Multi-color CL images of nanoparticle samples may be generated, by irradiating with a scanning electron beam a nanoparticle sample that containing a plurality of spectrally distinct optical emitters configured to generate CL light at respective different color channels, then detecting the CL light from the nanoparticles to generate multi-color NP-CL images of the nanoparticle sample. In some embodiments, SE (secondary electron) images of the sample may be acquire, substantially simultaneously with the acquisition of the CL images, so as to generate correlative NP-CL and SE images of the nanoparticle sample. In some embodiments, the nanoparticles may be surface-functionalized so that the nanoparticles selectively bind only to particular structures of interest.