Abstract: A system and method for encoded microparticles is described. One embodiment includes an encoded microparticle comprising a plurality of segments, wherein the plurality of segments form a spatial code; contrast coating on at least one segment of the plurality of segments, wherein the contrast coating further encodes the microparticle; an outer surface, wherein the outer surface encloses the spatial code and contrast coating, and wherein the spatial code and contrast coating are detectable through the outer surface.

Abstract: A system and method for encoded microparticles is described. One embodiment includes an encoded microparticle comprising a plurality of segments, wherein the plurality of segments form a spatial code; contrast coating on at least one segment of the plurality of segments, wherein the contrast coating further encodes the microparticle; an outer surface, wherein the outer surface encloses the spatial code and contrast coating, and wherein the spatial code and contrast coating are detectable through the outer surface.

Abstract: The present invention provides methods to detect biomolecules on a microarray using a scanning electron microscope. In one embodiment of the invention, errors in oligonucleotide synthesis during manufacturing of microarrays are detected by monitoring synthesis of control probes on the chips. In another embodiment, misalignment of features on the chip is determined. In yet another embodiment, the size, shape and edge definition of features on the chip is determined. In further embodiments, methods are provided for analyzing interactions between an oligonucleotide target and an oligonucleotide probe on a microarray and methods for testing conditions in a microarray manufacturing process.