In the medical field, instead of mentally combining information in the images displayed side-by-side, Dual-Bootstrap can automatically merge information in the images into a single image, improving a physician's ability to diagnose and monitor disease. For example Dual-Bootstrap can:

• Align retinal fundus images taken of the same patient but several years apart, and then flicker the images in such a way that enables physicians to diagnose glaucoma earlier than any other available method.
• Align retinal fundus images and fluorescein angiography images in order to visualize and evaluate blood flow through the retina.
• Align images of patient's skin taken months or years apart as the basis for visualizing early signs of skin cancer.
• Align images taken at different times to enable a physician to monitor the progress of disease. Such is the case when looking at images of cervical cancer patients.
• Align CT scans of a patient's lungs in order to automatically detect changes and monitor the growth of the small nodules that may be early indications of cancer.
• Align images of a patient's brain taken using different imaging modalities including, potentially, functional images, as the basis for providing physicians with the timely and accurate information needed to diagnose or treat brain abnormalities.

Furthermore, it may be possible to use the Dual-Bootstrap in image-guided surgery, which will also heavily depend on information in multiple images. Integrating these into a single, precisely merged image will be of critical importance.

Similar to the above, Dual-Bootstrap can be used to register images during clinical trials to monitor the impact of a drug on a patient or animal.