X-ray microscopy is capable of imaging particles in the colloidal size range directly in their aqueous environment with high spatial resolution. It is possible to combine this with high spectral resolution for spectromicroscopic studies. Two types of microscopes are common in X-ray microscopy

the transmission X-ray microscope and the scanning transmission X-ray microscope

whose setup is shown in this paper. While an X-ray microscope quickly takes high resolution images from an object

a scanning X-ray microscope as an analytical instrument is suited for spectromicroscopy. As an example for visualization of morphology

clay and soil samples have been imaged with a transmission X-ray microscope. Images from a cryotomography experiment based on X-ray microscopy images to obtain information about the 3D structure of microhabitats formed by bacteria and other soil colloids are shown. The analysis of a stack of images taken with a scanning transmission X-ray microscope to bring together morphology and chemistry within a soil sample is given.