Methods for manufacturing and using an apparatus for manipulating and analyzing a large number of microscopic samples of a liquid or materials, including cells, in liquid suspension. Parallel through-holes are formed in a platen and loaded with a liquid. Loading may be performed in such a way as to create a gradient, with respect to the position of the through-holes, of the concentration of a particular substance or of another quantity. Mixing of the contents of through-holes may be obtained by bringing filled microwell arrays into contact with each other with registration of individual through-holes.