  Analogies between non-trivial topologies of matter and light have inspired
numerous studies, including defect formation in structured light and
topological photonic band-structures. Three-dimensional topological objects of
localized particle-like nature attract broad interest across discipline
boundaries from elementary particle physics and cosmology to condensed matter
physics. Here we show how simple structured light beams can be transformed into
optical excitations of atoms with considerably more complex topologies
representing three-dimensional particle-like Skyrmions. This construction can
also be described in terms of linked Hopf maps, analogous to knotted solitons
of the Skyrme-Faddeev model. We identify the transverse polarization density
current as the effective magnetic gauge potential for the Chern-Simons helicity
term. While we prepare simpler two-dimensional baby-Skyrmions and singular
defects using the traditional Stokes vectors on the Poincar\'e sphere for
light, particle-like topologies can only be achieved in the full optical
hypersphere description that no longer discards the variation of the total
electromagnetic phase of vibration.
