A semiconductor nanocrystal compound capable of linking to one or more affinity molecules comprising (1) one or more semiconductor nanocrystals capable of, in response to exposure to a first energy, providing a second energy, and (2) one or more linking agents, having a first portion linked to the one or more semiconductor nanocrystals and a second portion capable of linking to one or more affinity molecules. One or more of semiconductor nanocrystal compounds linked to one or more affinity molecules to form a semiconductor nanocrystal probe capable of bonding with one or more detectable substances in a material being analyzed, and are capable of, in response to exposure to a first energy, providing a second energy. The probe is capable of emitting electromagnetic radiation in a narrow wavelength band and/or absorbing, scattering, or diffracting energy when excited by an electromagnetic radiation source of narrow or broad bandwidth, or a particle beam. The probe is stable to repeated exposure to energy in the presence of oxygen and/or other radicals.