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The Zeta TMS Navigation System is a stereotaxic, image-guided planning and guidance system enabling computer-assisted procedures. The system assists the trained clinical professionals with accurate positioning of the coils of TMS treatment systems relative to patient anatomy by displaying the position of a navigated TMS coil relative to 3D neuroimaging scans. The system provides navigation in three planes (axial, sagittal, and coronal) and enables the selection of target anatomical points. The underlying RealTrack algorithm allows for real-time tracking of head movement using only the patient’s native anatomical features, eliminating the need for rigid head immobilization, body-mounted frames, or facial fiducials.