Nanomaterials originate from both naturally occurring as well as human-engineered sources. The number of technologies that utilize engineered nanoparticles is increasing despite unknown environmental impacts. Therefore, sustainable growth of nanotechnology relies upon the development of analytical techniques for studying nanomaterials, particularly within biologically relevant systems. Traditional analytical tools designed for bulk or ensemble measurements in pristine environments struggle with the detection of signal from nanoparticles in these conditions. The work presented here focuses on addressing this challenge by developing background-free, selective detection and imaging of nanomaterials in noisy, optically crowded environments. Optically detected magnetic resonance (ODMR) is a background-free, selective optical detection technique enabled by the unique electronic structure of a fluorescent defect in diamond known as a nitrogen vacancy (NV) center. NV centers in nanodiamond offer an opportunity to study nanodiamonds in systems with heterogenous backgrounds by exploiting the spin-sensitive fluorescence emission of the negative charge state, NV-. This work aimed at enabling ODMR imaging of nanodiamonds as an analytical method in, first, materials systems and with particular attention to the impact of nanodiamond diameter on emissive properties of NV centers and, in turn, the effect on ODMR contrast and signal-to-noise ratio. Secondly, ODMR was performed in a biological system, Oncorhynchus mykiss (rainbow trout) gill epithelial cells exposed to NV-nanodiamond by two methods for manipulating the spin-sensitive fluorescence emission: static magnetic field (SMF) and resonant microwave field (ODMR). We found that the SMF-modulation approach achieved a higher contrast and signal-to-noise ratio than the microwave-modulation technique. These results were discussed in the context of expanding the used of quantum-based imaging techniques into fields that may benefit from selective detection of signals from nanomaterials amongst high background noise. Finally, the syntheses and characterizations of luminescent, photostable ruby nanoflakes and nanospheres are presented. The ruby nanospheres showed microsecond-long phosphorescence lifetime and the origin this surprising property was investigated through further materials and optical characterizations. We demonstrate time-gated imaging of ruby nanospheres associated with rainbow trout gill cells. These results are important for enabling fast, background-free time-gated imaging of ruby nanospheres in biological samples.