A cell culture vessel (100) includes a wall including an inner surface defining a cell culture chamber of the vessel. A substrate (215) of non-porous material is positioned in the cell culture chamber between a first region of the cell culture chamber and a second region of the cell culture chamber. The substrate includes a plurality of microcavities (220), each microcavity of the plurality of microcavities includes a concave surface defining a well and an opening, the concave surface of each microcavity includes at least one aperture including a dimension less than or equal to about 15 microns defining a path from the well to the second region. A cell culture vessel including a substrate including a plurality of microcavities and a layer of porous material is also provided. Methods of culturing cells in the cell culture vessel are also provided.