1. A method for generating motion corrected tomographic images, comprising the steps of: illuminating a region to of interest (ROI) to be imaged being part of an unrestrained live subject located in a burrow and having at least three spaced apart optical markers thereon; acquiring first and second sets of simultaneous images of said markers, wherein both the first and the second set of simultaneous images are acquired from a first and a second camera from different angles; determining an initial reference position of said markers using said first set of simultaneous images; calculating motion data using said second set of simultaneous images, said motion data comprising 3D position and orientation of said markers in the second set of simultaneous images relative to said initial reference position of said markers, and motion correcting tomographic data obtained from said ROI using said motion data, wherein motion corrected tomographic images are obtained, wherein said calculating motion data step comprises processing said second set of simultaneous images using segmentation, followed by object features extraction and filtering, said segmentation comprising removing reflections from a surface of the burrow with size and shape filtering.