This dissertation documents work done in two different fields, both of which are related through their studies of objects measured on the order of nanometers. The first part discusses efforts at automating image reconstruction of objects studied through coherent X-ray imaging experiments. Data collected at the Linac Coherent Light Source are used to reconstruct hundreds of images of soot particles in flight. The second part discusses efforts at protein structure prediction and generating collections of building blocks necessary for the prediction algorithm. Data from the Protein Data Bank are processed to generate large numbers of building blocks, which are then used to predict protein structures with some initial success.