Quantitative characterization of images of nanocrystals and nanostructures is a challenging but important task. The development and optimization of methods for the construction of complex nanostructures rely on imaging techniques. Computer programs were developed to quantify TEM images of nanocrystal/DNA nanostructures, and results are presented for heterodimers and trimers of gold nanocrystals. The programs presented here have also been used to analyze more complex trimers and tetramers linked by branched DNA, as well as for structures made from attaching gold nanocrystals to CdSe/ZnS core-shell quantum dots. This work has the additional goal of enabling others to quickly and easily adapt the methods for their own use.