Systems and methods are described for the fully automatic, template-free locating and extracting of a plurality of two-dimensional projections of particles in a micrograph image. A set of reference images is automatically assembled from a micrograph image by analyzing the image data in each of a plurality of partially overlapping windows and identifying a subset of windows with image data satisfying at least one statistic criterion compared to other windows. A normalized cross-correlation is then calculated between the image data in each reference image and the image data in each of a plurality of query image windows. Based on this cross-correlation analysis, a plurality of locations in the micrograph is automatically identified as containing a two-dimensional projection of a different instance of the particle of the first type. The two-dimensional projections identified in the micrograph are then used to determine the three-dimensional structure of the particle.