An apparatus and method of measuring biofilm and biological activity on a surface is disclosed. The apparatus includes a biofilm, which includes one or more microorganisms, grown on a substrate. A viewing window is placed on a surface of the biofilm and a gas bubble is introduced between the viewing window and the surface of the biofilm. The space between the substrate and the viewing window may be enclosed in a casing that has an inlet and an outlet, forming a flow cell. A microscope system, such as a white light interferometer, captures data of the biofilm in situ and non-destructively. The 3D images of biofilm surface have high resolution while maintaining a large field of view. This invention will be useful for fundamental studies of biofilms, biomedical and environmental screening, and many other applications in biology and the life sciences.
STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT
 This invention was made with Government support under Contract DE-AC0576RL01830 awarded by the U.S. Department of Energy. The Government has certain rights in the invention.