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Shakil completed his PhD at the University of Sydney, School of Physics with Professor Colin Sheppard in 2004 and since then has worked at various international organizations. In 2005, he joined, as a JSPS research fellow, at National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan for a couple of years and then joined National University of Singapore at Bioengineering Department in 2007 and held a joint appointment as a research fellow at Singapore Eye Research Institute. Later in 2011, he joined a newly established institute: Singapore-MIT Alliance for Research and Technology (SMART), doing research in the fields of optical imaging and microscopy in Singapore and at MIT, USA.

In 2017, he returned to Australia and joined LASTEK Pty Ltd., where he is involved in the design and development of advanced imaging and microscopy systems. Shakil has built various optical imaging systems for biological and medical applications and is expert in physical optics, coherent and incoherent light sources, optical microscopy, multi-photon microscopy and digital holography. At LASTEK, he is involved in the design and development of high-resolution imaging and visualization tools, including optical microscopy, confocal and multi-photon systems.