arXiv subjects

Antony J. Lomax

Publications and source records attributed to Antony J. Lomax.

8 recordsLinked to original sources

arXiv2026

Portable surrogate-free 4D MRI from standard fast multi-slice 2D MRI via implicit neural representations

Four-dimensional MRI (4D MRI) characterizes respiratory organ motion, yet existing reconstruction pipelines are tightly coupled to specific acquisition platforms (e.g., non-Cartesian trajectories with self-gating, vendor-specific navigators, or external respiratory hardware), limiting broad adoption across diverse clinical and research settings, including low-field, open-bore, and non-supine imaging. We present SIMPLE-4D (Surrogate-free, IMplicit, PortabLE 4D MRI), a software-first portable workflow that operates entirely on reconstructed slices from standard fast multi-slice 2D MRI and requires no pulse-sequence modification, no non-Cartesian trajectory, no navigator, and no external hardware. SIMPLE-4D combines an acquisition-agnostic front end consuming standard 2D protocols, a surrogate-free variational motion encoder that extracts a compact motion code directly from each 2D slice, and a physics-aware continuous spatio-temporal reconstruction based on a hash-encoded implicit neural representation (INR) with a SIREN deformation network producing bidirectional cycle-consistent DVFs and motion-dependent Gauss-Legendre thick-slice quadrature. Bidirectionality yields a complete inter-frame motion model by composition, supporting downstream tasks such as dose accumulation without retraining. We validate the identical pipeline on two contrasting datasets: a 1.5 T clinical bSSFP dataset (5 volunteers, 3 sessions each) and a 0.5 T open-bore HASTE dataset (5 volunteers, supine and upright). To our knowledge, this is the first per-frame 4D volumetric respiratory MRI reconstruction on a weight-bearing upright open-bore low-field scanner from reconstructed 2D Cartesian slices alone. On low-field data the INR template additionally acts as an implicit denoiser, yielding +132% SNR. Systematic ablations isolate each component's contribution.

physics.med-ph↗

arXiv2025

CPT-4DMR: Continuous sPatial-Temporal Representation for 4D-MRI Reconstruction

Four-dimensional MRI (4D-MRI) is an promising technique for capturing respiratory-induced motion in radiation therapy planning and delivery. Conventional 4D reconstruction methods, which typically rely on phase binning or separate template scans, struggle to capture temporal variability, complicate workflows, and impose heavy computational loads. We introduce a neural representation framework that considers respiratory motion as a smooth, continuous deformation steered by a 1D surrogate signal, completely replacing the conventional discrete sorting approach. The new method fuses motion modeling with image reconstruction through two synergistic networks: the Spatial Anatomy Network (SAN) encodes a continuous 3D anatomical representation, while a Temporal Motion Network (TMN), guided by Transformer-derived respiratory signals, produces temporally consistent deformation fields. Evaluation using a free-breathing dataset of 19 volunteers demonstrates that our template- and phase-free method accurately captures both regular and irregular respiratory patterns, while preserving vessel and bronchial continuity with high anatomical fidelity. The proposed method significantly improves efficiency, reducing the total processing time from approximately five hours required by conventional discrete sorting methods to just 15 minutes of training. Furthermore, it enables inference of each 3D volume in under one second. The framework accurately reconstructs 3D images at any respiratory state, achieves superior performance compared to conventional methods, and demonstrates strong potential for application in 4D radiation therapy planning and real-time adaptive treatment.

cs.CV↗

arXiv2025

Continuous sPatial-Temporal Deformable Image Registration (CPT-DIR) for motion modelling in radiotherapy: beyond classic voxel-based methods

Deformable image registration (DIR) is a crucial tool in radiotherapy for analyzing anatomical changes and motion patterns. Current DIR implementations rely on discrete volumetric motion representation, which often leads to compromised accuracy and uncertainty when handling significant anatomical changes and sliding boundaries. This limitation affects the reliability of subsequent contour propagation and dose accumulation procedures, particularly in regions with complex anatomical interfaces such as the lung-chest wall boundary. Given that organ motion is inherently a continuous process in both space and time, we aimed to develop a model that preserves these fundamental properties. Drawing inspiration from fluid mechanics, we propose a novel approach using implicit neural representation (INR) for continuous modeling of patient anatomical motion. This approach ensures spatial and temporal continuity while effectively unifying Eulerian and Lagrangian specifications to enable natural continuous motion modeling and frame interpolation. The integration of these specifications provides a more comprehensive understanding of anatomical deformation patterns. By leveraging the continuous representations, the CPT-DIR method significantly enhances registration and interpolation accuracy, automation, and speed. The method demonstrates superior performance in landmark and contour precision, particularly in challenging anatomical regions, representing a substantial advancement over conventional approaches in deformable image registration. The improved efficiency and accuracy of CPT-DIR make it particularly suitable for real-time adaptive radiotherapy applications.

physics.med-ph↗

arXiv2024

GAMBAS -- Fast Beam Arrangement Selection for Proton Therapy using a Nearest Neighbour Model

Purpose: Beam angle selection is critical in proton therapy treatment planning, yet automated approaches remain underexplored. This study presents and evaluates GAMBAS, a novel, fast machine learning model for automatic beam angle selection. Methods: The model extracts a predefined set of anatomical features from a patient's CT and structure contours. Using these features, it identifies the most similar patient from a training database and suggests that patient's beam arrangement. A retrospective study with 19 patients was conducted, comparing this model's suggestions to human planners' choices and randomly selected beam arrangements from the training dataset. An expert treatment planner evaluated the plans on quality (scale 1-5), ranked them, and guessed the method used. Results: The number of acceptable (score 4 or 5) plans was comparable between human-chosen 17 (89%) and model-selected 16(84%) beam arrangements. The fully automatic treatment planning took between 4 - 7 min (mean 5 min). Conclusion: The model produces beam arrangements of comparable quality to those chosen by human planners, demonstrating its potential as a fast tool for quality assurance and patient selection, although it is not yet ready for clinical use.

physics.med-ph↗

arXiv2024

JulianA.jl -- A Julia package for radiotherapy

The importance of computers is continually increasing in radiotherapy. Efficient algorithms, implementations and the ability to leverage advancements in computer science are crucial to improve cancer care even further and deliver the best treatment to each patient. Yet, the software landscape for radiotherapy is fragmented into proprietary systems that do not share a common interface. Further, the radiotherapy community does not have access to the vast possibilities offered by modern programming languages and their ecosystem of libraries yet. We present JulianA.jl, a novel Julia package for radiotherapy. It aims to provide a modular and flexible foundation for the development and efficient implementation of algorithms and workflows for radiotherapy researchers and clinicians. JulianA.jl can be interfaced with any scriptable treatment planning system, be it commercial, open source or in-house developed. This article highlights our design choices and showcases the package's simplicity and powerful automatic treatment planning capabilities.

physics.med-ph↗

arXiv2024

A Unified Generation-Registration Framework for Improved MR-based CT Synthesis in Proton Therapy

Background: In MR-guided proton therapy planning, aligning MR and CT images is key for MR-based CT synthesis, especially in mobile regions like the head-and-neck. Misalignments here can lead to less accurate synthetic CT (sCT) images, impacting treatment precision. Purpose: This study introduces a novel network that cohesively unifies image generation and registration processes to enhance the quality and anatomical fidelity of sCTs derived from better-aligned MR images. Methods: The approach synergizes a generation network (G) with a deformable registration network (R), optimizing them jointly in MR-to-CT synthesis. This goal is achieved by alternately minimizing the discrepancies between the generated/registered CT images and their corresponding reference CT counterparts. The generation network employs a UNet architecture, while the registration network leverages an implicit neural representation of the Deformable Vector Fields (DVFs). We validated this method on a dataset comprising 60 Head-and-Neck patients, reserving 12 cases for holdout testing. Results: Compared to the baseline Pix2Pix method with MAE 124.95\pm 30.74 HU, the proposed technique demonstrated 80.98\pm 7.55 HU. The unified translation-registration network produced sharper and more anatomically congruent outputs, showing superior efficacy in converting MR images to sCTs. Additionally, from a dosimetric perspective, the plan recalculated on the resulting sCTs resulted in a remarkably reduced discrepancy to the reference proton plans. Conclusions: This study conclusively demonstrates that a holistic MR-based CT synthesis approach, integrating both image-to-image translation and deformable registration, significantly improves the precision and quality of sCT generation, particularly for the challenging body area with varied anatomic changes between corresponding MR and CT.

physics.med-ph↗

arXiv2023

JulianA: An automatic treatment planning platform for intensity-modulated proton therapy and its application to intra- and extracerebral neoplasms

Creating high quality treatment plans is crucial for a successful radiotherapy treatment. However, it demands substantial effort and special training for dosimetrists. Existing automated treatment planning systems typically require either an explicit prioritization of planning objectives, human-assigned objective weights, large amounts of historic plans to train an artificial intelligence or long planning times. Many of the existing auto-planning tools are difficult to extend to new planning goals. A new spot weight optimisation algorithm, called JulianA, was developed. The algorithm minimises a scalar loss function that is built only based on the prescribed dose to the tumour and organs at risk (OARs), but does not rely on historic plans. The objective weights in the loss function have default values that do not need to be changed for the patients in our dataset. The system is a versatile tool for researchers and clinicians without specialised programming skills. Extending it is as easy as adding an additional term to the loss function. JulianA was validated on a dataset of 19 patients with intra- and extracerebral neoplasms within the cranial region that had been treated at our institute. For each patient, a reference plan which was delivered to the cancer patient, was exported from our treatment database. Then JulianA created the auto plan using the same beam arrangement. The reference and auto plans were given to a blinded independent reviewer who assessed the acceptability of each plan, ranked the plans and assigned the human-/machine-made labels. The auto plans were considered acceptable in 16 out of 19 patients and at least as good as the reference plan for 11 patients. Whether a plan was crafted by a dosimetrist or JulianA was only recognised for 9 cases. The median time for the spot weight optimisation is approx. 2 min (range: 0.5 min - 7 min).

physics.med-ph↗

arXiv2023

Feasibility of the J-PET to monitor range of therapeutic proton beams

Objective: The aim of this work is to investigate the feasibility of the Jagiellonian Positron Emission Tomography (J-PET) scanner for intra-treatment proton beam range monitoring. Approach: The Monte Carlo simulation studies with GATE and PET image reconstruction with CASToR were performed in order to compare six J-PET scanner geometries (three dual-heads and three cylindrical). We simulated proton irradiation of a PMMA phantom with a Single Pencil Beam (SPB) and Spread-Out Bragg Peak (SOBP) of various ranges. The sensitivity and precision of each scanner were calculated, and considering the setup's cost-effectiveness, we indicated potentially optimal geometries for the J-PET scanner prototype dedicated to the proton beam range assessment. Main results: The investigations indicate that the double-layer cylindrical and triple-layer double-head configurations are the most promising for clinical application. We found that the scanner sensitivity is of the order of 10$^{-5}$ coincidences per primary proton, while the precision of the range assessment for both SPB and SOBP irradiation plans was found below 1 mm. Among the scanners with the same number of detector modules, the best results are found for the triple-layer dual-head geometry. Significance: We performed simulation studies demonstrating that the feasibility of the J-PET detector for PET-based proton beam therapy range monitoring is possible with reasonable sensitivity and precision enabling its pre-clinical tests in the clinical proton therapy environment. Considering the sensitivity, precision and cost-effectiveness, the double-layer cylindrical and triple-layer dual-head J-PET geometry configurations seem promising for the future clinical application. Experimental tests are needed to confirm these findings.

physics.med-ph↗