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Transbronchial biopsy of peripheral lung nodules is hindered by the inability to access lesions endoluminally due to the large diameter of conventional bronchoscopes. An ultrathin scanning fiber bronchoscope has recently been developed to advance image-guided biopsy several branching generations deeper into the peripheral airways. However, navigating a potentially complex 3-D path to the region of interest presents a challenge to the bronchoscopist. An accompanying guidance system has also been developed to track the bronchoscope through the airways, and display its position and intended path on a virtual display. Intraoperative localization of the bronchoscope was achieved by combining electromagnetic tracking (EMT) and image-based tracking (IBT). An error-state Kalman filter was used to model the disagreement between the two tracking sources. The positional tracking error was reduced from 14.22 and 14.92 mm by independent EMT and IBT, respectively, to 6.74 mm using the hybrid approach. Hybrid tracking of the scope orientation and respiratory motion compensation further improved tracking accuracy and stability, resulting in an average tracking error of 3.33 mm and 10.01??.