Embodiments provide method and systems for determining alignment of a patient's body part, such as an eye, in an external coordinate system of a treatment or diagnostic device, such as a radiotherapy device, so as to define a reference axis for guiding device operation. Additional embodiments provide image-based methods and systems for aligning, tracking and monitoring motion of a body part and a treatment target in relation to a radiation beam axis. Particular ophthalmic embodiments provide method and systems including an eye-contact guide device and imaging system for aligning and tracking motion of an eye and ocular treatment target in relation to an orthovoltage X-ray beam axis, so as to monitor application of radiation to a lesion, such as a macular lesion of the retina. Particular methods for controlling radiation in response to motion of the target during treatment are described, such as algorithms for gating or interrupting radiation emission, both to ensure treatment goals and to avoid exposure to sensitive structures.