arXiv subjects

Nil Stolt-Ansó

Publications and source records attributed to Nil Stolt-Ansó.

11 recordsLinked to original sources

arXiv2026

Implicit representations are dead. Long live explicit primitives!

Continuous parameterization of medical data has emerged as a powerful paradigm for resolution-independent image representation. While Implicit Neural Representations offer high fidelity and compact storage, their reliance on global Multi-Layer Perceptrons incurs sizeable computational costs, large memory requirements, and extensive optimization times. As medical imaging trends towards ever-more detailed, high-resolution volumes, these costs impose significant bottlenecks in the applicability of implicit approaches. Recently, explicit Gaussian-based primitives have revolutionized the representation learning paradigm by trading deep network evaluations for localized, rasterization-friendly primitives. In this paper, we present a comprehensive, cross-dimensional evaluation of Gaussian representations against implicit approaches for medical imaging applications. First, we outline a theoretical overview on the mathematical properties offered by explicit primitives beyond what is capable under the implicit neural paradigm. Subsequently, we benchmark the computational performance on two demanding image datasets: 2D microscopy histology and 3D lung Computed Tomography (CT). Our experiments demonstrate that Gaussian representations consistently match or surpass reconstruction metrics compared to implicit methods across all compression factors, while displaying significantly lower optimization times, and memory requirements. Together with the compelling mathematical properties offered by explicit primitives, these findings motivate the wider adoption of Gaussian representations and position them as an attractive direction for future research in medical imaging.

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arXiv2026

NISF++: Geometrically-grounded implicit representations of 3D+time cardiac function from 2D short- and long-axis MR views

Clinical acquisition in cardiac magnetic resonance (CMR) imaging involves obtaining cross-sectional planes of the heart along the radial and longitudinal directions. Despite these planes being 2D cross-sectional images of the heart, radiologists understand the 3D spatial and continuous temporal nature of the organ being imaged. The same can not be said about the conventional deep learning architectures used to process CMR images, which rely on in-plane and grid-based operations, and are hence unable to organically integrate information from all imaging planes. This paper builds upon previous work on neural implicit segmentation functions (NISF) to overcome unaddressed challenges in cardiac function modeling in the CMR domain. For a given subject, our architecture builds a shared 3D+time representations from all available acquisition planes regardless of orientation. By design, predictions along any imaging plane orientation are cross-sections of the same 3D representation, leading to spatio-temporal consistency across all slices. Moreover, our architecture makes the rotation and translation parameters of imaging planes learnable, allowing us to correct for the commonplace respiratory and patient motion between slice acquisitions under a rigid assumption. Furthermore, interpolation of intensities and segmentation can be performed in 4D at any desired resolution. We perform our study on a 120 subject sub-cohort of CMR imaging data from the UK-Biobank. Our in-plane segmentation performance is on-par with existing CMR segmentation methods and explore how the majority of failure cases arise from limitations in the ground-truth segmentation, for which our representations make predictions with better anatomical accuracy than its original training data. We also evaluate our motion-correction capabilities, displaying quantitative and qualitative improvements in slice alignment.

cs.CV↗

arXiv2026

Gabor Primitives for Accelerated Cardiac Cine MRI Reconstruction

Accelerated cardiac cine MRI requires reconstructing spatiotemporal images from highly undersampled k-space data. Implicit neural representations (INRs) enable scan-specific reconstruction without large training datasets, but encode content implicitly in network weights without physically interpretable parameters. Gaussian primitives provide an explicit and geometrically interpretable alternative, but their spectra are confined near the k-space origin, limiting high-frequency representation. We propose Gabor primitives for MRI reconstruction, modulating each Gaussian envelope with a complex exponential to place its spectral support at an arbitrary k-space location, enabling efficient representation of both smooth structures and sharp boundaries. To exploit spatiotemporal redundancy in cardiac cine, we decompose per-primitive temporal variation into a low-rank geometry basis capturing cardiac motion and a signal-intensity basis modeling contrast changes. Experiments on cardiac cine data with Cartesian and radial trajectories show that Gabor primitives consistently outperform compressed sensing, Gaussian primitives, and hash-grid INR baselines, while providing a compact, continuous-resolution representation with physically meaningful parameters.

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arXiv2025

Fast and Explicit: Slice-to-Volume Reconstruction via 3D Gaussian Primitives with Analytic Point Spread Function Modeling

Recovering high-fidelity 3D images from sparse or degraded 2D images is a fundamental challenge in medical imaging, with broad applications ranging from 3D ultrasound reconstruction to MRI super-resolution. In the context of fetal MRI, high-resolution 3D reconstruction of the brain from motion-corrupted low-resolution 2D acquisitions is a prerequisite for accurate neurodevelopmental diagnosis. While implicit neural representations (INRs) have recently established state-of-the-art performance in self-supervised slice-to-volume reconstruction (SVR), they suffer from a critical computational bottleneck: accurately modeling the image acquisition physics requires expensive stochastic Monte Carlo sampling to approximate the point spread function (PSF). In this work, we propose a shift from neural network based implicit representations to Gaussian based explicit representations. By parameterizing the HR 3D image volume as a field of anisotropic Gaussian primitives, we leverage the property of Gaussians being closed under convolution and thus derive a \textit{closed-form analytical solution} for the forward model. This formulation reduces the previously intractable acquisition integral to an exact covariance addition ($\mathbfΣ_{obs} = \mathbfΣ_{HR} + \mathbfΣ_{PSF}$), effectively bypassing the need for compute-intensive stochastic sampling while ensuring exact gradient propagation. We demonstrate that our approach matches the reconstruction quality of self-supervised state-of-the-art SVR frameworks while delivering a 5$\times$--10$\times$ speed-up on neonatal and fetal data. With convergence often reached in under 30 seconds, our framework paves the way towards translation into clinical routine of real-time fetal 3D MRI. Code will be public at {https://github.com/m-dannecker/Gaussian-Primitives-for-Fast-SVR}.

cs.CV↗

arXiv2025

Reconstruction-free segmentation from undersampled k-space using transformers

Motivation: High acceleration factors place a limit on MRI image reconstruction. This limit is extended to segmentation models when treating these as subsequent independent processes. Goal: Our goal is to produce segmentations directly from sparse k-space measurements without the need for intermediate image reconstruction. Approach: We employ a transformer architecture to encode global k-space information into latent features. The produced latent vectors condition queried coordinates during decoding to generate segmentation class probabilities. Results: The model is able to produce better segmentations across high acceleration factors than image-based segmentation baselines. Impact: Cardiac segmentation directly from undersampled k-space samples circumvents the need for an intermediate image reconstruction step. This allows the potential to assess myocardial structure and function on higher acceleration factors than methods that rely on images as input.

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arXiv2025

Global and Local Contrastive Learning for Joint Representations from Cardiac MRI and ECG

An electrocardiogram (ECG) is a widely used, cost-effective tool for detecting electrical abnormalities in the heart. However, it cannot directly measure functional parameters, such as ventricular volumes and ejection fraction, which are crucial for assessing cardiac function. Cardiac magnetic resonance (CMR) is the gold standard for these measurements, providing detailed structural and functional insights, but is expensive and less accessible. To bridge this gap, we propose PTACL (Patient and Temporal Alignment Contrastive Learning), a multimodal contrastive learning framework that enhances ECG representations by integrating spatio-temporal information from CMR. PTACL uses global patient-level contrastive loss and local temporal-level contrastive loss. The global loss aligns patient-level representations by pulling ECG and CMR embeddings from the same patient closer together, while pushing apart embeddings from different patients. Local loss enforces fine-grained temporal alignment within each patient by contrasting encoded ECG segments with corresponding encoded CMR frames. This approach enriches ECG representations with diagnostic information beyond electrical activity and transfers more insights between modalities than global alignment alone, all without introducing new learnable weights. We evaluate PTACL on paired ECG-CMR data from 27,951 subjects in the UK Biobank. Compared to baseline approaches, PTACL achieves better performance in two clinically relevant tasks: (1) retrieving patients with similar cardiac phenotypes and (2) predicting CMR-derived cardiac function parameters, such as ventricular volumes and ejection fraction. Our results highlight the potential of PTACL to enhance non-invasive cardiac diagnostics using ECG. The code is available at: https://github.com/alsalivan/ecgcmr

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arXiv2025

Interpretable deformable image registration: A geometric deep learning perspective

Deformable image registration poses a challenging problem where, unlike most deep learning tasks, a complex relationship between multiple coordinate systems has to be considered. Although data-driven methods have shown promising capabilities to model complex non-linear transformations, existing works employ standard deep learning architectures assuming they are general black-box solvers. We argue that understanding how learned operations perform pattern-matching between the features in the source and target domains is the key to building robust, data-efficient, and interpretable architectures. We present a theoretical foundation for designing an interpretable registration framework: separated feature extraction and deformation modeling, dynamic receptive fields, and a data-driven deformation functions awareness of the relationship between both spatial domains. Based on this foundation, we formulate an end-to-end process that refines transformations in a coarse-to-fine fashion. Our architecture employs spatially continuous deformation modeling functions that use geometric deep-learning principles, therefore avoiding the problematic approach of resampling to a regular grid between successive refinements of the transformation. We perform a qualitative investigation to highlight interesting interpretability properties of our architecture. We conclude by showing significant improvement in performance metrics over state-of-the-art approaches for both mono- and multi-modal inter-subject brain registration, as well as the challenging task of longitudinal retinal intra-subject registration. We make our code publicly available

cs.CV↗

arXiv2024

Direct Cardiac Segmentation from Undersampled K-space Using Transformers

The prevailing deep learning-based methods of predicting cardiac segmentation involve reconstructed magnetic resonance (MR) images. The heavy dependency of segmentation approaches on image quality significantly limits the acceleration rate in fast MR reconstruction. Moreover, the practice of treating reconstruction and segmentation as separate sequential processes leads to artifact generation and information loss in the intermediate stage. These issues pose a great risk to achieving high-quality outcomes. To leverage the redundant k-space information overlooked in this dual-step pipeline, we introduce a novel approach to directly deriving segmentations from sparse k-space samples using a transformer (DiSK). DiSK operates by globally extracting latent features from 2D+time k-space data with attention blocks and subsequently predicting the segmentation label of query points. We evaluate our model under various acceleration factors (ranging from 4 to 64) and compare against two image-based segmentation baselines. Our model consistently outperforms the baselines in Dice and Hausdorff distances across foreground classes for all presented sampling rates.

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arXiv2024

Intensity-based 3D motion correction for cardiac MR images

Cardiac magnetic resonance (CMR) image acquisition requires subjects to hold their breath while 2D cine images are acquired. This process assumes that the heart remains in the same position across all slices. However, differences in breathhold positions or patient motion introduce 3D slice misalignments. In this work, we propose an algorithm that simultaneously aligns all SA and LA slices by maximizing the pair-wise intensity agreement between their intersections. Unlike previous works, our approach is formulated as a subject-specific optimization problem and requires no prior knowledge of the underlying anatomy. We quantitatively demonstrate that the proposed method is robust against a large range of rotations and translations by synthetically misaligning 10 motion-free datasets and aligning them back using the proposed method.

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arXiv2023

Global k-Space Interpolation for Dynamic MRI Reconstruction using Masked Image Modeling

In dynamic Magnetic Resonance Imaging (MRI), k-space is typically undersampled due to limited scan time, resulting in aliasing artifacts in the image domain. Hence, dynamic MR reconstruction requires not only modeling spatial frequency components in the x and y directions of k-space but also considering temporal redundancy. Most previous works rely on image-domain regularizers (priors) to conduct MR reconstruction. In contrast, we focus on interpolating the undersampled k-space before obtaining images with Fourier transform. In this work, we connect masked image modeling with k-space interpolation and propose a novel Transformer-based k-space Global Interpolation Network, termed k-GIN. Our k-GIN learns global dependencies among low- and high-frequency components of 2D+t k-space and uses it to interpolate unsampled data. Further, we propose a novel k-space Iterative Refinement Module (k-IRM) to enhance the high-frequency components learning. We evaluate our approach on 92 in-house 2D+t cardiac MR subjects and compare it to MR reconstruction methods with image-domain regularizers. Experiments show that our proposed k-space interpolation method quantitatively and qualitatively outperforms baseline methods. Importantly, the proposed approach achieves substantially higher robustness and generalizability in cases of highly-undersampled MR data. For video presentation, poster, GIF results and code please check our project page: https://jzpeterpan.github.io/k-gin.github.io/.

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arXiv2023

NISF: Neural Implicit Segmentation Functions

Segmentation of anatomical shapes from medical images has taken an important role in the automation of clinical measurements. While typical deep-learning segmentation approaches are performed on discrete voxels, the underlying objects being analysed exist in a real-valued continuous space. Approaches that rely on convolutional neural networks (CNNs) are limited to grid-like inputs and not easily applicable to sparse or partial measurements. We propose a novel family of image segmentation models that tackle many of CNNs' shortcomings: Neural Implicit Segmentation Functions (NISF). Our framework takes inspiration from the field of neural implicit functions where a network learns a mapping from a real-valued coordinate-space to a shape representation. NISFs have the ability to segment anatomical shapes in high-dimensional continuous spaces. Training is not limited to voxelized grids, and covers applications with sparse and partial data. Interpolation between observations is learnt naturally in the training procedure and requires no post-processing. Furthermore, NISFs allow the leveraging of learnt shape priors to make predictions for regions outside of the original image plane. We go on to show the framework achieves dice scores of 0.87 $\pm$ 0.045 on a (3D+t) short-axis cardiac segmentation task using the UK Biobank dataset. We also provide a qualitative analysis on our frameworks ability to perform segmentation and image interpolation on unseen regions of an image volume at arbitrary resolutions.

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