OctoMap for collision avoidance / using point clouds

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OctoMap by defatult does not store individual points but rather integrates them into an occupancy map for maximum compression in order to reduce memory usage. Have a look at http://octomap.sourceforge.net/ and the paper there for a detailed description.

You can continuously update this map with further sensor readings but the original point clouds are not stored (which you could do yourself instead). If you need individual points, you would need to extend your own octree class. If you are only interested in the points and need the octree just for adressing or neighbor search, then I would suggest the PCL octree instead.

The occupancy map can be used for a variety of tasks such as localization, arm navigation and navigation in cluttered environments. The 3D_navigation stack can serve you as a starting point but it's not quite ready yet to be deployed out of the box directly.