This study focuses on the application of infra-red thermography to visualise the heat transfer dynamics of diabatic flows in multi-microchannels etched into silicon wafers. The 100 parallel channels were 50 micron wide, 100 microns deep, and with a pitch of 50 microns. The length of the channels was 10mm, and was limited by transverse inlet and outlet slits. A copper manifold was used to provide and remove fluid from the test section. This manifold was also designed to provide optical access to both the top and bottom surfaces of the test section. With the use of a temperature controlled water bath, a novel in-situ ‘pixel by pixel’ technique has been developed to calibrate the raw infra-red images thus converting them into accurate two-dimensional temperature fields of the test section surface. Preliminary tests, involving pumping hot water through the test section, have shown that this technique is able to provide detailed spatio-temporal information on the surface temperature field.