We report methods to synthesize sub-micron- and micron-sized patchy silica particles with fluorescently labeled hemispherical titania protrusions, as well as routes to efficiently characterize these particles and self-assemble these particles into non-close-packed structures. The synthesis methods expand upon earlier work in the literature, in which silica particles packed in a colloidal crystal were surface-patterned with a silane coupling agent. Here, hemispherical amorphous titania protrusions were successfully labeled with fluorescent dyes, allowing for imaging by confocal microscopy and super-resolution techniques. Confocal microscopy was exploited to experimentally determine the numbers of protrusions per particle over large numbers of particles for good statistical significance, and these distributions were compared to simulations predicting the number of patches as a function of core particle polydispersity and maximum separation between the particle surfaces. We self-assembled these patchy particles into open percolating gel networks by exploiting solvophobic attractions between the protrusions.