The family sold their estate and moved to Breslau (Wrocław) where, in 1872, eleven-year-old Czapski began attending school at the Maria Magdalenen Gymnasium.
At the start of his second semester he switched to the University of Breslau, studying physics under Oskar Emil Meyer, Ernst Dorn and Felix Auerbach, mathematics under Jakob Rosanes and philosophy under Jacob Freudenthal.
In 1882 Czapski began work for the Normal-Eichungskommission (Imperial Institute for Weights and Measures) which was headed by the astronomer Wilhelm Julius Foerster.
In December he embarked on his doctoral exams which were held by Helmholtz and Kirchhoff in physics, Leopold Kronecker in mathematics and Eduard Zeller in philosophy.
Abbe soon appointed Czapski as his assistant – a post he held until 1886 – and involved him in his discussions with the physicist Leonhard Sohncke from the University of Jena.
He subsequently worked on the technical implementation of a binocular microscope based on ideas put forward by the American biologist Horatio S. Greenough.
Working closely with Abbe and a foundation inspector from the Grand-Ducal Saxon State Ministry in Weimar (initially Karl Rothe and from 1899 onwards the Government Privy Council Max Vollert), Czapski played an ever greater role in managing the company, something that took an increasing toll on his health.
Margarete's father was a professor at a grammar school in Paris and a nephew of Juliette Drouet, who was Victor Hugo's partner for much of his life.
Their marriage produced eight children: Czapski had long been suffering from ill health, and his huge workload made the situation even more difficult.