Weixun Luo

Weixun Luo, Alexandre Triay Bagur, Paul Aljabar et al.

Background and Objective: The lack of benchmark datasets has impeded the development of slice-to-volume registration algorithms. Such datasets are difficult to annotate, primarily due to the dimensional difference within data and the dearth of task-specific software. We aim to develop a user-friendly tool to streamline dataset annotation for slice-to-volume registration. Methods: The proposed tool, named SVRDA, is an installation-free web application for platform-agnostic collaborative dataset annotation. It enables efficient transformation manipulation via keyboard shortcuts and smooth case transitions with auto-saving. SVRDA supports configuration-based data loading and adheres to the separation of concerns, offering great flexibility and extensibility for future research. Various supplementary features have been implemented to facilitate slice-to-volume registration. Results: We validated the effectiveness of SVRDA by indirectly evaluating the post-registration segmentation quality on UK Biobank data, observing a dramatic overall improvement (24.02% in the Dice Similarity Coefficient and 48.93% in the 95th percentile Hausdorff distance, respectively) supported by highly statistically significant evidence ($p<0.001$).We further showcased the clinical usage of SVRDA by integrating it into test-retest T1 quantification on in-house magnetic resonance images, leading to more consistent results after registration. Conclusions: SVRDA can facilitate collaborative annotation of benchmark datasets while being potentially applicable to other pipelines incorporating slice-to-volume registration. Full source code and documentation are available at https://github.com/Roldbach/SVRDA

Weixun Luo, Xiaodan Xing, Guang Yang

Featured by a bottleneck structure, autoencoder (AE) and its variants have been largely applied in various medical image analysis tasks, such as segmentation, reconstruction and de-noising. Despite of their promising performances in aforementioned tasks, in this paper, we claim that AE models are not applicable to single image super-resolution (SISR) for 3D CT data. Our hypothesis is that the bottleneck architecture that resizes feature maps in AE models degrades the details of input images, thus can sabotage the performance of super-resolution. Although U-Net proposed skip connections that merge information from different levels, we claim that the degrading impact of feature resizing operations could hardly be removed by skip connections. By conducting large-scale ablation experiments and comparing the performance between models with and without the bottleneck design on a public CT lung dataset , we have discovered that AE models, including U-Net, have failed to achieve a compatible SISR result ($p<0.05$ by Student's t-test) compared to the baseline model. Our work is the first comparative study investigating the suitability of AE architecture for 3D CT SISR tasks and brings a rationale for researchers to re-think the choice of model architectures especially for 3D CT SISR tasks. The full implementation and trained models can be found at: https://github.com/Roldbach/Autoencoder-3D-CT-SISR