The 3rd International Multidisciplinary Microscopy Congress (InterM2015), held from 19 to 23 October 2015, focused on the latest developments concerning applications of microscopy in the biological, physical and chemical sciences at all dimensional scales, advances in instrumentation, techniques in and educational materials on microscopy. These proceedings gather 17 peer-reviewed technical papers submitted by leading academic and research institutions from nine countries and representing some of the most cutting-edge research available.