Microarray is an ordered and highly dense arrangement of gene segments on a laboratory slide and is used for the analysis of thousands of genes in a single experiment. The genes are placed on the slide through a process of liquid spotting using techniques such as dispensing pins. Contact pin spotting technology is primarily used because high spot-density is attainable. On the other hand, pin spotting requires the accommodation of the following time-consuming processes:​ (i) cleaning of pins, (ii) loading the solutions onto the pins, (iii) removing the excess solution from pins for a uniform spot size, and (iv) spotting.

This thesis specifically investigates optimization of the first three aforementioned time-consuming processes in order to increase the productivity of the pin-based microarray slides preparation. Analysis and simulation performed in this research show that the optimal hole-diameter of the vacuum-based cleaning system for stealth microspotting pin is 2.4 mm. For this diameter the highest shear stress on the entire pin can be obtained. Two newly proposed patterns to remove the excess solution from the pins are compared with an existing technology. One of the proposed patterns generates the highest spot-density as opposed to existing technologies. Furthermore, another contribution of this research is the development of a statistical approach for estimating the transferred solution volumes in loading/spotting procedures.