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Berlin city authorities had sought to block the opening of the museum, citing burial laws that ban the public display of human corpses.
The court said the creators of the law did not intend for it to be applied to bodies preserved using plastination, a process that replaces water and fat with plastic.
Von Hagens, nicknamed "Dr. Death" by some critics, said the museum is scheduled to open in January and will feature 20 preserved bodies and up to 200 preserved body parts.