AFM images of DNA deposited on mica surface were recorded and single molecules were traced using an automated program developed with the improved thinning algorithm of Brugal and Chassery. This program dramatically improves throughput such that thousands of DNA traces may be obtained within a day. The program was used to analyze AFM images of DNA-186 repressor nucleoprotein complexes relevant to the regulation of the 186 bacteriophage genetic switch. The location of protein particles on the DNA, their size and volume could be generated automatically. The result showed that the 186 bacteriophage repressor, 186 CI, aggregates into a disc-shaped heptamer with the help of DNA and explains why this oligomerization state of the repressor had not been observed in sedimentation equilibrium experiments performed on protein solutions. Furthermore, the high statistics achievable with this program allowed probing cooperative interactions between distant DNA regulatory sites that would have been difficult to test otherwise.