Daniël M. Pelt

Jiayang Shi, Lincen Yang, Zhong Li et al.

Generative models, particularly Diffusion Models (DM), have shown strong potential for Computed Tomography (CT) reconstruction serving as expressive priors for solving ill-posed inverse problems. However, diffusion-based reconstruction relies on Stochastic Differential Equations (SDEs) for forward diffusion and reverse denoising, where such stochasticity can interfere with repeated data consistency corrections in CT reconstruction. Since CT reconstruction is often time-critical in clinical and interventional scenarios, improving reconstruction efficiency is essential. In contrast, Flow Matching (FM) models sampling as a deterministic Ordinary Differential Equation (ODE), yielding smooth trajectories without stochastic noise injection. This deterministic formulation is naturally compatible with repeated data consistency operations. Furthermore, we observe that FM-predicted velocity fields exhibit strong correlations across adjacent steps. Motivated by this, we propose an FM-based CT reconstruction framework (FMCT) and an efficient variant (EFMCT) that reuses previously predicted velocity fields over consecutive steps to substantially reduce the number of Neural network Function Evaluations (NFEs), thereby improving inference efficiency. We provide theoretical analysis showing that the error introduced by velocity reuse is bounded when combined with data consistency operations. Extensive experiments demonstrate that FMCT/EFMCT achieve competitive reconstruction quality while significantly improving computational efficiency compared with diffusion-based methods. The codebase is open-sourced at https://github.com/EFMCT/EFMCT.

Kay Gijzen, Gertjan J. Burghouts, Daniël M. Pelt

Severe occlusions of objects pose a major challenge for computer vision. We show that two root causes are (1) the loss of visible information and (2) the distracting patterns caused by the occluders. Our approach addresses both causes at the same time. First, the distracting patterns are removed at test-time, via masking of the occluding patterns. This masking is independent of the type of occlusion, by handling the occlusion through the lens of visual anomalies w.r.t. the object of interest. Second, to deal with less visual details, we follow standard practice by masking random parts of the object during training, for various degrees of occlusions. We discover that (a) it is possible to estimate the degree of the occlusion (i.e. severity) at test-time, and (b) that a model optimized for a specific degree of occlusion also performs best on a similar degree during test-time. Combining these two insights brings us to a severity-informed classification model called OASIC: Occlusion Agnostic Severity Informed Classification. We estimate the severity of occlusion for a test image, mask the occluder, and select the model that is optimized for the degree of occlusion. This strategy performs better than any single model optimized for any smaller or broader range of occlusion severities. Experiments show that combining gray masking with adaptive model selection improves $\text{AUC}_\text{occ}$ by +18.5 over standard training on occluded images and +23.7 over finetuning on unoccluded images.

Xingyi Cheng, Julien Maufront, Aurélie Di Cicco et al.

Cryo-electron tomography (cryo-ET) enables high resolution, three-dimensional reconstruction of biological structures, including membranes and membrane proteins. Identification of regions of interest (ROIs) is central to scientific imaging, as it enables isolation and quantitative analysis of specific structural features within complex datasets. In practice, however, ROIs are typically derived indirectly through full structure segmentation followed by post hoc analysis. This limitation is especially apparent for continuous and geometrically complex structures such as membranes, which are segmented as single entities. Here, we developed TomoROIS-SurfORA, a two step framework for direct, shape-agnostic ROI segmentation and morphological surface analysis. TomoROIS performs deep learning-based ROI segmentation and can be trained from scratch using small annotated datasets, enabling practical application across diverse imaging data. SurfORA processes segmented structures as point clouds and surface meshes to extract quantitative morphological features, including inter-membrane distances, curvature, and surface roughness. It supports both closed and open surfaces, with specific considerations for open surfaces, which are common in cryo-ET due to the missing wedge effect. We demonstrate both tools using in vitro reconstituted membrane systems containing deformable vesicles with complex geometries, enabling automatic quantitative analysis of membrane contact sites and remodeling events such as invagination. While demonstrated here on cryo-ET membrane data, the combined approach is applicable to ROI detection and surface analysis in broader scientific imaging contexts.

Jiayang Shi, Junyi Zhu, Daniel M. Pelt et al.

Computed Tomography (CT) is pivotal in industrial quality control and medical diagnostics. Sparse-view CT, offering reduced ionizing radiation, faces challenges due to its under-sampled nature, leading to ill-posed reconstruction problems. Recent advancements in Implicit Neural Representations (INRs) have shown promise in addressing sparse-view CT reconstruction. Recognizing that CT often involves scanning similar subjects, we propose a novel approach to improve reconstruction quality through joint reconstruction of multiple objects using INRs. This approach can potentially utilize the advantages of INRs and the common patterns observed across different objects. While current INR joint reconstruction techniques primarily focus on speeding up the learning process, they are not specifically tailored to enhance the final reconstruction quality. To address this gap, we introduce a novel INR-based Bayesian framework integrating latent variables to capture the common patterns across multiple objects under joint reconstruction. The common patterns then assist in the reconstruction of each object via latent variables, thereby improving the individual reconstruction. Extensive experiments demonstrate that our method achieves higher reconstruction quality with sparse views and remains robust to noise in the measurements as indicated by common numerical metrics. The obtained latent variables can also serve as network initialization for the new object and speed up the learning process.

Jiayang Shi, Daniel M. Pelt, K. Joost Batenburg

Computed tomography (CT) is a widely used non-invasive medical imaging technique for disease diagnosis. The diagnostic accuracy is often affected by image resolution, which can be insufficient in practice. For medical CT images, the through-plane resolution is often worse than the in-plane resolution and there can be overlap between slices, causing difficulties in diagnoses. Self-supervised methods for through-plane resolution enhancement, which train on in-plane images and infer on through-plane images, have shown promise for both CT and MRI imaging. However, existing self-supervised methods either neglect overlap or can only handle specific cases with fixed combinations of resolution and overlap. To address these limitations, we propose a self-supervised method called SR4ZCT. It employs the same off-axis training approach while being capable of handling arbitrary combinations of resolution and overlap. Our method explicitly models the relationship between resolutions and voxel spacings of different planes to accurately simulate training images that match the original through-plane images. We highlight the significance of accurate modeling in self-supervised off-axis training and demonstrate the effectiveness of SR4ZCT using a real-world dataset.

Aniss Aiman Medbouhi, Alejandro García-Castellanos, Giovanni Luca Marchetti et al.

We study the problem of constructing Steiner Minimal Trees (SMTs) in hyperbolic space. Exact SMT computation is NP-hard, and existing hyperbolic heuristics such as HyperSteiner are deterministic and often get trapped in locally suboptimal configurations. We introduce Randomized HyperSteiner (RHS), a stochastic Delaunay triangulation heuristic that incorporates randomness into the expansion process and refines candidate trees via Riemannian gradient descent optimization. Experiments on synthetic data sets and a real-world single-cell transcriptomic data show that RHS outperforms Minimum Spanning Tree (MST), Neighbour Joining, and vanilla HyperSteiner (HS). In near-boundary configurations, RHS can achieve a 32% reduction in total length over HS, demonstrating its effectiveness and robustness in diverse data regimes.

Alejandro García-Castellanos, David R. Wessels, Nicky J. van den Berg et al.

We introduce Equivariant Neural Eikonal Solvers, a novel framework that integrates Equivariant Neural Fields (ENFs) with Neural Eikonal Solvers. Our approach employs a single neural field where a unified shared backbone is conditioned on signal-specific latent variables - represented as point clouds in a Lie group - to model diverse Eikonal solutions. The ENF integration ensures equivariant mapping from these latent representations to the solution field, delivering three key benefits: enhanced representation efficiency through weight-sharing, robust geometric grounding, and solution steerability. This steerability allows transformations applied to the latent point cloud to induce predictable, geometrically meaningful modifications in the resulting Eikonal solution. By coupling these steerable representations with Physics-Informed Neural Networks (PINNs), our framework accurately models Eikonal travel-time solutions while generalizing to arbitrary Riemannian manifolds with regular group actions. This includes homogeneous spaces such as Euclidean, position-orientation, spherical, and hyperbolic manifolds. We validate our approach through applications in seismic travel-time modeling of 2D, 3D, and spherical benchmark datasets. Experimental results demonstrate superior performance, scalability, adaptability, and user controllability compared to existing Neural Operator-based Eikonal solver methods.

Jiayang Shi, Daniel M. Pelt, K. Joost Batenburg

Computed Tomography (CT) using synchrotron radiation is a powerful technique that, compared to lab-CT techniques, boosts high spatial and temporal resolution while also providing access to a range of contrast-formation mechanisms. The acquired projection data is typically processed by a computational pipeline composed of multiple stages. Artifacts introduced during data acquisition can propagate through the pipeline, and degrade image quality in the reconstructed images. Recently, deep learning has shown significant promise in enhancing image quality for images representing scientific data. This success has driven increasing adoption of deep learning techniques in CT imaging. Various approaches have been proposed to incorporate deep learning into computational pipelines, but each has limitations in addressing artifacts effectively and efficiently in synchrotron CT, either in properly addressing the specific artifacts, or in computational efficiency. Recognizing these challenges, we introduce a novel method that incorporates separate deep learning models at each stage of the tomography pipeline-projection, sinogram, and reconstruction-to address specific artifacts locally in a data-driven way. Our approach includes bypass connections that feed both the outputs from previous stages and raw data to subsequent stages, minimizing the risk of error propagation. Extensive evaluations on both simulated and real-world datasets illustrate that our approach effectively reduces artifacts and outperforms comparison methods.

Mathé T. Zeegers, Tristan van Leeuwen, Daniël M. Pelt et al.

Detection of unwanted (`foreign') objects within products is a common procedure in many branches of industry for maintaining production quality. X-ray imaging is a fast, non-invasive and widely applicable method for foreign object detection. Deep learning has recently emerged as a powerful approach for recognizing patterns in radiographs (i.e., X-ray images), enabling automated X-ray based foreign object detection. However, these methods require a large number of training examples and manual annotation of these examples is a subjective and laborious task. In this work, we propose a Computed Tomography (CT) based method for producing training data for supervised learning of foreign object detection, with minimal labour requirements. In our approach, a few representative objects are CT scanned and reconstructed in 3D. The radiographs that have been acquired as part of the CT-scan data serve as input for the machine learning method. High-quality ground truth locations of the foreign objects are obtained through accurate 3D reconstructions and segmentations. Using these segmented volumes, corresponding 2D segmentations are obtained by creating virtual projections. We outline the benefits of objectively and reproducibly generating training data in this way compared to conventional radiograph annotation. In addition, we show how the accuracy depends on the number of objects used for the CT reconstructions. The results show that in this workflow generally only a relatively small number of representative objects (i.e., fewer than 10) are needed to achieve adequate detection performance in an industrial setting. Moreover, for real experimental data we show that the workflow leads to higher foreign object detection accuracies than with standard radiograph annotation.

Richard Schoonhoven, Allard A. Hendriksen, Daniël M. Pelt et al.

Neural network pruning techniques can substantially reduce the computational cost of applying convolutional neural networks (CNNs). Common pruning methods determine which convolutional filters to remove by ranking the filters individually, i.e., without taking into account their interdependence. In this paper, we advocate the viewpoint that pruning should consider the interdependence between series of consecutive operators. We propose the LongEst-chAiN (LEAN) method that prunes CNNs by using graph-based algorithms to select relevant chains of convolutions. A CNN is interpreted as a graph, with the operator norm of each operator as distance metric for the edges. LEAN pruning iteratively extracts the highest value path from the graph to keep. In our experiments, we test LEAN pruning on several image-to-image tasks, including the well-known CamVid dataset, and a real-world X-ray CT dataset. Results indicate that LEAN pruning can result in networks with similar accuracy, while using 1.7-12x fewer convolutional filters than existing approaches.

Marinus J. Lagerwerf, Daniel M Pelt, Willem Jan Palenstijn et al.

Circular cone-beam (CCB) Computed Tomography (CT) has become an integral part of industrial quality control, materials science and medical imaging. The need to acquire and process each scan in a short time naturally leads to trade-offs between speed and reconstruction quality, creating a need for fast reconstruction algorithms capable of creating accurate reconstructions from limited data. In this paper we introduce the Neural Network Feldkamp-Davis-Kress (NN-FDK) algorithm. This algorithm adds a machine learning component to the FDK algorithm to improve its reconstruction accuracy while maintaining its computational efficiency. Moreover, the NN-FDK algorithm is designed such that it has low training data requirements and is fast to train. This ensures that the proposed algorithm can be used to improve image quality in high throughput CT scanning settings, where FDK is currently used to keep pace with the acquisition speed using readily available computational resources. We compare the NN-FDK algorithm to two standard CT reconstruction algorithms and to two popular deep neural networks trained to remove reconstruction artifacts from the 2D slices of an FDK reconstruction. We show that the NN-FDK reconstruction algorithm is substantially faster in computing a reconstruction than all the tested alternative methods except for the standard FDK algorithm and we show it can compute accurate CCB CT reconstructions in cases of high noise, a low number of projection angles or large cone angles. Moreover, we show that the training time of an NN-FDK network is orders of magnitude lower than the considered deep neural networks, with only a slight reduction in reconstruction accuracy.

D. M. Pelt, K. J. Batenburg

In many applications of tomography, the acquired projections are either limited in number or contain a significant amount of noise. In these cases, standard reconstruction methods tend to produce artifacts that can make further analysis difficult. Advanced regularized iterative methods, such as total variation minimization, are often able to achieve a higher reconstruction quality by exploiting prior knowledge about the scanned object. In practice, however, these methods often have prohibitively long computation times or large memory requirements. Furthermore, since they are based on minimizing a global objective function, regularized iterative methods need to reconstruct the entire scanned object, even when one is only interested in a (small) region of the reconstructed image. In this paper, we present a method to approximate regularized iterative reconstruction methods inside a (small) region of the scanned object. The method only performs computations inside the region of interest, ensuring low computational requirements. Reconstruction results for different phantom images and types of regularization are given, showing that reconstructions of the proposed local method are almost identical to those of the global regularized iterative methods that are approximated, even for relatively small regions of interest. Furthermore, we show that larger regions can be reconstructed efficiently by reconstructing several small regions in parallel and combining them into a single reconstruction afterwards.