A computer-implemented method is provided for anatomically indexing a subject. The method includes: receiving image scan data representing a volume of a subject, where the image scan data is comprised of a plurality of image slices of the subject and includes at least a portion of a vertebral column of the subject; identifying the vertebral canal of the vertebral column of the subject in the image scan data; determining a plurality of markers for the vertebral column, where each marker is indicative of a different vertebral body of the vertebral column and includes its location in the image scan data defined in a coordinate system, such that the plurality of markers define a vertebral level coordinate system; and storing each marker along with its location in a database. The markers can subsequently be used to reference other anatomical components of the subject across different image scans.