arXiv subjects

Timothy Cootes

Publications and source records attributed to Timothy Cootes.

4 recordsLinked to original sources

arXiv2026

Landmark-free Assessment of Lower-limb Alignment with Implicit Neural Shape Functions from Knee Radiographs

Radiographic assessment of lower-limb alignment (LLA) is important for predicting joint health and surgical outcomes in total knee arthroplasty. Traditional measurement methods are manual and time-consuming, while recent machine learning approaches typically rely on locating a fixed set of anatomical landmarks. This dependence limits flexibility and may require re-annotation when clinical definitions change. To address this, we propose an automated workflow using Implicit Neural Shape Functions (INSF). Rather than relying on explicit landmark coordinates, we encode the anatomy into a compact latent space and regress clinical alignment measurements directly from these latent codes. This architecture allows for rapid extendability to new tasks without altering the backbone representation. We trained our method on an internal dataset of 566 knee radiographs, each annotated with the outline of the femur and tibia. We evaluated it on both an internal test dataset of 50 patients and a separate external set of 402 preoperative cases from the MRKR dataset. Manual clinical measurements are available for these data, and the MRKR measurements will be made publicly accessible. Performance was comparable to state-of-the-art landmark-based methods and manual agreement, while offering a flexible shape representation that can be extended to additional measurement tasks.

cs.CV↗

arXiv2025

An Efficient Model-Driven Groupwise Approach for Atlas Construction

Atlas construction is fundamental to medical image analysis, offering a standardized spatial reference for tasks such as population-level anatomical modeling. While data-driven registration methods have recently shown promise in pairwise settings, their reliance on large training datasets, limited generalizability, and lack of true inference phases in groupwise contexts hinder their practical use. In contrast, model-driven methods offer training-free, theoretically grounded, and data-efficient alternatives, though they often face scalability and optimization challenges when applied to large 3D datasets. In this work, we introduce DARC (Diffeomorphic Atlas Registration via Coordinate descent), a novel model-driven groupwise registration framework for atlas construction. DARC supports a broad range of image dissimilarity metrics and efficiently handles arbitrary numbers of 3D images without incurring GPU memory issues. Through a coordinate descent strategy and a centrality-enforcing activation function, DARC produces unbiased, diffeomorphic atlases with high anatomical fidelity. Beyond atlas construction, we demonstrate two key applications: (1) One-shot segmentation, where labels annotated only on the atlas are propagated to subjects via inverse deformations, outperforming state-of-the-art few-shot methods; and (2) shape synthesis, where new anatomical variants are generated by warping the atlas mesh using synthesized diffeomorphic deformation fields. Overall, DARC offers a flexible, generalizable, and resource-efficient framework for atlas construction and applications.

cs.CV↗

arXiv2025

Deep Learning-based Alignment Measurement in Knee Radiographs

Radiographic knee alignment (KA) measurement is important for predicting joint health and surgical outcomes after total knee replacement. Traditional methods for KA measurements are manual, time-consuming and require long-leg radiographs. This study proposes a deep learning-based method to measure KA in anteroposterior knee radiographs via automatically localized knee anatomical landmarks. Our method builds on hourglass networks and incorporates an attention gate structure to enhance robustness and focus on key anatomical features. To our knowledge, this is the first deep learning-based method to localize over 100 knee anatomical landmarks to fully outline the knee shape while integrating KA measurements on both pre-operative and post-operative images. It provides highly accurate and reliable anatomical varus/valgus KA measurements using the anatomical tibiofemoral angle, achieving mean absolute differences ~1{\deg} when compared to clinical ground truth measurements. Agreement between automated and clinical measurements was excellent pre-operatively (intra-class correlation coefficient (ICC) = 0.97) and good post-operatively (ICC = 0.86). Our findings demonstrate that KA assessment can be automated with high accuracy, creating opportunities for digitally enhanced clinical workflows.

cs.CV↗

arXiv2024

From Diagnostic CT to DTI Tractography labels: Using Deep Learning for Corticospinal Tract Injury Assessment and Outcome Prediction in Intracerebral Haemorrhage

The preservation of the corticospinal tract (CST) is key to good motor recovery after stroke. The gold standard method of assessing the CST with imaging is diffusion tensor tractography. However, this is not available for most intracerebral haemorrhage (ICH) patients. Non-contrast CT scans are routinely available in most ICH diagnostic pipelines, but delineating white matter from a CT scan is challenging. We utilise nnU-Net, trained on paired diagnostic CT scans and high-directional diffusion tractography maps, to segment the CST from diagnostic CT scans alone, and we show our model reproduces diffusion based tractography maps of the CST with a Dice similarity coefficient of 57%. Surgical haematoma evacuation is sometimes performed after ICH, but published clinical trials to date show that whilst surgery reduces mortality, there is no evidence of improved functional recovery. Restricting surgery to patients with an intact CST may reveal a subset of patients for whom haematoma evacuation improves functional outcome. We investigated the clinical utility of our model in the MISTIE III clinical trial dataset. We found that our model's CST integrity measure significantly predicted outcome after ICH in the acute and chronic time frames, therefore providing a prognostic marker for patients to whom advanced diffusion tensor imaging is unavailable. This will allow for future probing of subgroups who may benefit from surgery.

eess.IV↗