His areas of research are in optics, microscopy and imaging, including confocal and multiphoton microscopy, diffraction, 3D imaging and reconstruction, superresolution, beam propagation, and pulse propagation.

Then, from 1968 to 1972 he completed a PhD, also at the University of Cambridge, titled A reflection scanning electron diffractometer and its application to the oxidation of metals[1] under the direction of Charles William Oatley.

Sheppard is currently senior scientist at the Italian Institute of Technology in Genoa, Italy.

Previously, he was professor in the Department of Bioengineering and Faculty of Engineering for National University of Singapore[3] (2003–2012).

He was professor of physics at the University of Sydney (1989–2003), and research director of the Australian Key Centre for Microscopy & Microanalysis (1995–2001).