A non-transitory computer-readable storage medium storing instructions which, when executed by a computer, cause the computer to: receive image data of a patient's chest; identify the patient's lungs in the image data; determine locations of a luminal network in the patient's lungs in the image data; identify a target location in the patient's lungs, based on a selection received from a clinician or on image processing and analysis performed by the computer; generate, automatically or with input from a clinician, a pathway to the target location; generate a three-dimensional model of the patient's lungs based on the image data, the 3D model showing the luminal network in the patient's lungs and the pathway to the target location; determine a location of a tool based on an electromagnetic sensor as the tool is navigated within the patient's chest; cause a display device to display a view of the 3D model and showing the determined location of the tool on the 3D model; receive cone beam computed tomography (CBCT) image data of a portion of the patient's chest based on an intra-procedural scan performed after the tool has at least partially been navigated within the patient's chest; update at least a portion of the 3D model based on the CBCT image data; and cause the display device to display a view of the updated 3D model; wherein the instructions further cause the computer to: identify an actual location of the tool based on the CBCT image data; identify an actual position of the target location based on the CBCT image data; generate an updated pathway between the actual location of the tool and the actual position of the target location; and cause the display device to display the updated pathway on the updated 3D model. receive image data of a patient's chest; identify the patient's lungs in the image data; determine locations of a luminal network in the patient's lungs in the image data; identify a target location in the patient's lungs, based on a selection received from a clinician or on image processing and analysis performed by the computer; generate, automatically or with input from a clinician, a pathway to the target location; generate a three-dimensional model of the patient's lungs based on the image data, the 3D model showing the luminal network in the patient's lungs and the pathway to the target location; determine a location of a tool based on an electromagnetic sensor as the tool is navigated within the patient's chest; cause a display device to display a view of the 3D model and showing the determined location of the tool on the 3D model; receive cone beam computed tomography (CBCT) image data of a portion of the patient's chest based on an intra-procedural scan performed after the tool has at least partially been navigated within the patient's chest; update at least a portion of the 3D model based on the CBCT image data; and cause the display device to display a view of the updated 3D model; identify an actual location of the tool based on the CBCT image data; identify an actual position of the target location based on the CBCT image data; generate an updated pathway between the actual location of the tool and the actual position of the target location; and cause the display device to display the updated pathway on the updated 3D model.