In this paper, we aim to design an automatic camera pose estimation pipeline for clinical spaces such as catheterization laboratories. Our proposed pipeline exploits Scaled-YOLOv4 to detect fixed objects. We adopt the self-supervised key-point detector SuperPoint in combination with SuperGlue, a keypoint matching technique based on graph neural networks. Thus, we match key-points on input images with annotated reference points. Reference points are chosen on fixed objects in the scene, such as corners of door posts or windows. The point-correspondences between the image coordinates and the 3D coordinates are applied to the Perspective-n-Point algorithm to estimate the pose of each camera. Compared with other camera pose estimation methods, the proposed pipeline does not require the construction of 3D point-cloud model of the scene or placing a polyhedron object in the scene before each required calibration. Using videos from real procedures, we show that the pipeline can estimate the camera pose with high accuracy.