Because atoms are really microscopic (nanometer scale), it is not possible to view them directly with the eye. They can however be seen indirectly with the Scanning Electron Microscope, SEM, and with the Scanning Tunneling Microscope, STM. In either case, while the images created are highly accurate, they are computer enhanced processed images -- not real-time. So, in that sense, it is not possible to view atoms as anything other than highly accurate animations. That is my current understanding anyway.
See: Atomic Resolution with Scanning Tunneling Microscopy
http://www.cns.cornell.edu/documents/ScanningTunnelingMicroscopy.pdf
See: Atomic Force Microscopy
http://virtual.itg.uiuc.edu/training/AFM_tutorial/
See: Atom-By-Atom Extraction Using the Scanning Tunneling Microscope ...
http://www.phy.ohiou.edu/~hla/HLA-46.pdf
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