We study a granular-sized magnetic flux emergence event that occurred in NOAA 11024 in July 2009. The observations were made with the CRISP spectropolarimeter at the Swedish 1 m Solar Telescope achieving a spatial resolution of 0.14. Simultaneous full Stokes observations of the two photospheric Fe I lines at 630.2 nm and the chromospheric Ca II 854.2 nm line allow us to describe in detail the emergence process across the solar atmosphere. We report here on 3D semi-spherical bubble events, where instead of simple magnetic footpoints, we observe complex semi-circular feet straddling a few granules. The most characteristic signature in these events is the observation of a dark bubble in filtergrams taken in the wings of the Ca II 854.2 nm line. We can infer how the bubble rises through the solar atmosphere as we see it progressing from the wings to the core of Ca II 854.2 nm. In the photosphere, the magnetic bubble shows mean upward Doppler velocities of 2 km/s. In about 3.5 minutes it travels some 1100 km to reach the mid chromosphere, implying an average ascent speed of 5.2 km/s. To aid the interpretation of the observations, we carry out 3D numerical simulations of the evolution of a horizontal, untwisted magnetic flux sheet injected in the convection zone, using the Bifrost code. The computational domain spans from the upper convection zone to the lower corona. In the modeled chromosphere the rising flux sheet produces a large, cool, magnetized bubble. We compare this bubble with the observed ones and find excellent agreement, including similar field strengths and velocity signals in the photosphere and chromosphere, temperature deficits, ascent speeds, expansion velocities, and lifetimes.