A three-dimensional (3-D) culture “Petri-dish” for research in regenerative medicine, biotechnology and clinical translation is described. This 3-D perfusion culture dish is to advance in vitro culture tools from static 2-D to dynamic 3-D perfusion culture. Interwoven hollow fiber capillary membranes divide the “Petri-dish” culture space into a controllable 3-D pattern of different compartments, serving the functions of the organ's larger vasculature. These physically active scaffolds, which can be suitable for cell adhesion or cell aggregate immobilization, offer a supply of cells with high-performance mass exchange including gas supply and under perfusion conditions. In contrast to static and discontinuous medium supply, a dynamic culture can be achieved with continuous or alternating medium supply and integral oxygenation. They provide a more physiologic supply in the cell macro environment, including homeostasis of oxygen, pH, nutrition, soluble factors, and gradients of metabolites for the cells. Also, medium perfusion can be achieved. Consequently the invention was made for cultures at tissue density, especially stem cells and support cells, which strive to create their own stem cell niche.