This dataset contains experimental recordings on neuronal cultures grown on PDMS topographical cultures, as well as the corresponding numerical simulations. Data is in the form of raster plots and includes a representative full analysis for the extraction of important properties such as activity and effective connectivity. Experimental data was obtained from rat primary neuronal cultures grown on topographical PDMS patterns. Spontaneous activity of neurons grown on different pattern configurations was then recorded using fluorescence calcium imaging. Data was then analyzed with the NETCAL toolbox run in Matlab (available at Zenodo, DOI: 10.5281/zenodo.1119026) to extract the raster plots and properties such as collective activity and effective connectivity. Numerical simulations were based on the articles Orlandi et al., Nature Physics 9, 582–590 (2013) and Ludl and Soriano, Front. Comput. Neurosci. 14, article 77 (2020), and were extended to include spatial constraints in network connectivity that mimic the experimental PDMS patterns.