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Thanks for the reply Mr. Moore, the issue was indeed a missing reference of the fiducial markers to our world position. Thanks to your suggestion now it works! We simply add static transforms marker --> world_marker and then lookup the tf between world_marker and base_link. Finally we gave to the Ekf as input the corresponding message for that transform, by using as a message frame_id the map and that was it. The final output is now the base_link position seen from the map frame.

Cheers