1. A method to determine a position of a probe in a surgical site with a plurality of reference structures, comprising: receiving a three-dimensional image of the surgical site generated before the probe enters the surgical site, wherein the three-dimensional image is associated with a first coordinate system; receiving a first two-dimensional image generated by the probe from a position within the surgical site, wherein the first two-dimensional image is associated with a second coordinate system; acquiring registration to the plurality of reference structures based on the first two-dimensional image to obtain a permissible set of probe pose parameters; extracting a second two-dimensional image from the three-dimensional image based on the permissible set of probe pose parameters; and computing a correlation between the first two-dimensional image and the extracted second two-dimensional image to map the position of the probe represented by the second coordinate system to a position represented by the first coordinate system with respect to the three-dimensional image.