This data set contains raw video files (.avi) of gold spherical nanoparticles with diameter of 100nm diffusing above a human mesenchymal stem cell monolayer in standard cell culture solutions. Nanoparticles were visualised using the technique developed by Patterson and Whelan (2008) using a Zeiss Axio Observer inverted microscope. Videos were taken using the Zeiss Axio Cam 305 mono and 40x objective lens. The pixel size is 0.086µm x 0.086µm. T1, 2 and 3 refers to three timepoints which were 15, 60, and 105 minutes respectively. H1, 2, 3 and 4 refer to heights above the top surface of the monolayer at which nanoparticles were tracked which were 25, 50, 75 and 100µm. Nanoparticles were visualised whilst inside an incubator stage maintained at 37C throughout the tracking process.