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The data on "batch_clouds" sends the clouds one by one, in the camera coordinate frame, along with a tf transformation of the camera pose. You probably only get one frame, because you (over)write the file for every received cloud.

The "save" and "save as" commands also publish the registered and merged point cloud on the topic /rgbdslam/aggregate_clouds.

By the way, the octomap documentation is pretty good, just not on ros.org. Have a look at their hompage.