Disclosed are two different approaches for immobilization of beads on a substrate, one of which involves forming a bead-nanoparticle composite by cross-linking of the bead mixture with nanoparticles. The other method involves surface modification of the substrate, using multi-layered polyelectrolytes. With either method, the beads are immobilized on the substrate in a manner suitable for viewing, as when the beads are used in assays and need to be analyzed following the assay. Different designs of depressions are also disclosed, some of which are suitable for holding beads in place without any deposition of nanoparticles or polyelectrolytes.