Can we really see the bonds?
All credit to Zhang et al. "Real-Space Identification of Intermolecular Bonding with Atomic Force Microscopy" Science Vol. 342  no. 6158  pp. 611-614.

Yes, direct images of bonds, not only covalent bonds but also intermolecular hydrogen bonds have been recorded.

It is the electron density that is being observed, covalent and hydrogen bonds involving high electron density between the atoms.

Scanning Tunneling Microscopy can also be utilized to directly observe the electron density of bonds.