Bacteria can adapt to stresses by aggregating into colonies and biofilms. Within these aggregates bacteria are protected against killing by antibiotics, phages, or predators. How does aggregation confer tolerance against antibiotics? Are physical properties of colonies correlated with bacterial survivability? We address these questions in the framework of the Center for Molecular Medicine Cologne. We develop tools for 3D live-cell tracking, combine them with transcriptomics, and apply them to a clinical strain collection of the human pathogen Neisseria gonorrhoeae.