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Edinburgh Napier University opened its doors to students as Napier Technical College in 1964, taking its name from John Napier, the inventor of logarithms and the decimal point, who was born in 1550 in the medieval tower house of Merchiston Castle (the site of the University's Merchiston campus).

In 1966, it was renamed Napier College of Science and Technology. Three years later, it merged with the Sighthill-based Edinburgh College of Commerce to form Napier College of Commerce and Technology, which became a Central Institution in 1985.

The college was renamed Napier Polytechnic in 1986 and in the same year acquired the former Hydropathic hospital buildings at Craiglockhart.

In June 1992 the institution officially became Napier University.

In 1994, Napier University acquired its Craighouse campus. In 1996, the university gained a new Faculty of Health Studies through a merger between the Scottish Borders College of Nursing and Lothian College of Health Studies.

In February 2009 the University launched its new title, Edinburgh Napier University, to reflect its location in Scotland's capital city.