The integration of a surgical robotic instrument tracking module within optical microscopes holds the potential to advance microsurgery practices, as it facilitates automated camera movements, thereby augmenting the surgeon's capability in executing surgical procedures. In the present work, an innovative detection backbone based on spatial attention module is implemented to enhance the detection accuracy of small objects within the image. Additionally, we have introduced a robust data association technique, capable to re-track surgical instrument, mainly based on the knowledge of the dual-instrument robotics system, Intersection over Union metric and Kalman filter. The effectiveness of this pipeline was evaluated through testing on a dataset comprising ten manually annotated videos of anastomosis procedures involving either animal or phantom vessels, exploiting the Symani®Surgical System-a dedicated robotic platform designed for microsurgery. The multiple object tracking precision (MOTP) and the multiple object tracking accuracy (MOTA) are used to evaluate the performance of the proposed approach, and a new metric is computed to demonstrate the efficacy in stabilizing the tracking result along the video frames. An average MOTP of 74±0.06% and a MOTA of 99±0.03% over the test videos were found. These results confirm the potential of the proposed approach in enhancing precision and reliability in microsurgical instrument tracking. Thus, the integration of attention mechanisms and a tailored data association module could be a solid base for automatizing the motion of optical microscopes.