Systems, devices, and methods for generating, culturing, and using magnetically-controlled three-dimensional (3D) tissues are described. A magnetically-enabled transwell system for immobilizing and supplying perfusion to a 3D mini-tissue includes a cell culture vessel with at least a first chamber and a second chamber, the mini-tissue being disposed in the first chamber, and a perfusion mechanism defining an elongate perfusion channel with a proximal end in the first chamber and a distal end in fluid communication with the second chamber, with a magnetic element configured to immobilize a magnetically-controlled 3D mini-tissue such that the proximal end is in fluid communication with basolateral space of the immobilized mini-tissue.