A method and a system are disclosed for labeling an anatomical point associated with a lesion in an organ such as a lung. The method includes: a segmentation of a vessel tree anatomical structure starting from an autonomously determined initial image point; labeling the vessel segments of the vessel tree segmentation with segment labels based on a priori anatomical knowledge, thereby creating an individualized anatomical model; receiving a user-specified image point having a location from a user and locating a nearby vessel structure; tracking along the vessel structure in a direction towards a root of a parent vessel tree until a prior labeled vessel segment is encountered in the anatomical model, and assigning the label of the encountered prior labeled vessel segment from the anatomical model as an anatomical location label of the user-specified image point.