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Super-resolution imaging has emerged as a rapidly advancing field in diagnostic ultrasound. Ultrasound Localization Microscopy (ULM) achieves sub-wavelength precision in microvasculature imaging by tracking gas microbubbles (MBs) flowing through blood vessels. However, MB localization faces challenges due to dynamic point spread functions (PSFs) caused by harmonic and sub-harmonic emissions, as well as depth-dependent PSF variations in ultrasound imaging. Additionally, deep learning models often struggle to generalize from simulated to in vivo data due to significant disparities between the two domains. To address these issues, we propose a novel approach using the DEformable DEtection TRansformer (DE-DETR). This object detection network tackles object deformations by utilizing multi-scale feature maps and incorporating a deformable attention module. We further refine the super-resolution map by employing a KDTree algorithm for efficient MB tracking across consecutive frames. We evaluated our method using both simulated and in vivo data, demonstrating improved precision and recall compared to current state-of-the-art methodologies. These results highlight the potential of our approach to enhance ULM performance in clinical applications.