A cell culture vessel (100) has walls and a substrate having a plurality of microcavities (120), where each microcavity of the plurality of microcavities includes a concave well and an opening to allow the microcavity to be filled with liquid. A flange (170) surrounds the substrate having an array of microcavities. A channel (175, 176) surrounds the flange, providing a moat around the microcavity substrate. The flange is angled. Methods of culturing cells in the cell culture vessel are also provided.