Mesenchymal stem cells (MSCs) were found to be effective in repairing the damaged brain of animals with ischemic brain injury. However, the behavior, distribution and fate of these cells after implantation which gives very important information on cell dynamics and interactions with the host central nervous system is still unknown. Minimally-invasive functional imaging techniques have driven much advancement in medical sciences. One of the challenges in minimally-invasive functional imaging is to achieve both high resolution and SNR. Multi-modal imaging is emerging as a strategy to overcome this challenge by combining two or more imaging modalities. In this project, we seek to combine shortwave infrared (SWIR) and photoacoustic (PA) imaging into one versatile minimally-invasive molecular imaging platform utilizing polymer coated Rare Earth Doped Nanoparticles (REDNs), as imaging probes. Not only do the REDNs enhance SNR and improve resolution, but the REDNs also provide an added analytic ability at the cellular level using the functional relationships between the probes and biological systems.