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During the construction of university buildings on the territory of Toomemägi Park in 1808, it was also the turn to build an observatory. Originally it was planned to be built in one of the towers of the Dome Cathedral, but these plans were not fulfilled. The building committee decided that the site for the future building observatory on the highest point of Toomemägi at 66.8 metres above sea level, where the building of the Bishop's Castle used to be.

The beginning of construction dates back to 1808. By the spring, when already some of the university buildings had already been constructed and the main building, it was time for the observatory to be built. Its project was prepared by university architect I.B. Krause. According to the project, the building was to be be practical, with simple austere lines.

In addition to I.B. Krause, other specialists took part in the construction of the building - Г. F. F. Parrott, I. W. Pfaff and E. C. F. Knorre. The project was based on models of the observatories of the German cities of Göttingen and Gotha.

Tartu Observatory was made of powerful stone pillars, and was completed in 1810. The finished building was a one-storey brick structure with a hip roof. On one side there was round two-storey tower, which was originally covered with a dome. However, in 1824, when a large telescope arrived, the fixed tower had to be to be rebuilt. The new tower rotated on rollers and was ready as early as 1825. The observatory building has not undergone any further alterations since that year.

Inside, the building was just as utilitarian and simple. In the centre were the working rooms, and on the sides were large halls. In 1819, astronomers' lodge was built next to the observatory, which 2 years later was connected to it by a passage. К The observatory also includes a round pavilion built in 1897. In it Petzval's astrograph, a device for photographing celestial objects.

The Tartu Observatory soon became world-famous, mainly due to the efforts of Friedrich Georg Wilhelm Struve, director of the Tartu and later Pulkovo Observatory. He worked in Tartu from 1913 to 1939. When he arrived at the observatory, it was not yet operational. Some of the instruments had not been assembled, some had not yet arrived, and some had not even been ordered. And so, Struve began his work here by installing the instruments that were in stock and ordering the necessary ones. It was to his credit that he was able to equip the observatory in the best possible and state-of-the-art at the time. This contributed greatly to the fact that the scientists working at the observatory were able to rise to a world-class level of science. When Struve was in charge of the observatory, it was equipped with the Reichenbach and Ernst meridian circle and the Fraunhofer refractor, at the time the largest in the world at the time. Because of the presence of these devices, the observatory was considered the best in the world in terms of technical equipment. Regular observations at the Tartu Observatory began in 1814.

Struve also became known for his work on double stars. Although the discovery of double stars belongs to the English astronomer W. Herschel, Struve Struve made a major contribution to the study of these cosmic objects. In particular, the scientist did a great deal of work to develop a precise method of observing double stars. His works have not lost their relevance to this day. Under Struve, a catalogue of 3,112 double stars with descriptions, 2,343 was compiled, of which were discovered by him. He was also the first to prove the existence of light-absorbing matter in interstellar space. He also studied planets and comets.

Struve's merit also lies in the fact that the Tartu Observatory became a centre where many Tartu Observatory became a centre where many scientists who later went on to direct other observatories received their training. In addition to Struve, many other scientists worked here, who contributed to science: O. Backlund, E. Hartwig, T. Clausen, T. Banajevich, E. Schönberg et al.

All instruments used throughout the history of the observatory have survived to this day. They can be seen in the east hall of the Tartu Observatory, which has now been turned into a museum.

Gradually the institution lost its leading importance. The First World War World War I and the political situation in Estonia in the 20s and 30s did not favour the development of the Tartu Observatory. The leading place was taken by research of a theoretical nature. Later, the building constructed on Toomemägi, did not fulfil the requirements of modern research work. A new building was built 25 kilometres away from the existing one in Tyravere. The new observatory was opened in 1964 and is named after Struve. The new observatory also has a park near it, with the belief that it would become as wonderful as the park on the hill of the Toomemägi.

Due to the construction of the new building, the old observatory has lost its original significance and is being turned into a museum. On 27 April 2011, Tartu celebrated the bicentenary of the observatory. The institution has been undergoing restoration work since 2009, and once they are completed, the observatory will reopen as a museum.