is accomplished by optimizing features and parameters in the flow cell to minimize unwanted refraction or reflection of light used in the array synthesis process the design of the flow cell can be better understood with reference to an exemplary array synthesis instrument one exemplary instrument using a flow cell with a single reaction chamber and a optical elements light array is shown generally at 110 in fig1 the apparatus includes a two dimensional array image former 112 and a flow cell or reaction chamber 114 into which an array image is projected by the image former 112 the flow cell also shown in schematic fashion in fig1 includes a planar substrate 116 on the rear surface of which the microarray is synthesized the substrate 116 is placed over a chamber 18 formed in the front of an enclosure 120 an inlet port 122 and an outlet port 124 provide fluid communication into and out of the flow cell 114 the image formed is constructed to direct the light pattern to the substrate 116 where the reactions occur in the interior or rear surface of the substrate 116 the areas of the substrate on which the nucleic acid probes are constructed are indicated schematically in fig1 at 126 the image former.