A sample run of ArrayD. The inputs given to the program were: type of plate-384; number of samples-2304; number of replicates-2; number of pins in X-axis-2; number of pins in Y-axis-2. A total of 67 solutions were offered. Two solutions are shown: top ranking solution with inter-spot distance 170 μm and an alternative design solution with inter-spot distance 200 μm. The ArrayD output was subsequently fed to the companion program 'ArraySolution' to classify each design based on its geometry and the report generated is displayed in Table 2 [see Additional file 1].