arXiv subjects

Thomas Wendler

Publications and source records attributed to Thomas Wendler.

At least 19 recordsLinked to original sources

arXiv2026

Implicit Neural Representations for Multimodal Longitudinal Image Imputation and Interpolation

Longitudinal multiparametric MRI is central to follow-up imaging in oncology, yet real-world clinical data are characterised by missing sequences, heterogeneous acquisition protocols, and varying spatial resolutions across time points. We propose a patient-specific conditional implicit neural representation (INR) that models multimodal longitudinal MRI as a continuous function of world coordinates, time, and modality conditioning. The model is trained with stochastic modality dropout to handle incomplete data, and its continuous coordinate-space formulation enables both spatial and temporal interpolation without resampling to a fixed voxel grid. A self-consistency-based confidence estimator is derived from cross-modal reconstruction performance at inference time. We evaluate the framework on longitudinal MRI from paediatric brain tumour patients, demonstrating statistically significant improvements over linear interpolation for T1CE and FLAIR (p < 0.05), with mean MS-SSIM of 0.95 $\pm$ 0.02 for T1CE. Predicted confidence correlates strongly with true reconstruction quality (Pearson r up to 0.996), suggesting reliable deployment potential in heterogeneous clinical settings.

cs.CV↗

arXiv2026

Inverse Bayesian Inference for Extracting Lesion Dynamics from Longitudinal Spectral CT

Longitudinal medical imaging captures temporal evolution of lesions, yet extracting the underlying dynamical parameters governing this evolution remains challenging. We propose an inverse Bayesian framework for inferring lesion dynamics from longitudinal spectral CT. We decompose spectral feature ($x$) evolution into three components: \begin{equation*} \frac{dx_i}{dt} = A_i x_i + B \cdot n + C \cdot \Delta x_{\text{sat}} \end{equation*} where $A_i$ captures intrinsic dynamics (lesion-autonomous evolution), $B$ captures local environment tumour burden (organ tumour burden through satellite count coupling), and $C$ captures environment/satellite state change (i.e., whether surrounding lesions move similarly or not). We demonstrate the framework on photon-counting NSCLC CT data from metastases, recovering distinct dynamical regimes: lung lesions exhibit significant satellite count coupling ($B=-0.34$, $p<0.05$) suggesting competitive dynamics, while liver lesions show synergistic satellite behaviour coupling ($C\approx+1.0$, $p<0.05$). Synthetic validation confirms parameter recovery, and cross-coupling analysis validates that our method detects non-zero coupling when present. This work establishes inverse dynamical inference as a principled methodology for extracting interpretable parameters from longitudinal imaging, moving beyond static feature extraction toward mechanistic characterisation of lesion behaviour. The code and data are available at: https://github.com/lukasf98/inverse-bayesian-inference

cs.CV↗

arXiv2026

Performance and Explainability Requirements of Evolutionary Algorithms in Real-World Physics-Informed Optimization

Evolutionary computation offers a variety of tools to solve complex real-world optimization problems. However, research often focuses on smaller, simplified problems and optimization algorithms that sometimes miss expectations in real-world scenarios. Additionally, trust in the applied algorithm and the solutions it provides is often essential in such settings, but requires an understanding of the search process itself. This leads to evolutionary computation often not being seriously considered by practitioners in many application contexts, among them physics-based modeling. In this article, techniques from evolutionary computation are detailed that can alleviate these problems. First, five real-world physics-based optimization problems are introduced and described by domain experts. For each of these, the requirements for the evolutionary algorithm regarding performance and explainability to increase trust and usability are presented. We found that all domain experts expect fast convergence to a good solution and want some explanations for how the results were formed, while other requirements strongly depend on the respective problem. Finally, we present existing approaches that can be leveraged to improve those aspects of evolutionary algorithms but have to our knowledge never been employed in complex real-world scenarios. This implies a gap between both domains that needs to be closed to exploit the full potential of evolutionary computation.

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arXiv2026

Bridging MRI and PET physiology: Untangling complementarity through orthogonal representations

Multimodal imaging analysis often relies on joint latent representations, yet these approaches rarely define what information is shared versus modality-specific. Clarifying this distinction is clinically relevant, as it delineates the irreducible contribution of each modality and informs rational acquisition strategies. We propose a subspace decomposition framework that reframes multimodal fusion as a problem of orthogonal subspace separation rather than translation. We decompose Prostate-Specific Membrane Antigen (PSMA) PET uptake into an MRI-explainable physiological envelope and an orthogonal residual reflecting signal components not expressible within the MRI feature manifold. Using multiparametric MRI, we train an intensity-based, non-spatial implicit neural representation (INR) to map MRI feature vectors to PET uptake. We introduce a projection-based regularization using singular value decomposition to penalize residual components lying within the span of the MRI feature manifold. This enforces mathematical orthogonality between tissue-level physiological properties (structure, diffusion, perfusion) and intracellular PSMA expression. Tested on 13 prostate cancer patients, the model demonstrates that residual components spanned by MRI features are absorbed into the learned envelope, while the orthogonal residual is largest in tumour regions. This indicates that PSMA PET contains signal components not recoverable from MRI-derived physiological descriptors. The resulting decomposition provides a structured characterization of modality complementarity grounded in representation geometry rather than image translation.

cs.CV↗

arXiv2026

Energy-based Tissue Manifolds for Longitudinal Multiparametric MRI Analysis

We propose a geometric framework for longitudinal multi-parametric MRI analysis based on patient-specific energy modelling in sequence space. Rather than operating on images with spatial networks, each voxel is represented by its multi-sequence intensity vector ($T1$, $T1c$, $T2$, FLAIR, ADC), and a compact implicit neural representation is trained via denoising score matching to learn an energy function $E_{\theta}(\mathbf{u})$ over $\mathbb{R}^d$ from a single baseline scan. The learned energy landscape provides a differential-geometric description of tissue regimes without segmentation labels. Local minima define tissue basins, gradient magnitude reflects proximity to regime boundaries, and Laplacian curvature characterises local constraint structure. Importantly, this baseline energy manifold is treated as a fixed geometric reference: it encodes the set of contrast combinations observed at diagnosis and is not retrained at follow-up. Longitudinal assessment is therefore formulated as evaluation of subsequent scans relative to this baseline geometry. Rather than comparing anatomical segmentations, we analyse how the distribution of MRI sequence vectors evolves under the baseline energy function. In a paediatric case with later recurrence, follow-up scans show progressive deviation in energy and directional displacement in sequence space toward the baseline tumour-associated regime before clear radiological reappearance. In a case with stable disease, voxel distributions remain confined to established low-energy basins without systematic drift. The presented cases serve as proof-of-concept that patient-specific energy manifolds can function as geometric reference systems for longitudinal mpMRI analysis without explicit segmentation or supervised classification, providing a foundation for further investigation of manifold-based tissue-at-risk tracking in neuro-oncology.

cs.CV↗

arXiv2025

Learn2Reg 2024: New Benchmark Datasets Driving Progress on New Challenges

Medical image registration is critical for clinical applications, and fair benchmarking of different methods is essential for monitoring ongoing progress in the field. To date, the Learn2Reg 2020-2023 challenges have released several complementary datasets and established metrics for evaluations. Building on this foundation, the 2024 edition expands the challenge's scope to cover a wider range of registration scenarios, particularly in terms of modality diversity and task complexity, by introducing three new tasks, including large-scale multi-modal registration and unsupervised inter-subject brain registration, as well as the first microscopy-focused benchmark within Learn2Reg. The new datasets also inspired new method developments, including invertibility constraints, pyramid features, keypoints alignment and instance optimisation. Visit Learn2Reg at https://learn2reg.grand-challenge.org.

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arXiv2025

Beyond the LUMIR challenge: The pathway to foundational registration models

Medical image challenges have played a transformative role in advancing the field, catalyzing innovation and establishing new performance benchmarks. Image registration, a foundational task in neuroimaging, has similarly advanced through the Learn2Reg initiative. Building on this, we introduce the Large-scale Unsupervised Brain MRI Image Registration (LUMIR) challenge, a next-generation benchmark for unsupervised brain MRI registration. Previous challenges relied upon anatomical label maps, however LUMIR provides 4,014 unlabeled T1-weighted MRIs for training, encouraging biologically plausible deformation modeling through self-supervision. Evaluation includes 590 in-domain test subjects and extensive zero-shot tasks across disease populations, imaging protocols, and species. Deep learning methods consistently achieved state-of-the-art performance and produced anatomically plausible, diffeomorphic deformation fields. They outperformed several leading optimization-based methods and remained robust to most domain shifts. These findings highlight the growing maturity of deep learning in neuroimaging registration and its potential to serve as a foundation model for general-purpose medical image registration.

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arXiv2025

Anatomy-constrained modelling of image-derived input functions in dynamic PET using multi-organ segmentation

Accurate kinetic analysis of [$^{18}$F]FDG distribution in dynamic positron emission tomography (PET) requires anatomically constrained modelling of image-derived input functions (IDIFs). Traditionally, IDIFs are obtained from the aorta, neglecting anatomical variations and complex vascular contributions. This study proposes a multi-organ segmentation-based approach that integrates IDIFs from the aorta, portal vein, pulmonary artery, and ureters. Using high-resolution CT segmentations of the liver, lungs, kidneys, and bladder, we incorporate organ-specific blood supply sources to improve kinetic modelling. Our method was evaluated on dynamic [$^{18}$F]FDG PET data from nine patients, resulting in a mean squared error (MSE) reduction of $13.39\%$ for the liver and $10.42\%$ for the lungs. These initial results highlight the potential of multiple IDIFs in improving anatomical modelling and fully leveraging dynamic PET imaging. This approach could facilitate the integration of tracer kinetic modelling into clinical routine.

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arXiv2025

Physiological neural representation for personalised tracer kinetic parameter estimation from dynamic PET

Dynamic positron emission tomography (PET) with [$^{18}$F]FDG enables non-invasive quantification of glucose metabolism through kinetic analysis, often modelled by the two-tissue compartment model (TCKM). However, voxel-wise kinetic parameter estimation using conventional methods is computationally intensive and limited by spatial resolution. Deep neural networks (DNNs) offer an alternative but require large training datasets and significant computational resources. To address these limitations, we propose a physiological neural representation based on implicit neural representations (INRs) for personalized kinetic parameter estimation. INRs, which learn continuous functions, allow for efficient, high-resolution parametric imaging with reduced data requirements. Our method also integrates anatomical priors from a 3D CT foundation model to enhance robustness and precision in kinetic modelling. We evaluate our approach on an [$^{18}$F]FDG dynamic PET/CT dataset and compare it to state-of-the-art DNNs. Results demonstrate superior spatial resolution, lower mean-squared error, and improved anatomical consistency, particularly in tumour and highly vascularized regions. Our findings highlight the potential of INRs for personalized, data-efficient tracer kinetic modelling, enabling applications in tumour characterization, segmentation, and prognostic assessment.

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arXiv2024

Fine-Tuning TransMorph with Gradient Correlation for Anatomical Alignment

Unsupervised deep learning is a promising method in brain MRI registration to reduce the reliance on anatomical labels, while still achieving anatomically accurate transformations. For the Learn2Reg2024 LUMIR challenge, we propose fine-tuning of the pre-trained TransMorph model to improve the convergence stability as well as the deformation smoothness. The former is achieved through the FAdam optimizer, and consistency in structural changes is incorporated through the addition of gradient correlation in the similarity measure, improving anatomical alignment. The results show slight improvements in the Dice and HdDist95 scores, and a notable reduction in the NDV compared to the baseline TransMorph model. These are also confirmed by inspecting the boundaries of the tissue. Our proposed method highlights the effectiveness of including Gradient Correlation to achieve smoother and structurally consistent deformations for interpatient brain MRI registration.

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arXiv2024

Shape Completion in the Dark: Completing Vertebrae Morphology from 3D Ultrasound

Purpose: Ultrasound (US) imaging, while advantageous for its radiation-free nature, is challenging to interpret due to only partially visible organs and a lack of complete 3D information. While performing US-based diagnosis or investigation, medical professionals therefore create a mental map of the 3D anatomy. In this work, we aim to replicate this process and enhance the visual representation of anatomical structures. Methods: We introduce a point-cloud-based probabilistic DL method to complete occluded anatomical structures through 3D shape completion and choose US-based spine examinations as our application. To enable training, we generate synthetic 3D representations of partially occluded spinal views by mimicking US physics and accounting for inherent artifacts. Results: The proposed model performs consistently on synthetic and patient data, with mean and median differences of 2.02 and 0.03 in CD, respectively. Our ablation study demonstrates the importance of US physics-based data generation, reflected in the large mean and median difference of 11.8 CD and 9.55 CD, respectively. Additionally, we demonstrate that anatomic landmarks, such as the spinous process (with reconstruction CD of 4.73) and the facet joints (mean distance to GT of 4.96mm) are preserved in the 3D completion. Conclusion: Our work establishes the feasibility of 3D shape completion for lumbar vertebrae, ensuring the preservation of level-wise characteristics and successful generalization from synthetic to real data. The incorporation of US physics contributes to more accurate patient data completions. Notably, our method preserves essential anatomic landmarks and reconstructs crucial injections sites at their correct locations. The generated data and source code will be made publicly available (https://github.com/miruna20/Shape-Completion-in-the-Dark).

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arXiv2023

Interactive Segmentation for COVID-19 Infection Quantification on Longitudinal CT scans

Consistent segmentation of COVID-19 patient's CT scans across multiple time points is essential to assess disease progression and response to therapy accurately. Existing automatic and interactive segmentation models for medical images only use data from a single time point (static). However, valuable segmentation information from previous time points is often not used to aid the segmentation of a patient's follow-up scans. Also, fully automatic segmentation techniques frequently produce results that would need further editing for clinical use. In this work, we propose a new single network model for interactive segmentation that fully utilizes all available past information to refine the segmentation of follow-up scans. In the first segmentation round, our model takes 3D volumes of medical images from two-time points (target and reference) as concatenated slices with the additional reference time point segmentation as a guide to segment the target scan. In subsequent segmentation refinement rounds, user feedback in the form of scribbles that correct the segmentation and the target's previous segmentation results are additionally fed into the model. This ensures that the segmentation information from previous refinement rounds is retained. Experimental results on our in-house multiclass longitudinal COVID-19 dataset show that the proposed model outperforms its static version and can assist in localizing COVID-19 infections in patient's follow-up scans.

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arXiv2023

AutoPaint: A Self-Inpainting Method for Unsupervised Anomaly Detection

Robust and accurate detection and segmentation of heterogenous tumors appearing in different anatomical organs with supervised methods require large-scale labeled datasets covering all possible types of diseases. Due to the unavailability of such rich datasets and the high cost of annotations, unsupervised anomaly detection (UAD) methods have been developed aiming to detect the pathologies as deviation from the normality by utilizing the unlabeled healthy image data. However, developed UAD models are often trained with an incomplete distribution of healthy anatomies and have difficulties in preserving anatomical constraints. This work intends to, first, propose a robust inpainting model to learn the details of healthy anatomies and reconstruct high-resolution images by preserving anatomical constraints. Second, we propose an autoinpainting pipeline to automatically detect tumors, replace their appearance with the learned healthy anatomies, and based on that segment the tumoral volumes in a purely unsupervised fashion. Three imaging datasets, including PET, CT, and PET-CT scans of lung tumors and head and neck tumors, are studied as benchmarks for evaluation. Experimental results demonstrate the significant superiority of the proposed method over a wide range of state-of-the-art UAD methods. Moreover, the unsupervised method we propose produces comparable results to a robust supervised segmentation method when applied to multimodal images.

cs.CV↗

arXiv2023

Self-Supervised Learning for Physiologically-Based Pharmacokinetic Modeling in Dynamic PET

Dynamic positron emission tomography imaging (dPET) provides temporally resolved images of a tracer enabling a quantitative measure of physiological processes. Voxel-wise physiologically-based pharmacokinetic (PBPK) modeling of the time activity curves (TAC) can provide relevant diagnostic information for clinical workflow. Conventional fitting strategies for TACs are slow and ignore the spatial relation between neighboring voxels. We train a spatio-temporal UNet to estimate the kinetic parameters given TAC from F-18-fluorodeoxyglucose (FDG) dPET. This work introduces a self-supervised loss formulation to enforce the similarity between the measured TAC and those generated with the learned kinetic parameters. Our method provides quantitatively comparable results at organ-level to the significantly slower conventional approaches, while generating pixel-wise parametric images which are consistent with expected physiology. To the best of our knowledge, this is the first self-supervised network that allows voxel-wise computation of kinetic parameters consistent with a non-linear kinetic model. The code will become publicly available upon acceptance.

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arXiv2022

Precise Repositioning of Robotic Ultrasound: Improving Registration-based Motion Compensation using Ultrasound Confidence Optimization

Robotic ultrasound (US) imaging has been seen as a promising solution to overcome the limitations of free-hand US examinations, i.e., inter-operator variability. However, the fact that robotic US systems cannot react to subject movements during scans limits their clinical acceptance. Regarding human sonographers, they often react to patient movements by repositioning the probe or even restarting the acquisition, in particular for the scans of anatomies with long structures like limb arteries. To realize this characteristic, we proposed a vision-based system to monitor the subject's movement and automatically update the scan trajectory thus seamlessly obtaining a complete 3D image of the target anatomy. The motion monitoring module is developed using the segmented object masks from RGB images. Once the subject is moved, the robot will stop and recompute a suitable trajectory by registering the surface point clouds of the object obtained before and after the movement using the iterative closest point algorithm. Afterward, to ensure optimal contact conditions after repositioning US probe, a confidence-based fine-tuning process is used to avoid potential gaps between the probe and contact surface. Finally, the whole system is validated on a human-like arm phantom with an uneven surface, while the object segmentation network is also validated on volunteers. The results demonstrate that the presented system can react to object movements and reliably provide accurate 3D images.

cs.RO↗

arXiv2022

U-PET: MRI-based Dementia Detection with Joint Generation of Synthetic FDG-PET Images

Alzheimer's disease (AD) is the most common cause of dementia. An early detection is crucial for slowing down the disease and mitigating risks related to the progression. While the combination of MRI and FDG-PET is the best image-based tool for diagnosis, FDG-PET is not always available. The reliable detection of Alzheimer's disease with only MRI could be beneficial, especially in regions where FDG-PET might not be affordable for all patients. To this end, we propose a multi-task method based on U-Net that takes T1-weighted MR images as an input to generate synthetic FDG-PET images and classifies the dementia progression of the patient into cognitive normal (CN), cognitive impairment (MCI), and AD. The attention gates used in both task heads can visualize the most relevant parts of the brain, guiding the examiner and adding interpretability. Results show the successful generation of synthetic FDG-PET images and a performance increase in disease classification over the naive single-task baseline.

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arXiv2022

Weakly-supervised Biomechanically-constrained CT/MRI Registration of the Spine

CT and MRI are two of the most informative modalities in spinal diagnostics and treatment planning. CT is useful when analysing bony structures, while MRI gives information about the soft tissue. Thus, fusing the information of both modalities can be very beneficial. Registration is the first step for this fusion. While the soft tissues around the vertebra are deformable, each vertebral body is constrained to move rigidly. We propose a weakly-supervised deep learning framework that preserves the rigidity and the volume of each vertebra while maximizing the accuracy of the registration. To achieve this goal, we introduce anatomy-aware losses for training the network. We specifically design these losses to depend only on the CT label maps since automatic vertebra segmentation in CT gives more accurate results contrary to MRI. We evaluate our method on an in-house dataset of 167 patients. Our results show that adding the anatomy-aware losses increases the plausibility of the inferred transformation while keeping the accuracy untouched.

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arXiv2022

VesNet-RL: Simulation-based Reinforcement Learning for Real-World US Probe Navigation

Ultrasound (US) is one of the most common medical imaging modalities since it is radiation-free, low-cost, and real-time. In freehand US examinations, sonographers often navigate a US probe to visualize standard examination planes with rich diagnostic information. However, reproducibility and stability of the resulting images often suffer from intra- and inter-operator variation. Reinforcement learning (RL), as an interaction-based learning method, has demonstrated its effectiveness in visual navigating tasks; however, RL is limited in terms of generalization. To address this challenge, we propose a simulation-based RL framework for real-world navigation of US probes towards the standard longitudinal views of vessels. A UNet is used to provide binary masks from US images; thereby, the RL agent trained on simulated binary vessel images can be applied in real scenarios without further training. To accurately characterize actual states, a multi-modality state representation structure is introduced to facilitate the understanding of environments. Moreover, considering the characteristics of vessels, a novel standard view recognition approach based on the minimum bounding rectangle is proposed to terminate the searching process. To evaluate the effectiveness of the proposed method, the trained policy is validated virtually on 3D volumes of a volunteer's in-vivo carotid artery, and physically on custom-designed gel phantoms using robotic US. The results demonstrate that proposed approach can effectively and accurately navigate the probe towards the longitudinal view of vessels.

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