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After earning his degree, he worked as a physician in Vienna where he befriended Ludwig van Beethoven and married Wilhelmine Polborn. During that time, Troxler discovered a phenomenon of visual perception that now bears his name, Troxler's fading. In 1811 he returned to Beromünster.
Troxler represented Switzerland at the Congress of Vienna in 1815. In 1820 he became a professor for philosophy and history at the lyceum in Lucerne but had to leave after a year due to political problems. He founded an educational institution in Aarau and continued working as a physician.
In 1830, he became a professor again – this time in Basel –, and he had to leave again the next year due to political problems. In 1832 he was elected to the legislative assembly of the canton of Aargau. He became a professor at the just established University of Berne in 1834 and stayed there until 1850.
In 1848, Troxler succeeded in altering the Swiss Federal Constitution to include elements of the United States Constitution.