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