To better understand the extrinsic signals that control neural stem cell (NSC) fate, here we applied a microwell array platform which allows high-throughput clonal analyses of NSCs, cultured either as neurospheres or as adherent clones, exposed to poly(ethylene glycol) (PEG) hydrogel substrates functionalized with selected signaling molecules. We analyzed by time-lapse microscopy and retrospective immunostaining the role of integrin and Notch ligands, two key NSC niche components, in altering the behavior of several hundred single stem cells isolated from a previously described Hes5::GFP reporter mouse. NSC self-renewal was increased by 1.5-fold upon exposure to covalently tethered Laminin-1 and fibronectin fragment 9–10 (FN_9–10), where 60–65% of single cells proliferated extensively and remained Nestin positive. Tethering of the Notch ligand Jagged-1 induced activation of Notch signaling. While Jagged-1 alone increased cell survival and proliferation, no further increase in the clonogenic potential of Hes5::GFP cells was observed upon co-stimulation with Laminin-1 and Jagged-1. We believe that the bioengineering of such in vitro niche analogues is a powerful approach to elucidate single stem cell fate regulation in a well-controlled fashion.