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The short answer is that in the case of robots moving in a 2D plane which the navigation package is designed for a 2D laser scan is sufficient in most cases.

SLAM in 3D is far more complex than SLAM in 2D, so if it's a safe assumption that the robot remains in a 2D plane then this is the best choice. There is no need spending orders of magnitude more processing power to localise in 3D if that's not a task you really need to do.

However if you're moving in 3D space with 6 degrees of freedom, then you'll have to use the 3D information with a package such as RGB-D-SLAM or R-TAB-MAP, but this is not what the navigation stack is designed for.