Fig. 3.

Simulation of polony adjacency reconstruction. (A) Lattice diagram of primer lawn and polonies denoted with color and Voronoi cell boundaries. Solid circles indicate seed locations. (B) Illustration of random site pairing between adjacent primer sites. (C) Alignment between a priori and a posteriori points from A. (D) Larger simulated surface with a polony density $\lambda$ = 2,000 polonies per unit area and a relative site density $\rho$ = 50 sites per polony on average. (E) Reconstructed graph (red lines) and corresponding Voronoi tessellation (gray lines) computed using the Tutte embedding approach from scrambled edges derived from the simulated surface in D.