A cell culture article has substrate that is predominantly opaque and that provides a three-dimensional (e.g., irregular) surface, but incorporates an optically transparent, substantially regular (e.g., two-dimensional) surface to serve as a microscopic observation and imaging window for the 3D cell culture. In many embodiments, the 3D portion of the substrate occupies greater than 99% of the surface while the 2D portion occupies less than 1% of the surface so as not to substantially disrupt the general 3D culture environment.