Lecture notes on methodology for measuring surface ligand density, investigating the surfaces of biomaterials, assays of proteins adsorbed on biomaterials surfaces, quantitative methods for measuring the ligand density of surfaces, the need for a measurement of density of bound ligands in cell-seeded scaffolds, the need for a three-dimensional (3D) description of cell-scaffold interactions, choice of microscopy method for study of cell-seeded surfaces of biomaterials, and the molecular mechanism by which collagen-GAG scaffolds modify cell phenotypes in four cases.