the comparison of different types of learned methods. To address this gap, we use the 2DeteCT dataset, a real-world experimental computed tomography dataset, for benchmarking machine learning based CT image reconstruction algorithms. We categorize these methods into post-processing networks, learned/unrolled iterative methods, learned regularizer methods, and plug-and-play methods, and provide a pipeline for easy implementation and evaluation. Using key performance metrics, including SSIM and PSNR, our benchmarking results showcase the effectiveness of various algorithms on tasks such as full data reconstruction, limited-angle reconstruction, sparse-angle reconstruction, low-dose reconstruction, and beam-hardening corrected reconstruction. With this benchmarking study, we provide an evaluation of a range of algorithms representative for different categories of learned reconstruction methods on a recently published dataset of real-world experimental CT measurements. The reproducible setup of methods and CT image reconstruction tasks in an open-source toolbox enables straightforward addition and comparison of new methods later on. The toolbox also provides the option to load the 2DeteCT dataset differently for extensions to other problems and different CT reconstruction tasks.

Nadja Gruber, Johannes Schwab, Markus Haltmeier et al.

We propose Noisier2Inverse, a correction-free self-supervised deep learning approach for general inverse problems. The proposed method learns a reconstruction function without the need for ground truth samples and is applicable in cases where measurement noise is statistically correlated. This includes computed tomography, where detector imperfections or photon scattering create correlated noise patterns, as well as microscopy and seismic imaging, where physical interactions during measurement introduce dependencies in the noise structure. Similar to Noisier2Noise, a key step in our approach is the generation of noisier data from which the reconstruction network learns. However, unlike Noisier2Noise, the proposed loss function operates in measurement space and is trained to recover an extrapolated image instead of the original noisy one. This eliminates the need for an extrapolation step during inference, which would otherwise suffer from ill-posedness. We numerically demonstrate that our method clearly outperforms previous self-supervised approaches that account for correlated noise.

Chu Chen, Ander Biguri, Jean-Michel Morel et al.

X-ray Computed Laminography (CL) is essential for non-destructive inspection of plate-like structures in applications such as microchips and composite battery materials, where traditional computed tomography (CT) struggles due to geometric constraints. However, reconstructing high-quality volumes from laminographic projections remains challenging, particularly under highly sparse-view acquisition conditions. In this paper, we propose a reconstruction algorithm, namely LamiGauss, that combines Gaussian Splatting radiative rasterization with a dedicated detector-to-world transformation model incorporating the laminographic tilt angle. LamiGauss leverages an initialization strategy that explicitly filters out common laminographic artifacts from the preliminary reconstruction, preventing redundant Gaussians from being allocated to false structures and thereby concentrating model capacity on representing the genuine object. Our approach effectively optimizes directly from sparse projections, enabling accurate and efficient reconstruction with limited data. Extensive experiments on both synthetic and real datasets demonstrate the effectiveness and superiority of the proposed method over existing techniques. LamiGauss uses only 3$\%$ of full views to achieve superior performance over the iterative method optimized on a full dataset.

Christina Runkel, Natacha Kuete Meli, Jovita Lukasik et al.

Compressing and pruning large machine learning models has become a critical step towards their deployment in real-world applications. Standard pruning and compression techniques are typically designed without taking the structure of the network's weights into account, limiting their effectiveness. We explore the impact of smooth regularization on neural network training and model compression. By applying nuclear norm, first- and second-order derivative penalties of the weights during training, we encourage structured smoothness while preserving predictive performance on par with non-smooth models. We find that standard pruning methods often perform better when applied to these smooth models. Building on this observation, we apply a Singular-Value-Decomposition-based compression method that exploits the underlying smooth structure and approximates the model's weight tensors by smaller low-rank tensors. Our approach enables state-of-the-art compression without any fine-tuning - reaching up to $91\%$ accuracy on a smooth ResNet-18 on CIFAR-10 with $70\%$ fewer parameters.

Christina Runkel, Ander Biguri, Carola-Bibiane Schönlieb

Neural ordinary differential equations (Neural ODEs) propose the idea that a sequence of layers in a neural network is just a discretisation of an ODE, and thus can instead be directly modelled by a parameterised ODE. This idea has had resounding success in the deep learning literature, with direct or indirect influence in many state of the art ideas, such as diffusion models or time dependant models. Recently, a continuous version of the U-net architecture has been proposed, showing increased performance over its discrete counterpart in many imaging applications and wrapped with theoretical guarantees around its performance and robustness. In this work, we explore the use of Neural ODEs for learned inverse problems, in particular with the well-known Learned Primal Dual algorithm, and apply it to computed tomography (CT) reconstruction.