a microwell assembly that includes a tray that supports well inserts . the tray has an array of cylindrical cavities , each having an optically opaque cylindrical wall and an open base . the well inserts have wells having an optically clear bottom . the cylindrical cavities are sized to receive the well inserts such that the bottom of the wells does not extend beyond the cylindrical walls of the cavities . the opaque walls of the tray optically isolates the wells . in one embodiment , the entire structure of the well insert is economically made of the same material such as clear polymer . the tray may be reusable , and the well inserts are disposable . in one embodiment , the well insert may be configured in the form of a multi - well strip that includes wells at a spacing conforming to the inter - well spacing of a standard microplate .