A method of building an anatomical branch model comprises receiving anatomical image data comprising a plurality of graphical units associated with an anatomical structure and determining a plurality of parent segments and child segments. The method also comprises determining a set of relationships between the parent segments and the child segments by determining a first set of connection costs of connecting at least one of the parent segments to a first subset of the child segments, the child segments of the first subset are separated from the at least one of the parent segments by one or more gaps, identifying a first child segment from the first subset of the child segments based on a first connection cost, and connecting the first child segment to the at least one parent segment. The method further comprising generating an image of the anatomical branch model based on the determined set of relationships.