Dear Hyperspy users,
The solution was just there. Thermo provides a software to convert their format (.csi) into rpl format (.rpl). The program is call "SIConvert.exe" and can be found in "C:\Program Files (x86)\Thermo Scientific\NSS".
All metadata are loss. They can be retreived using the program called "SIAttributes.exe" in the same folder and have to be manually added in hyperspy. For example:
>>> s = hs.load('Map.rpl')
>>> s.set_signal_type('EDS_SEM')
>>>names = ['x', 'y','Energy']
>>>units = ['${\mu}m$','${\mu}m$','keV']
>>>scales = [0.466, 0.466, 0.01]
>>> ax.name = names[i]
>>> ax.units = units[i]
>>> ax.scale = scales[i]
>>> elements = ['Ti', 'Cu']
>>> s.set_elements(elements)
>>> s.set_microscope_parameters(beam_energy=10)