We report a simple, low cost and environmentally friendly method to prepare NaYF4:Yb3+, Tm3+ upconversion microphosphors (UCMPs) by thermal decomposition of rare earth-trifluoroacetate precursors using paraffin as the high boiling non-coordinating solvent. The UCMPs exhibited cubic phase with defined shape and bright upconversion luminescence. After coating with amphiphilic polymers of phospholipid-polyethylene glycol, the NaYF4:Yb3+, Tm3+ UCMPs were highly dispersed in aqueous solutions and exhibited low cytotoxicity. Furthermore, we explored the use of the micro-injected micro sized NaYF4:Yb3+, Tm3+ particles for converting of near infrared into blue light in mice brain. The in vivo macroscopic upconversion luminescence imaging results showed that UCMPs located at 1 mm depth in the brain could be clearly distinguished. Microscopic upconversion luminescence imaging of the brain sections in vitro revealed that the UCMPs embedded at the particular location in brain tissues of mice were stable without significant diffusion in two weeks. (C) 2017 Elsevier Inc. All rights reserved.