Micro-CT scans generate three-dimensional images consisting of the order of 10003 voxels (3D picture elements), each cubic voxel being sub-micron to 100 micrometer on a side. The gray-scale modulation within tomographic images reflects the local attenuation of the x-ray. This allows for differentiation of different tissues by virtue of their elemental content. However, the elements in blood vessel walls and within blood differ little from organ parenchyma, hence they are not readily distinguishable unless the attenuation of blood is enhanced by injecting a heavy element (such as iodine) into the blood stream or by staining the vessel wall tissues with heavy metals such as osmium tetroxide. Three-dimensional micro-CT images a volume (of light-opaque tissue) large enough to include entire, intact, vascular trees without the need to destroy the 3D tissue specimen. Hence, the fluid dynamic and the perfusion territory size consequences, as well the micro-anatomic relationship of the vascular branching geometry and interconnectivity to parenchymal structures (e.g., nephron, hepatic lobule or cancer) can be readily appreciated and quantified. The permeability of microvasculature can also be imaged by virtue of the increased contrast resulting from the fraction of the injected contrast agent passing through the endothelium into the surrounding extravascular tissue. In recent years micro-CT based on the imaging of coherent x-ray scatter and on x-ray phase shift caused by local electron density distributions (reflecting molecular bond type in some cases) provide greater inherent image contrast than does x-ray attenuation. These new capabilities are now active avenues of research and development.