Mixing efficiency is lower in passive micromixers due to viscous forces and substantial research effort is focused on designing high performance micromixers. Active micromixers make use of external forces to enhance mixing efficiency. Among these, magnetic forces are popular because they are non-contact and therefore the micromixer design can be kept simple. Laser-based diagnostic tools have great potential in providing multi-parameter information in microfluidics research on mixing. MicroPIV experiments are performed to investigate the transient flow field in a magnetic micromixer undergoing labyrinthine instability. Velocity and interface front information is extracted from a sequence of time-resolved particle images. The use of image pre-processing functions proves to be essential in two-phase flow microfluidics: Velocity measurements are obtained using an adaptive cross-correlation algorithm, where particle image contrast was enhanced using local contrast normalization and difference of Gaussian filters. Interface location is estimated using Prewitt edge detection filter together with a combination of standard image processing functions. A detailed uncertainty analysis is provided. Time resolved information on velocity and interface location provides a new understanding of the mixing processes in microscale and opens new possibilities for validation for computational and theoretical studies.