A method of mapping a plurality of marker points identified in a sequence of projection images to a physical marker placed on a patient or other scanned object, the method executed by an imaging system including a scanner, a computer with an electronic processing unit, and a memory module storing a marker physical mapping module executable by the electronic processing unit, the method comprising: obtaining, at the computer, a sequence of images based on image data generated by the scanner, each image in the sequence of images representing an angle of rotation by the scanner and including a plurality of marker points each having a U position and a V position; calculating, with the electronic processing unit, an expected U position and an expected V position for the physical marker for each image in the sequence of images and an expected U range and an expected V range for each image in the sequence of images based on the expected U position and the expected V position for each image; creating, with the electronic processing unit, a candidate point list that includes each marker point in each image that has a U position within the expected U range of the image and a V position within the expected V range of the image; subtracting, with the electronic processing unit, for each marker point in the candidate point list, the expected U position from the U position and the expected V position from the V position to create a tracking error value assigned to each point in the candidate point list; creating, with the electronic processing unit, an empty good point list for tracking marker points in the sequence of images mapped to the physical marker; adding, with the electronic processing unit, a marker point from an initial image to the good point list as a good point and designating the marker point as a reference good point; and processing, with the electronic processing unit, a next image in the sequence of images based on the good point list; characterised by the processing including: determining a derivative value between the reference good point and each marker point in the candidate point list associated with the next image, and adding the marker point associated with a lowest derivative value to the good point list. obtaining, at the computer, a sequence of images based on image data generated by the scanner, each image in the sequence of images representing an angle of rotation by the scanner and including a plurality of marker points each having a U position and a V position; calculating, with the electronic processing unit, an expected U position and an expected V position for the physical marker for each image in the sequence of images and an expected U range and an expected V range for each image in the sequence of images based on the expected U position and the expected V position for each image; creating, with the electronic processing unit, a candidate point list that includes each marker point in each image that has a U position within the expected U range of the image and a V position within the expected V range of the image; subtracting, with the electronic processing unit, for each marker point in the candidate point list, the expected U position from the U position and the expected V position from the V position to create a tracking error value assigned to each point in the candidate point list; creating, with the electronic processing unit, an empty good point list for tracking marker points in the sequence of images mapped to the physical marker; adding, with the electronic processing unit, a marker point from an initial image to the good point list as a good point and designating the marker point as a reference good point; and processing, with the electronic processing unit, a next image in the sequence of images based on the good point list; characterised by the processing including: determining a derivative value between the reference good point and each marker point in the candidate point list associated with the next image, and adding the marker point associated with a lowest derivative value to the good point list. determining a derivative value between the reference good point and each marker point in the candidate point list associated with the next image, and adding the marker point associated with a lowest derivative value to the good point list.