The invention relates to a combination hybrid computer tomography (CT) system that is particularly suited for elucidating stages in pulmonary diseases, notably cystic fibrosis and lung cancer. Improved visualization of lung parenchyma and the margins of lung cysts (non-invasive “virtual biopsy”) may provide sufficient detail to distinguish the types of cystic lesions such that the typical lung tissue pathologic biopsy would not be needed to make a diagnosis. The system includes placing one or more x-ray detector panels near the patient’s body initially outside the view of a CT scanner and then moved into place for a secondary scan. An initial low dose scan, CT scan or X-ray, can be performed and if a high-resolution CT scan is then necessary a flat panel detector is positioned near the area of interest. It is preferable that the flat panel detector be transparent to high-energy x-ray photons. The plurality of acquired images are then reconstructed into a low and high-resolution image.