The present embodiments provides improved devices, systems, and methods for affecting changes in pupil sizes before a laser eye procedure and using those images for alignment before and/or during a diagnostic and/or treatment procedure of the eye, particularly during laser eye surgery procedures. The embodiments provide methods and systems for tracking pupil position and torsional cyclorotation of a patient's eye. In one exemplary embodiment, the present embodiments provides methods and software for registering a photopic image of an eye captured by a laser device to the eye images of the patient's eye using a scotopic image and a photopic image captured simultaneously during wavefront exam.
