After MSc in Electrical Engineering and Computer Sciences, Pekka Hänninen moved in 1988 to European Molecular Biology Laboratory in Heidelberg. In Heidelberg P.H. was a part of a team building confocal microscopes. In 1992 P.H. moved to Turku and to the team of Prof. Erkki Soini. Pekka's colleague Stefan Hell from Heidelberg followed early 1993 and the three gentlemen formed a team with distinct roles. Prof. Erkki Soini told Stefan and Pekka: "You guys take care of the science and I will get you funding". The work of the team with resolution enhancement lead into several innovations in two-photon microscopy and super-resolution - work for which Stefan Hell was awarded the Nobel Prize in Chemistry in 2014. While Stefan went on with super-resolution and returned to Germany in 1997, PH together with prof. Erkki Soini concentrated on development of new in-vitro diagnostics system based on two-photon excitation. In 2002 Pekka Hänninen took over the laboratory of Biophysics as Erkki Soini retired - and since 2005 he has been appointed as full professor of Medical Physics and Engineering. Currently Pekka Hänninen is also the vice-dean of the faculty and as of 1.8. 2019 the Dean.

Prof. Pekka Hänninen has a long experience in applied research that has also lead into industrial exploitation. The previous work related application of microscopy based detection methods to specific detection of microbes has lead into the birth of Arctic Diagnostics and their product MariPOC. The invention of fingerprinting technology has lead into commercialization of the ideas within industrial processes at a startup Aqsens Oy – and later on with Aqsens Health Oy and preventive health care in India. His background is in signal processing, electronic engineering and instrumentation and he has worked within instrumentally solving biological problems since his engagement to EMBL in 1988. Prof Hänninen has more than 20 patents majority of which have lead into industrial exploitation and products.

Prof. Pekka Hänninen is the responsible professor for International Masters Program in Biomedical Imaging. The program attracts science fascinated students from around the globe - more information can be found in http://www.bioimaging.fi