1. An image-guided radiation therapy system for treating a target within a patient, the system comprising: a treatment delivery system having a radiation source configured to generate treatment radiation beams and a collimator configured to collimate the treatment radiation beams; a multi-energy imaging system configured to generate a first set of image data of part or all of the patient using imaging radiation at a first energy level and a second set of image data of part or all of the patient using imaging radiation at a second energy level; and a system processor configured to process the first and second sets of image data to generate an enhanced image of part or all of the patient, the system processor further configured to direct the treatment delivery system based on information obtained from the enhanced image.