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Ideally, I think we would like to use both the 3D SLAM and 2D SLAM (or is this wildly computationally expensive/redundant?).
If your robot is restricted to motion in the plane you can get the pose of the kinect from 2D SLAM and the extrinsic calibration of the Robot and Kinect. This allows to correctly backproject the point clouds. This approach is computationally cheaper and makes it easy to align the origins of 2D and 3D map than mapping 2D and 3D seperately.
If your floor is not level, consider using 3D SLAM and downprojection of the map to 2D.
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