For in-vivo imaging applications the use of conventional confocal microscope systems are simply not practical due to their relatively large size and weight. There is, however, great interest from both the life science research community and the clinical profession for the development of compact and portable micro-optical instrumentation capable of achieving minimally invasive, in-vivo imaging of tissue with sub-cellular resolution. In this paper we describe a novel confocal micro-imaging system incorporating, at its core, a thermally driven, non-resonant two-axis MEMS scanner which serves as a substitute for the two single-axis galvanometer scanners commonly used in standard confocal imaging systems. In this paper we describe the non-linearity of such devices and a number of techniques to compensate for this.© (2009) COPYRIGHT SPIE--The International Society for Optical Engineering. Downloading of the abstract is permitted for personal use only.