arXiv subjects

Jo Hajnal

Publications and source records attributed to Jo Hajnal.

5 recordsLinked to original sources

arXiv2026

SPARC: Slice-to-volume Pipeline for Automated Reconstruction of gated 3D+time fetal Cardiac MRI

Fetal cardiac MRI (fCMR) provides valuable diagnostic information complementary to echocardiography, particularly for complex congenital heart disease (CHD). Dynamic cine imaging captures cardiac motion essential for assessment of cardiac function; however, the reconstruction of 3D+time cine volumes from 2D+time acquired slices remains challenging due to unpredictable fetal motion and the absence of automated and robust processing tools suitable for clinical deployment. We present the SPARC pipeline (Slice-to-volume Pipeline for Automated Reconstruction of gated 3D+time fetal Cardiac MRI) which combines physics-informed slice-to-volume reconstruction (SVR) of Doppler ultrasound (DUS) gated stacks of slices, assisted by deep learning (DL) models for thoracic segmentation and anatomical reorientation. The proposed SVR algorithm achieves a tenfold reduction in reconstruction time relative to existing frame-wise approaches ($4.8 \pm 1.0$ vs $49.0 \pm 14.1$ min, $p < 0.0001$) while improving the reconstruction quality. Thoracic segmentation performance using ensemble aggregation exceeded inter-rater agreement (Dice $84.7 \pm 3.9\%$ vs $81.4 \pm 7.7\%$, $p<0.05$), while anatomical reorientation achieved a success rate of $90.1\%$. End-to-end evaluation on a large held-out clinical cohort ($n = 121$) demonstrated fully automatic processing in $82.6\%$ of cases with a mean runtime of $7.1 \pm 1.3$ min, compatible with clinical deployment. The complete SPARC pipeline is publicly available as a Docker container https://hub.docker.com/r/aboutill/sparc and is currently deployed at our institution as a clinical research tool.

cs.CV↗

arXiv2021

PRETUS: A plug-in based platform for real-time ultrasound imaging research

We present PRETUS -a Plugin-based Real Time UltraSound software platform for live ultrasound image analysis and operator support. The software is lightweight; functionality is brought in via independent plug-ins that can be arranged in sequence. The software allows to capture the real-time stream of ultrasound images from virtually any ultrasound machine, applies computational methods and visualises the results on-the-fly. Plug-ins can run concurrently without blocking each other. They can be implemented in C ++ and Python. A graphical user interface can be implemented for each plug-in, and presented to the user in a compact way. The software is free and open source, and allows for rapid prototyping and testing of real-time ultrasound imaging methods in a manufacturer-agnostic fashion. The software is provided with input, output and processing plug-ins, as well as with tutorials to illustrate how to develop new plug-ins for PRETUS.

physics.med-ph↗

arXiv2020

Deep Generative Models to Simulate 2D Patient-Specific Ultrasound Images in Real Time

We present a computational method for real-time, patient-specific simulation of 2D ultrasound (US) images. The method uses a large number of tracked ultrasound images to learn a function that maps position and orientation of the transducer to ultrasound images. This is a first step towards realistic patient-specific simulations that will enable improved training and retrospective examination of complex cases. Our models can simulate a 2D image in under 4ms (well within real-time constraints), and produce simulated images that preserve the content (anatomical structures and artefacts) of real ultrasound images.

eess.IV↗

arXiv2019

Interpretable Convolutional Neural Networks for Preterm Birth Classification

The use of convolutional neural networks (CNNs) for classification tasks has become dominant in various medical imaging applications. At the same time, recent advances in interpretable machine learning techniques have shown great potential in explaining classifiers' decisions. Layer-wise relevance propagation (LRP) has been introduced as one of these novel methods that aim to provide visual interpretation for the network's decisions. In this work we propose the application of 3D CNNs with LRP for the first time for neonatal T2-weighted magnetic resonance imaging (MRI) data analysis. Through LRP, the decisions of our trained classifier are transformed into heatmaps indicating each voxel's relevance for the outcome of the decision. Our resulting LRP heatmaps reveal anatomically plausible features in distinguishing preterm neonates from term ones.

eess.IV↗

arXiv2018

Human-level Performance On Automatic Head Biometrics In Fetal Ultrasound Using Fully Convolutional Neural Networks

Measurement of head biometrics from fetal ultrasonography images is of key importance in monitoring the healthy development of fetuses. However, the accurate measurement of relevant anatomical structures is subject to large inter-observer variability in the clinic. To address this issue, an automated method utilizing Fully Convolutional Networks (FCN) is proposed to determine measurements of fetal head circumference (HC) and biparietal diameter (BPD). An FCN was trained on approximately 2000 2D ultrasound images of the head with annotations provided by 45 different sonographers during routine screening examinations to perform semantic segmentation of the head. An ellipse is fitted to the resulting segmentation contours to mimic the annotation typically produced by a sonographer. The model's performance was compared with inter-observer variability, where two experts manually annotated 100 test images. Mean absolute model-expert error was slightly better than inter-observer error for HC (1.99mm vs 2.16mm), and comparable for BPD (0.61mm vs 0.59mm), as well as Dice coefficient (0.980 vs 0.980). Our results demonstrate that the model performs at a level similar to a human expert, and learns to produce accurate predictions from a large dataset annotated by many sonographers. Additionally, measurements are generated in near real-time at 15fps on a GPU, which could speed up clinical workflow for both skilled and trainee sonographers.

cs.CV↗